From nkxirainbow at gmail.com Sat Aug 1 03:25:37 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 1 Aug 2009 09:25:37 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <4A730EE2.7000107@democritos.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> Message-ID: <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/0d104e4f/attachment.htm From lidonglin556 at 163.com Sat Aug 1 05:59:09 2009 From: lidonglin556 at 163.com (lidonglin556) Date: Sat, 1 Aug 2009 11:59:09 +0800 (CST) Subject: [Pw_forum] about larger system's frequence calculation Message-ID: <17438791.56011249099149105.JavaMail.coremail@app177.163.com> 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 From baroni at sissa.it Sat Aug 1 06:59:11 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 1 Aug 2009 06:59:11 +0200 Subject: [Pw_forum] Volume in a supercell In-Reply-To: References: Message-ID: <37B540D3-CF20-4242-9299-D15ED719FC07@sissa.it> 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 From giannozz at democritos.it Sat Aug 1 08:29:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 Aug 2009 08:29:42 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> Message-ID: 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 From giannozz at democritos.it Sat Aug 1 08:37:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 Aug 2009 08:37:40 +0200 Subject: [Pw_forum] about larger system's frequence calculation In-Reply-To: <17438791.56011249099149105.JavaMail.coremail@app177.163.com> References: <17438791.56011249099149105.JavaMail.coremail@app177.163.com> Message-ID: <8E6B4C32-472E-4442-ACCF-051A8033A22B@democritos.it> 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 From nkxirainbow at gmail.com Sat Aug 1 09:12:42 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 1 Aug 2009 15:12:42 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> Message-ID: <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> 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 From giannozz at democritos.it Sat Aug 1 09:33:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 Aug 2009 09:33:42 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> Message-ID: <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> 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 From degironc at sissa.it Sat Aug 1 09:35:20 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 01 Aug 2009 09:35:20 +0200 Subject: [Pw_forum] Volume in a supercell In-Reply-To: References: Message-ID: <4A73F038.9080200@sissa.it> 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 > From degironc at sissa.it Sat Aug 1 09:54:56 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 01 Aug 2009 09:54:56 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> Message-ID: <4A73F4D0.7070802@sissa.it> 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 From nkxirainbow at gmail.com Sat Aug 1 10:21:43 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 1 Aug 2009 16:21:43 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> Message-ID: <21fbc4790908010121m74037abbmc89925b0208a13f4@mail.gmail.com> 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 From neelphysics at yahoo.in Sat Aug 1 10:35:02 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Sat, 1 Aug 2009 14:05:02 +0530 (IST) Subject: [Pw_forum] Epsilon error Message-ID: <494812.26458.qm@web95006.mail.in2.yahoo.com> 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 From nkxirainbow at gmail.com Sat Aug 1 11:04:22 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 1 Aug 2009 17:04:22 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <4A73F4D0.7070802@sissa.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> Message-ID: <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/27feabd4/attachment.htm From lidonglin556 at 163.com Sat Aug 1 11:03:14 2009 From: lidonglin556 at 163.com (null) Date: Sat, 1 Aug 2009 17:03:14 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 26, Issue 2 In-Reply-To: References: Message-ID: <12410951.216991249117394352.JavaMail.coremail@bj163app79.163.com> 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 From degironc at sissa.it Sat Aug 1 11:24:35 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 01 Aug 2009 11:24:35 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> Message-ID: <4A7409D3.7030302@sissa.it> 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 > From nkxirainbow at gmail.com Sat Aug 1 14:39:01 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 1 Aug 2009 20:39:01 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <4A7409D3.7030302@sissa.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <4A7409D3.7030302@sissa.it> Message-ID: <21fbc4790908010539q6072b508t23cf94248fe16b42@mail.gmail.com> 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 From giannozz at democritos.it Sat Aug 1 14:59:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 Aug 2009 14:59:38 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 26, Issue 2 In-Reply-To: <12410951.216991249117394352.JavaMail.coremail@bj163app79.163.com> References: <12410951.216991249117394352.JavaMail.coremail@bj163app79.163.com> Message-ID: <5129ED4E-9195-4115-A373-670AD2204D64@democritos.it> 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 From giannozz at democritos.it Sat Aug 1 15:03:51 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 Aug 2009 15:03:51 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790908010121m74037abbmc89925b0208a13f4@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <21fbc4790908010121m74037abbmc89925b0208a13f4@mail.gmail.com> Message-ID: <0690881B-FD46-4127-B12E-A33722E8CB83@democritos.it> 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 From neelphysics at yahoo.in Sat Aug 1 15:04:54 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Sat, 1 Aug 2009 18:34:54 +0530 (IST) Subject: [Pw_forum] error in running epsilon Message-ID: <85654.5548.qm@web95004.mail.in2.yahoo.com> 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 From giannozz at democritos.it Sat Aug 1 15:07:11 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 Aug 2009 15:07:11 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> Message-ID: 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 From eariel99 at gmail.com Sat Aug 1 15:08:48 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Sat, 1 Aug 2009 09:08:48 -0400 Subject: [Pw_forum] failure with npool Message-ID: 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 >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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/e95cdf4a/attachment.htm From nkxirainbow at gmail.com Sun Aug 2 03:11:21 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 2 Aug 2009 09:11:21 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> Message-ID: <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> Dear Paolo Giannozzi: > >what is the meaning of "force constants"? ( hint: second derivative of > >the energy with respect to atomic displacements ) Thanks for your hint. I got it:) > ____________________________________ > 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/20090802/94cf6415/attachment-0001.htm From neelphysics at yahoo.in Sun Aug 2 10:00:52 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Sun, 2 Aug 2009 13:30:52 +0530 (IST) Subject: [Pw_forum] USPP are not implemented Message-ID: <332104.49514.qm@web95008.mail.in2.yahoo.com> 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 Looking for local information? Find it on Yahoo! Local -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum 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/20090802/ccf208e2/attachment.htm From neelphysics at yahoo.in Sun Aug 2 10:10:35 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Sun, 2 Aug 2009 13:40:35 +0530 (IST) Subject: [Pw_forum] USPP are not implemented Message-ID: <23397.64655.qm@web95012.mail.in2.yahoo.com> 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 Looking for local information? Find it on Yahoo! Local -----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. 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/20090802/6d493049/attachment.htm From yaldachem at gmail.com Sun Aug 2 10:31:45 2009 From: yaldachem at gmail.com (yaldaa kh) Date: Sun, 2 Aug 2009 01:31:45 -0700 Subject: [Pw_forum] average.x and workfunction calculations Message-ID: <47431d9f0908020131l473fd6bdn35e8dbf9734614b6@mail.gmail.com> Dear all How can I write an input file for average.x code in order to calculation of workfunction? thanks a lot Yalda Kh. (chemistry student) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090802/42747e5a/attachment.htm From kazempoor2000 at yahoo.com Sun Aug 2 12:13:44 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Sun, 2 Aug 2009 03:13:44 -0700 (PDT) Subject: [Pw_forum] occupation In-Reply-To: <4A71E3FB.406@umn.edu> Message-ID: <736374.41939.qm@web112508.mail.gq1.yahoo.com> Dear Matteo I follow? your link and is useful for me, but when I want to study a? nonmagnetic material like Tio2 ,how do I change the format of pos_file.? for NiO it is in tutorial ,but NiO is antiferromagnetic and in pos_nio.r16 you add a switch 1,-1 and 0 in front of atomic type. but for TiO2, it is nonmagnetic. How can I define the differnet type? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Thu, 7/30/09, Matteo Cococcioni wrote: From: Matteo Cococcioni Subject: Re: [Pw_forum] occupation To: "PWSCF Forum" Date: Thursday, July 30, 2009, 11:18 AM the new tutorial on the calculation of U can be downloaded from this webpage: http://www.quantum-espresso.org/wiki/index.php/QESB09#First_week Matteo Cococcioni wrote: > Dear Ali, > > on the wiki page of quantum-espresso you should be able to find a new > tutorial on the calculation of U. Please download it > and run the scripts in there following the instructions. > > > > ali kazempour wrote: >??? >> Dear all >> >> From Linear response calculation ,I get for TiO2 bulk U=5.73, But when >> I double the unit cell in z direction and again compute U ,I get three >> different value for Ti atoms.(U=5.63,5.46,5.70). >> >>? ??? > > what are these three values? I assume they are what you get with > supercells of three different sizes. is this correct? if it is the only > strange thing is that the intermediate value is lower than the other > two. otherwise you got pretty nice convergence of U which is what you > want to achieve. Is there any particular reason (apart computational > cost) why you only enlarge the cell in z direction? > >??? >> Why these values are not same . what is the main reason? Does it in >> numerical variation errors? >> ANother question: >> When we perturb D level by alpha, it give rise to change in d >> occupancy . Is it correct that if we impose negative alpha , the >> occupation becomes less than initial state .? >> >>? ??? > > no. positive alpha -- > decrease in total n. but you need to look at the > right n.... > >??? >> for Ti isolated atom for apha=0.1? tr[ns(na)] after first-iteration >> equal to the 0.002 and at the end of calculation is 2.327 while we >> know that for Ti,? tr[ns(na)] =2.000. Does it seems to be correct.? >> >>? ? ? Number of iteration with fixed ns =? 0 >>? ? ? Starting ns and Hubbard U : >>? enter write_ns >> U( 1) =? 0.0000 >> alpha( 1) =? 0.1000 >> atom? 1???Tr[ns(na)]=???2.0000000 >> atom? 1? spin? 1 >> eigenvalues:? 0.4000000 0.4000000 0.4000000 0.4000000 0.4000000 >>? eigenvectors >>? 1???1.0000000? 0.0000000? 0.0000000? 0.0000000? 0.0000000 >>? 2???0.0000000? 1.0000000? 0.0000000? 0.0000000? 0.0000000 >>? 3???0.0000000? 0.0000000? 1.0000000? 0.0000000? 0.0000000 >>? 4???0.0000000? 0.0000000? 0.0000000? 1.0000000? 0.0000000 >>? 5???0.0000000? 0.0000000? 0.0000000? 0.0000000? 1.0000000 >>? occupations >>? 0.400? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.400? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.400? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.400? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.400 >> atom? 1? spin? 2 >> eigenvalues:? 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>? eigenvectors >>? 1???1.0000000? 0.0000000? 0.0000000? 0.0000000? 0.0000000 >>? 2???0.0000000? 1.0000000? 0.0000000? 0.0000000? 0.0000000 >>? 3???0.0000000? 0.0000000? 1.0000000? 0.0000000? 0.0000000 >>? 4???0.0000000? 0.0000000? 0.0000000? 1.0000000? 0.0000000 >>? 5???0.0000000? 0.0000000? 0.0000000? 0.0000000? 1.0000000 >>? occupations >>? 0.000? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >> nsum =???2.0000000 >>? exit write_ns >> >>? ??? > > this is not the first iteration. this is what the initial guess of the > on-site occupations the code does to start the calculation > > >??? >>? Atomic wfc used for LDA+U Projector are NOT orthogonalized >>? ? ? Starting wfc are? ? 9 atomic +? ? 1 random wfc >> >>? ? ? total cpu time spent up to now is? ???13.34 secs >> >>? ? ? per-process dynamical memory:???326.3 Mb >> >>? ? ? Self-consistent Calculation >> >>? ? ? iteration #? 1? ???ecut=? ? 45.00 Ry? ???beta=0.70 >>? ? ? CG style diagonalization >>? ? ? c_bands:? 3 eigenvalues not converged >>? ? ? c_bands:? 2 eigenvalues not converged >>? ? ? ethr =? 1.00E-12,? avg # of iterations = 40.4 >>? enter write_ns >> U( 1) =? 0.0000 >> alpha( 1) =? 0.1000 >> atom? 1???Tr[ns(na)]=???0.0021401 >> atom? 1? spin? 1 >> eigenvalues:? 0.0000001 0.0000001 0.0000001 0.0009883 0.0009883 >>? eigenvectors >>? 1???0.0000000 -0.8803392 -0.4743427? 0.0000000? 0.0013927 >>? 2???0.0000000 -0.4743432? 0.8803400? 0.0000000 -0.0000040 >>? 3???0.0000000? 0.0012242? 0.0006642? 0.0000000? 0.9999990 >>? 4? -0.8886820? 0.0000000? 0.0000000 -0.4585240? 0.0000000 >>? 5???0.4585240? 0.0000000? 0.0000000 -0.8886820? 0.0000000 >>? occupations >>? 0.001? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.001? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.000 >> >>? ??? > > this is the first iteration! the problem is, in my opinion, that you > didn't start this calculation from wfc and potential saved from the scf > unperturbed run, but from scratch (that's why the code has to make the > initial guess for the n). > > regards, > > Matteo >??? >> ---------------------------------- and end of the file is >> : >>? ? ? End of self-consistent calculation >>? enter write_ns >> U( 1) =? 0.0000 >> alpha( 1) =? 0.1000 >> atom? 1???Tr[ns(na)]=???2.3270531 >> atom? 1? spin? 1 >> eigenvalues:? 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825 >>? eigenvectors >>? 1???0.0000000 -0.4359030 -0.7986559? 0.0000000? 0.4148945 >>? 2???0.0000000? 0.7269732 -0.0406891? 0.0000000? 0.6854592 >>? 3???0.0000000 -0.5305643? 0.6004109? 0.0000000? 0.5983379 >>? 4? -0.9258933? 0.0000000? 0.0000000 -0.3777851? 0.0000000 >>? 5???0.3777851? 0.0000000? 0.0000000 -0.9258933? 0.0000000 >>? occupations >>? 0.927? 0.000? 0.000? 0.000? 0.000 >>? 0.000? 0.157? 0.000? 0.000? 0.000 >>? 0.000? 0.000? 0.157? 0.000? 0.000 >>? 0.000? 0.000? 0.000? 0.927? 0.000 >>? 0.000? 0.000? 0.000? 0.000? 0.157 >> >> >> Ali Kazempour >> Physics department, Isfahan University of Technology >> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >>??? >>? ??? > > >??? -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056? ? Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% _______________________________________________ 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/20090802/1eb4b10d/attachment-0001.htm From lanhaiping at gmail.com Sun Aug 2 14:53:20 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sun, 2 Aug 2009 20:53:20 +0800 Subject: [Pw_forum] average.x and workfunction calculations In-Reply-To: <47431d9f0908020131l473fd6bdn35e8dbf9734614b6@mail.gmail.com> References: <47431d9f0908020131l473fd6bdn35e8dbf9734614b6@mail.gmail.com> Message-ID: Hi , Please have a look at $QE/examples/WorkFct_example . Or, read source code of average.x regards On Sun, Aug 2, 2009 at 4:31 PM, yaldaa kh wrote: > Dear all > How can I write an input file for average.x code in order to calculation of > workfunction? > > thanks a lot > Yalda Kh. > (chemistry student) > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090802/00569eaf/attachment.htm From baroni at sissa.it Sun Aug 2 15:59:55 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 2 Aug 2009 15:59:55 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> Message-ID: <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> Dear Hui Wang, dear All: I am extremely glad that the youngest among you find expert advice on this forum about such basic issues as discussed in this thread. You should be advised, though, that the human resources of the QE developers' team are extremely limited, and none of them gets any rewards for the their work other than the knowledge thay they are providing a (great) service to the community. You will have noticed that most of feedback comes from a very small number of members of this forum, and guess what? from the 3-4 individuals who do most of the development, maintanance, planning for future improvements. A simple application of a simple conservation law should suggest that every second they spend to answer trivial questions is a second less spent for more technical work that does require their expert contribution. I think that all of us can give a bit more to this community. To start with: 1) For the youngest - Do not think that a free resource (the advice you can obtain on this forum) is unlimited. Use it sparingly and judiciously, after making YOURSELF a serious effort to answer your question. Remember that there is no better teacher than oneself. It may be painful to teach / learn from oneself, but a self-taught thing is learnt forever (not to mention your local mentors, senior colleagues, etc) 2) For the not-so-young - Many of the questions asked on this forum are general enough to be answered by any knowledgeable senior graduate student / young postdoc. Please, give back to this community by keeping the discussion alive without forcing the same 3-4 people to give all the advice that is requested here. 3) For the bravest. Join the developers' efforts by volunteering some of your time and help fix bugs / implement new features / start new projects based on QE. For the time being, enjoy being with us as much as we enjoy being with you. Stefano B On Aug 2, 2009, at 3:11 AM, xirainbow wrote: > Dear Paolo Giannozzi: > > > >what is the meaning of "force constants"? ( hint: second derivative > of > >the energy with respect to atomic displacements ) > > Thanks for your hint. I got it:) > > > ____________________________________ > 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 --- 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/20090802/c5f56fdc/attachment.htm From matteo at umn.edu Sun Aug 2 17:31:55 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Sun, 02 Aug 2009 10:31:55 -0500 Subject: [Pw_forum] occupation In-Reply-To: <736374.41939.qm@web112508.mail.gq1.yahoo.com> References: <736374.41939.qm@web112508.mail.gq1.yahoo.com> Message-ID: <4A75B16B.6030702@umn.edu> Dear Ali, 1, -1, 0 are just spin indexes to tell the code what is the relative magnetization of the atoms (parallel, antiparallel, or none). if your system is non magnetic put all 0. or set magn = .false. and put nothing. you should look at the examples on Fe and Si as well and learn from there by comparison. Matteo ali kazempour wrote: > Dear Matteo > I follow your link and is useful for me, but when I want to study a > nonmagnetic material like Tio2 ,how do I change the format of > pos_file.? for NiO it is in tutorial ,but NiO is antiferromagnetic and > in pos_nio.r16 you add a switch 1,-1 and 0 in front of atomic type. > but for TiO2, it is nonmagnetic. How can I define the differnet type? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Thu, 7/30/09, Matteo Cococcioni //* wrote: > > > From: Matteo Cococcioni > Subject: Re: [Pw_forum] occupation > To: "PWSCF Forum" > Date: Thursday, July 30, 2009, 11:18 AM > > > the new tutorial on the calculation of U can be downloaded from this > webpage: > > http://www.quantum-espresso.org/wiki/index.php/QESB09#First_week > > > Matteo Cococcioni wrote: > > Dear Ali, > > > > on the wiki page of quantum-espresso you should be able to find > a new > > tutorial on the calculation of U. Please download it > > and run the scripts in there following the instructions. > > > > > > > > ali kazempour wrote: > > > >> Dear all > >> > >> From Linear response calculation ,I get for TiO2 bulk U=5.73, > But when > >> I double the unit cell in z direction and again compute U ,I > get three > >> different value for Ti atoms.(U=5.63,5.46,5.70). > >> > >> > > > > what are these three values? I assume they are what you get with > > supercells of three different sizes. is this correct? if it is > the only > > strange thing is that the intermediate value is lower than the > other > > two. otherwise you got pretty nice convergence of U which is > what you > > want to achieve. Is there any particular reason (apart > computational > > cost) why you only enlarge the cell in z direction? > > > > > >> Why these values are not same . what is the main reason? Does > it in > >> numerical variation errors? > >> ANother question: > >> When we perturb D level by alpha, it give rise to change in d > >> occupancy . Is it correct that if we impose negative alpha , the > >> occupation becomes less than initial state .? > >> > >> > > > > no. positive alpha -- > decrease in total n. but you need to > look at the > > right n.... > > > > > >> for Ti isolated atom for apha=0.1 tr[ns(na)] after > first-iteration > >> equal to the 0.002 and at the end of calculation is 2.327 while we > >> know that for Ti, tr[ns(na)] =2.000. Does it seems to be correct.? > >> > >> Number of iteration with fixed ns = 0 > >> Starting ns and Hubbard U : > >> enter write_ns > >> U( 1) = 0.0000 > >> alpha( 1) = 0.1000 > >> atom 1 Tr[ns(na)]= 2.0000000 > >> atom 1 spin 1 > >> eigenvalues: 0.4000000 0.4000000 0.4000000 0.4000000 0.4000000 > >> eigenvectors > >> 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > >> 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 > >> 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 > >> 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 > >> 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 > >> occupations > >> 0.400 0.000 0.000 0.000 0.000 > >> 0.000 0.400 0.000 0.000 0.000 > >> 0.000 0.000 0.400 0.000 0.000 > >> 0.000 0.000 0.000 0.400 0.000 > >> 0.000 0.000 0.000 0.000 0.400 > >> atom 1 spin 2 > >> eigenvalues: 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > >> eigenvectors > >> 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > >> 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 > >> 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 > >> 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 > >> 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 > >> occupations > >> 0.000 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> nsum = 2.0000000 > >> exit write_ns > >> > >> > > > > this is not the first iteration. this is what the initial guess > of the > > on-site occupations the code does to start the calculation > > > > > > > >> Atomic wfc used for LDA+U Projector are NOT orthogonalized > >> Starting wfc are 9 atomic + 1 random wfc > >> > >> total cpu time spent up to now is 13.34 secs > >> > >> per-process dynamical memory: 326.3 Mb > >> > >> Self-consistent Calculation > >> > >> iteration # 1 ecut= 45.00 Ry beta=0.70 > >> CG style diagonalization > >> c_bands: 3 eigenvalues not converged > >> c_bands: 2 eigenvalues not converged > >> ethr = 1.00E-12, avg # of iterations = 40.4 > >> enter write_ns > >> U( 1) = 0.0000 > >> alpha( 1) = 0.1000 > >> atom 1 Tr[ns(na)]= 0.0021401 > >> atom 1 spin 1 > >> eigenvalues: 0.0000001 0.0000001 0.0000001 0.0009883 0.0009883 > >> eigenvectors > >> 1 0.0000000 -0.8803392 -0.4743427 0.0000000 0.0013927 > >> 2 0.0000000 -0.4743432 0.8803400 0.0000000 -0.0000040 > >> 3 0.0000000 0.0012242 0.0006642 0.0000000 0.9999990 > >> 4 -0.8886820 0.0000000 0.0000000 -0.4585240 0.0000000 > >> 5 0.4585240 0.0000000 0.0000000 -0.8886820 0.0000000 > >> occupations > >> 0.001 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> 0.000 0.000 0.000 0.001 0.000 > >> 0.000 0.000 0.000 0.000 0.000 > >> > >> > > > > this is the first iteration! the problem is, in my opinion, that > you > > didn't start this calculation from wfc and potential saved from > the scf > > unperturbed run, but from scratch (that's why the code has to > make the > > initial guess for the n). > > > > regards, > > > > Matteo > > > >> ---------------------------------- and end of the file is > >> : > >> End of self-consistent calculation > >> enter write_ns > >> U( 1) = 0.0000 > >> alpha( 1) = 0.1000 > >> atom 1 Tr[ns(na)]= 2.3270531 > >> atom 1 spin 1 > >> eigenvalues: 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825 > >> eigenvectors > >> 1 0.0000000 -0.4359030 -0.7986559 0.0000000 0.4148945 > >> 2 0.0000000 0.7269732 -0.0406891 0.0000000 0.6854592 > >> 3 0.0000000 -0.5305643 0.6004109 0.0000000 0.5983379 > >> 4 -0.9258933 0.0000000 0.0000000 -0.3777851 0.0000000 > >> 5 0.3777851 0.0000000 0.0000000 -0.9258933 0.0000000 > >> occupations > >> 0.927 0.000 0.000 0.000 0.000 > >> 0.000 0.157 0.000 0.000 0.000 > >> 0.000 0.000 0.157 0.000 0.000 > >> 0.000 0.000 0.000 0.927 0.000 > >> 0.000 0.000 0.000 0.000 0.157 > >> > >> > >> Ali Kazempour > >> Physics department, Isfahan University of Technology > >> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > >> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > >> > >> > >> > ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > >> > > > > > > > > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From paulatto at sissa.it Sun Aug 2 20:26:46 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 2 Aug 2009 20:26:46 +0200 (CEST) Subject: [Pw_forum] USPP are not implemented In-Reply-To: <23397.64655.qm@web95012.mail.in2.yahoo.com> References: <23397.64655.qm@web95012.mail.in2.yahoo.com> Message-ID: <55471.78.12.167.22.1249237606.squirrel@webmail.sissa.it> On Sun, August 2, 2009 10:10, Neel Singh wrote: > I was calculating the optical properties and during > epsilon calculation, I got > ???? from grid_build : error #???????? 1 > ???? USPP are not implemented Dear Neel, why are you sending the same email over and over? We got it correctly the first time. The error means that the calculation you are trying to do is not implemented for USPP (ultra-soft pseudo-potential). Either use norm-conserving only, or develop it for ultrasoft. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From marzari at MIT.EDU Mon Aug 3 02:09:00 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 02 Aug 2009 20:09:00 -0400 Subject: [Pw_forum] advice from Stefano Baroni In-Reply-To: <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A730EE2.7000107@democritos.it> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> Message-ID: <4A762A9C.8020309@mit.edu> Dear All, please read very carefully the piece of advice below - in particular, if you are an experienced user of QE, it would be a worthy endeavour if you were to give back to this community by providing advice to the forum (too many are silent, in my opinion). For all the QE-developers: I've heard it too many times that experienced people do not post for fear of being unpleasantly chastised. This, as well, should not happen - and it would be great to recognize that written words always sound harsher than you think. Can we all make an effort ? Pretty please, nicola > Dear Hui Wang, dear All: > > I am extremely glad that the youngest among you find expert advice on > this forum about such basic issues as discussed in this thread. You > should be advised, though, that the human resources of the QE > developers' team are extremely limited, and none of them gets any > rewards for the their work other than the knowledge thay they are > providing a (great) service to the community. > > You will have noticed that most of feedback comes from a very small > number of members of this forum, and guess what? from the 3-4 > individuals who do most of the development, maintanance, planning for > future improvements. A simple application of a simple conservation law > should suggest that every second they spend to answer trivial questions > is a second less spent for more technical work that does require their > expert contribution. > > I think that all of us can give a bit more to this community. To start with: > > 1) For the youngest - Do not think that a free resource (the advice you > can obtain on this forum) is unlimited. Use it sparingly and > judiciously, after making YOURSELF a serious effort to answer your > question. Remember that there is no better teacher than oneself. It may > be painful to teach / learn from oneself, but a self-taught thing is > learnt forever (not to mention your local mentors, senior colleagues, etc) > > 2) For the not-so-young - Many of the questions asked on this forum are general > enough to be answered by any knowledgeable senior graduate student / young postdoc. > Please, give back to this community by keeping the discussion alive without forcing > the same 3-4 people to give all the advice that is requested here. > > 3) For the bravest. Join the developers' efforts by volunteering some of > your time and help fix bugs / implement new features / start new > projects based on QE. > > For the time being, enjoy being with us as much as we enjoy being with you. > > Stefano B -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From nkxirainbow at gmail.com Mon Aug 3 07:32:16 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 3 Aug 2009 13:32:16 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> Message-ID: <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> Dear Stefano Baroni? I read your reply intensively. I'm very grateful to you for your adivce. Through you reply, I know more about the PW_forum. I have translated it to my native language and posted to the other PWscf forum in my country. Once again, thanks you, paolo, Stefano de Gironcoli and other developers of QE. ____________________________________ 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/20090803/f43aa4b1/attachment.htm From mahasinalam at yahoo.co.uk Mon Aug 3 07:47:38 2009 From: mahasinalam at yahoo.co.uk (MAHASIN ALAM) Date: Mon, 3 Aug 2009 05:47:38 +0000 (GMT) Subject: [Pw_forum] Bandstructure Message-ID: <304603.90685.qm@web24102.mail.ird.yahoo.com> Dear Friends, ? I am working on nanowires and try to calculate the bandstructure using PWSCF (QE). I have finished the calcutations.?Can any one please help me how to draw the bandstructures? Thanks a lot for your help. ? Regards ? Mahasin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090803/1840a89c/attachment.htm From baroni at sissa.it Mon Aug 3 09:10:31 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 3 Aug 2009 09:10:31 +0200 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> Message-ID: Thank you for your consideration, Hui Wang. I am curious (maybe many of us are curious) to kow more about "the other PWscf forum in my country": how does it work? where is it it hosted? how many subscribers does it have? ... I have kinda presentiment that not many of the QE developers do contribute to it? (at least, not many of those that I know) Thanks again - SB On Aug 3, 2009, at 7:32 AM, xirainbow wrote: > Dear Stefano Baroni? > I read your reply intensively. > I'm very grateful to you for your adivce. > Through you reply, I know more about the PW_forum. > I have translated it to my native language and posted to the other > PWscf forum in my country. > Once again, thanks you, paolo, Stefano de Gironcoli and other > developers of QE. > > ____________________________________ > 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 --- 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/20090803/e6131e27/attachment.htm From baroni at sissa.it Mon Aug 3 09:12:11 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 3 Aug 2009 09:12:11 +0200 Subject: [Pw_forum] Bandstructure In-Reply-To: <304603.90685.qm@web24102.mail.ird.yahoo.com> References: <304603.90685.qm@web24102.mail.ird.yahoo.com> Message-ID: <9135641A-1738-4EB4-AD05-EFA15031FCAB@sissa.it> Send us the data. I will draw a picture for you, do you prefer pencil, or pen, Sir? Which color? SB On Aug 3, 2009, at 7:47 AM, MAHASIN ALAM wrote: > Dear Friends, > > I am working on nanowires and try to calculate the bandstructure > using PWSCF (QE). I have finished the calcutations. Can any one > please help me how to draw the bandstructures? Thanks a lot for your > help. > > Regards > > Mahasin > > _______________________________________________ > 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/20090803/526558d6/attachment.htm From giannozz at democritos.it Mon Aug 3 09:23:02 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 3 Aug 2009 09:23:02 +0200 Subject: [Pw_forum] Bandstructure In-Reply-To: <304603.90685.qm@web24102.mail.ird.yahoo.com> References: <304603.90685.qm@web24102.mail.ird.yahoo.com> Message-ID: <6AE63A51-10DD-425B-B9B5-38E1193D6C1B@democritos.it> On Aug 3, 2009, at 7:47 , MAHASIN ALAM wrote: > Can any one please help me how to draw the bandstructures? see examples/example01 P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mahasinalam at yahoo.co.uk Mon Aug 3 09:29:52 2009 From: mahasinalam at yahoo.co.uk (MAHASIN ALAM) Date: Mon, 3 Aug 2009 07:29:52 +0000 (GMT) Subject: [Pw_forum] Bandstructure Message-ID: <656613.92444.qm@web24103.mail.ird.yahoo.com> Dear Dr. Baroni, ? Thank you very much. I am sending you one of the output file. I am a new user of PWSCF (QE). Do you need other data? I use 1x1x4 k-points mess for the calculation. Can you please tell me also the steps how to draw it, because?I need to draw for lot of systems. ? ? Warm regards ? Mahasin ? --- On Mon, 3/8/09, Stefano Baroni wrote: From: Stefano Baroni Subject: Re: [Pw_forum] Bandstructure To: "PWSCF Forum" Date: Monday, 3 August, 2009, 12:42 PM Send us the data.? I will draw a picture for you, do you prefer pencil, or pen, Sir? Which color? SB On Aug 3, 2009, at 7:47 AM, MAHASIN ALAM wrote: Dear Friends, ? I am working on nanowires and try to calculate the bandstructure using PWSCF (QE). I have finished the calcutations.?Can any one please help me how to draw the bandstructures? Thanks a lot for your help. ? Regards ? Mahasin _______________________________________________ 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 -----Inline Attachment Follows----- _______________________________________________ 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/20090803/232f4b50/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: band.pw.out Type: application/octet-stream Size: 14604 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090803/232f4b50/attachment-0001.obj From paulatto at sissa.it Mon Aug 3 09:47:17 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 03 Aug 2009 09:47:17 +0200 Subject: [Pw_forum] average.x and workfunction calculations In-Reply-To: <47431d9f0908020131l473fd6bdn35e8dbf9734614b6@mail.gmail.com> References: <47431d9f0908020131l473fd6bdn35e8dbf9734614b6@mail.gmail.com> Message-ID: In data 02 agosto 2009 alle ore 10:31:45, yaldaa kh ha scritto: > How can I write an input file for average.x code in order to calculation > of workfunction? I recond that average.x is not documented properly, although if you open its source file you find this brief explanation: !----------------------------------------------------------------------- PROGRAM average !----------------------------------------------------------------------- ! ! This program calculates planar and macroscopic averages ! of a quantity defined on a 3D-FFT mesh. ! The planar average is done on FFT mesh planes. ! It reads the quantity to average, or several quantities, from ! one or several files and adds them with the given weights. ! It computes the planar average of the resulting quantity ! averaging on planes defined by the FFT mesh points and by one ! direction perpendicular to the planes. ! The planar average can be interpolated on a ! 1D-mesh with an arbitrary number of points. ! Finally, it computes the macroscopic average. The size ! of the averaging window is given as input. ! ! It receive as input the following variables: ! ! nfile ! the number of 3D-FFT files ! for each file: ! filename ! the name of the 3D-FFT file ! weight ! the weight of the quantity in this file ! . ! . ! end ! npt ! the number of points of the thick mesh ! idir ! 1,2 or 3. It is the fixed index which defines ! ! the planes of the planar average ! awin ! the size of the window for macroscopic averages. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From marzari at MIT.EDU Mon Aug 3 09:47:03 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 03 Aug 2009 03:47:03 -0400 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <21fbc4790907311825l11fe6adbj5400bda8410c316e@mail.gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> Message-ID: <4A7695F7.6050205@mit.edu> Stefano Baroni wrote: > Thank you for your consideration, Hui Wang. > I am curious (maybe many of us are curious) to kow more about "the > other PWscf forum in my country": how does it work? where is it it > hosted? how many subscribers does it have? ... > I have kinda presentiment that not many of the QE developers do > contribute to it? (at least, not many of those that I know) > Thanks again - SB ?????????. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From nkxirainbow at gmail.com Mon Aug 3 11:16:35 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 3 Aug 2009 17:16:35 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <4A7695F7.6050205@mit.edu> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> <4A7695F7.6050205@mit.edu> Message-ID: <21fbc4790908030216h7aa22fd5s920c86fc03396081@mail.gmail.com> Dear Nicola Marzari? I think I did not express clearly.Sorry. The "forum" I mentioned is a website, or a BBS. Some people ask questions about PWscf, Abinit and other calculation software; and hope other people to answer it. And the bbs has nothing relation with QE developers. I am not sure whether I describe the bbs clearly. On 8/3/09, Nicola Marzari wrote: > > Stefano Baroni wrote: > > Thank you for your consideration, Hui Wang. > > I am curious (maybe many of us are curious) to kow more about "the > > other PWscf forum in my country": how does it work? where is it it > > hosted? how many subscribers does it have? ... > > I have kinda presentiment that not many of the QE developers do > > contribute to it? (at least, not many of those that I know) > > Thanks again - SB > > > ?????????. > > nicola > > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ____________________________________ 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/20090803/387a2da7/attachment.htm From lanhaiping at gmail.com Mon Aug 3 11:33:17 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 3 Aug 2009 17:33:17 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <21fbc4790908010012i4670cccbi523ded34f37e933f@mail.gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> Message-ID: Dear Stefano and Nicola : As far as i know , there are several Chinese bulletins or web forums for electronic structural calculations, i.e. http://www.materialssimulation.com . But almost efforts are done by graduate students or postdoctors for exchanging experience on softwares such as QE, abinit and vasp . Cheers, Hai-Ping On Mon, Aug 3, 2009 at 3:10 PM, Stefano Baroni wrote: > Thank you for your consideration, Hui Wang.I am curious (maybe many of us > are curious) to kow more about "the other PWscf forum in my country": how > does it work? where is it it hosted? how many subscribers does it have? ... > I have kinda presentiment that not many of the QE developers do contribute > to it? (at least, not many of those that I know) > Thanks again - SB > > On Aug 3, 2009, at 7:32 AM, xirainbow wrote: > > Dear Stefano Baroni? > I read your reply intensively. > I'm very grateful to you for your adivce. > Through you reply, I know more about the PW_forum. > I have translated it to my native language and posted to the other PWscf > forum in my country. > Once again, thanks you, paolo, Stefano de Gironcoli and other developers of > QE. > > ____________________________________ > 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 > > > --- > 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 > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090803/9ab428ad/attachment.htm From lanhaiping at gmail.com Mon Aug 3 11:34:58 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 3 Aug 2009 17:34:58 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: <4A7695F7.6050205@mit.edu> References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> <4A7695F7.6050205@mit.edu> Message-ID: Hi, Nicola . I am surprised that you are good at both Simplied Chinese and Traditional Chinese Characteres. Best, Hai-Ping On Mon, Aug 3, 2009 at 3:47 PM, Nicola Marzari wrote: > Stefano Baroni wrote: > > Thank you for your consideration, Hui Wang. > > I am curious (maybe many of us are curious) to kow more about "the > > other PWscf forum in my country": how does it work? where is it it > > hosted? how many subscribers does it have? ... > > I have kinda presentiment that not many of the QE developers do > > contribute to it? (at least, not many of those that I know) > > Thanks again - SB > > > ?????????. > > nicola > > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090803/a773d92a/attachment.htm From nkxirainbow at gmail.com Mon Aug 3 13:11:30 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 3 Aug 2009 19:11:30 +0800 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> <4A7695F7.6050205@mit.edu> Message-ID: <21fbc4790908030411v1dddfc32pbad808edb24915f7@mail.gmail.com> Dear NIcola: I post translated issue at http://emuch.net/bbs/viewthread.php?tid=1466138&fpage=1. Lan Haiping said you are good at simplified Chinese Characters. I think you can understand the http://emuch.net/bbs/ (???) On 8/3/09, lan haiping wrote: > > Hi, Nicola . > I am surprised that you are good at both Simplied Chinese and Traditional > Chinese Characteres. > > Best, > > Hai-Ping > > -- ____________________________________ 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/20090803/dc762b5b/attachment-0001.htm From paulatto at sissa.it Mon Aug 3 13:47:54 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 03 Aug 2009 13:47:54 +0200 Subject: [Pw_forum] generating k point weights In-Reply-To: References: Message-ID: In data 31 luglio 2009 alle ore 16:25:39, Manoj Srivastava ha scritto: > Dear All, > I was wondering if someone can tell me, how to generate k point weights > in the BZ. Reference of a paper would be great! Dear Manoj, you can find the algorithm tha tgenerates points and weights in pwtools/kpoints.f The obvious reference is the original article from Monkhorst and Pack: Phys. Rev. B 13, 5188 - 5192 (1976), although I don't know if they give an explicit formulation for the weights there (weights depend on how many symmetry-equivalent copies of a point are present in the set, not on the generation algorithm). cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mansourehp at gmail.com Mon Aug 3 14:19:36 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Mon, 3 Aug 2009 15:49:36 +0330 Subject: [Pw_forum] t2g and eg states from output Message-ID: Dear all Please help me to describe this output. Output of a GGA+U nsf run is as follows. (This system has a trigonally distorted (D3d) of octahedral symmetry (MO6) with). ( orbital 3d6) Is my description correct? In this output for atom1 all majority spins (spin1) are occupied. The majority spins contains one singlet (eigenvector 1) and two doublets (eigenvectors 1,2 and eigenvector 3, 4). For atom1 (spin2), one of minority spin is occupied and other minority spins are empty. The occupied minority spin is singlet and Two doublets in minority spin are unoccupied. The singlet is lower than doublets. Thanks in advance for your helping Mansoureh Pashangpour Islamic Azad University, Science & research branch Tehran, IRAN. Parameters of the lda+U calculation: Number of iteration with fixed ns = 0 Starting ns and Hubbard U : enter write_ns U( 1) = 0.0000 U( 2) = 0.0000 U( 3) = 4.0500 U( 4) = 4.0500 alpha( 1) = 0.0000 alpha( 2) = 0.0000 alpha( 3) = 0.0000 alpha( 4) = 0.0000 atom 1 Tr[ns(na)]= 6.5161025 atom 1 spin 1 eigenvalues: 0.9939275 0.9939275 0.9944132 0.9944132 0.9960317 eigenvectors 1 0.0000000 -0.6391294 -0.3462545 -0.3271294 -0.6038276 2 0.0000000 -0.3462545 0.6391294 0.6038276 -0.3271294 3 0.0000000 -0.0863314 0.6812990 -0.7211301 0.0913786 4 -0.0000000 -0.6812990 -0.0863314 0.0913786 0.7211301 5 1.0000000 -0.0000000 -0.0000000 0.0000000 0.0000000 occupations 0.996 0.000 -0.000 0.000 0.000 0.000 0.994 0.000 -0.000 -0.000 -0.000 0.000 0.994 -0.000 -0.000 0.000 -0.000 -0.000 0.994 -0.000 0.000 -0.000 -0.000 -0.000 0.994 atom 1 spin 2 eigenvalues: 0.0634753 0.0634753 0.2104542 0.2104542 0.9955304 eigenvectors 1 -0.0000000 0.0317884 -0.6764254 0.7350136 -0.0345418 2 -0.0000000 -0.6764254 -0.0317884 0.0345418 0.7350136 3 0.0000000 -0.6541234 -0.3369878 -0.3101263 -0.6019830 4 0.0000000 -0.3369878 0.6541234 0.6019830 -0.3101263 5 1.0000000 0.0000000 -0.0000000 0.0000000 0.0000000 occupations 0.996 0.000 -0.000 0.000 0.000 0.000 0.143 0.000 -0.000 0.073 -0.000 0.000 0.143 0.073 -0.000 0.000 -0.000 0.073 0.131 -0.000 0.000 0.073 -0.000 -0.000 0.131 atom 2 Tr[ns(na)]= 6.5161680 atom 2 spin 1 eigenvalues: 0.0634805 0.0634805 0.2104807 0.2104807 0.9955312 eigenvectors 1 -0.0000000 0.0316770 -0.6764602 0.7349922 -0.0344179 2 -0.0000000 -0.6764602 -0.0316770 0.0344179 0.7349922 3 0.0000000 -0.6544993 -0.3361977 -0.3094241 -0.6023774 4 0.0000000 -0.3361977 0.6544993 0.6023774 -0.3094241 5 1.0000000 0.0000000 -0.0000000 0.0000000 0.0000000 occupations 0.996 0.000 -0.000 0.000 0.000 0.000 0.143 0.000 -0.000 0.073 -0.000 0.000 0.143 0.073 -0.000 0.000 -0.000 0.073 0.131 -0.000 0.000 0.073 -0.000 -0.000 0.131 atom 2 spin 2 eigenvalues: 0.9939283 0.9939283 0.9944132 0.9944132 0.9960313 eigenvectors 1 0.0000000 -0.6382822 -0.3467668 -0.3280918 -0.6039077 2 0.0000000 -0.3467668 0.6382822 0.6039077 -0.3280918 3 0.0000000 -0.0865899 0.6817997 -0.7206079 0.0915186 4 -0.0000000 -0.6817997 -0.0865899 0.0915186 0.7206079 5 1.0000000 -0.0000000 -0.0000000 0.0000000 0.0000000 occupations 0.996 0.000 -0.000 0.000 0.000 0.000 0.994 0.000 -0.000 -0.000 -0.000 0.000 0.994 -0.000 -0.000 0.000 -0.000 -0.000 0.994 -0.000 0.000 -0.000 -0.000 -0.000 0.994 nsum = 13.0322704 exit write_ns -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090803/5b31c542/attachment.htm From manoj at phys.ufl.edu Mon Aug 3 16:16:55 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Mon, 3 Aug 2009 10:16:55 -0400 (EDT) Subject: [Pw_forum] generating k point weights In-Reply-To: Message-ID: Dear Lorenzo, Thanks a lot. I will look into the code. In the mean time I found a paper which talks about generation of special k points and evaluation of their weight. Its by Chadi & Cohen, Phys. Rev. B, 8,5747-5753 (1973). They have some examples in it too. Regards, Manoj Srivastava University of Florida, Gainesville, FL On Mon, 3 Aug 2009, Lorenzo Paulatto wrote: > In data 31 luglio 2009 alle ore 16:25:39, Manoj Srivastava > ha scritto: > > > Dear All, > > I was wondering if someone can tell me, how to generate k point weights > > in the BZ. Reference of a paper would be great! > > Dear Manoj, > you can find the algorithm tha tgenerates points and weights in > pwtools/kpoints.f > The obvious reference is the original article from Monkhorst and Pack: > Phys. Rev. B 13, 5188 - 5192 (1976), although I don't know if they give an > explicit formulation for the weights there (weights depend on how many > symmetry-equivalent copies of a point are present in the set, not on the > generation algorithm). > > cheers > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From matteo at umn.edu Mon Aug 3 16:38:41 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 03 Aug 2009 09:38:41 -0500 Subject: [Pw_forum] t2g and eg states from output In-Reply-To: References: Message-ID: <4A76F671.1070308@umn.edu> Hi Mansoureh to me your interpretation looks right. I would add that the singlet state has a z^2 symmetry. In fact the order of the d states in the code is: z^2 xz yz x^2-y^2 xy and the singlet occupied state has components 1 0 0 0 0 Matteo Mansoureh Pashangpour wrote: > > Dear all > > Please help me to describe this output. Output of a GGA+U nsf run is > as follows. (This system has a trigonally distorted (D3d) of > octahedral symmetry (MO6) with). ( orbital 3d6) > > Is my description correct? > > In this output for atom1 all majority spins (spin1) are occupied. The > majority spins contains one singlet (eigenvector 1) and two doublets > (eigenvectors 1,2 and eigenvector 3, 4). For atom1 (spin2), one of > minority spin is occupied and other minority spins are empty. The > occupied minority spin is singlet and Two doublets in minority spin > are unoccupied. The singlet is lower than doublets. > > Thanks in advance for your helping > > Mansoureh Pashangpour > > Islamic Azad University, > > Science & research branch > > Tehran, IRAN. > > Parameters of the lda+U calculation: > Number of iteration with fixed ns = 0 > Starting ns and Hubbard U : > enter write_ns > U( 1) = 0.0000 U( 2) = 0.0000 U( 3) = 4.0500 U( 4) > = 4.0500 > alpha( 1) = 0.0000 alpha( 2) = 0.0000 alpha( 3) = > 0.0000 alpha( 4) = 0.0000 > atom 1 Tr[ns(na)]= 6.5161025 > atom 1 spin 1 > eigenvalues: 0.9939275 0.9939275 0.9944132 0.9944132 0.9960317 > eigenvectors > 1 0.0000000 -0.6391294 -0.3462545 -0.3271294 -0.6038276 > 2 0.0000000 -0.3462545 0.6391294 0.6038276 -0.3271294 > 3 0.0000000 -0.0863314 0.6812990 -0.7211301 0.0913786 > 4 -0.0000000 -0.6812990 -0.0863314 0.0913786 0.7211301 > 5 1.0000000 -0.0000000 -0.0000000 0.0000000 0.0000000 > occupations > 0.996 0.000 -0.000 0.000 0.000 > 0.000 0.994 0.000 -0.000 -0.000 > -0.000 0.000 0.994 -0.000 -0.000 > 0.000 -0.000 -0.000 0.994 -0.000 > 0.000 -0.000 -0.000 -0.000 0.994 > atom 1 spin 2 > eigenvalues: 0.0634753 0.0634753 0.2104542 0.2104542 0.9955304 > eigenvectors > 1 -0.0000000 0.0317884 -0.6764254 0.7350136 -0.0345418 > 2 -0.0000000 -0.6764254 -0.0317884 0.0345418 0.7350136 > 3 0.0000000 -0.6541234 -0.3369878 -0.3101263 -0.6019830 > 4 0.0000000 -0.3369878 0.6541234 0.6019830 -0.3101263 > 5 1.0000000 0.0000000 -0.0000000 0.0000000 0.0000000 > occupations > 0.996 0.000 -0.000 0.000 0.000 > 0.000 0.143 0.000 -0.000 0.073 > -0.000 0.000 0.143 0.073 -0.000 > 0.000 -0.000 0.073 0.131 -0.000 > 0.000 0.073 -0.000 -0.000 0.131 > atom 2 Tr[ns(na)]= 6.5161680 > atom 2 spin 1 > eigenvalues: 0.0634805 0.0634805 0.2104807 0.2104807 0.9955312 > eigenvectors > 1 -0.0000000 0.0316770 -0.6764602 0.7349922 -0.0344179 > 2 -0.0000000 -0.6764602 -0.0316770 0.0344179 0.7349922 > 3 0.0000000 -0.6544993 -0.3361977 -0.3094241 -0.6023774 > 4 0.0000000 -0.3361977 0.6544993 0.6023774 -0.3094241 > 5 1.0000000 0.0000000 -0.0000000 0.0000000 0.0000000 > occupations > 0.996 0.000 -0.000 0.000 0.000 > 0.000 0.143 0.000 -0.000 0.073 > -0.000 0.000 0.143 0.073 -0.000 > 0.000 -0.000 0.073 0.131 -0.000 > 0.000 0.073 -0.000 -0.000 0.131 > atom 2 spin 2 > eigenvalues: 0.9939283 0.9939283 0.9944132 0.9944132 0.9960313 > eigenvectors > 1 0.0000000 -0.6382822 -0.3467668 -0.3280918 -0.6039077 > 2 0.0000000 -0.3467668 0.6382822 0.6039077 -0.3280918 > 3 0.0000000 -0.0865899 0.6817997 -0.7206079 0.0915186 > 4 -0.0000000 -0.6817997 -0.0865899 0.0915186 0.7206079 > 5 1.0000000 -0.0000000 -0.0000000 0.0000000 0.0000000 > occupations > 0.996 0.000 -0.000 0.000 0.000 > 0.000 0.994 0.000 -0.000 -0.000 > -0.000 0.000 0.994 -0.000 -0.000 > 0.000 -0.000 -0.000 0.994 -0.000 > 0.000 -0.000 -0.000 -0.000 0.994 > nsum = 13.0322704 > exit write_ns > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From mahasinalam at yahoo.co.uk Mon Aug 3 18:44:51 2009 From: mahasinalam at yahoo.co.uk (MAHASIN ALAM) Date: Mon, 3 Aug 2009 16:44:51 +0000 (GMT) Subject: [Pw_forum] Fermi enery Message-ID: <676800.87577.qm@web24105.mail.ird.yahoo.com> Dear Friends, ? Can any one tell me how to get the Fermi Energy from PWSCF (QE) result files. Thank you. ? Warm regards ? Mahasin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090803/848e2e39/attachment.htm From manoj at phys.ufl.edu Mon Aug 3 18:58:34 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Mon, 3 Aug 2009 12:58:34 -0400 (EDT) Subject: [Pw_forum] Fermi enery In-Reply-To: <676800.87577.qm@web24105.mail.ird.yahoo.com> Message-ID: Dear Mahasin, 'grep' is very useful to find stuff around, for example if you have a SCF output file, just grep Fermi. -manoj On Mon, 3 Aug 2009, MAHASIN ALAM wrote: > Dear Friends, > ? > Can any one tell me how to get the Fermi Energy from PWSCF (QE) result files. Thank you. > ? > Warm regards > ? > Mahasin From paulatto at sissa.it Mon Aug 3 19:07:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 03 Aug 2009 19:07:34 +0200 Subject: [Pw_forum] Fermi enery In-Reply-To: <676800.87577.qm@web24105.mail.ird.yahoo.com> References: <676800.87577.qm@web24105.mail.ird.yahoo.com> Message-ID: In data 03 agosto 2009 alle ore 18:44:51, MAHASIN ALAM ha scritto: > Can any one tell me how to get the Fermi Energy from PWSCF (QE) result > files. Thank you. You only get the fermi energy if you used smearing to define the occupations; it is somewhere in the output of pw.x, just a couple of lines over "total energy". Otherwise, if you used fixed occupation you will get the energies of HOMO and LUMO orbitals (but only if nbands>nelec*2, otherwise LUMO would be impossible to compute) If you have specified fixed occupations, I think there is neither the fermi energy nor the HOME and LUMO, but I could be wrong. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From hande at newton.physics.metu.edu.tr Mon Aug 3 18:58:47 2009 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Mon, 3 Aug 2009 19:58:47 +0300 (EEST) Subject: [Pw_forum] Fermi enery In-Reply-To: <676800.87577.qm@web24105.mail.ird.yahoo.com> Message-ID: Dear Mahasin Try grep Fermi for metals. This won't work for semiconductors in which case you can grep for "highest" and "lowest" to get the HOMO and LUMO respectively. Regards, Hande On Mon, 3 Aug 2009, MAHASIN ALAM wrote: > Dear Friends, > ? > Can any one tell me how to get the Fermi Energy from PWSCF (QE) result files. Thank you. > ? > Warm regards > ? > Mahasin -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From vtmtrinh at caltech.edu Tue Aug 4 04:20:59 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Mon, 3 Aug 2009 19:20:59 -0700 (PDT) Subject: [Pw_forum] printing wavefunction on real grid Message-ID: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> Dear PWSCF Users, I would like to print out the wavefunction with both real and imaginary parts in real space. I started to look first at 'postproc.f90', 'punch_plot.f90', and 'local_dos.f90' (in directory PP). I started from there, because with the plot_num=7 |psi|^2 can be printed out, and thus I think I can hard code, adding a few lines to print out psi in real space. There is one part in the code 'local_dos' I don't understand is the case where ', lsign=true', i.e. k=gamma and iflag=0, write |psi|^2*sign(psi), why |psi|^2 has to multiply by sign(psi). I read thru the code at this part, but I still could not get it. MyTrinh Vo JPL/CalTech From marzari at MIT.EDU Tue Aug 4 05:00:50 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 03 Aug 2009 23:00:50 -0400 Subject: [Pw_forum] *.fc file in PW_SCF help. In-Reply-To: References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com> <5038BB04-82D7-4CC2-A1A3-8FD46EC44A95@democritos.it> <4A73F4D0.7070802@sissa.it> <21fbc4790908010204n6a1d1253qeed82255dca66d4a@mail.gmail.com> <21fbc4790908011811m405b99a5o35aef4638e9298cc@mail.gmail.com> <9DDAB292-6AF5-4EAA-BBF4-D358802D2737@sissa.it> <21fbc4790908022232s5158665fubeda733bb1345cfb@mail.gmail.com> <4A7695F7.6050205@mit.edu> Message-ID: <4A77A462.4030308@mit.edu> lan haiping wrote: > Hi, Nicola . > I am surprised that you are good at both Simplied Chinese and > Traditional Chinese Characteres. > > Best, > > Hai-Ping ??????. ???babelfish . nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From shobhana at jncasr.ac.in Tue Aug 4 07:20:30 2009 From: shobhana at jncasr.ac.in (shobhana at jncasr.ac.in) Date: Tue, 4 Aug 2009 10:50:30 +0530 (IST) Subject: [Pw_forum] generating k-point weights In-Reply-To: References: Message-ID: <53585.172.16.1.8.1249363230.squirrel@172.16.1.8> > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 03 Aug 2009 13:47:54 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] generating k point weights > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 31 luglio 2009 alle ore 16:25:39, Manoj Srivastava > ha scritto: > >> Dear All, >> I was wondering if someone can tell me, how to generate k point weights >> in the BZ. Reference of a paper would be great! > > Dear Manoj, > you can find the algorithm tha tgenerates points and weights in > pwtools/kpoints.f > The obvious reference is the original article from Monkhorst and Pack: Phys. Rev. B 13, 5188 - 5192 (1976), although I don't know if they give an > explicit formulation for the weights there (weights depend on how many symmetry-equivalent copies of a point are present in the set, not on the generation algorithm). > > cheers > > Hello, I would like to point out that pwscf generates k-points slightly differently from the way it was done by Monkhorst and Pack in their original paper. For them, the k-point grid either included or did not include Gamma (zone center) depending on whether the number of divisions was odd or even. However, in PWscf, 'unshifted' grids always include Gamma, and 'shifted' ones do not, regardless of whether the number of divisions is odd or even. To get weights: you have to see how many k points in the full BZ are equivalent to the given point in the IBZ. I have a slide illustrating this in my recent talk at the UCSB Q-E summer school, see my first lecture, slides available at http://www.quantum-espresso.org/wiki/index.php/QESB09 Shobhana Narasimhan Theoretical Sciences Unit Jawaharlal Nehru Centre for Advanced Scientific Research Bangalore From paulatto at sissa.it Tue Aug 4 08:55:10 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 4 Aug 2009 08:55:10 +0200 (CEST) Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> Message-ID: <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> On Tue, August 4, 2009 04:20, vtmtrinh at caltech.edu wrote: > I think I can hard code, adding a few lines to print out psi in real > space. Dear MyTrin, You definitely can! > > There is one part in the code 'local_dos' I don't understand is the case > where ', lsign=true', i.e. k=gamma and iflag=0, write |psi|^2*sign(psi), > why |psi|^2 has to multiply by sign(psi). I read thru the code at this > part, but I still could not get it. Maybe I've misunderstood your question, but that's exactly what the option lsign is supposed to do. Wavefunctions in Gamma can be defined ti be real, hence they have a well defined sign. Although, they can always be multiplied by any complex number (-1 included) and still remain perfectly good eigenvalues. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Tue Aug 4 08:57:07 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 4 Aug 2009 08:57:07 +0200 (CEST) Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> Message-ID: <56775.78.12.161.81.1249369027.squirrel@webmail.sissa.it> On Tue, August 4, 2009 08:55, Lorenzo Paulatto wrote: > good eigenvalues. This slipped me, I mean "good eigenvector". -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From bipulrr at gmail.com Tue Aug 4 09:10:56 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 4 Aug 2009 12:40:56 +0530 Subject: [Pw_forum] CVS vs released versions Message-ID: <3a749910908040010t3f3a767cw9a455b7a9d48663f@mail.gmail.com> Dear PWSCF users, Is it good to use cvs version of espresso or the latest release of espresso? I just installed the cvs and keep on updating it time to time and dont use the latest release of espresso. So does the cvs version also give all the information (in terms of calculation) which the latest release will do? regards -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090804/8a693e43/attachment.htm From giannozz at democritos.it Tue Aug 4 09:34:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Aug 2009 09:34:38 +0200 Subject: [Pw_forum] CVS vs released versions In-Reply-To: <3a749910908040010t3f3a767cw9a455b7a9d48663f@mail.gmail.com> References: <3a749910908040010t3f3a767cw9a455b7a9d48663f@mail.gmail.com> Message-ID: On Aug 4, 2009, at 9:10 , Bipul Rakshit wrote: > Is it good to use cvs version of espresso or the > latest release of espresso? you should use the cvs version only in the following cases: - if you plan to add something new to the distribution - if you need some new development that is not yet available in the stable version. If you just want to perform "normal" calculations, the latest release is all you need. The latest release and the cvs version will produce the same numbers, especially if you perform "normal" calculations, but on bad days the cvs version may not even compile. This is usually fixed in hours, but it may happen that a change introduces a bug that is not noticed before a few days or weeks or months. Right now there are few differences between the cvs version and the latest release, but this will not last. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From kazempoor2000 at yahoo.com Tue Aug 4 10:07:44 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 4 Aug 2009 01:07:44 -0700 (PDT) Subject: [Pw_forum] U for Oxygen In-Reply-To: <4A75B16B.6030702@umn.edu> Message-ID: <622958.53055.qm@web112508.mail.gq1.yahoo.com> Dear Matteo I used your comment and followed?? your example for NiO and I succeed? to get U for TiO2. But in file Ur16.out I see three column . The first is number of atom in supercell , second is U value for Ni atom and I don,t know? the third? does the third belong to? U value for Oxygen or not? Because the third column kas big value? another question is for isolated atom Hubbard parameter. What do you expect about the value of U for Isolated atom? Is this big value (greater than 10 eV) or? it would be tiny value? should we choose for running the script for isolated atom only gamma point or we have to choose a fine mesh? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Sun, 8/2/09, Matteo Cococcioni wrote: From: Matteo Cococcioni Subject: Re: [Pw_forum] occupation To: "PWSCF Forum" Date: Sunday, August 2, 2009, 8:31 AM Dear Ali, 1, -1, 0 are just spin indexes to tell the code what is the relative magnetization of the atoms (parallel, antiparallel, or none). if your system is non magnetic put all 0. or set magn = .false. and put nothing. you should look at the examples on Fe and Si as well and learn from there by comparison. Matteo ali kazempour wrote: > Dear Matteo > I follow? your link and is useful for me, but when I want to study a? > nonmagnetic material like Tio2 ,how do I change the format of > pos_file.? for NiO it is in tutorial ,but NiO is antiferromagnetic and > in pos_nio.r16 you add a switch 1,-1 and 0 in front of atomic type. > but for TiO2, it is nonmagnetic. How can I define the differnet type? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Thu, 7/30/09, Matteo Cococcioni //* wrote: > > >? ???From: Matteo Cococcioni >? ???Subject: Re: [Pw_forum] occupation >? ???To: "PWSCF Forum" >? ???Date: Thursday, July 30, 2009, 11:18 AM > > >? ???the new tutorial on the calculation of U can be downloaded from this >? ???webpage: > >? ???http://www.quantum-espresso.org/wiki/index.php/QESB09#First_week > > >? ???Matteo Cococcioni wrote: >? ???> Dear Ali, >? ???> >? ???> on the wiki page of quantum-espresso you should be able to find >? ???a new >? ???> tutorial on the calculation of U. Please download it >? ???> and run the scripts in there following the instructions. >? ???> >? ???> >? ???> >? ???> ali kazempour wrote: >? ???>??? >? ???>> Dear all >? ???>> >? ???>> From Linear response calculation ,I get for TiO2 bulk U=5.73, >? ???But when >? ???>> I double the unit cell in z direction and again compute U ,I >? ???get three >? ???>> different value for Ti atoms.(U=5.63,5.46,5.70). >? ???>> >? ???>>? ??? >? ???> >? ???> what are these three values? I assume they are what you get with >? ???> supercells of three different sizes. is this correct? if it is >? ???the only >? ???> strange thing is that the intermediate value is lower than the >? ???other >? ???> two. otherwise you got pretty nice convergence of U which is >? ???what you >? ???> want to achieve. Is there any particular reason (apart >? ???computational >? ???> cost) why you only enlarge the cell in z direction? >? ???> >? ???>??? >? ???>> Why these values are not same . what is the main reason? Does >? ???it in >? ???>> numerical variation errors? >? ???>> ANother question: >? ???>> When we perturb D level by alpha, it give rise to change in d >? ???>> occupancy . Is it correct that if we impose negative alpha , the >? ???>> occupation becomes less than initial state .? >? ???>> >? ???>>? ??? >? ???> >? ???> no. positive alpha -- > decrease in total n. but you need to >? ???look at the >? ???> right n.... >? ???> >? ???>??? >? ???>> for Ti isolated atom for apha=0.1? tr[ns(na)] after >? ???first-iteration >? ???>> equal to the 0.002 and at the end of calculation is 2.327 while we >? ???>> know that for Ti,? tr[ns(na)] =2.000. Does it seems to be correct.? >? ???>> >? ???>>? ? ? Number of iteration with fixed ns =? 0 >? ???>>? ? ? Starting ns and Hubbard U : >? ???>>? enter write_ns >? ???>> U( 1) =? 0.0000 >? ???>> alpha( 1) =? 0.1000 >? ???>> atom? 1???Tr[ns(na)]=???2.0000000 >? ???>> atom? 1? spin? 1 >? ???>> eigenvalues:? 0.4000000 0.4000000 0.4000000 0.4000000 0.4000000 >? ???>>? eigenvectors >? ???>>? 1???1.0000000? 0.0000000? 0.0000000? 0.0000000? 0.0000000 >? ???>>? 2???0.0000000? 1.0000000? 0.0000000? 0.0000000? 0.0000000 >? ???>>? 3???0.0000000? 0.0000000? 1.0000000? 0.0000000? 0.0000000 >? ???>>? 4???0.0000000? 0.0000000? 0.0000000? 1.0000000? 0.0000000 >? ???>>? 5???0.0000000? 0.0000000? 0.0000000? 0.0000000? 1.0000000 >? ???>>? occupations >? ???>>? 0.400? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.400? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.400? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.400? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.400 >? ???>> atom? 1? spin? 2 >? ???>> eigenvalues:? 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >? ???>>? eigenvectors >? ???>>? 1???1.0000000? 0.0000000? 0.0000000? 0.0000000? 0.0000000 >? ???>>? 2???0.0000000? 1.0000000? 0.0000000? 0.0000000? 0.0000000 >? ???>>? 3???0.0000000? 0.0000000? 1.0000000? 0.0000000? 0.0000000 >? ???>>? 4???0.0000000? 0.0000000? 0.0000000? 1.0000000? 0.0000000 >? ???>>? 5???0.0000000? 0.0000000? 0.0000000? 0.0000000? 1.0000000 >? ???>>? occupations >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>> nsum =???2.0000000 >? ???>>? exit write_ns >? ???>> >? ???>>? ??? >? ???> >? ???> this is not the first iteration. this is what the initial guess >? ???of the >? ???> on-site occupations the code does to start the calculation >? ???> >? ???> >? ???>??? >? ???>>? Atomic wfc used for LDA+U Projector are NOT orthogonalized >? ???>>? ? ? Starting wfc are? ? 9 atomic +? ? 1 random wfc >? ???>> >? ???>>? ? ? total cpu time spent up to now is? ???13.34 secs >? ???>> >? ???>>? ? ? per-process dynamical memory:???326.3 Mb >? ???>> >? ???>>? ? ? Self-consistent Calculation >? ???>> >? ???>>? ? ? iteration #? 1? ???ecut=? ? 45.00 Ry? ???beta=0.70 >? ???>>? ? ? CG style diagonalization >? ???>>? ? ? c_bands:? 3 eigenvalues not converged >? ???>>? ? ? c_bands:? 2 eigenvalues not converged >? ???>>? ? ? ethr =? 1.00E-12,? avg # of iterations = 40.4 >? ???>>? enter write_ns >? ???>> U( 1) =? 0.0000 >? ???>> alpha( 1) =? 0.1000 >? ???>> atom? 1???Tr[ns(na)]=???0.0021401 >? ???>> atom? 1? spin? 1 >? ???>> eigenvalues:? 0.0000001 0.0000001 0.0000001 0.0009883 0.0009883 >? ???>>? eigenvectors >? ???>>? 1???0.0000000 -0.8803392 -0.4743427? 0.0000000? 0.0013927 >? ???>>? 2???0.0000000 -0.4743432? 0.8803400? 0.0000000 -0.0000040 >? ???>>? 3???0.0000000? 0.0012242? 0.0006642? 0.0000000? 0.9999990 >? ???>>? 4? -0.8886820? 0.0000000? 0.0000000 -0.4585240? 0.0000000 >? ???>>? 5???0.4585240? 0.0000000? 0.0000000 -0.8886820? 0.0000000 >? ???>>? occupations >? ???>>? 0.001? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.001? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.000 >? ???>> >? ???>>? ??? >? ???> >? ???> this is the first iteration! the problem is, in my opinion, that >? ???you >? ???> didn't start this calculation from wfc and potential saved from >? ???the scf >? ???> unperturbed run, but from scratch (that's why the code has to >? ???make the >? ???> initial guess for the n). >? ???> >? ???> regards, >? ???> >? ???> Matteo >? ???>??? >? ???>> ---------------------------------- and end of the file is >? ???>> : >? ???>>? ? ? End of self-consistent calculation >? ???>>? enter write_ns >? ???>> U( 1) =? 0.0000 >? ???>> alpha( 1) =? 0.1000 >? ???>> atom? 1???Tr[ns(na)]=???2.3270531 >? ???>> atom? 1? spin? 1 >? ???>> eigenvalues:? 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825 >? ???>>? eigenvectors >? ???>>? 1???0.0000000 -0.4359030 -0.7986559? 0.0000000? 0.4148945 >? ???>>? 2???0.0000000? 0.7269732 -0.0406891? 0.0000000? 0.6854592 >? ???>>? 3???0.0000000 -0.5305643? 0.6004109? 0.0000000? 0.5983379 >? ???>>? 4? -0.9258933? 0.0000000? 0.0000000 -0.3777851? 0.0000000 >? ???>>? 5???0.3777851? 0.0000000? 0.0000000 -0.9258933? 0.0000000 >? ???>>? occupations >? ???>>? 0.927? 0.000? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.157? 0.000? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.157? 0.000? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.927? 0.000 >? ???>>? 0.000? 0.000? 0.000? 0.000? 0.157 >? ???>> >? ???>> >? ???>> Ali Kazempour >? ???>> Physics department, Isfahan University of Technology >? ???>> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >? ???>> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >? ???>> >? ???>> >? ???>> >? ???------------------------------------------------------------------------ >? ???>> >? ???>> _______________________________________________ >? ???>> Pw_forum mailing list >? ???>> Pw_forum at pwscf.org >? ???>> http://www.democritos.it/mailman/listinfo/pw_forum >? ???>>??? >? ???>>? ??? >? ???> >? ???> >? ???>??? > > >? ???-- >? ???%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >? ???Matteo Cococcioni >? ???Department of Chemical Engineering and Materials Science, >? ???University of Minnesota >? ???421 Washington Av. SE >? ???Minneapolis, MN 55455 >? ???Tel. +1 612 624 9056? ? Fax +1 612 626 7246 >? ???%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >? ???_______________________________________________ >? ???Pw_forum mailing list >? ???Pw_forum at pwscf.org >? ???http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >??? -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056? ? Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% _______________________________________________ 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/20090804/8f02beba/attachment-0001.htm From bipulrr at gmail.com Tue Aug 4 11:06:52 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 4 Aug 2009 14:36:52 +0530 Subject: [Pw_forum] LOOP WAS VECTORISE Message-ID: <3a749910908040206m211b6483hd743d8c94c01ea0e@mail.gmail.com> Dear Pwscf users, I am using mpif90 and /mkl/10.0.3.020/lib/em64t and trying to compile espresso-4.1 During compilation, there comes LOOP WAS VECTORISED I have gone through the previous pwscf post and use all the solution which the users said, but still the remark comes. So is that some error in compilation? If so how can i remove it. Following is my make.sys file # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA FDFLAGS = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS = -I../include # MODFLAGS = flag used by f90 compiler to locate modules # You need to search for modules in ./, in ../iotk/src, in ../Modules # Some applications also need modules in ../PW and ../PH MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH -I../EE -I../GIPAW # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpif90 #F90 = ifort CC = mpicc F77 = mpif90 # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD = mpif90 LDFLAGS = -i-static -openmp LD_LIBS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : ../flib/blas.a BLAS_LIBS = -L/opt/intel/mkl/10.0.3.020/lib/em64t -lmkl_em64t # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = -L/opt/intel/mkl/10.0.3.020/lib/em64t -lmkl_lapack -lmkl_ia32 -lguide -lpthread -lmkl_core -lmkl_em64t # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW in DFLAGS) FFT_LIBS = # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = # pgplot libraries (used by some post-processing tools) PGPLOT_LIBS = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv # ARFLAGS_DYNAMIC is used in iotk to produce a dynamical library, # for Mac OS-X with PowerPC and xlf compiler. In all other cases # ARFLAGS_DYNAMIC = $(ARFLAGS) AR = ar ARFLAGS = ruv ARFLAGS_DYNAMIC= ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a ../Multigrid/mglib.a LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090804/11c65089/attachment.htm From giannozz at democritos.it Tue Aug 4 11:41:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Aug 2009 11:41:52 +0200 Subject: [Pw_forum] LOOP WAS VECTORISE In-Reply-To: <3a749910908040206m211b6483hd743d8c94c01ea0e@mail.gmail.com> References: <3a749910908040206m211b6483hd743d8c94c01ea0e@mail.gmail.com> Message-ID: <3385C284-548D-4AC9-B19D-83E0CF28A5CE@democritos.it> On Aug 4, 2009, at 11:06 , Bipul Rakshit wrote: > During compilation, there comes LOOP WAS VECTORISED never heard about good old "vector computers"? once upon a time, everybody was happy to see such messages P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From bipulrr at gmail.com Tue Aug 4 11:58:36 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 4 Aug 2009 15:28:36 +0530 Subject: [Pw_forum] LOOP WAS VECTORISE In-Reply-To: <3385C284-548D-4AC9-B19D-83E0CF28A5CE@democritos.it> References: <3a749910908040206m211b6483hd743d8c94c01ea0e@mail.gmail.com> <3385C284-548D-4AC9-B19D-83E0CF28A5CE@democritos.it> Message-ID: <3a749910908040258l201c631di4ab6bf919c504caa@mail.gmail.com> Dear Paolo, Actually I have joined a new institute and not at all familiar with the MPI version which is installed. So I think they use some old versions of mpif90, and that's why these error comes.. Am i right?? On Tue, Aug 4, 2009 at 3:11 PM, Paolo Giannozzi wrote: > > On Aug 4, 2009, at 11:06 , Bipul Rakshit wrote: > > > During compilation, there comes LOOP WAS VECTORISED > > never heard about good old "vector computers"? once > upon a time, everybody was happy to see such messages > > 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 mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090804/6e142f7a/attachment.htm From paulatto at sissa.it Tue Aug 4 12:03:37 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 04 Aug 2009 12:03:37 +0200 Subject: [Pw_forum] LOOP WAS VECTORISE In-Reply-To: <3a749910908040258l201c631di4ab6bf919c504caa@mail.gmail.com> References: <3a749910908040206m211b6483hd743d8c94c01ea0e@mail.gmail.com> <3385C284-548D-4AC9-B19D-83E0CF28A5CE@democritos.it> <3a749910908040258l201c631di4ab6bf919c504caa@mail.gmail.com> Message-ID: In data 04 agosto 2009 alle ore 11:58:36, Bipul Rakshit ha scritto: > and that's why these error comes.. Am i right?? Dear Bipul, they are not errors... it is the compiler boasting its awesome optimization features. Those messages are supposed to tell you that the compiler is using vectorization to improve code performance. Although the real effectiveness of vectorization on modern hardware is debated, they are at least harmless messages. best regards P.S. If you are getting any errors, they are not related to the "loop was vectorized" messages. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Tue Aug 4 12:06:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Aug 2009 12:06:16 +0200 Subject: [Pw_forum] LOOP WAS VECTORISE In-Reply-To: <3a749910908040258l201c631di4ab6bf919c504caa@mail.gmail.com> References: <3a749910908040206m211b6483hd743d8c94c01ea0e@mail.gmail.com> <3385C284-548D-4AC9-B19D-83E0CF28A5CE@democritos.it> <3a749910908040258l201c631di4ab6bf919c504caa@mail.gmail.com> Message-ID: <73089C08-E340-48AD-A631-F0F8B8283707@democritos.it> On Aug 4, 2009, at 11:58 , Bipul Rakshit wrote: > Actually I have joined a new institute and not at all familiar > with the MPI version which is installed. So I think they use > some old versions of mpif90, and that's why these error > comes.. Am i right?? no, you are wrong --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From matteo at umn.edu Tue Aug 4 15:59:19 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 04 Aug 2009 08:59:19 -0500 Subject: [Pw_forum] U for Oxygen In-Reply-To: <622958.53055.qm@web112508.mail.gq1.yahoo.com> References: <622958.53055.qm@web112508.mail.gq1.yahoo.com> Message-ID: <4A783EB7.9060902@umn.edu> Dear Ali, ali kazempour wrote: > Dear Matteo > I used your comment and followed your example for NiO and I succeed > to get U for TiO2. But in file Ur16.out I see three column . > I don't have any three column section in any of my files. so if you want me to help you you have to report at least a section of your output file. This is a good habit actually in consideration of the fact that this is not a private conversation (I would have asked you in any case as I don't remember by heart the format of any file) between me and you but a message to the forum and you want other people to understand what you are saying. > The first is number of atom in supercell , second is U value for Ni > atom and I don,t know the third? does the third belong to U value > for Oxygen or not? Because the third column kas big value? > > > another question is for isolated atom Hubbard parameter. What do you > expect about the value of U for Isolated atom? Is this big value > (greater than 10 eV) or it would be tiny value? > I think it will be meaningless for the reasons I explained in my last email. To obtain a meaningful number for the isolated atom you probably have to abandon the idea to use a perturbation in the potential and change instead the number of electrons directly. This means you will have to do calculations on atoms having fractional charges which requires additional corrections if you use a code designed for periodic systems (crystals). However I have never done this isolated atom calculation of U before so I don't have more details about it. I see (from a private email) you are thinking of computing U for the isolated atom and to obtain a value for the crystal just by dividing by the epsilon_inft. the method is proposed in http://link.aps.org/doi/10.1103/PhysRevB.74.045202 (which I haven't re-read yet). I see a couple of problems: 1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and Fe3+. these Fe ions likely have different U. how do you obtain a different number from the atomic code? would you do the calculation for isolated Fe2+ and Fe3+? 2) how do you get epsilon? since it's a linear response property I don't think its calculation is any cheaper than the direct calculation of U. regards, Matteo > should we choose for running the script for isolated atom only gamma > point or we have to choose a fine mesh? > thanks a lot > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Sun, 8/2/09, Matteo Cococcioni //* wrote: > > > From: Matteo Cococcioni > Subject: Re: [Pw_forum] occupation > To: "PWSCF Forum" > Date: Sunday, August 2, 2009, 8:31 AM > > > Dear Ali, > > 1, -1, 0 are just spin indexes to tell the code what is the relative > magnetization of the atoms (parallel, antiparallel, or none). if > your system is non magnetic put all 0. or set magn = .false. and put > nothing. > you should look at the examples on Fe and Si as well and learn from > there by comparison. > > Matteo > > > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From jjr19 at uakron.edu Tue Aug 4 16:14:07 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Tue, 4 Aug 2009 07:14:07 -0700 (PDT) Subject: [Pw_forum] References for damped dynamics structural minimization? Message-ID: <835044.69547.qm@web50905.mail.re2.yahoo.com> I've been trying to find references for the damped quick-min Verlet algorithm used by PWscf in structural relaxation (when calculation = 'relax' and ion_dynamics = 'damp'), but about the only references that I find relate to the quick-min Verlet minimization often used in NEB calculations. Is the same damped dynamics algorithm used in both the NEB calculations and structural relaxation? Where might I find references (journal articles, textbooks, etc.) on the damped dynamics algorithm? University of Akron Civil Engineering (!) Dept. From kazempoor2000 at yahoo.com Tue Aug 4 17:40:40 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 4 Aug 2009 08:40:40 -0700 (PDT) Subject: [Pw_forum] U for Oxygen Message-ID: <916113.6562.qm@web112505.mail.gq1.yahoo.com> Dear Matteo Thanks for your help. In attachment there is outout file for U for NiO that I get from wiki.This file has three column. thanks Ali Kazempour Physics de 8/4/09, Matteo Cococcioni wrote: From: Matteo Cococcioni Subject: Re: [Pw_forum] U for Oxygen To: "PWSCF Forum" Date: Tuesday, August 4, 2009, 6:59 AM Dear Ali, ali kazempour wrote: > Dear Matteo > I used your comment and followed???your example for NiO and I succeed? > to get U for TiO2. But in file Ur16.out I see three column . > I don't have any three column section in any of my files. so if you want me to help you you have to report at least a section of your output file. This is a good habit actually in consideration of the fact that this is not a private conversation (I would have asked you in any case as I don't remember by heart the format of any file) between me and you but a message to the forum and you want other people to understand what you are saying. > The first is number of atom in supercell , second is U value for Ni > atom and I don,t know? the third? does the third belong to? U value > for Oxygen or not? Because the third column kas big value? > > > another question is for isolated atom Hubbard parameter. What do you > expect about the value of U for Isolated atom? Is this big value > (greater than 10 eV) or? it would be tiny value? > I think it will be meaningless for the reasons I explained in my last email. To obtain a meaningful number for the isolated atom you probably have to abandon the idea to use a perturbation in the potential and change instead the number of electrons directly. This means you will have to do calculations on atoms having fractional charges which requires additional corrections if you use a code designed for periodic systems (crystals). However I have never done this isolated atom calculation of U before so I don't have more details about it. I see (from a private email) you are thinking of computing U for the isolated atom and to obtain a value for the crystal just by dividing by the epsilon_inft. the method is proposed in http://link.aps.org/doi/10.1103/PhysRevB.74.045202 (which I haven't re-read yet). I see a couple of problems: 1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and Fe3+. these Fe ions likely have different U. how do you obtain a different number from the atomic code? would you do the calculation for isolated Fe2+ and Fe3+? 2) how do you get epsilon? since it's a linear response property I don't think its calculation is any cheaper than the direct calculation of U. regards, Matteo > should we choose for running the script for isolated atom only gamma > point or we have to choose a fine mesh? > thanks a lot > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Sun, 8/2/09, Matteo Cococcioni //* wrote: > > >? ???From: Matteo Cococcioni >? ???Subject: Re: [Pw_forum] occupation >? ???To: "PWSCF Forum" >? ???Date: Sunday, August 2, 2009, 8:31 AM > > >? ???Dear Ali, > >? ???1, -1, 0 are just spin indexes to tell the code what is the relative >? ???magnetization of the atoms (parallel, antiparallel, or none). if >? ???your system is non magnetic put all 0. or set magn = .false. and put >? ???nothing. >? ???you should look at the examples on Fe and Si as well and learn from >? ???there by comparison. > >? ???Matteo > > > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056? ? Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% _______________________________________________ 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/20090804/db4f7653/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Ur16.out Type: application/octet-stream Size: 191 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090804/db4f7653/attachment.obj From matteo at umn.edu Tue Aug 4 17:48:11 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 04 Aug 2009 10:48:11 -0500 Subject: [Pw_forum] U for Oxygen In-Reply-To: <916113.6562.qm@web112505.mail.gq1.yahoo.com> References: <916113.6562.qm@web112505.mail.gq1.yahoo.com> Message-ID: <4A78583B.5040702@umn.edu> Dear Ali, this is a file where we collected the results from the calculation of U. first column is the number of atom in the supercell, second column is the U of Ni third column the U of O. Matteo ali kazempour wrote: > Dear Matteo > Thanks for your help. In attachment there is outout file for U for NiO > that I get from wiki.This file has three column. > thanks > > Ali Kazempour > Physics de *8/4/09, Matteo Cococcioni //* wrote: > > > From: Matteo Cococcioni > Subject: Re: [Pw_forum] U for Oxygen > To: "PWSCF Forum" > Date: Tuesday, August 4, 2009, 6:59 AM > > > > Dear Ali, > > > > ali kazempour wrote: > > Dear Matteo > > I used your comment and followed your example for NiO and I > succeed > > to get U for TiO2. But in file Ur16.out I see three column . > > > > I don't have any three column section in any of my files. so if > you want > me to help you you have to report at least a section of your output > file. This is a good habit actually in consideration of the fact that > this is not a private conversation (I would have asked you in any > case > as I don't remember by heart the format of any file) between me > and you > but a message to the forum and you want other people to understand > what you are saying. > > > The first is number of atom in supercell , second is U value for Ni > > atom and I don,t know the third? does the third belong to U value > > for Oxygen or not? Because the third column kas big value? > > > > > > another question is for isolated atom Hubbard parameter. What do > you > > expect about the value of U for Isolated atom? Is this big value > > (greater than 10 eV) or it would be tiny value? > > > > I think it will be meaningless for the reasons I explained in my last > email. To obtain a meaningful number for the isolated atom you > probably > have to abandon the idea to use a perturbation in the potential and > change instead the number of electrons directly. This means you will > have to do calculations on atoms having fractional charges which > requires additional corrections if you use a code designed for > periodic > systems (crystals). However I have never done this isolated atom > calculation of U before so I don't have more details about it. > I see (from a private email) you are thinking of computing U for the > isolated atom and to obtain a value for the crystal just by > dividing by > the epsilon_inft. the method is proposed in > > http://link.aps.org/doi/10.1103/PhysRevB.74.045202 > > (which I haven't re-read yet). > > I see a couple of problems: > > 1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and > Fe3+. > these Fe ions likely have different U. how do you obtain > a different number from the atomic code? would you do the calculation > for isolated Fe2+ and Fe3+? > > 2) how do you get epsilon? since it's a linear response property I > don't > think its calculation is any cheaper than the direct calculation of U. > > regards, > > Matteo > > > should we choose for running the script for isolated atom only > gamma > > point or we have to choose a fine mesh? > > thanks a lot > > > > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > --- On *Sun, 8/2/09, Matteo Cococcioni / >/* wrote: > > > > > > From: Matteo Cococcioni > > > Subject: Re: [Pw_forum] occupation > > To: "PWSCF Forum" > > > Date: Sunday, August 2, 2009, 8:31 AM > > > > > > Dear Ali, > > > > 1, -1, 0 are just spin indexes to tell the code what is the > relative > > magnetization of the atoms (parallel, antiparallel, or none). if > > your system is non magnetic put all 0. or set magn = .false. > and put > > nothing. > > you should look at the examples on Fe and Si as well and > learn from > > there by comparison. > > > > Matteo > > > > > > > > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From kazempoor2000 at yahoo.com Tue Aug 4 18:05:26 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 4 Aug 2009 09:05:26 -0700 (PDT) Subject: [Pw_forum] change the refeeeeeeeeence Message-ID: <867633.10516.qm@web112519.mail.gq1.yahoo.com> Dear All ?For Zn (d=10) the d orbital is fully occupied. I want to change the reference to d=9. Which parameter should be modified? If then I want to do LDA+U calculation,should I also modify the occ_loc=5 in tabd.f90 and set_hubbard.f90 thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090804/e2136e5d/attachment.htm From matteo at umn.edu Tue Aug 4 18:14:58 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 04 Aug 2009 11:14:58 -0500 Subject: [Pw_forum] change the refeeeeeeeeence In-Reply-To: <867633.10516.qm@web112519.mail.gq1.yahoo.com> References: <867633.10516.qm@web112519.mail.gq1.yahoo.com> Message-ID: <4A785E82.6020801@umn.edu> dear Ali, set_hubbard_l doesn't need any change. you can try to set occ_loc to 9 (for Zn) in tabd.f90. But I suspect that you won't get a big change in your results. maybe not even if you changed the reference configuration of the pseudopotential. just try and let us know. Matteo ali kazempour wrote: > Dear All > For Zn (d=10) the d orbital is fully occupied. I want to change the > reference to d=9. Which parameter should be modified? > If then I want to do LDA+U calculation,should I also modify the > //occ_loc=5 in tabd.f90 and set_hubbard.f90 > thanks a lot > // > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From kazempoor2000 at yahoo.com Tue Aug 4 18:30:49 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 4 Aug 2009 09:30:49 -0700 (PDT) Subject: [Pw_forum] change the refeeeeeeeeence In-Reply-To: <4A785E82.6020801@umn.edu> Message-ID: <97361.31764.qm@web112502.mail.gq1.yahoo.com> Dear Matteo I decide to go to the common calculation of U for isolated atom.As noted in refference paper atomic U is? : Uat = {Etot[d(n+1)] ? Etot[d(n)]} ? {Etot[d(n)] ? Etot[d(n?1])} this mean that I need to calculate differrent systems with various occupation of d orbital for i.e Etot[d(10)] and Etot[d(9)] and Etot[d(8)] for doing this ,is it enough to only change in tabd.f90 the occ_loc from 10 to 9? or should I do? additional modifications? thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Tue, 8/4/09, Matteo Cococcioni wrote: From: Matteo Cococcioni Subject: Re: [Pw_forum] change the refeeeeeeeeence To: "PWSCF Forum" Date: Tuesday, August 4, 2009, 9:14 AM dear Ali, set_hubbard_l doesn't need any change. you can try to set occ_loc to 9 (for Zn) in tabd.f90. But I suspect that you won't get a big change in your results. maybe not even if you changed the reference configuration of the pseudopotential. just try and let us know. Matteo ali kazempour wrote: > Dear All >? For Zn (d=10) the d orbital is fully occupied. I want to change the > reference to d=9. Which parameter should be modified? > If then I want to do LDA+U calculation,should I also modify the > //occ_loc=5 in tabd.f90 and set_hubbard.f90 >? thanks a lot > // > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >??? -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056? ? Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% _______________________________________________ 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/20090804/f9447e64/attachment-0001.htm From matteo at umn.edu Tue Aug 4 18:39:38 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 04 Aug 2009 11:39:38 -0500 Subject: [Pw_forum] change the refeeeeeeeeence In-Reply-To: <97361.31764.qm@web112502.mail.gq1.yahoo.com> References: <97361.31764.qm@web112502.mail.gq1.yahoo.com> Message-ID: <4A78644A.3060903@umn.edu> Dear Ali, this is not directly possible in pwscf because the occupation of atomic states is not something we can control by hand. you need to implement and use constraints on the total atomic occupations if you want to do this. Matteo ali kazempour wrote: > Dear Matteo > I decide to go to the common calculation of U for isolated atom.As > noted in refference paper atomic U is : > > Uat = {Etot[d(n+1)] ? Etot[d(n)]} ? {Etot[d(n)] ? Etot[d(n?1])} > this mean that I need to calculate differrent systems with various > occupation of d orbital for i.e Etot[d(10)] and Etot[d(9)] and Etot[d(8)] > for doing this ,is it enough to only change in tabd.f90 the occ_loc > from 10 to 9 or should I do additional modifications? > thanks > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Tue, 8/4/09, Matteo Cococcioni //* wrote: > > > From: Matteo Cococcioni > Subject: Re: [Pw_forum] change the refeeeeeeeeence > To: "PWSCF Forum" > Date: Tuesday, August 4, 2009, 9:14 AM > > > dear Ali, > > set_hubbard_l doesn't need any change. you can try to set occ_loc > to 9 > (for Zn) in tabd.f90. > But I suspect that you won't get a big change in your results. > maybe not > even if you changed the reference configuration > of the pseudopotential. > > just try and let us know. > > Matteo > > > > ali kazempour wrote: > > Dear All > > For Zn (d=10) the d orbital is fully occupied. I want to change > the > > reference to d=9. Which parameter should be modified? > > If then I want to do LDA+U calculation,should I also modify the > > //occ_loc=5 in tabd.f90 and set_hubbard.f90 > > thanks a lot > > // > > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From kazempoor2000 at yahoo.com Tue Aug 4 18:41:54 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 4 Aug 2009 09:41:54 -0700 (PDT) Subject: [Pw_forum] U for Oxygen In-Reply-To: <4A783EB7.9060902@umn.edu> Message-ID: <206083.36410.qm@web112512.mail.gq1.yahoo.com> Dear Matteo This means that hubbard parameter for oxygen is large (grater than Ni). Is it correct or originate from another challenge? thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Tue, 8/4/09, Matteo Cococcioni wrote: From: Matteo Cococcioni Subject: Re: [Pw_forum] U for Oxygen To: "PWSCF Forum" Date: Tuesday, August 4, 2009, 6:59 AM Dear Ali, ali kazempour wrote: > Dear Matteo > I used your comment and followed???your example for NiO and I succeed? > to get U for TiO2. But in file Ur16.out I see three column . > I don't have any three column section in any of my files. so if you want me to help you you have to report at least a section of your output file. This is a good habit actually in consideration of the fact that this is not a private conversation (I would have asked you in any case as I don't remember by heart the format of any file) between me and you but a message to the forum and you want other people to understand what you are saying. > The first is number of atom in supercell , second is U value for Ni > atom and I don,t know? the third? does the third belong to? U value > for Oxygen or not? Because the third column kas big value? > > > another question is for isolated atom Hubbard parameter. What do you > expect about the value of U for Isolated atom? Is this big value > (greater than 10 eV) or? it would be tiny value? > I think it will be meaningless for the reasons I explained in my last email. To obtain a meaningful number for the isolated atom you probably have to abandon the idea to use a perturbation in the potential and change instead the number of electrons directly. This means you will have to do calculations on atoms having fractional charges which requires additional corrections if you use a code designed for periodic systems (crystals). However I have never done this isolated atom calculation of U before so I don't have more details about it. I see (from a private email) you are thinking of computing U for the isolated atom and to obtain a value for the crystal just by dividing by the epsilon_inft. the method is proposed in http://link.aps.org/doi/10.1103/PhysRevB.74.045202 (which I haven't re-read yet). I see a couple of problems: 1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and Fe3+. these Fe ions likely have different U. how do you obtain a different number from the atomic code? would you do the calculation for isolated Fe2+ and Fe3+? 2) how do you get epsilon? since it's a linear response property I don't think its calculation is any cheaper than the direct calculation of U. regards, Matteo > should we choose for running the script for isolated atom only gamma > point or we have to choose a fine mesh? > thanks a lot > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Sun, 8/2/09, Matteo Cococcioni //* wrote: > > >? ???From: Matteo Cococcioni >? ???Subject: Re: [Pw_forum] occupation >? ???To: "PWSCF Forum" >? ???Date: Sunday, August 2, 2009, 8:31 AM > > >? ???Dear Ali, > >? ???1, -1, 0 are just spin indexes to tell the code what is the relative >? ???magnetization of the atoms (parallel, antiparallel, or none). if >? ???your system is non magnetic put all 0. or set magn = .false. and put >? ???nothing. >? ???you should look at the examples on Fe and Si as well and learn from >? ???there by comparison. > >? ???Matteo > > > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056? ? Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% _______________________________________________ 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/20090804/9ddb73bf/attachment.htm From matteo at umn.edu Tue Aug 4 18:52:01 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 04 Aug 2009 11:52:01 -0500 Subject: [Pw_forum] U for Oxygen In-Reply-To: <206083.36410.qm@web112512.mail.gq1.yahoo.com> References: <206083.36410.qm@web112512.mail.gq1.yahoo.com> Message-ID: <4A786731.8070504@umn.edu> this is what comes out from the calculation (U(O) > U(Ni)). whether it's reasonable to apply U on O or not, I'm not sure. I think the U shouldn't be used on states that are completely occupied. Matteo ali kazempour wrote: > Dear Matteo > This means that hubbard parameter for oxygen is large (grater than > Ni). Is it correct or originate from another challenge? > thanks > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Tue, 8/4/09, Matteo Cococcioni //* wrote: > > > From: Matteo Cococcioni > Subject: Re: [Pw_forum] U for Oxygen > To: "PWSCF Forum" > Date: Tuesday, August 4, 2009, 6:59 AM > > > > Dear Ali, > > > > ali kazempour wrote: > > Dear Matteo > > I used your comment and followed your example for NiO and I > succeed > > to get U for TiO2. But in file Ur16.out I see three column . > > > > I don't have any three column section in any of my files. so if > you want > me to help you you have to report at least a section of your output > file. This is a good habit actually in consideration of the fact that > this is not a private conversation (I would have asked you in any > case > as I don't remember by heart the format of any file) between me > and you > but a message to the forum and you want other people to understand > what you are saying. > > > The first is number of atom in supercell , second is U value for Ni > > atom and I don,t know the third? does the third belong to U value > > for Oxygen or not? Because the third column kas big value? > > > > > > another question is for isolated atom Hubbard parameter. What do > you > > expect about the value of U for Isolated atom? Is this big value > > (greater than 10 eV) or it would be tiny value? > > > > I think it will be meaningless for the reasons I explained in my last > email. To obtain a meaningful number for the isolated atom you > probably > have to abandon the idea to use a perturbation in the potential and > change instead the number of electrons directly. This means you will > have to do calculations on atoms having fractional charges which > requires additional corrections if you use a code designed for > periodic > systems (crystals). However I have never done this isolated atom > calculation of U before so I don't have more details about it. > I see (from a private email) you are thinking of computing U for the > isolated atom and to obtain a value for the crystal just by > dividing by > the epsilon_inft. the method is proposed in > > http://link.aps.org/doi/10.1103/PhysRevB.74.045202 > > (which I haven't re-read yet). > > I see a couple of problems: > > 1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and > Fe3+. > these Fe ions likely have different U. how do you obtain > a different number from the atomic code? would you do the calculation > for isolated Fe2+ and Fe3+? > > 2) how do you get epsilon? since it's a linear response property I > don't > think its calculation is any cheaper than the direct calculation of U. > > regards, > > Matteo > > > should we choose for running the script for isolated atom only > gamma > > point or we have to choose a fine mesh? > > thanks a lot > > > > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > --- On *Sun, 8/2/09, Matteo Cococcioni / >/* wrote: > > > > > > From: Matteo Cococcioni > > > Subject: Re: [Pw_forum] occupation > > To: "PWSCF Forum" > > > Date: Sunday, August 2, 2009, 8:31 AM > > > > > > Dear Ali, > > > > 1, -1, 0 are just spin indexes to tell the code what is the > relative > > magnetization of the atoms (parallel, antiparallel, or none). if > > your system is non magnetic put all 0. or set magn = .false. > and put > > nothing. > > you should look at the examples on Fe and Si as well and > learn from > > there by comparison. > > > > Matteo > > > > > > > > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From vtmtrinh at caltech.edu Tue Aug 4 20:11:33 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Tue, 4 Aug 2009 11:11:33 -0700 (PDT) Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> Message-ID: <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> Dear Lorenzo, Thank you for your help. I am still confused (I may be dump :-)). Yes, I agree that wavefunction at Gamma is real and thus will have a sign with it. However, |psi|^2 is a positive quantity. If we multiply |psi|^2 by sign(psi) (which is segno in the code), then |psi|^2*sign(psi) will have a sign of sign(psi). Why we want to have a sign with |psi|^2? Best, Trinh > On Tue, August 4, 2009 04:20, vtmtrinh at caltech.edu wrote: >> I think I can hard code, adding a few lines to print out psi in real >> space. > > Dear MyTrin, > You definitely can! > >> >> There is one part in the code 'local_dos' I don't understand is the >> case >> where ', lsign=true', i.e. k=gamma and iflag=0, write >> |psi|^2*sign(psi), >> why |psi|^2 has to multiply by sign(psi). I read thru the code at this >> part, but I still could not get it. > > Maybe I've misunderstood your question, but that's exactly what the option > lsign is supposed to do. Wavefunctions in Gamma can be defined ti be real, > hence they have a well defined sign. Although, they can always be > multiplied by any complex number (-1 included) and still remain perfectly > good eigenvalues. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Tue Aug 4 20:41:47 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Aug 2009 20:41:47 +0200 Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> Message-ID: <3150FD58-5D27-4755-86AB-928E06B152A9@democritos.it> On Aug 4, 2009, at 20:11 , vtmtrinh at caltech.edu wrote: > Why we want to have a sign with |psi|^2? because somebody wanted to have that piece of information and implemented that option. If you don't like it, don't use it. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vtmtrinh at caltech.edu Tue Aug 4 20:46:48 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Tue, 4 Aug 2009 11:46:48 -0700 (PDT) Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <3150FD58-5D27-4755-86AB-928E06B152A9@democritos.it> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> <3150FD58-5D27-4755-86AB-928E06B152A9@democritos.it> Message-ID: <3810.137.78.73.28.1249411608.squirrel@webmail.caltech.edu> Oh, I see. Thanks, Paolo. Trinh > > On Aug 4, 2009, at 20:11 , vtmtrinh at caltech.edu wrote: > >> Why we want to have a sign with |psi|^2? > > because somebody wanted to have that piece of information > and implemented that option. If you don't like it, don't use it. > > 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 mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From jjr19 at uakron.edu Tue Aug 4 22:19:44 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Tue, 4 Aug 2009 13:19:44 -0700 (PDT) Subject: [Pw_forum] Trying to clarify the dipole correction (again!) Message-ID: <96033.30039.qm@web50909.mail.re2.yahoo.com> In the reference on the dipole correction used in QE, L. Bengtsson, PRB 59, 12301 (1999), the dipole potential is given as V_dip(z) = 4*pi*m*(z/z_m - 0.5), 0 < z < z_m where z_m is the height of the box, and there is a discontinuity in the potential at z = 0,z_m. I'm not sure how this fits into the QE documentation on the dipole correction. Is V_dip in QE supposed to be something like this?: V_dip(z) = 4*pi*m*[z/z_m - (emaxpos + eopreg -1)], emaxpos + eopreg -1 < z/z_m < emaxpos; = something with a steep but finite slope, otherwise My guess is probably wrong, but the explanations in the documentation of the roles of emaxpos and eopreg appear to be tied to the case where eamp is nonzero. I'm not sure if the documentation for the dipfield variable is supposed to indicate that the actual slope of the potential is supposed to be eamp + 4*pi*m/z_m. University of Akron Civil Engineering (!) Dept. From haoweipeng at gmail.com Wed Aug 5 01:48:52 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Tue, 4 Aug 2009 18:48:52 -0500 Subject: [Pw_forum] Does the dos.x only work with npool=1 Message-ID: <7559eb240908041648n3d236363va62ffd40028df499@mail.gmail.com> as the title. thanks a lot.. -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090804/5db7b1f2/attachment.htm From mambom1902 at yahoo.com Wed Aug 5 03:52:06 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 4 Aug 2009 18:52:06 -0700 (PDT) Subject: [Pw_forum] Difinition of V_bare and electric field potential Message-ID: <105892.39138.qm@web38804.mail.mud.yahoo.com> Dear all, I wonder what is definition of V_bare and electric field?potential in PWscf?code. The electric field potential in Pwscf is the same as electrostatic potential? It may be a stupid question but I can not find the consistence in the name of potential?as usual call. ? I?appreciate your explaination! ?? Sincerely,?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From mansourehp at gmail.com Wed Aug 5 07:50:54 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Wed, 5 Aug 2009 09:20:54 +0330 Subject: [Pw_forum] transition Message-ID: Dear all I have perorm GGA+U for a system with trigonally distorted (D3d) of octahedral symmetry (MO6) (with orbital 3d6). using PDOS for this system perdict two transition. How can I find which transion is allowed or forbbiden? I am looking forward to hearing from you. Mansoureh Pashangpour Islamic Azad University Science & Reaserch Branch, Tehran, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/840fefd7/attachment.htm From nahidbd1 at in.com Wed Aug 5 08:55:03 2009 From: nahidbd1 at in.com (nahid bd) Date: Wed, 05 Aug 2009 12:25:03 +0530 Subject: [Pw_forum] =?utf-8?q?Atom_projected_phonon_DOS?= Message-ID: <1249455303.5bf73bc6c6e6775d472621264309a88b@mail.in.com> Dear Prof. Eyvaz Isaev,Sir, I have calculated EP coupling and Tc successfully using your codes and also calculated total phonon DOS.Now I would like to calculate atom projected phonon DOS.Please send me the code by which I can calculate atom projected phonon DOS.Sincerely yoursNahid ParvezResearch studentCondensed Matter Physics LabRajshahi UniversityBangladesh.Dear pwforum! Get Yourself a cool, short @in.com Email ID now! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/74057814/attachment.htm From baroni at sissa.it Wed Aug 5 09:06:52 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 5 Aug 2009 09:06:52 +0200 Subject: [Pw_forum] transition In-Reply-To: References: Message-ID: <4C751718-0EE6-4CB5-AEEE-BFC01A8FA7B0@sissa.it> Using Fermi's golden rule + selection rules + common sense 1) Fermi golden rule: (All: can everybody read the formula above?) where (cv) are conduction and valence states 2) selection rules tell you which ones of the above matrix elements vanish and which don't 3) common sense: in an extended system, many occupied (v) and empty (c) states contribute to the sum, so that selection rules are of little help, in general. when the spectrum is dominated by localized states, an analysis based on symmetry and selection rules is usually much more meaningful ... hope this helps Stefano B On Aug 5, 2009, at 7:50 AM, Mansoureh Pashangpour wrote: > Dear all > I have perorm GGA+U for a system with trigonally distorted (D3d) > of octahedral symmetry (MO6) (with orbital 3d6). > using PDOS for this system perdict two transition. How can I find > which transion is allowed or forbbiden? > > I am looking forward to hearing from you. > > Mansoureh Pashangpour > > Islamic Azad University > Science & Reaserch Branch, > Tehran, Iran. > _______________________________________________ > 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/20090805/6eeda397/attachment-0002.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: latex-image-1.pdf Type: application/pdf Size: 53254 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090805/6eeda397/attachment-0001.pdf -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/6eeda397/attachment-0003.htm From kazempoor2000 at yahoo.com Wed Aug 5 11:03:09 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 5 Aug 2009 02:03:09 -0700 (PDT) Subject: [Pw_forum] add or subtract electron Message-ID: <781663.66645.qm@web112507.mail.gq1.yahoo.com> Dear users Does anyone knows that how possible is the computation of total energy of a system with same total number of electron when we add a electron to the orbital OR subtract electron from that orbital? I mean? how we? put for example 1 additional electron to the orbital d. I want this to compute? U(hubbard)? from U=E(dn+1) + E(dn1)-2E(dn) thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/cbb206f4/attachment.htm From degironc at sissa.it Wed Aug 5 11:07:08 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 05 Aug 2009 11:07:08 +0200 Subject: [Pw_forum] add or subtract electron In-Reply-To: <781663.66645.qm@web112507.mail.gq1.yahoo.com> References: <781663.66645.qm@web112507.mail.gq1.yahoo.com> Message-ID: <4A794BBC.2030907@sissa.it> Cococcioni M, de Gironcoli S Linear response approach to the calculation of the effective interaction parameters in the LDA+U method Phys. Rev. B *71*, 035105 (2005) ali kazempour wrote: > Dear users > Does anyone knows that how possible is the computation of total energy > of a system with same total number of electron when we add a electron > to the orbital OR subtract electron from that orbital? I mean how we > put for example 1 additional electron to the orbital d. > I want this to compute U(hubbard) from > U=E(dn+1) + E(dn1)-2E(dn) > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bipulrr at gmail.com Wed Aug 5 11:14:34 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 5 Aug 2009 14:44:34 +0530 Subject: [Pw_forum] nspin=2 for GGA Pseudopotential Message-ID: <3a749910908050214u69b779b0l9270ed2982915433@mail.gmail.com> Dear PWSCF users, Can we use nspin=2 for GGA type PP?? Because in the manual it is written that, nspin = 2 : spin-polarized calculation, *LSDA* -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/655fa3d2/attachment.htm From kazempoor2000 at yahoo.com Wed Aug 5 11:26:49 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 5 Aug 2009 02:26:49 -0700 (PDT) Subject: [Pw_forum] add or subtract electron In-Reply-To: <4A794BBC.2030907@sissa.it> Message-ID: <931197.72557.qm@web112518.mail.gq1.yahoo.com> Dear Stefano I am familier with the linear response in pwscf, but this approach don't response for computation of U for isolated atoms, So I have to switch? directly the occupation .But it is not possible in espresso to control the occupation of orbital by hand. So, indirectly,? I have to use constraints on the total atomic occupations if I want to do this. But I don't know how can I do that? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Wed, 8/5/09, Stefano de Gironcoli wrote: From: Stefano de Gironcoli Subject: Re: [Pw_forum] add or subtract electron To: "PWSCF Forum" Date: Wednesday, August 5, 2009, 2:07 AM Cococcioni M, de Gironcoli S Linear response approach to the calculation of the effective interaction parameters in the LDA+U method Phys. Rev. B *71*, 035105 (2005) ali kazempour wrote: > Dear users > Does anyone knows that how possible is the computation of total energy > of a system with same total number of electron when we add a electron > to the orbital OR subtract electron from that orbital? I mean? how we? > put for example 1 additional electron to the orbital d. > I want this to compute? U(hubbard)? from > U=E(dn+1) + E(dn1)-2E(dn) > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >??? _______________________________________________ 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/20090805/8eb6b608/attachment.htm From tone.kokalj at ijs.si Wed Aug 5 12:19:27 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 Aug 2009 12:19:27 +0200 Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> Message-ID: <1249467567.1465.4.camel@walk.ijs.si> On Tue, 2009-08-04 at 11:11 -0700, vtmtrinh at caltech.edu wrote: > Dear Lorenzo, > > Thank you for your help. I am still confused (I may be dump :-)). > Yes, I agree that wavefunction at Gamma is real and thus will have a sign > with it. However, |psi|^2 is a positive quantity. If we multiply |psi|^2 > by sign(psi) (which is segno in the code), then |psi|^2*sign(psi) will > have a sign of sign(psi). Why we want to have a sign with |psi|^2? Perhaps, because you may then plot: sign(psi)\sqrt(|psi|^2) ... Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From bipulrr at gmail.com Wed Aug 5 12:20:15 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 5 Aug 2009 15:50:15 +0530 Subject: [Pw_forum] IBM-AIX vs ifort Message-ID: <3a749910908050320x7c3c9f49i157300089f548e81@mail.gmail.com> Hello PWSCF users, I have installed espresso-4.1 version in parallel Machine complier AIX-IBM mpxlf95 and mpicc Linux ifort and icc I am doing a relax calculation of LaMnO3, the linux doing Entering Dynamics: iteration =2 while the AIX-IBM is doing Entering Dynamics: iteration =12 Can any body suggest why it is happening? I am attaching the two make.sys files -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/9ad42481/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: make.sys-IBM Type: application/octet-stream Size: 4996 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090805/9ad42481/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: make.sys-Linux Type: application/octet-stream Size: 4661 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090805/9ad42481/attachment-0003.obj From vamsi.iisc at gmail.com Wed Aug 5 12:38:10 2009 From: vamsi.iisc at gmail.com (vamsi kv) Date: Wed, 5 Aug 2009 16:08:10 +0530 Subject: [Pw_forum] chargedensity Message-ID: <84ff69170908050338g5dd38f3bxcf37aa630d1b06fd@mail.gmail.com> Dear PWScf users, 1. Can i print the chargedensity information after every iteration in the scf or relax calculation? or can we know waht is the initial charge density gues and how it changes during the simulation. 2. What is bonding chargedensity? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090805/82d2c63f/attachment.htm From nkxirainbow at gmail.com Wed Aug 5 13:12:02 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 5 Aug 2009 19:12:02 +0800 Subject: [Pw_forum] nspin=2 for GGA Pseudopotential In-Reply-To: <3a749910908050214u69b779b0l9270ed2982915433@mail.gmail.com> References: <3a749910908050214u69b779b0l9270ed2982915433@mail.gmail.com> Message-ID: <21fbc4790908050412q7abc694ctfff1726609d6280b@mail.gmail.com> Dear Bipul Rakshit Look this? http://www.democritos.it/pipermail/pw_forum/2005-December/003365.html On Monday 28 November 2005 09:24, W. YU wrote: Paolo said:" *of course it is. Not all functionals are implemented, though, but the most important are this is for the LDA part-only. * *You can combine these with various gradient corrections. * *Several popular gradient-corrected functionals are available * *(Becke86-Perdew88, Perdew-Wang 91, PBE). * *BLYP with spin polarization is also implemented in 3.0"* >* By the way, I couldn't find this source file in espresso-3.0. *>* Where has it gone? * part in Modules/functionals.f90, part in flib/functionals.f90, flib/lsda_functionals.f90, flib/more_functionals.f90 . Paolo On 8/5/09, Bipul Rakshit wrote: > > Dear PWSCF users, > Can we use nspin=2 for GGA type PP?? > Because in the manual it is written that, > nspin = 2 : spin-polarized calculation, *LSDA* > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ 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/20090805/18dbd303/attachment.htm From nkxirainbow at gmail.com Wed Aug 5 13:22:03 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 5 Aug 2009 19:22:03 +0800 Subject: [Pw_forum] nspin=2 for GGA Pseudopotential In-Reply-To: <21fbc4790908050412q7abc694ctfff1726609d6280b@mail.gmail.com> References: <3a749910908050214u69b779b0l9270ed2982915433@mail.gmail.com> <21fbc4790908050412q7abc694ctfff1726609d6280b@mail.gmail.com> Message-ID: <21fbc4790908050422n8c733f1uc0ce1ee0f45aa95c@mail.gmail.com> Sorry, the second half of the upper email is not concerned with the question;) ____________________________________ 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/20090805/a19cdf94/attachment.htm From nkxirainbow at gmail.com Wed Aug 5 14:37:11 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 5 Aug 2009 20:37:11 +0800 Subject: [Pw_forum] chargedensity In-Reply-To: <84ff69170908050338g5dd38f3bxcf37aa630d1b06fd@mail.gmail.com> References: <84ff69170908050338g5dd38f3bxcf37aa630d1b06fd@mail.gmail.com> Message-ID: <21fbc4790908050537y45b2b47i1858e5b6de9aa4c@mail.gmail.com> Dear vamsi kv: > >can we know waht is the initial charge density guess May be you can get it by setting "Convergence threshold for selfconsistency" very large. 2. What is bonding chargedensity? I think "Partial charge density." may help you;) -- > ____________________________________ > 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/20090805/a2b15ff8/attachment.htm From dmitry at korotin.name Wed Aug 5 14:13:49 2009 From: dmitry at korotin.name (Dmitry Korotin) Date: Wed, 5 Aug 2009 18:13:49 +0600 Subject: [Pw_forum] inter_pool_comm Message-ID: <166cd7c60908050513m670080d2hc358a4df5ecb1bb1@mail.gmail.com> Dear QE developers, could anyone explain to me in a few words a difference between inter_pool_comm and intra_pool_comm variables. I am not really familiar with MPI, but I need to sum some variable over k-points. Should I use mp_sum(variable_name,inter_pool_comm) or mp_sum(variable_name,intra_pool_comm)? Does mp_sum take into account k-point weights? (As I understood from the source this routine is used for summation over k-points?) Thank you in advance. -- Best regards, Dmitry Korotin Ph. D. Student, Institute of Metal Physics S. Kovalevskaya, 18 620041 Ekaterinburg GSP-170 Russia From l.salimi at ph.iut.ac.ir Wed Aug 5 18:32:15 2009 From: l.salimi at ph.iut.ac.ir (leila salimi) Date: Wed, 5 Aug 2009 20:02:15 +0330 (IRST) Subject: [Pw_forum] Segmentation fault Message-ID: <16175338.379491249489935359.JavaMail.root@mta.iut.ac.ir> Hi every body I use espresso-4.0.5 on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. If I use calculation='scf' no problem and the result matches our testdata. If we use calculation='relax? we get the right value for the energy after the first loop and then the application should start with the second loop but it stops with the following error: ====== energy new = -121.3312114461 Ry new trust radius = .5000000000 bohr ERROR: 0031-250 task 0: Segmentation fault ERROR: 0031-250 task 4: Terminated ERROR: 0031-250 task 7: Terminated ERROR: 0031-250 task 6: Terminated ERROR: 0031-250 task 2: Terminated ERROR: 0031-250 task 1: Terminated ERROR: 0031-250 task 5: Terminated ERROR: 0031-250 task 3: Terminated We use the following command line: poe ~/espresso/bin/pw.x -procs 8 -npool 2 < input.relax > InAs-relax.out 2>&1 Do you have any idea with this problem? Best Regards, Leila Salimi Isfahan University of Technology, Isfahan, Iran. From paulatto at sissa.it Wed Aug 5 18:59:52 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 5 Aug 2009 18:59:52 +0200 (CEST) Subject: [Pw_forum] add or subtract electron In-Reply-To: <931197.72557.qm@web112518.mail.gq1.yahoo.com> References: <931197.72557.qm@web112518.mail.gq1.yahoo.com> Message-ID: <36515.78.12.161.81.1249491592.squirrel@webmail.sissa.it> In data 05 agosto 2009 alle ore 11:26:49, ali kazempour ha scritto:So I have to switch > But it is not possible in espresso to control > the occupation of orbital by hand. Is is possible, in the atomic code. It only solves spherical atoms, though, so you have to think if it applies to your case. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Wed Aug 5 19:02:14 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 5 Aug 2009 19:02:14 +0200 (CEST) Subject: [Pw_forum] Does the dos.x only work with npool=1 In-Reply-To: <7559eb240908041648n3d236363va62ffd40028df499@mail.gmail.com> References: <7559eb240908041648n3d236363va62ffd40028df499@mail.gmail.com> Message-ID: <40517.78.12.161.81.1249491734.squirrel@webmail.sissa.it> On Wed, August 5, 2009 01:48, Haowei Peng wrote: > as the title. I think you are right, but it is not a big deal. You can do the scf calculation with any number of pools, using the option wf_collect=.true. in the control namelist. Than you can compute the dos using a single pool (it is a short calculation). regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Wed Aug 5 19:10:28 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 5 Aug 2009 19:10:28 +0200 (CEST) Subject: [Pw_forum] Segmentation fault In-Reply-To: <16175338.379491249489935359.JavaMail.root@mta.iut.ac.ir> References: <16175338.379491249489935359.JavaMail.root@mta.iut.ac.ir> Message-ID: <36441.78.12.161.81.1249492228.squirrel@webmail.sissa.it> On Wed, August 5, 2009 18:32, leila salimi wrote: > ERROR: 0031-250 task 0: Segmentation fault Dear Leila, from the information you provide all I can say is that task #0 caused a segmentation fault, then the other tasks were killed. Seriously, without at least the full input there is nothing I can add, it may just be that you ran out of ram! regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From vtmtrinh at caltech.edu Thu Aug 6 02:27:36 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Wed, 5 Aug 2009 17:27:36 -0700 (PDT) Subject: [Pw_forum] printing wavefunction on real grid In-Reply-To: <1249467567.1465.4.camel@walk.ijs.si> References: <2053.137.78.73.28.1249352459.squirrel@webmail.caltech.edu> <56736.78.12.161.81.1249368910.squirrel@webmail.sissa.it> <3559.137.78.73.28.1249409493.squirrel@webmail.caltech.edu> <1249467567.1465.4.camel@walk.ijs.si> Message-ID: <2732.137.78.73.28.1249518456.squirrel@webmail.caltech.edu> Thanks, Tone. MyTrinh > On Tue, 2009-08-04 at 11:11 -0700, vtmtrinh at caltech.edu wrote: >> Dear Lorenzo, >> >> Thank you for your help. I am still confused (I may be dump :-)). >> Yes, I agree that wavefunction at Gamma is real and thus will have a >> sign >> with it. However, |psi|^2 is a positive quantity. If we multiply |psi|^2 >> by sign(psi) (which is segno in the code), then |psi|^2*sign(psi) will >> have a sign of sign(psi). Why we want to have a sign with |psi|^2? > > Perhaps, because you may then plot: sign(psi)\sqrt(|psi|^2) ... > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mahasinalam at yahoo.co.uk Thu Aug 6 10:54:12 2009 From: mahasinalam at yahoo.co.uk (MAHASIN ALAM) Date: Thu, 6 Aug 2009 08:54:12 +0000 (GMT) Subject: [Pw_forum] Geometry Optimization Message-ID: <276859.52500.qm@web24107.mail.ird.yahoo.com> Dear Friends, ? For geometry opimization in PWSCF (QE) it mentioned in the manual that we have to set calculation = 'relax'. If I set it, it will only relax the ions. But if I have a system with vacuum cell and if I need to relax the ions as well as vacuum cell, can I do it using PWSCF? If yes can any one tell me what I have to set in calculation type? Thank you for your help. ? Regards ? Mahasin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/6846ba65/attachment.htm From l.salimi at ph.iut.ac.ir Thu Aug 6 11:59:20 2009 From: l.salimi at ph.iut.ac.ir (leila salimi) Date: Thu, 6 Aug 2009 13:29:20 +0330 (IRST) Subject: [Pw_forum] Segmentation fault Message-ID: <19999719.386181249552760044.JavaMail.root@mta.iut.ac.ir> Dear Lorenzo, Thanks for your reply, this is my input file: &control calculation='relax' restart_mode='from_scratch' prefix='NW-WZH6-1' pseudo_dir = '/home/mokhles/espresso-4.0.5/pseudo', outdir='/home/mokhles/leila/' tstress = .true. tprnfor = .true. / &system ibrav=4, celldm(1) =31.9,celldm(3)= 0.40925,nat=12, ntyp= 2, ecutwfc = 48.0, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &IONS ion_dynamics='bfgs' / ATOMIC_SPECIES In 114.8 In.pz-n-bhs.UPF As 74.9216 As.pz-bhs.UPF ATOMIC_POSITIONS (crystal) In 0.50000000 0.25000000 0.00000000 In 0.41666666 0.33333333 0.50000000 In 0.50000000 0.50000000 0.00000000 In 0.66666666 0.58333333 0.50000000 In 0.75000000 0.50000000 0.00000000 In 0.66666666 0.33333333 0.50000000 As 0.50000000 0.25000000 0.37500000 As 0.41666666 0.33333333 0.87500000 As 0.50000000 0.50000000 0.37500000 As 0.66666666 0.58333333 0.87500000 As 0.75000000 0.50000000 0.37500000 As 0.66666666 0.33333333 0.87500000 K_POINTS (automatic) 1 1 8 1 1 1 this is the end of output : one-electron contribution = -321.15692571 Ry hartree contribution = 165.82317284 Ry xc contribution = -49.84034576 Ry ewald contribution = 83.84288718 Ry convergence has been achieved in 37 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = .00000000 .03498356 .00975168 atom 2 type 1 force = .03029665 .01749178 .00975168 atom 3 type 1 force = .03029665 -.01749178 .00975168 atom 4 type 1 force = .00000000 -.03498356 .00975168 atom 5 type 1 force = -.03029665 -.01749178 .00975168 atom 6 type 1 force = -.03029665 .01749178 .00975168 atom 7 type 2 force = .00000000 -.02738364 -.00975168 atom 8 type 2 force = -.02371492 -.01369182 -.00975168 atom 9 type 2 force = -.02371492 .01369182 -.00975168 atom 10 type 2 force = .00000000 .02738364 -.00975168 atom 11 type 2 force = .02371492 .01369182 -.00975168 atom 12 type 2 force = .02371492 -.01369182 -.00975168 Total force = .113945 Total SCF correction = .000019 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= -3.80 -.00000941 .00000000 .00000000 -1.38 .00 .00 .00000000 -.00000941 .00000000 .00 -1.38 .00 .00000000 .00000000 -.00005866 .00 .00 -8.63 BFGS Geometry Optimization number of scf cycles = 1 number of bfgs steps = 0 energy new = -121.3312114461 Ry new trust radius = .5000000000 bohr ERROR: 0031-250 task 0: Segmentation fault ERROR: 0031-250 task 4: Terminated ERROR: 0031-250 task 7: Terminated ERROR: 0031-250 task 6: Terminated ERROR: 0031-250 task 2: Terminated ERROR: 0031-250 task 1: Terminated ERROR: 0031-250 task 5: Terminated ERROR: 0031-250 task 3: Terminated From paulatto at sissa.it Thu Aug 6 11:03:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 06 Aug 2009 11:03:11 +0200 Subject: [Pw_forum] Geometry Optimization In-Reply-To: <276859.52500.qm@web24107.mail.ird.yahoo.com> References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: In data 06 agosto 2009 alle ore 10:54:12, MAHASIN ALAM ha scritto: > But if I have a system with vacuum cell and if I need to relax the ions > as well as vacuum cell, can I do it using PWSCF? If yes can any one tell > me what I have to set in calculation type? Thank you for your help. You can use vc-relax to relax both the ions and the unit cell (mainatining its symmetry); but it does NOT do what you want. What you want to do is find the smaller amount of vacuum that guarantees a negligible interaction between periodic copies along the vacuum direction. This is equivalent to minimize forces between peridic images, but does not keep stress in account and will likely /increase/ the total energy. On the other hand, vc-relax only tries to minimize stress and minimize energy. In practice, you have to do a few tryes with different amounts of vacuum and see when the total energy becomes stable. This may reuire as little as 5 Angstrom of empty space, for a simple slab geometry, but may be much more if you have dipolar molecules. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kazempoor2000 at yahoo.com Thu Aug 6 11:06:20 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 6 Aug 2009 02:06:20 -0700 (PDT) Subject: [Pw_forum] U for Oxygen In-Reply-To: <4A786731.8070504@umn.edu> Message-ID: <461162.40692.qm@web112508.mail.gq1.yahoo.com> Dear Matteo In your tutorial about LDA_U, you mentioned that the perturbation should be isolated. and? said that we normally use supercell of increasing size up to when convergence of is reached. I don't understand how do you increase the size of the cell and how do you compute the U in larger supercell.? I mean how do you apply perturbation to bigger size or how to extrapolate the U to converge? Another question according to prior email for computation of U by common method(not linear response) is : you mentioned that espresso cann't directly change the occupation of special orbital by hand, but it is possible to do by using constraint on total number of electron(total occupation) indirectly . Do you mean that( for example for Ti atom that has 2 electron in d orbital) ,what can i do is change the of number of nelup and neldw? without change in nelec? or I have to do another switch? Would you please tell me in more details. Thank you very much for your aids Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Tue, 8/4/09, Matteo Cococcioni wrote: From: Matteo Cococcioni Subject: Re: [Pw_forum] U for Oxygen To: "PWSCF Forum" Date: Tuesday, August 4, 2009, 9:52 AM this is what comes out from the calculation (U(O) > U(Ni)). whether it's reasonable to apply U on O or not, I'm not sure. I think the U shouldn't be used on states that are completely occupied. Matteo ali kazempour wrote: > Dear Matteo > This means that hubbard parameter for oxygen is large (grater than > Ni). Is it correct or originate from another challenge? > thanks > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Tue, 8/4/09, Matteo Cococcioni //* wrote: > > >? ???From: Matteo Cococcioni >? ???Subject: Re: [Pw_forum] U for Oxygen >? ???To: "PWSCF Forum" >? ???Date: Tuesday, August 4, 2009, 6:59 AM > > > >? ???Dear Ali, > > > >? ???ali kazempour wrote: >? ???> Dear Matteo >? ???> I used your comment and followed???your example for NiO and I >? ???succeed >? ???> to get U for TiO2. But in file Ur16.out I see three column . >? ???> > >? ???I don't have any three column section in any of my files. so if >? ???you want >? ???me to help you you have to report at least a section of your output >? ???file. This is a good habit actually in consideration of the fact that >? ???this is not a private conversation (I would have asked you in any >? ???case >? ???as I don't remember by heart the format of any file) between me >? ???and you >? ???but a message to the forum and you want other people to understand >? ???what you are saying. > >? ???> The first is number of atom in supercell , second is U value for Ni >? ???> atom and I don,t know? the third? does the third belong to? U value >? ???> for Oxygen or not? Because the third column kas big value? >? ???> >? ???> >? ???> another question is for isolated atom Hubbard parameter. What do >? ???you >? ???> expect about the value of U for Isolated atom? Is this big value >? ???> (greater than 10 eV) or? it would be tiny value? >? ???> > >? ???I think it will be meaningless for the reasons I explained in my last >? ???email. To obtain a meaningful number for the isolated atom you >? ???probably >? ???have to abandon the idea to use a perturbation in the potential and >? ???change instead the number of electrons directly. This means you will >? ???have to do calculations on atoms having fractional charges which >? ???requires additional corrections if you use a code designed for >? ???periodic >? ???systems (crystals). However I have never done this isolated atom >? ???calculation of U before so I don't have more details about it. >? ???I see (from a private email) you are thinking of computing U for the >? ???isolated atom and to obtain a value for the crystal just by >? ???dividing by >? ???the epsilon_inft. the method is proposed in > >? ???http://link.aps.org/doi/10.1103/PhysRevB.74.045202 > >? ???(which I haven't re-read yet). > >? ???I see a couple of problems: > >? ???1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and >? ???Fe3+. >? ???these Fe ions likely have different U. how do you obtain >? ???a different number from the atomic code? would you do the calculation >? ???for isolated Fe2+ and Fe3+? > >? ???2) how do you get epsilon? since it's a linear response property I >? ???don't >? ???think its calculation is any cheaper than the direct calculation of U. > >? ???regards, > >? ???Matteo > >? ???> should we choose for running the script for isolated atom only >? ???gamma >? ???> point or we have to choose a fine mesh? >? ???> thanks a lot >? ???> >? ???> >? ???> Ali Kazempour >? ???> Physics department, Isfahan University of Technology >? ???> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >? ???> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >? ???> >? ???> --- On *Sun, 8/2/09, Matteo Cococcioni /? ???>/* wrote: >? ???> >? ???> >? ???>? ???From: Matteo Cococcioni ? ???> >? ???>? ???Subject: Re: [Pw_forum] occupation >? ???>? ???To: "PWSCF Forum" ? ???> >? ???>? ???Date: Sunday, August 2, 2009, 8:31 AM >? ???> >? ???> >? ???>? ???Dear Ali, >? ???> >? ???>? ???1, -1, 0 are just spin indexes to tell the code what is the >? ???relative >? ???>? ???magnetization of the atoms (parallel, antiparallel, or none). if >? ???>? ???your system is non magnetic put all 0. or set magn = .false. >? ???and put >? ???>? ???nothing. >? ???>? ???you should look at the examples on Fe and Si as well and >? ???learn from >? ???>? ???there by comparison. >? ???> >? ???>? ???Matteo >? ???> >? ???> >? ???> > > >? ???-- >? ???%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >? ???Matteo Cococcioni >? ???Department of Chemical Engineering and Materials Science, >? ???University of Minnesota >? ???421 Washington Av. SE >? ???Minneapolis, MN 55455 >? ???Tel. +1 612 624 9056? ? Fax +1 612 626 7246 >? ???%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >? ???_______________________________________________ >? ???Pw_forum mailing list >? ???Pw_forum at pwscf.org >? ???http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >??? -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056? ? Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% _______________________________________________ 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/20090806/7884c208/attachment-0001.htm From Michael at ihpc.a-star.edu.sg Thu Aug 6 10:59:24 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Thu, 6 Aug 2009 16:59:24 +0800 Subject: [Pw_forum] Geometry Optimization In-Reply-To: <276859.52500.qm@web24107.mail.ird.yahoo.com> References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: Mahasin: You are very close. Trying using calculation='vc-relax'. Don't forget to add an &CELL section to your input. Here is the relevant section of the manual: http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id3667252 Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of MAHASIN ALAM Sent: Thursday, August 06, 2009 4:54 PM To: pwscf Subject: [Pw_forum] Geometry Optimization Dear Friends, For geometry opimization in PWSCF (QE) it mentioned in the manual that we have to set calculation = 'relax'. If I set it, it will only relax the ions. But if I have a system with vacuum cell and if I need to relax the ions as well as vacuum cell, can I do it using PWSCF? If yes can any one tell me what I have to set in calculation type? Thank you for your help. Regards Mahasin ________________________________ This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/20652b79/attachment.htm From bipulrr at gmail.com Thu Aug 6 11:23:56 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 6 Aug 2009 14:53:56 +0530 Subject: [Pw_forum] relaxation of perovskite structure Message-ID: <3a749910908060223j10738f6fu2c6d25c81aec14f5@mail.gmail.com> Dear PWSCF users, I want to do structural relaxation calculation on LaMnO3 (insulating antiferromagnet). And I am having few question for doing relaxation of a=b#c type of compounds. 1. Do I have to simply run the vc-relax calculation and the results at the end gives relaxed structure? 2. Do after relaxation the final Pressure P= , I got very low? 3. I have run the vc-relax calculation (still running). During calculation I find that although pressure reaches comparitively lower value ~ -2.01 kbar, but the (3x3) stress tensor matrix, the off diagonal although zero, but the on-diagonal elements do show 11.52 Kbar pressure also............ So my question is, why I am not getting total pressure P and all the on-diagonal element appreciable of some very low value? What more option I have to use in input file for my point 3? Kindly guide me for the same. regards -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/62735127/attachment.htm From bipulrr at gmail.com Thu Aug 6 11:27:43 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 6 Aug 2009 14:57:43 +0530 Subject: [Pw_forum] Fwd: relaxation of perovskite structure In-Reply-To: <3a749910908060223j10738f6fu2c6d25c81aec14f5@mail.gmail.com> References: <3a749910908060223j10738f6fu2c6d25c81aec14f5@mail.gmail.com> Message-ID: <3a749910908060227k5804bb0bj47a6039edefae0b6@mail.gmail.com> SOrry, now the input file is attached ---------- Forwarded message ---------- From: Bipul Rakshit Date: Thu, Aug 6, 2009 at 2:53 PM Subject: relaxation of perovskite structure To: PWSCF Forum Dear PWSCF users, I want to do structural relaxation calculation on LaMnO3 (insulating antiferromagnet). And I am having few question for doing relaxation of a=b#c type of compounds. 1. Do I have to simply run the vc-relax calculation and the results at the end gives relaxed structure? 2. Do after relaxation the final Pressure P= , I got very low? 3. I have run the vc-relax calculation (still running). During calculation I find that although pressure reaches comparitively lower value ~ -2.01 kbar, but the (3x3) stress tensor matrix, the off diagonal although zero, but the on-diagonal elements do show 11.52 Kbar pressure also............ So my question is, why I am not getting total pressure P and all the on-diagonal element appreciable of some very low value? What more option I have to use in input file for my point 3? Kindly guide me for the same. regards -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/0c01f139/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.vc-relax.in Type: application/octet-stream Size: 2593 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090806/0c01f139/attachment.obj From Michael at ihpc.a-star.edu.sg Thu Aug 6 11:32:58 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Thu, 6 Aug 2009 17:32:58 +0800 Subject: [Pw_forum] Geometry Optimization In-Reply-To: References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: Prof Paulatto: Very good point. Mahasin: Listen to the master. :) For slabs, I usually optimize the bulk cell and use that lattice constant to generate a surface. With this surface, I don't change the cell (ie I use calculation='relax'). Hope that helps and sorry for the confusion. Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Lorenzo Paulatto Sent: Thursday, August 06, 2009 5:03 PM To: PWSCF Forum Subject: Re: [Pw_forum] Geometry Optimization In data 06 agosto 2009 alle ore 10:54:12, MAHASIN ALAM ha scritto: > But if I have a system with vacuum cell and if I need to relax the ions > as well as vacuum cell, can I do it using PWSCF? If yes can any one tell > me what I have to set in calculation type? Thank you for your help. You can use vc-relax to relax both the ions and the unit cell (mainatining its symmetry); but it does NOT do what you want. What you want to do is find the smaller amount of vacuum that guarantees a negligible interaction between periodic copies along the vacuum direction. This is equivalent to minimize forces between peridic images, but does not keep stress in account and will likely /increase/ the total energy. On the other hand, vc-relax only tries to minimize stress and minimize energy. In practice, you have to do a few tryes with different amounts of vacuum and see when the total energy becomes stable. This may reuire as little as 5 Angstrom of empty space, for a simple slab geometry, but may be much more if you have dipolar molecules. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From paulatto at sissa.it Thu Aug 6 11:33:54 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 06 Aug 2009 11:33:54 +0200 Subject: [Pw_forum] Geometry Optimization In-Reply-To: References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: In data 06 agosto 2009 alle ore 11:32:58, Michael Sullivan ha scritto: > Prof Paulatto: graduate student :-) -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nkxirainbow at gmail.com Thu Aug 6 12:22:50 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 6 Aug 2009 18:22:50 +0800 Subject: [Pw_forum] Geometry Optimization In-Reply-To: References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: <21fbc4790908060322u45ac36b9w1a11647eb5c05d8@mail.gmail.com> Dear Lorenzo Paulatto: > >On the other hand, vc-relax only tries to minimize stress and minimize > >energy. I think vc-relax tries to minimize stress, energy and force at the same time. And there is a parameter "*forc_conv_thr*". Am I wrong? ____________________________________ > 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/20090806/eb0252e9/attachment-0001.htm From paulatto at sissa.it Thu Aug 6 12:24:48 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 06 Aug 2009 12:24:48 +0200 Subject: [Pw_forum] Geometry Optimization In-Reply-To: <21fbc4790908060322u45ac36b9w1a11647eb5c05d8@mail.gmail.com> References: <276859.52500.qm@web24107.mail.ird.yahoo.com> <21fbc4790908060322u45ac36b9w1a11647eb5c05d8@mail.gmail.com> Message-ID: In data 06 agosto 2009 alle ore 12:22:50, xirainbow ha scritto: > I think vc-relax tries to minimize stress, energy and force at the same > time. > And there is a parameter "*forc_conv_thr*". > Am I wrong? You are right, there are also etot_conv_thr and press_conv_thr, although the latter is not in the same namelist as the others. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nkxirainbow at gmail.com Thu Aug 6 12:27:43 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 6 Aug 2009 18:27:43 +0800 Subject: [Pw_forum] Geometry Optimization In-Reply-To: <276859.52500.qm@web24107.mail.ird.yahoo.com> References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: <21fbc4790908060327hefd551dm11ee5df6b0cb2734@mail.gmail.com> Dear MAHASIN ALAM: > >If I need to relax the ions as well as vacuum cell, can I do it using > PWSCF? > I think the following parameter can help you:) *"* *cell_dofree CHARACTER Default: 'all'* * Select which of the cell parameters should be moved:* * all = all axis and angles are propagated volume = the cell is simply rescaled, without changing the shape x = only the x axis is moved y = only the y axis is moved z = only the z axis is moved xy = only the x and y axis are moved, angles are unchanged xz = only the x and z axis are moved, angles are unchanged yz = only the y and z axis are moved, angles are unchanged xyz = x, y and z axis are moved, angles are unchanged xyt = x1, x2, y2 (i.e. lower xy triangle of the 2 vectors) xys = x1, y1, x2, y2 (i.e. xy square of the 2 vectors) xyzt = x1, x2, y2, x3, y3, z3 (i.e. lower xyz triangle of the 3 vectors) * " - > ____________________________________ > 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/20090806/6b2ed8e5/attachment.htm From baroni at sissa.it Thu Aug 6 16:11:44 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 6 Aug 2009 16:11:44 +0200 Subject: [Pw_forum] Geometry Optimization In-Reply-To: References: <276859.52500.qm@web24107.mail.ird.yahoo.com> Message-ID: <930AFD84-C5D4-4671-9475-0ECB0374390D@sissa.it> On Aug 6, 2009, at 11:33 AM, Lorenzo Paulatto wrote: > In data 06 agosto 2009 alle ore 11:32:58, Michael Sullivan > ha scritto: >> Prof Paulatto: > > graduate student :-) @SISSA we have _EXTREMELY_ well qualified graduate students ... ;-) S. > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > 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/20090806/d5e680da/attachment.htm From matteo at umn.edu Thu Aug 6 17:15:09 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 06 Aug 2009 10:15:09 -0500 Subject: [Pw_forum] U for Oxygen In-Reply-To: <461162.40692.qm@web112508.mail.gq1.yahoo.com> References: <461162.40692.qm@web112508.mail.gq1.yahoo.com> Message-ID: <4A7AF37D.9050304@umn.edu> Dear Ali ali kazempour wrote: > Dear Matteo > In your tutorial about LDA_U, you mentioned that the perturbation > should be isolated. and said that we normally use supercell of > increasing size up to when convergence of is reached. I don't > understand how do you increase the size of the cell and how do you > compute the U in larger supercell.? I mean how do you apply > perturbation to bigger size or how to extrapolate the U to converge? > just like to the small one. please run the examples in the tutorial > Another question according to prior email for computation of U by > common method(not linear response) is : you mentioned that espresso > cann't directly change the occupation of special orbital by hand, but > it is possible to do by using constraint on total number of > electron(total occupation) indirectly . Do you mean that( for example > for Ti atom that has 2 electron in d orbital) ,what can i do is change > the of number of nelup and neldw without change in nelec? or I have > to do another switch? Would you please tell me in more details. > Thank you very much for your aids > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Tue, 8/4/09, Matteo Cococcioni //* wrote: > > > From: Matteo Cococcioni > Subject: Re: [Pw_forum] U for Oxygen > To: "PWSCF Forum" > Date: Tuesday, August 4, 2009, 9:52 AM > > > this is what comes out from the calculation (U(O) > U(Ni)). > whether it's > reasonable to apply U on O or not, I'm not sure. > > I think the U shouldn't be used on states that are completely > occupied. > > Matteo > > > > ali kazempour wrote: > > Dear Matteo > > This means that hubbard parameter for oxygen is large (grater than > > Ni). Is it correct or originate from another challenge? > > thanks > > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > --- On *Tue, 8/4/09, Matteo Cococcioni / >/* wrote: > > > > > > From: Matteo Cococcioni > > > Subject: Re: [Pw_forum] U for Oxygen > > To: "PWSCF Forum" > > > Date: Tuesday, August 4, 2009, 6:59 AM > > > > > > > > Dear Ali, > > > > > > > > ali kazempour wrote: > > > Dear Matteo > > > I used your comment and followed your example for NiO and I > > succeed > > > to get U for TiO2. But in file Ur16.out I see three column . > > > > > > > I don't have any three column section in any of my files. so if > > you want > > me to help you you have to report at least a section of your > output > > file. This is a good habit actually in consideration of the > fact that > > this is not a private conversation (I would have asked you > in any > > case > > as I don't remember by heart the format of any file) between me > > and you > > but a message to the forum and you want other people to > understand > > what you are saying. > > > > > The first is number of atom in supercell , second is U > value for Ni > > > atom and I don,t know the third? does the third belong > to U value > > > for Oxygen or not? Because the third column kas big value? > > > > > > > > > another question is for isolated atom Hubbard parameter. > What do > > you > > > expect about the value of U for Isolated atom? Is this big > value > > > (greater than 10 eV) or it would be tiny value? > > > > > > > I think it will be meaningless for the reasons I explained > in my last > > email. To obtain a meaningful number for the isolated atom you > > probably > > have to abandon the idea to use a perturbation in the > potential and > > change instead the number of electrons directly. This means > you will > > have to do calculations on atoms having fractional charges which > > requires additional corrections if you use a code designed for > > periodic > > systems (crystals). However I have never done this isolated atom > > calculation of U before so I don't have more details about it. > > I see (from a private email) you are thinking of computing U > for the > > isolated atom and to obtain a value for the crystal just by > > dividing by > > the epsilon_inft. the method is proposed in > > > > http://link.aps.org/doi/10.1103/PhysRevB.74.045202 > > > > (which I haven't re-read yet). > > > > I see a couple of problems: > > > > 1) (not important for ZnO). suppose you have Fe3O4 with Fe2+ and > > Fe3+. > > these Fe ions likely have different U. how do you obtain > > a different number from the atomic code? would you do the > calculation > > for isolated Fe2+ and Fe3+? > > > > 2) how do you get epsilon? since it's a linear response > property I > > don't > > think its calculation is any cheaper than the direct > calculation of U. > > > > regards, > > > > Matteo > > > > > should we choose for running the script for isolated atom only > > gamma > > > point or we have to choose a fine mesh? > > > thanks a lot > > > > > > > > > Ali Kazempour > > > Physics department, Isfahan University of Technology > > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > > > --- On *Sun, 8/2/09, Matteo Cococcioni / > > >>/* wrote: > > > > > > > > > From: Matteo Cococcioni > > >> > > > Subject: Re: [Pw_forum] occupation > > > To: "PWSCF Forum" > > >> > > > Date: Sunday, August 2, 2009, 8:31 AM > > > > > > > > > Dear Ali, > > > > > > 1, -1, 0 are just spin indexes to tell the code what > is the > > relative > > > magnetization of the atoms (parallel, antiparallel, or > none). if > > > your system is non magnetic put all 0. or set magn = > .false. > > and put > > > nothing. > > > you should look at the examples on Fe and Si as well and > > learn from > > > there by comparison. > > > > > > Matteo > > > > > > > > > > > > > > > -- > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Matteo Cococcioni > > Department of Chemical Engineering and Materials Science, > > University of Minnesota > > 421 Washington Av. SE > > Minneapolis, MN 55455 > > Tel. +1 612 624 9056 Fax +1 612 626 7246 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From paulatto at sissa.it Thu Aug 6 18:13:27 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 6 Aug 2009 18:13:27 +0200 (CEST) Subject: [Pw_forum] chargedensity In-Reply-To: <84ff69170908050338g5dd38f3bxcf37aa630d1b06fd@mail.gmail.com> References: <84ff69170908050338g5dd38f3bxcf37aa630d1b06fd@mail.gmail.com> Message-ID: <50299.78.12.161.81.1249575207.squirrel@webmail.sissa.it> On Wed, August 5, 2009 12:38, vamsi kv wrote: > 1. Can i print the chargedensity information after every iteration in the > scf or relax calculation? or can we know waht is the initial charge > density gues and how it changes during the simulation. Not without modifying the code; I wouldn't take too much effort to program it, but you'll need a good reason if you wish someone to do it for free ;-). The initial charge density is a superposition of atomic charge densities (as defined in the pseudopotential file), if necessary renormalized (in Fourier space, e.g. rescaling the G=0 component) > 2. What is bonding chargedensity? The fraction of charge density that cannot be assigned to a specific atom. It is an ill defined quantity in plane-wave based codes (such as quantum-espresso). Actually I think it is an ill defined quantity in every code, although it helps chemical intuition. Computing maximally-localized Wannier functions, to see which are centered far off the ions, is probably more meaningful. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From decboy9 at gmail.com Thu Aug 6 18:31:30 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 6 Aug 2009 22:01:30 +0530 Subject: [Pw_forum] line crossing Valance bands (VB) & CB Message-ID: Hi to all, I have successfully calculated the band structure of my system. It is also matching the results. But when I plot my band structure in ps format only one line from conduction band and valance band is showing fluctuations. Means one line ,in ps output, from conduction band has apparently come down to valance band and vice versa. And this fluctuation is just at the end of graph. (means i have given 41 k points in calculations= 'bands' and in only last 3 there is some fluctuations, the whole other graphs is smooth otherwsie). Please help or give any suggestion. Thankful to all of you. With regards, Dev sharma. University of Delhi, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/c4e69f27/attachment.htm From spmmal at gmail.com Thu Aug 6 19:01:53 2009 From: spmmal at gmail.com (Caloma Trumica) Date: Thu, 6 Aug 2009 13:01:53 -0400 Subject: [Pw_forum] About cut-off energy Message-ID: Dear All, I would like to know whether there is some default plane-wave cut-off energy starting to test for each element. Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/bcb00117/attachment.htm From lshulenburger at gmail.com Thu Aug 6 19:34:47 2009 From: lshulenburger at gmail.com (Luke Shulenburger) Date: Thu, 6 Aug 2009 13:34:47 -0400 Subject: [Pw_forum] About cut-off energy In-Reply-To: References: Message-ID: Hello, You appear to be new to this mailing list and probably new to density functional theory as well. Welcome. The answer to your question is definitely no. The plane-wave cutoff is highly dependent on the nature of the pseudopotential used for each species in your simulation. There may be recommended cut off values for each of the pseudopotentials that you are using and then you should start with the largest of those values. If you are not familiar with these concepts I would recommend the book Electronic Structure: Basic Theory and Practical Methods by Richard Martin or any number of review articles that might be suggested by members of this list. Good luck. Luke Shulenburger Geophysical Laboratory Carnegie Institute of Washington PS It is customary on this list to include your name and affiliation in all messages. On Thu, Aug 6, 2009 at 1:01 PM, Caloma Trumica wrote: > Dear All, > > I would like to know whether there is some default plane-wave?cut-off energy > starting to test for each element. > > Thanks. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From waleed_abusin at hotmail.com Thu Aug 6 19:45:14 2009 From: waleed_abusin at hotmail.com (Alwaleed Adllan) Date: Thu, 6 Aug 2009 20:45:14 +0300 Subject: [Pw_forum] bond length Message-ID: Dear all I want to calculate the bond length of come material how can I do that I try example03 but the out but not clear or may be I don't understand it i need help thans _________________________________________________________________ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/7941a16a/attachment.htm From waleed_abusin at hotmail.com Thu Aug 6 20:33:35 2009 From: waleed_abusin at hotmail.com (Alwaleed Adllan) Date: Thu, 6 Aug 2009 21:33:35 +0300 Subject: [Pw_forum] bond length Message-ID: Dear all I want to calculate the bond length of some material how can I do that I try example03 but the output not clear or may be I didn't understand it i need help thanks for all See all the ways you can stay connected to friends and family _________________________________________________________________ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090806/bdf0c43a/attachment.htm From matteo at umn.edu Thu Aug 6 21:05:14 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 06 Aug 2009 14:05:14 -0500 Subject: [Pw_forum] bond length In-Reply-To: References: Message-ID: <4A7B296A.9090003@umn.edu> Dear Alwaleed with the little information you provide it's difficult to give you an answer. probably one of the relaxation algorithms in the pwscf code is what you need. whether or not you need a relaxation of ions only or of the unit cell as well depends on your system and how much you already know about it. please include your affiliation in your posts. Matteo Alwaleed Adllan wrote: > > > Dear all > > I want to calculate the bond length of some material > how can I do that I try example03 > but the output not clear or may be > I didn't understand it i need help > > thanks for all > > See all the ways you can stay connected to friends and family > > See all the ways you can stay connected to friends and family > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From daijiayu at nudt.edu.cn Fri Aug 7 05:49:50 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Fri, 07 Aug 2009 11:49:50 +0800 Subject: [Pw_forum] TDDFT and GW Message-ID: <449616990.04837@nudt.edu.cn> Dear all, It's so exciting to see the new release of espresso-4.1, and a lot of new parts in the code. But i would like to know if it includes the parts of TDDFT and GW? They have been discussed a lot before, and expected to be done soon? By the way, if we want change something about the exchange-correction functions in the code, what's the step to do it? It should be a big job? Best wishes. Jiayu ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From nkxirainbow at gmail.com Fri Aug 7 06:56:19 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 7 Aug 2009 12:56:19 +0800 Subject: [Pw_forum] TDDFT and GW In-Reply-To: <449616990.04837@nudt.edu.cn> References: <449616990.04837@nudt.edu.cn> Message-ID: <21fbc4790908062156t4063fc3cq7ee1dabfb3b3d43@mail.gmail.com> Dear Jiayu Dai? > It's so exciting to see the new release of espresso-4.1, and a lot of new > parts in > the code. But i would like to know if it includes the parts of TDDFT and > GW? They > have been discussed a lot before, and expected to be done soon? As I only use 4.0.5, I do not know whether QE 4.1can perform GW and TDDFT calculation. If you want to do GW and TDDFT righti now, you can try Yambo. Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo can take PWscf output files as its input file and do GW and TDDFT calculation. And Yambo is free. You can find it here http://www.yambo-code.org/index.php . From metaljobpar at gmail.com Fri Aug 7 08:05:14 2009 From: metaljobpar at gmail.com (Parveen Kr) Date: Fri, 7 Aug 2009 01:05:14 -0500 Subject: [Pw_forum] About cut-off energy In-Reply-To: References: Message-ID: <923fa5bc0908062305p71e13d59gac4ccb6297ddb81@mail.gmail.com> Dear Luke, I am a newbie in DFT just starting out. You mentioned review articles in response to another member's query. Can you suggest me some. Thanks Par On 8/6/09, Luke Shulenburger wrote: > Hello, > > You appear to be new to this mailing list and probably new to density > functional theory as well. Welcome. The answer to your question is > definitely no. The plane-wave cutoff is highly dependent on the > nature of the pseudopotential used for each species in your > simulation. There may be recommended cut off values for each of the > pseudopotentials that you are using and then you should start with the > largest of those values. If you are not familiar with these concepts > I would recommend the book Electronic Structure: Basic Theory and > Practical Methods by Richard Martin or any number of review articles > that might be suggested by members of this list. Good luck. > > Luke Shulenburger > Geophysical Laboratory > Carnegie Institute of Washington > > PS It is customary on this list to include your name and affiliation > in all messages. > > On Thu, Aug 6, 2009 at 1:01 PM, Caloma Trumica wrote: >> Dear All, >> >> I would like to know whether there is some default plane-wave?cut-off >> energy >> starting to test for each element. >> >> Thanks. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From Michael at ihpc.a-star.edu.sg Fri Aug 7 09:09:08 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Fri, 7 Aug 2009 15:09:08 +0800 Subject: [Pw_forum] TDDFT and GW In-Reply-To: <21fbc4790908062156t4063fc3cq7ee1dabfb3b3d43@mail.gmail.com> References: <449616990.04837@nudt.edu.cn> <21fbc4790908062156t4063fc3cq7ee1dabfb3b3d43@mail.gmail.com> Message-ID: I was looking into this a bit this week? If I understand it correctly, both YAMBO and SaX can perform GW calculations. Is there any reason to use one over the other and in what situations? By the way, information about SaX can be found here: http://www.sax-project.org/ Mike Sullivan Institute of High Performance Computing, Singapore http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of xirainbow Sent: Friday, August 07, 2009 12:56 PM To: Jiayu Dai; PWSCF Forum Subject: Re: [Pw_forum] TDDFT and GW Dear Jiayu Dai? It's so exciting to see the new release of espresso-4.1, and a lot of new parts in the code. But i would like to know if it includes the parts of TDDFT and GW? They have been discussed a lot before, and expected to be done soon? As I only use 4.0.5, I do not know whether QE 4.1can perform GW and TDDFT calculation. If you want to do GW and TDDFT righti now, you can try Yambo. Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo can take PWscf output files as its input file and do GW and TDDFT calculation. And Yambo is free. You can find it here http://www.yambo-code.org/index.php . From you address, I know you are Chinese. You can visit blog.sina.com.cn/nkasir to find some information about Yambo installaiton. -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From nkxirainbow at gmail.com Fri Aug 7 10:01:28 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 7 Aug 2009 16:01:28 +0800 Subject: [Pw_forum] TDDFT and GW In-Reply-To: References: <449616990.04837@nudt.edu.cn> <21fbc4790908062156t4063fc3cq7ee1dabfb3b3d43@mail.gmail.com> Message-ID: <21fbc4790908070101t6b1d577dt4a4611b34bd2b962@mail.gmail.com> Dear Michael Sullivan: Your reply widens my horizon:) But I think Sax can not do TDDFT calculation. On 8/7/09, Michael Sullivan wrote: > > I was looking into this a bit this week? > > If I understand it correctly, both YAMBO and SaX can perform GW > calculations. Is there any reason to use one over the other and in what > situations? > > By the way, information about SaX can be found here: > http://www.sax-project.org/ > > Mike Sullivan > Institute of High Performance Computing, Singapore > http://www.sullivan.sg/ > > > ____________________________________ > 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/20090807/7481b2d2/attachment.htm From baroni at sissa.it Fri Aug 7 10:11:54 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 7 Aug 2009 10:11:54 +0200 Subject: [Pw_forum] TDDFT and GW In-Reply-To: References: <449616990.04837@nudt.edu.cn> <21fbc4790908062156t4063fc3cq7ee1dabfb3b3d43@mail.gmail.com> Message-ID: <1F21499B-03BA-44DB-9A5D-C8FD834AE241@sissa.it> On Aug 7, 2009, at 9:09 AM, Michael Sullivan wrote: > I was looking into this a bit this week? > > If I understand it correctly, both YAMBO and SaX can perform GW > calculations. Is there any reason to use one over the other and in > what situations? > > By the way, information about SaX can be found here: http://www.sax-project.org/ You are right, Mike. Both yambo and sax have gw/bse capabilities. I think it is an exciting opportunity for the QE community to give both codes a try, and a great opportuniy for their respective developers' groups to get feedback from us. As for the announced GW/tddft capabilities in QE. They are both on their way, and they will address a different target from yambo and sax. The tddft module in QE implements a new Lanczos approach to time- dependent density-functional (perturbation) theory, particularly designed to cope with large systems (several hundreds atoms). See: JChemPhys 128, 154105 ( 2008). Our implementation of GW will be based on new algorithms to address large systems (a few hundreds atoms). see: PRB 79, 201104 (2009), and to be published. Both codes will presumably have fewer features/capabilities than generalist codes such as sax/yambo. Stay tuned! SB Both modules will be made available in the next few weeks/months (Q4-2009) > > Mike Sullivan > Institute of High Performance Computing, Singapore > http://www.sullivan.sg/ > > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] > On Behalf Of xirainbow > Sent: Friday, August 07, 2009 12:56 PM > To: Jiayu Dai; PWSCF Forum > Subject: Re: [Pw_forum] TDDFT and GW > > Dear Jiayu Dai? > It's so exciting to see the new release of espresso-4.1, and a lot > of new parts in > the code. But i would like to know if it includes the parts of TDDFT > and GW? They > have been discussed a lot before, and expected to be done soon? > > As I only use 4.0.5, I do not know whether QE 4.1can perform GW and > TDDFT calculation. > If you want to do GW and TDDFT righti now, you can try Yambo. > Yambo is a FORTRAN/C code for Many-Body calculations in solid state > and molecular physics. Yambo can take PWscf output files as its > input file and do GW and TDDFT calculation. And Yambo is free. You > can find it here http://www.yambo-code.org/index.php . > From you address, I know you are Chinese. You can visit > blog.sina.com.cn/nkasir to find some information about Yambo > installaiton. > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. > Please do not copy or use it for any purpose, or disclose its > contents to any other person. Thank you. > _______________________________________________ > 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/20090807/5c4bc9f4/attachment.htm From paulatto at sissa.it Fri Aug 7 12:31:54 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 07 Aug 2009 12:31:54 +0200 Subject: [Pw_forum] Fwd: relaxation of perovskite structure In-Reply-To: <3a749910908060227k5804bb0bj47a6039edefae0b6@mail.gmail.com> References: <3a749910908060223j10738f6fu2c6d25c81aec14f5@mail.gmail.com> <3a749910908060227k5804bb0bj47a6039edefae0b6@mail.gmail.com> Message-ID: Dear Bipul, In data 06 agosto 2009 alle ore 11:27:43, Bipul Rakshit ha scritto: > 1. Do I have to simply run the vc-relax calculation and the results at > the end gives relaxed structure? Yes > 2. Do after relaxation the final Pressure P= , I got very low? It depends on the threshold you've set. The default value is 0.5 Kbar > 3. I have run the vc-relax calculation (still running). During > calculation I find that although pressure reaches comparitively lower > value ~ -2.01 kbar, but the (3x3) stress tensor matrix, the off diagonal > although zero, but the on-diagonal elements do show 11.52 Kbar pressure > also............ Because you've set press=10.0 > So my question is, why I am not getting total pressure P and all the > on-diagonal element appreciable of some very low value? Because you've asked the code to find a configuration where pressure is 10.0 kbar, and that's what you will get! > What more option I have to use in input file for my point 3? I've noticed that you've set starting_magnetization=5.0 for two species, but the legal values are between -1 and 1 > Kindly guide me for the same. kindly read the manual (INPUT_PW.html) that you can find in the Doc/ directory! regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kazempoor2000 at yahoo.com Fri Aug 7 12:48:58 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 7 Aug 2009 03:48:58 -0700 (PDT) Subject: [Pw_forum] nelec Message-ID: <704182.51448.qm@web112505.mail.gq1.yahoo.com> Dear users I want to know( for example number of valence electrons? for isolated Zn is 12 ) If I put nelec=11 ,which orbital become free or if put nelec=13 which orbital is going to be full? If we change the number of electron from neutral state, does it means that we are doing charged atom calculation and we need to do? some correction like makov -payne or not? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090807/e659db89/attachment-0001.htm From baroni at sissa.it Fri Aug 7 14:26:21 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 7 Aug 2009 14:26:21 +0200 Subject: [Pw_forum] nelec In-Reply-To: <704182.51448.qm@web112505.mail.gq1.yahoo.com> References: <704182.51448.qm@web112505.mail.gq1.yahoo.com> Message-ID: <62A83CFB-1A5A-4958-BD8D-7057582C7662@sissa.it> On Aug 7, 2009, at 12:48 PM, ali kazempour wrote: > > Dear users > I want to know( for example number of valence electrons for > isolated Zn is 12 ) If I put nelec=11 ,which orbital become free the HOMO > or if put nelec=13 which orbital is going to be full? the LUMO (as Prof. Pauli would suggest) > If we change the number of electron from neutral state, does it > means that we are doing charged atom calculation what else? > and we need to do some correction like makov -payne or not? I would say so ... SB > thanks a lot > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > _______________________________________________ > 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 From kazempoor2000 at yahoo.com Fri Aug 7 15:37:03 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 7 Aug 2009 06:37:03 -0700 (PDT) Subject: [Pw_forum] nelec modify Message-ID: <245967.16076.qm@web112516.mail.gq1.yahoo.com> Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Fri, 8/7/09, ali kazempour wrote: From: ali kazempour Subject: nelec To: "pw" Date: Friday, August 7, 2009, 3:48 AM Dear users I want to know( for example number of valence electrons? for isolated Zn is 12 ) If I put nelec=11 ,which orbital become free or if put nelec=13 which orbital is going to be full? If we change the number of electron from neutral state, does it means that we are doing charged atom calculation and we need to do? some correction like makov -payne or not? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090807/1a56f8ca/attachment.htm From lanhaiping at gmail.com Fri Aug 7 16:27:20 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 7 Aug 2009 22:27:20 +0800 Subject: [Pw_forum] nelec modify In-Reply-To: <245967.16076.qm@web112516.mail.gq1.yahoo.com> References: <245967.16076.qm@web112516.mail.gq1.yahoo.com> Message-ID: Hi, Ali Why do you repeat your question ? Stefano has already replied the same question you droped to the list . I donot think it is proper to repeat the same thread several times . Regards On Fri, Aug 7, 2009 at 9:37 PM, ali kazempour wrote: > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Fri, 8/7/09, ali kazempour * wrote: > > > From: ali kazempour > Subject: nelec > To: "pw" > Date: Friday, August 7, 2009, 3:48 AM > > > Dear users > I want to know( for example number of valence electrons for isolated Zn is > 12 ) If I put nelec=11 ,which orbital become free or if put nelec=13 which > orbital is going to be full? > If we change the number of electron from neutral state, does it means that > we are doing charged atom calculation and we need to do some correction > like makov -payne or not? > thanks a lot > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090807/73aadd9a/attachment.htm From nlu at mail.ustc.edu.cn Fri Aug 7 16:37:17 2009 From: nlu at mail.ustc.edu.cn (nlu at mail.ustc.edu.cn) Date: Fri, 07 Aug 2009 22:37:17 +0800 Subject: [Pw_forum] Fwd:NMR of benzene Message-ID: <449655837.24653@ustc.edu.cn> >From: "" >Reply-To: "" >To: pw_forum at pwscf.org >Subject: NMR of benzene >Date:Fri, 07 Aug 2009 21:22:14 +0800 > >Dear all, > I have used GIPAW to calculate NMR of benzene recently. I have two question, the > first is why the mass of diamond C is 12 in the input file, in the examples of > GIPAW, why not 13? > The second is something strange happened in my calculation. When I increase the > ecutwfc, the shielding tensor of C did not converge: > 40ry:43ppm. 50ry:40ppm. 60ry:46ppm. 70ry:55ppm. 80ry:54ppm. 90ry: 43ppm. > 100ry:30ppm. 110ry:27ppm. 120ry:39ppm. 130ry:62ppm. 140ry:85ppm. > The input file is as following: > scf.in > &control > calculation='scf', > prefix='ben40', > tstress = .true., > tprnfor = .true., > restart_mode='from_scratch', > pseudo_dir ='/home/ustc/zyli/LuNing/NMR/pseudo', > outdir='/tmp/', > wf_collect = .true. > / > &system > ibrav= 0, celldm(1) = 1.889725989, > nat= 12, ntyp= 2, > nbnd= 50, > ecutwfc = 40, ecutrho = 160, > spline_ps = .true. > / > &electrons > diagonalization = 'david' > mixing_mode = 'plain' > mixing_beta = 0.4 > conv_thr = 1.0d-10 > / > ATOMIC_SPECIES > C 12.0107 C.pbe-tm-gipaw.UPF > H 1.00794 H.pbe-tm-gipaw.UPF > CELL_PARAMETERS > 15.000000 0.000000 0.000000 > 0.000000 15.000000 0.000000 > 0.000000 0.000000 10.000000 > K_POINTS (automatic) > 1 1 1 0 0 0 > ATOMIC_POSITIONS (crystal) > C 0.7308956360000001 0.9405381680000000 1.1476448430000001 > C 0.8213534039999999 0.9418137320000000 1.1835869040000000 > C 0.8707671719999998 0.8623363860000000 1.1842830870000001 > C 0.8297234940000000 0.7815763499999999 1.1490365249999999 > C 0.7392633260000001 0.7803012599999999 1.1130950639999999 > C 0.6898517000000000 0.8597802960000001 1.1123997629999998 > H 0.6194515180000000 0.8587884660000000 1.0844271930000002 > H 0.6924443960000000 1.0023908619999999 1.1471064960000001 > H 0.8532991100000000 1.0046622900000000 1.2110162340000004 > H 0.9411691480000000 0.8633331299999999 1.2122536769999999 > H 0.8681772059999999 0.7197198679999999 1.1495745989999999 > H 0.7073118900000002 0.7174531920000000 1.0856646179999998 > nmr.in > &inputgipaw > job = 'nmr' > prefix = 'ben40' > tmp_dir = '/tmp/' > isolve = 0 > iverbosity = 1 > q_gipaw = 0.01 > spline_ps = .true. > use_nmr_macroscopic_shape = .true. > / > I have already tested the supercell and the number of k-points. They are all > enough. Can someone tell the reason or the mistake of my calculation? > Thanks, Ning Lu > > > From ceresoli at MIT.EDU Fri Aug 7 16:49:53 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Fri, 07 Aug 2009 10:49:53 -0400 Subject: [Pw_forum] Fwd:NMR of benzene In-Reply-To: <449655837.24653@ustc.edu.cn> References: <449655837.24653@ustc.edu.cn> Message-ID: <4A7C3F11.5080700@mit.edu> nlu at mail.ustc.edu.cn wrote: >> From: "" >> Reply-To: "" >> To: pw_forum at pwscf.org >> Subject: NMR of benzene >> Date:Fri, 07 Aug 2009 21:22:14 +0800 >> >> Dear all, >> I have used GIPAW to calculate NMR of benzene recently. I have two question, > the >> first is why the mass of diamond C is 12 in the input file, in the examples of >> GIPAW, why not 13? Dear Lu, the NMR calculation is done at fixed atomic positions. The mass of the isotope matters only when computing phonons. Notice that in the NMR calculation, every nucleus is considered NMR active (with nuclear spin > 0). In reality, if the sample is not enriched, one should take into account the natural abundance of every isotope. >> The second is something strange happened in my calculation. When I increase the >> ecutwfc, the shielding tensor of C did not converge: >> 40ry:43ppm. 50ry:40ppm. 60ry:46ppm. 70ry:55ppm. 80ry:54ppm. 90ry: 43ppm. >> 100ry:30ppm. 110ry:27ppm. 120ry:39ppm. 130ry:62ppm. 140ry:85ppm. Your input looks correct, except for an isolated system you don't need the macroscopic shape correction. Later tonight or tomorrow, I'll investigate the problem. Cheers, Davide From haoweipeng at gmail.com Fri Aug 7 17:02:43 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Fri, 7 Aug 2009 10:02:43 -0500 Subject: [Pw_forum] nelec Message-ID: <7559eb240908070802i40509d94r7395fe59a9916590@mail.gmail.com> Hi ali, I think you can consider this issue step by step. First, figure out the band structure of the original materials. And then, you can find out where the added electrons or holes will be located. Corrections are needed if: 1, the cell is small; 2, the dielectric constants are very small; 3, the number of added electrons or holes is very large, eg 3 or 4.. But, the makov-payne correction itself is not correct, because it describe the added electrons as point charge. for more details, please see the paper Computational Materials Science 30 (2004) 337?348, especially Fig.1. So I think the best method is use a larger cell, and compare the results.... Best regards, -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 Message: 5 > Date: Fri, 7 Aug 2009 03:48:58 -0700 (PDT) > From: ali kazempour > Subject: [Pw_forum] nelec > To: pw > Message-ID: <704182.51448.qm at web112505.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > Dear users > I want to know( for example number of valence electrons? for isolated Zn is > 12 ) If I put nelec=11 ,which orbital become free or if put nelec=13 which > orbital is going to be full? > If we change the number of electron from neutral state, does it means that > we are doing charged atom calculation and we need to do? some correction > like makov -payne or not? > thanks a lot > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090807/e659db89/attachment.htm > > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090807/8fa87cab/attachment.htm From nlu at mail.ustc.edu.cn Sat Aug 8 10:55:14 2009 From: nlu at mail.ustc.edu.cn (nlu at mail.ustc.edu.cn) Date: Sat, 08 Aug 2009 16:55:14 +0800 Subject: [Pw_forum] Fwd:NMR of benzene Message-ID: <449721714.25334@ustc.edu.cn> Sincerely thanks to Davide for your explaination. I would hope your further investigation. Best wishes. Ning Lu ????????????????????: >From: Davide Ceresoli >Reply-To: >To: nlu at mail.ustc.edu.cn, PWSCF Forum >Subject: Re: [Pw_forum] Fwd:NMR of benzene >Date:Fri, 07 Aug 2009 10:49:53 -0400 > >nlu at mail.ustc.edu.cn wrote: > >> From: "" > >> Reply-To: "" > >> To: pw_forum at pwscf.org > >> Subject: NMR of benzene > >> Date:Fri, 07 Aug 2009 21:22:14 +0800 > >> > >> Dear all, > >> I have used GIPAW to calculate NMR of benzene recently. I have two question, > > the > >> first is why the mass of diamond C is 12 in the input file, in the examples of > >> GIPAW, why not 13? > Dear Lu, > the NMR calculation is done at fixed atomic positions. The > mass of the isotope matters only when computing phonons. > > Notice that in the NMR calculation, every nucleus is considered > NMR active (with nuclear spin > 0). In reality, if the sample is > not enriched, one should take into account the natural abundance > of every isotope. > > >> The second is something strange happened in my calculation. When I increase the > >> ecutwfc, the shielding tensor of C did not converge: > >> 40ry:43ppm. 50ry:40ppm. 60ry:46ppm. 70ry:55ppm. 80ry:54ppm. 90ry: 43ppm. > >> 100ry:30ppm. 110ry:27ppm. 120ry:39ppm. 130ry:62ppm. 140ry:85ppm. > Your input looks correct, except for an isolated system you don't > need the macroscopic shape correction. Later tonight or tomorrow, > I'll investigate the problem. > > > Cheers, > Davide > From ceresoli at MIT.EDU Sat Aug 8 18:24:43 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Sat, 08 Aug 2009 12:24:43 -0400 Subject: [Pw_forum] Fwd:NMR of benzene In-Reply-To: <449721714.25334@ustc.edu.cn> References: <449721714.25334@ustc.edu.cn> Message-ID: <4A7DA6CB.6080700@mit.edu> nlu at mail.ustc.edu.cn wrote: > > Sincerely thanks to Davide for your explaination. I would hope your further > investigation. > > Best wishes. > Ning Lu > Change your input to: celldm(1) = 18.89725989 CELL_PARAMETERS 1.500000 0.000000 0.000000 0.000000 1.500000 0.000000 0.000000 0.000000 1.000000 I apologize for the mysterious answer: I have an idea where the bug is, but I don't understand why. Bottom line: with ibrav = 0, please set celldm(1) to a not so small value. Davide From vamsi.iisc at gmail.com Sat Aug 8 19:40:46 2009 From: vamsi.iisc at gmail.com (vamsi kv) Date: Sat, 8 Aug 2009 23:10:46 +0530 Subject: [Pw_forum] running the parallel code Message-ID: <84ff69170908081040g53f305ffuca050bfc497ff8bc@mail.gmail.com> Dear PwScf users, I want to know how to run pwscf on parallel systems with shared memory. what type of libraries has to be used. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090808/fcaa2a94/attachment.htm From swblelia at ehu.es Sat Aug 8 19:41:07 2009 From: swblelia at ehu.es (Aritz Leonardo) Date: Sat, 8 Aug 2009 12:41:07 -0500 Subject: [Pw_forum] runtime error Message-ID: Hi all, I recently compiled the latest espresso in my macbook pro laptop using: 1.- g95 2.- gcc 4.2 3.- mpif90, mpicc etc... from mpich2 (compiled with the compilers above) All the compilations were done without problems. But when I run the examples in order to test the executables, something new for me happens. Running the 1st example (and only in this one) I get the error posted below. It crashes when calculating the band-structure of Si. The rest of the calculations are performed perfectly (even other band structure calcs for different elements) when compared to reference data provided. The most striking thing at least for me is that, when I run example05 where a band-structure calculation is done again for Silicon, I get NO errors. Any idea where to look for solutions? aritz OUTPUT from the screen: cleaning /Users/aritz/tmp_esp... done running the scf calculation for Si... done running the band-structure calculation for Si...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 done running the symmetry analysis for Si bands...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 done cleaning /Users/aritz/tmp_esp... done running the scf calculation for Al... done running the band-structure calculation for Al... done cleaning /Users/aritz/tmp_esp... done running the scf calculation for Cu... done running the band-structure calculation for Cu... done running the symmetry analysis for Cu bands... done cleaning /Users/aritz/tmp_esp... done running the scf calculation for Ni... done running the band-structure calculation for Ni... done cleaning /Users/aritz/tmp_esp... done running the scf calculation for Si... done running the band-structure calculation for Si...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 si.band.david.out : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%% from read_rho_xml : error # 1 dimensions do not match %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%% From bobjohn.lzu at gmail.com Sun Aug 9 04:32:46 2009 From: bobjohn.lzu at gmail.com (john Bob) Date: Sun, 9 Aug 2009 10:32:46 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation Message-ID: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> Dear Pwscf users: There are 3 questions about thermal calculation, need the answers. Q1: Does pwscf have tools to calculate internal energe, specific heat, entropy? Though I find fqha.x. Should I modify it to calculate the other properties myself? Q2: I have a system with soft mode (negative phonon freq) in phonon dispersion. Is it meaningful to calculate these thermal properties. If it still have physical meaning, how to deal with the DOS below zero, abandon it or just add into the integration? Q3: Using matdyn.x to get the full phonon dispersion, there are some discontiguous in phonon bands. Is there a convenient way to get continual phonon dispersion? Thank you Zhou Bo 2009.8.9 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090809/19d51bcb/attachment.htm From nkxirainbow at gmail.com Sun Aug 9 04:48:42 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 9 Aug 2009 10:48:42 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> References: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> Message-ID: <21fbc4790908081948u73e4f6b5ta5528c0c15a2be83@mail.gmail.com> Dear john Bob: > >Q1: Does pwscf have tools to calculate internal energe, specific heat, > entropy? > I do not think QE give the tools to calculate specific heat. > >Q2: I have a system with soft mode (negative phonon freq) in phonon > dispersion. Is it >meaningful to calculate these thermal properties. If it > still have physical meaning, how to >deal with the DOS below zero, abandon > it or just add into the integration? > I think negative phonon freq is meanless if you deal with a equilibrium state. You must elimilnate it. Maybe you can re-optimize the structure. > >Q3: Using matdyn.x to get the full phonon dispersion, there are some > discontiguous in >phonon bands. Is there a convenient way to get continual > phonon dispersion? > I never meet this condition, therefore I do not fully know what you mean. Can you upload the picture of phonon spectrum. -- ____________________________________ 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/20090809/cea186b3/attachment.htm From luotengf at msu.edu Sun Aug 9 06:04:11 2009 From: luotengf at msu.edu (Tengfei Luo) Date: Sun, 9 Aug 2009 00:04:11 -0400 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> References: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> Message-ID: <845E3780381744CD9902D690E9CE1BD0@WIN1DV2EQQQRS7> Hi, John: I know that the QHA package can be used to calculate specific heat. You can search the mailinglist for more details. Tengfei ----- Original Message ----- From: john Bob To: pw_forum at pwscf.org Sent: Saturday, August 08, 2009 10:32 PM Subject: [Pw_forum] Questions about Thermal properties calculation Dear Pwscf users: There are 3 questions about thermal calculation, need the answers. Q1: Does pwscf have tools to calculate internal energe, specific heat, entropy? Though I find fqha.x. Should I modify it to calculate the other properties myself? Q2: I have a system with soft mode (negative phonon freq) in phonon dispersion. Is it meaningful to calculate these thermal properties. If it still have physical meaning, how to deal with the DOS below zero, abandon it or just add into the integration? Q3: Using matdyn.x to get the full phonon dispersion, there are some discontiguous in phonon bands. Is there a convenient way to get continual phonon dispersion? Thank you Zhou Bo 2009.8.9 ------------------------------------------------------------------------------ _______________________________________________ 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/20090809/bf55d375/attachment.htm From nkxirainbow at gmail.com Sun Aug 9 06:45:31 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 9 Aug 2009 12:45:31 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <845E3780381744CD9902D690E9CE1BD0@WIN1DV2EQQQRS7> References: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> <845E3780381744CD9902D690E9CE1BD0@WIN1DV2EQQQRS7> Message-ID: <21fbc4790908082145y3639907ai859aa08c645bccbb@mail.gmail.com> Dear Tengfei? You reply enlarge my horizon:) But I find the following content at http://www.democritos.it/pipermail/pw_forum/2008-December/011083.html *"Hi, Eyvaz:* *Is the Debye.x removed from the package? I don't find it in the package. * *Hi Tengfei, Yes, it was removed intentionally. I was not sure for T_D at low temperatures. The last version I am going to release now includes Debye and Mean Square Displacements calculations."* Can you tell me whether Debye and Debye and Mean Square Displacements are available beyond 4.0.4? Thanks very much:) ____________________________________ 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/20090809/2724b7c7/attachment.htm From kyin.cn at gmail.com Sun Aug 9 08:36:43 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Sun, 09 Aug 2009 14:36:43 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> References: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> Message-ID: <1249799803.22510.44.camel@dejavu> Dear Zhou Bo: Please add your affiliation when you post email next time. > Q1: Does pwscf have tools to calculate internal energe, specific heat, > entropy? Though I find fqha.x. Should I modify it to calculate the > other properties myself? > > Yes for internal energy. No for specific heat, entropy at present. As I know fqha.x has bug until version 4.0.5. (Maybe fixed at version 4.1, you should check it by yourself). We modified matdyn.f90 to calculate thermal properties as we need. I think it is not so difficult if you know how to do numerical integration. Alternatively, you can try qha package provided by Eyvaz Isaev. Download at https://qe-forge.org/projects/qha/ > Q2: I have a system with soft mode (negative phonon freq) in phonon > dispersion. Is it meaningful to calculate these thermal properties. If > it still have physical meaning, how to deal with the DOS below zero, > abandon it or just add into the integration? > If you don't provide us what your system is, we can not answer negative frequency is meaningful or not. Generally, negative frequency has two reasons: numerical errors or unstable structure at your calculated condition. For the former case, the negative value should not far from zero, and you can add acoustic sum rule (asr=.crystal.) to eliminate it. For the latter case, negative frequency is meaningful. It shows the structure you calculated is unstable at some direction. You should analyze this 'soft mode' carefully. For both cases, when you do integration, I THINK negative value should be abandoned. > Q3: Using matdyn.x to get the full phonon dispersion, there are some > discontiguous in phonon bands. Is there a convenient way to get > continual phonon dispersion? > Calculate different path once a time, then connect them together when you plot. Or modify the matdyn.f90 to meet your need as I did. See matdyn2.f90 at attachment. The original qpoint list in matdyn input file is replaced by connected qpoint list of qpath. More details and sample input see HowTo.pdf. Example output graph as pdc-pdos.eps. Because the attachment size in this mailing list can not exceed 200 KB. So if you want other files, send me a personal email for request. Cheers, Kun Yin School of Earth Sciences and Engineering Nanjing University China email: kyin.cn at gmail.com -------------- next part -------------- A non-text attachment was scrubbed... Name: matdyn2.f90 Type: text/x-fortran Size: 67333 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090809/947fc64f/attachment-0001.bin From bobjohn.lzu at gmail.com Sun Aug 9 09:28:02 2009 From: bobjohn.lzu at gmail.com (john Bob) Date: Sun, 9 Aug 2009 15:28:02 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <1249799803.22510.44.camel@dejavu> References: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> <1249799803.22510.44.camel@dejavu> Message-ID: <401230aa0908090028v653ea7f1o70ba985a2f1a70c2@mail.gmail.com> Dear Yin: Thank you for your answers. Sorry, I didn't make myself clear. For A1: QHA is what I want. Thank you. For A2: The soft modes are not from numerical error. It is high temperature phase. For A3: It is not what I want. The discontinuity happens when two phonon bands cross. The phonon eigenvalues in the output file xxx.freq are always arranged ascendingly. When ploting with gnuplot, the cross two bands turn to two ugly separate lines. Another represention, how do you plot just a single phonon band among the phonon dispersion ? Zhou Bo 2009.8.9 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090809/3f50586a/attachment.htm From eyvaz_isaev at yahoo.com Sun Aug 9 11:08:03 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 9 Aug 2009 02:08:03 -0700 (PDT) Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> Message-ID: <700381.55386.qm@web65702.mail.ac4.yahoo.com> Dear Bob, Well, let me start to answer questions raiesed. --- On Sun, 8/9/09, john Bob wrote: ? > ? > Q1: Does pwscf have tools to calculate internal > energe, specific heat, entropy? Though I find > fqha.x.?Should I?modify it to calculate the other > properties myself? fqha.f90 is somewhat obsolete and was considerably enhanced in fqha.f90 from QHA package. QHA can calculate more you can expect. > Q2: I have a system with soft mode (negative phonon > freq) in phonon dispersion. Is it meaningful to calculate > these thermal properties. If it still have physical meaning, > how to deal with the DOS below zero, abandon it or just add > into the integration? You have imaginary phonon frequencies, not negative, i.e. \omega^2<0. As concerns calculation of thermal properties when you have soft (imaginary) modes, I think the trick you suggest is not correct. ? > Q3: Using matdyn.x to get the full phonon dispersion, > there are some discontiguous in phonon bands. Is there a > convenient way to get continual phonon dispersion? Most likely you have a semiconductor, so, you have LO-TO splitting at the \Gamma point. If you have these discontinious at q-points different from \Gamma, your q-path is incorrect. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From kyin.cn at gmail.com Sun Aug 9 11:13:44 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Sun, 09 Aug 2009 17:13:44 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908090028v653ea7f1o70ba985a2f1a70c2@mail.gmail.com> References: <401230aa0908081932ybcbeef3r17fdadd5b3306664@mail.gmail.com> <1249799803.22510.44.camel@dejavu> <401230aa0908090028v653ea7f1o70ba985a2f1a70c2@mail.gmail.com> Message-ID: <1249809224.500.9.camel@dejavu> Dear Zhou: > > Dear Yin: > > > Thank you for your answers. Sorry, I didn't make myself clear. > > For A1: > > QHA is what I want. Thank you. > > For A2: > The soft modes are not from numerical error. It is high temperature > phase. > > For A3: > It is not what I want. The discontinuity happens when two phonon > bands cross. The phonon eigenvalues in the output file xxx.freq are > always arranged ascendingly. When ploting with gnuplot, the cross two > bands turn to two ugly separate lines. I don't understand what you want. > Another represention, how do you plot just a single phonon band among > the phonon dispersion ? > The frequency is stored in a nband*nks array. xxx.freq file always starts with a line such as, &plot nbnd=??, nks=?? /. Then output loop each qpoint, at each qpoint, loop each band. > Zhou Bo Your affiliation? > 2009.8.9 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Sun Aug 9 11:15:24 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 9 Aug 2009 02:15:24 -0700 (PDT) Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <21fbc4790908082145y3639907ai859aa08c645bccbb@mail.gmail.com> Message-ID: <776074.63994.qm@web65703.mail.ac4.yahoo.com> Let me continue: --- On Sun, 8/9/09, xirainbow wrote: > ? > Can you tell me whether Debye and Debye and Mean > Square Displacements are available beyond 4.0.4? The right answer is "Yes". But it is not related to QE release number. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From bobjohn.lzu at gmail.com Sun Aug 9 11:48:32 2009 From: bobjohn.lzu at gmail.com (john Bob) Date: Sun, 9 Aug 2009 17:48:32 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <776074.63994.qm@web65703.mail.ac4.yahoo.com> References: <21fbc4790908082145y3639907ai859aa08c645bccbb@mail.gmail.com> <776074.63994.qm@web65703.mail.ac4.yahoo.com> Message-ID: <401230aa0908090248v47697408i894dee7440ad4bb4@mail.gmail.com> Dear Prof. Eyvaz Isaev: Thank you for your reply. From your answer. Do you mean, physical meaning of thermal properties calculation for "meta-stable" phase still need to be explored. The method of calculating these is not so simple ? as for my third question : the attached picture can explain. Zhou bo 2009.8.9 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090809/403a4bee/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: test.JPG Type: image/jpeg Size: 10695 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090809/403a4bee/attachment.jpeg From nkxirainbow at gmail.com Sun Aug 9 15:16:29 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 9 Aug 2009 21:16:29 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908090248v47697408i894dee7440ad4bb4@mail.gmail.com> References: <21fbc4790908082145y3639907ai859aa08c645bccbb@mail.gmail.com> <776074.63994.qm@web65703.mail.ac4.yahoo.com> <401230aa0908090248v47697408i894dee7440ad4bb4@mail.gmail.com> Message-ID: <21fbc4790908090616g20ae4e1an4b33dda73666258a@mail.gmail.com> Dear Bob: > as for my third question : the attached picture can explain. > It seems that QE does not arrange phonon eigenvalue according to their symmetry. You can deal with it by hand. For example, you can re-draw the picture in origin or gunplot:) ____________________________________ 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/20090809/98cd14f0/attachment-0001.htm From eyvaz_isaev at yahoo.com Sun Aug 9 16:08:59 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 9 Aug 2009 07:08:59 -0700 (PDT) Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <401230aa0908090248v47697408i894dee7440ad4bb4@mail.gmail.com> Message-ID: <288951.36316.qm@web65705.mail.ac4.yahoo.com> Dear Bob, --- On Sun, 8/9/09, john Bob wrote: > Do you mean, physical meaning of thermal properties calculation for > "meta-stable" phase still need to be explored. The > method?of calculating these is not so simple ? > Well, some metastable phases have no problems with phonons, i.e. they have no imaginary frequences. Diamond is a good example. In this case no problems with thermal property calculations. When frequences become imaginary, you will mix Real and Imaginary values, which seems to be meaningless. Omitting imaginary frequencies and then integrating of thermal properties one implicitly suppose another, dynamically stable phase. If you have high temperature phase (like bcc Ti, Zr), you can not avoid soft modes. In this case anharmonism plays the main role and phonon-phonon interaction corrects the phonon picture. ? > as for my third question : the attached picture can explain. Take more q-points and you will have better quality picture. Please, your affiliation. Bests, Eyvaz. From eyvaz_isaev at yahoo.com Sun Aug 9 16:29:05 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 9 Aug 2009 07:29:05 -0700 (PDT) Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <21fbc4790908090616g20ae4e1an4b33dda73666258a@mail.gmail.com> Message-ID: <634973.62349.qm@web65713.mail.ac4.yahoo.com> Hi, --- On Sun, 8/9/09, xirainbow wrote: > ?as for my third question : the attached picture can > explain. > ? > It seems that?QE does not arrange phonon eigenvalue according to their > symmetry. You can deal with it by hand. For example, you can > re-draw the picture in origin or gunplot:) QE makes a good job and discontiniuties in the figure can be avoided using more q-points (as it was pointed out in my previous e-mail). I do not think origin or gnuplot will help without extra effort. Even using option "smooth" in gnuplot may give worse result. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From nkxirainbow at gmail.com Sun Aug 9 16:39:24 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 9 Aug 2009 22:39:24 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <634973.62349.qm@web65713.mail.ac4.yahoo.com> References: <21fbc4790908090616g20ae4e1an4b33dda73666258a@mail.gmail.com> <634973.62349.qm@web65713.mail.ac4.yahoo.com> Message-ID: <21fbc4790908090739g6a0c3629m8ce278a5075b2659@mail.gmail.com> Dear Eyvas lsaev: >QE makes a good job and discontiniuties in the figure can be >avoided using more q-points (as it >was pointed out in my previous >e-mail). I do not think origin or gnuplot will help without extra effort. >Even using option "smooth" in gnuplot may give worse result. I know QE makes a good job?? When I deal with electronic band, I can avoid the discontiniuty by adding "lsym = .true." in prefix.bands.in file. I think phonon dispersion does take this privilage. : ? ____________________________________ 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/20090809/bc9e60a8/attachment.htm From eyvaz_isaev at yahoo.com Sun Aug 9 17:19:43 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 9 Aug 2009 08:19:43 -0700 (PDT) Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <21fbc4790908090739g6a0c3629m8ce278a5075b2659@mail.gmail.com> Message-ID: <160784.12211.qm@web65703.mail.ac4.yahoo.com> Dear Wang, > avoid the discontiniuty by?adding??"lsym = .true." in prefix.bands.in I never used bands.x or bands.in, so, I belive you are right. The only doubt is that in the case band structure calculations turning on the lsym=.true. option band.f90 calls sym_band.f90 which reads eigenfunctions and makes intensive symmerty calculations. If this takes place for phonon dispersion relations, too - so nice. If not? Bests, Eyvaz. --- On Sun, 8/9/09, xirainbow wrote: > From: xirainbow > Subject: Re: [Pw_forum] Questions about Thermal properties calculation > To: "PWSCF Forum" > Date: Sunday, August 9, 2009, 6:39 PM > Dear Eyvas > lsaev: > > >QE makes a good job and discontiniuties > in the figure can be > >avoided using more q-points (as it > >was pointed out in my previous > >e-mail). I do not think origin or > gnuplot will help without extra effort. > >Even using option > "smooth" in gnuplot may give worse result. > ? > I know QE makes a good job?? > When I deal with electronic band, I can > avoid the discontiniuty by?adding??"lsym = .true." in prefix.bands.in > file. > > I think phonon dispersion does take this privilage.? : > ? > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > From lmoreira at fc.unesp.br Sun Aug 9 23:23:47 2009 From: lmoreira at fc.unesp.br (Leandro Moreira de Campos Pinto) Date: Sun, 09 Aug 2009 18:23:47 -0300 Subject: [Pw_forum] Interpreting DOS Message-ID: <20090809182347.12964d5jyrzac5sz@webmail.fc.unesp.br> Dear people, could someone explain me if the area under the curve of a DOS projection have any physical meaning? Thanks. leandro -- ***************************************** * Leandro Moreira de Campos Pinto * * Lab. Eletrocatalise, Fac. de Ciencias * * UNESP, Bauru, SP, Brazil * * http://www.fc.unesp.br/grupo_dafc * ***************************************** ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From baroni at sissa.it Mon Aug 10 00:45:08 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 10 Aug 2009 00:45:08 +0200 Subject: [Pw_forum] Interpreting DOS In-Reply-To: <20090809182347.12964d5jyrzac5sz@webmail.fc.unesp.br> References: <20090809182347.12964d5jyrzac5sz@webmail.fc.unesp.br> Message-ID: The number of electrons in the orbital you are projecting onto. Stefano Baroni - SISSA Trieste --- swift text written and sent on the go On 09/ago/2009, at 23.23, "Leandro Moreira de Campos Pinto" wrote: > Dear people, > > could someone explain me if the area under the curve of a DOS > projection have any physical meaning? > > Thanks. > > leandro > > > -- > ***************************************** > * Leandro Moreira de Campos Pinto * > * Lab. Eletrocatalise, Fac. de Ciencias * > * UNESP, Bauru, SP, Brazil * > * http://www.fc.unesp.br/grupo_dafc * > ***************************************** > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From nkxirainbow at gmail.com Mon Aug 10 03:48:39 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 10 Aug 2009 09:48:39 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <160784.12211.qm@web65703.mail.ac4.yahoo.com> References: <21fbc4790908090739g6a0c3629m8ce278a5075b2659@mail.gmail.com> <160784.12211.qm@web65703.mail.ac4.yahoo.com> Message-ID: <21fbc4790908091848y508b39d9p6c42d3b2e8affc2e@mail.gmail.com> Dear Eyvaz lsaev: >The only doubt is that in the case band structure calculations turning on the lsym=.true. option >band.f90 calls sym_band.f90 which reads eigenfunctions and makes intensive symmerty >calculations. Including lsym=true makes certain additional calculation and takes more time. >If this takes place for phonon dispersion relations, too - so nice. >If not? Sorry, I am not familiar with QE. Therefore, I do not know the answer of your doubt :? I hope the developers can give certain explanation :? ____________________________________ 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/20090810/0719d23d/attachment.htm From dalcorso at sissa.it Mon Aug 10 06:35:20 2009 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Mon, 10 Aug 2009 06:35:20 +0200 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <21fbc4790908091848y508b39d9p6c42d3b2e8affc2e@mail.gmail.com> References: <21fbc4790908090739g6a0c3629m8ce278a5075b2659@mail.gmail.com> <160784.12211.qm@web65703.mail.ac4.yahoo.com> <21fbc4790908091848y508b39d9p6c42d3b2e8affc2e@mail.gmail.com> Message-ID: <20090810063520.ki7cghmhwkc4kwg8@webmail.sissa.it> Quoting xirainbow : > Dear Eyvaz lsaev: > >> The only doubt is that in the case band structure calculations turning on > the lsym=.true. option >> band.f90 calls sym_band.f90 which reads eigenfunctions and makes intensive > symmerty >calculations. > Including lsym=true makes certain additional calculation and takes more > time. > >> If this takes place for phonon dispersion relations, too - so nice. >> If not? > Sorry, I am not familiar with QE. Therefore, I do not know the answer of > your doubt :? > I hope the developers can give certain explanation :? The symmetry analysis of the displacement patterns is implemented only in ph.x. Presently matdyn.x does not use symmetry and cannot do the symmetry analysis as in bands.x. Andrea > > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From nkxirainbow at gmail.com Mon Aug 10 08:48:44 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 10 Aug 2009 14:48:44 +0800 Subject: [Pw_forum] Questions about Thermal properties calculation In-Reply-To: <20090810063520.ki7cghmhwkc4kwg8@webmail.sissa.it> References: <21fbc4790908090739g6a0c3629m8ce278a5075b2659@mail.gmail.com> <160784.12211.qm@web65703.mail.ac4.yahoo.com> <21fbc4790908091848y508b39d9p6c42d3b2e8affc2e@mail.gmail.com> <20090810063520.ki7cghmhwkc4kwg8@webmail.sissa.it> Message-ID: <21fbc4790908092348r712fd93ej3c59e8f92ca59df@mail.gmail.com> Dear Andrea: >The symmetry analysis of the displacement patterns is implemented only in ph.x. >Presently matdyn.x does not use symmetry and cannot do the >symmetry analysis as in bands.x. Thank you very much for you explanation :? ____________________________________ 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/20090810/dddd1769/attachment.htm From wangqj1 at 126.com Mon Aug 10 10:05:21 2009 From: wangqj1 at 126.com (wangqj1) Date: Mon, 10 Aug 2009 16:05:21 +0800 (CST) Subject: [Pw_forum] about U Message-ID: <13488300.515861249891521624.JavaMail.coremail@bj126app82.126.com> ---------- ?????? ---------- ????"wangqj1 " ?????2009-07-22 12:42:56 ????pw_forum ??? about U Dear pwscf users I want to compute the value of U,in the paper PRB 71, 035105 (2005),the Eq.(18),(19),but I don't know how to construct the response matrices. matrices \chi and \chi_0,I want to construct the matrices manually instead of programe pack like the example. And how do I extract the the date from the out file of unperturbed self-consistent calculation and the files of perturbed calculations(like pert-0.1.out ,pert-0.2.out and so on ) to construct the matrices of \chi and \chi_0 as in Eq.(18) ? Beat regards Q J Wang XiangTan University ??YEAH.NET????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/0d57f03f/attachment.htm From bipulrr at gmail.com Mon Aug 10 10:12:41 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 10 Aug 2009 13:42:41 +0530 Subject: [Pw_forum] davico error while calculating projected density of states Message-ID: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> Dear PWSCF users, I am doing calculation of LaMnO3. When I try to do the projected density of states, then it shows the error Calling projwave .... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I have first done the scf, nscf dos.x then projwfc.x kindly help me in this regard -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/ed54c055/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.nscf.in Type: application/octet-stream Size: 1881 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090810/ed54c055/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.pdos.in Type: application/octet-stream Size: 100 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090810/ed54c055/attachment-0001.obj From decboy9 at gmail.com Mon Aug 10 10:13:57 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 10 Aug 2009 13:43:57 +0530 Subject: [Pw_forum] Problem in parallel execution, please help Message-ID: Hi sir, Hope so that all of you will be fine, I am new to linux and I tried to install PWscf in parallel on a quad core machine but still facing problems . What I did sequentially, i am writing here 1) i download mpich2-1.0.4p1 from internet and install it. 2) then i installed espresso4.0.2 using the following two commands (a) env MPIF90=mpif77 ./configure (after this command finally it gave mssg, parallel envoirnment successful) (b) make all after that when i tried any example it is giving mssg as: Program PWSCF v.4.0.2 starts ... Today is 10Aug2009 at 18:51:21 Parallel version (MPI) Number of processors in use: 1 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Iterative solution of the eigenvalue problem Too few procs for parallel algorithm we need at least 4 procs per pool a serial algorithm will be used Planes per process (thick) : nr3 = 15 npp = 15 ncplane = 225 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 15 121 869 15 121 869 31 113 AND when i tried to execute my files using the command mpirun -np 4 /home/sushil/espresso-4.0.2/bin/pw.x -in yvo.inp> scf.out1 it is giving in output as: piexec_localhost.localdomain: cannot connect to local mpd (/tmp/mpd2.console_sushil); possible causes: 1. no mpd is running on this host 2. an mpd is running but was started without a "console" (-n option) In case 1, you can start an mpd on this host with: mpd & and you will be able to run jobs just on this host. For more details on starting mpds on a set of hosts, see the MPICH2 Installation Guide. please help me and guide me . Thanks Yours sincerly, Dev Sharma University of Delhi, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/464a2771/attachment.htm From nkxirainbow at gmail.com Mon Aug 10 10:49:20 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 10 Aug 2009 16:49:20 +0800 Subject: [Pw_forum] Problem in parallel execution, please help In-Reply-To: References: Message-ID: <21fbc4790908100149i16526938pb4500c9917bb3dd5@mail.gmail.com> Dear dev sharma: >(a) env MPIF90=mpif77 ./configure (after this command finally it gave mssg, parallel >envoirnment successful) Why not use mpif90 instead of mpif77 >piexec_localhost.localdomain: cannot connect to local mpd >(/tmp/mpd2.console_sushil); possible causes: >1. no mpd is running on this host >2. an mpd is running but was started without a "console" (-n option) >In case 1, you can start an mpd on this host with: > mpd & >and you will be able to run jobs just on this host. It is a problem of mpi, not QE. Simply follow the instruction: start an mpd on your host with "mpd" or you can try the following way: 0.down load mpich2-1.0.8.tar.gz on intelnet 1.enter directory /etc, then input "touch mpd.conf" using terminal. 2.input "vi mpd.conf" 3.add "MPD_SECRETWORD=XXXXX" (XXXXXX is your secrete number) 4.return to terminal and input mpdboot ____________________________________ 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/20090810/b5a0d37e/attachment.htm From padmaja_patnaik at yahoo.co.uk Mon Aug 10 11:01:53 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Mon, 10 Aug 2009 09:01:53 +0000 (GMT) Subject: [Pw_forum] Pseudopotential of Cr and Mn Message-ID: <895159.29199.qm@web26107.mail.ukl.yahoo.com> Dear all i am looking for ultrasoft or norm-conserving pseudopotential for V, Cr and Mn with LDA. Can anyone help me. Thanks in advance and regards, padmaja Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/c88194aa/attachment.htm From paulatto at sissa.it Mon Aug 10 11:15:58 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 10 Aug 2009 11:15:58 +0200 Subject: [Pw_forum] Problem in parallel execution, please help In-Reply-To: References: Message-ID: Hello Dev, > piexec_localhost.localdomain: cannot connect to local mpd > (/tmp/mpd2.console_sushil); possible causes: > 1. no mpd is running on this host > 2. an mpd is running but was started without a "console" (-n option) > In case 1, you can start an mpd on this host with: > mpd & > and you will be able to run jobs just on this host. > For more details on starting mpds on a set of hosts, see > the MPICH2 Installation Guide. Have you tried following those intructions? If yes, what went wrong at that point? If no, why? Anyway, it is a problem with mpich configuration, not with quantum espresso. I would suggest to invest some time in testing the mpich configuration. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From samirmeher at gmail.com Mon Aug 10 11:42:55 2009 From: samirmeher at gmail.com (Samir Ranjan Meher) Date: Mon, 10 Aug 2009 15:12:55 +0530 Subject: [Pw_forum] How to convert OCTOPUS generated PP to UPF format Message-ID: <8a4c6de60908100242v7a70a359lee455477ba1dbb04@mail.gmail.com> Hi, Can anyone plz tell me how to generate or find out the Troullier-Martins pseudopotential for Ga in UPF fromat. I am able to get it in OCTOPUS........but not able to convert it into UPF format. Waiting for ur reply........ Thanks in advance. Samir Ranjan Meher, IIT Madras -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/f30b48d9/attachment.htm From sclauzer at sissa.it Mon Aug 10 11:50:28 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 10 Aug 2009 11:50:28 +0200 Subject: [Pw_forum] davico error while calculating projected density of states In-Reply-To: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> References: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> Message-ID: <4A7FED64.8060308@sissa.it> Bipul Rakshit wrote: > Dear PWSCF users, > I am doing calculation of LaMnO3. When I try to do the projected density > of states, then it shows the error > > Calling projwave .... > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > error while reading from file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > I have first done the scf, > nscf > dos.x > then projwfc.x > > kindly help me in this regard First check if all the files containing the wavefunctions (outdir/prefix.wfc*) are present and are not corrupted. If so, please give more details (i.e. input files). If not, rerun scf and nscf steps. Regards GS > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From kazempoor2000 at yahoo.com Mon Aug 10 12:00:45 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 10 Aug 2009 03:00:45 -0700 (PDT) Subject: [Pw_forum] global U Message-ID: <333664.58290.qm@web112518.mail.gq1.yahoo.com> Dear users ?Is it possible to use the hubbard parametr obtained by another code (like wien2k) in espresso or not? is U a global or not? thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/28bd5525/attachment.htm From marzari at MIT.EDU Mon Aug 10 12:17:54 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 10 Aug 2009 13:17:54 +0300 Subject: [Pw_forum] How to convert OCTOPUS generated PP to UPF format In-Reply-To: <8a4c6de60908100242v7a70a359lee455477ba1dbb04@mail.gmail.com> References: <8a4c6de60908100242v7a70a359lee455477ba1dbb04@mail.gmail.com> Message-ID: <4A7FF3D2.9040506@mit.edu> Samir Ranjan Meher wrote: > Hi, > Can anyone please tell me how to generate or find out the Troullier-Martins > pseudopotential for Ga in UPF fromat. I am able to get it in > OCTOPUS, but not able to convert it into UPF format. Waiting for > your reply. > Thanks in advance. You can use the ld1 code distributed with espresso. Another alternative is to use fhi98pp, and use the espresso converter from fhi to upf. nicola PS: I've edited your text. -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From sclauzer at sissa.it Mon Aug 10 12:19:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 10 Aug 2009 12:19:51 +0200 Subject: [Pw_forum] Segmentation fault In-Reply-To: <16175338.379491249489935359.JavaMail.root@mta.iut.ac.ir> References: <16175338.379491249489935359.JavaMail.root@mta.iut.ac.ir> Message-ID: <4A7FF447.3020106@sissa.it> Hi, leila salimi wrote: > Hi every body > I use espresso-4.0.5 on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. > If I use calculation='scf' no problem and the result matches our testdata. > If we use calculation='relax? we get the right value for the energy after the first loop and then the application should start with the second loop but it stops with the following error: > > ====== > energy new = -121.3312114461 Ry > > new trust radius = .5000000000 bohr > ERROR: 0031-250 task 0: Segmentation fault > ERROR: 0031-250 task 4: Terminated > ERROR: 0031-250 task 7: Terminated > ERROR: 0031-250 task 6: Terminated > ERROR: 0031-250 task 2: Terminated > ERROR: 0031-250 task 1: Terminated > ERROR: 0031-250 task 5: Terminated > ERROR: 0031-250 task 3: Terminated > > We use the following command line: > > poe ~/espresso/bin/pw.x -procs 8 -npool 2 < input.relax > InAs-relax.out 2>&1 > > > Do you have any idea with this problem? Is the error reproducible? If so, you may have filled the physical memory of your node. I think that at the beginning of the second scf cycle the program needs to allocate more memory to mix old/new variables (wfcs, charge density...). Try to monitor memory usage and ,if this is the problem, use more computing nodes. regards GS > > Best Regards, > Leila Salimi > Isfahan University of Technology, Isfahan, Iran. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From marzari at MIT.EDU Mon Aug 10 12:21:10 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 10 Aug 2009 13:21:10 +0300 Subject: [Pw_forum] global U In-Reply-To: <333664.58290.qm@web112518.mail.gq1.yahoo.com> References: <333664.58290.qm@web112518.mail.gq1.yahoo.com> Message-ID: <4A7FF496.3040506@mit.edu> ali kazempour wrote: > > Dear users > Is it possible to use the hubbard parametr obtained by another code > (like wien2k) in espresso or not? is U a global or not? > thanks No, it's not, even remotely. Different codes use different implementations of U, different definitions (e.g. U-J, for QE), and even for the same implementation, U would depend on the pseudopotential used, with fairly large differences if the atomic calculations were done in different oxidation states (e.g. neutral Fe vs Fe+ vs Fe++ vs Fe+++). On the plus side, if you use the appropriate U for each pseudopotential, you recover broadly similar physical results. We have a brief summary in the appendix of Kulik/Marzari JCP 2008. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From sclauzer at sissa.it Mon Aug 10 15:50:11 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 10 Aug 2009 15:50:11 +0200 Subject: [Pw_forum] generating k point weights In-Reply-To: References: Message-ID: <4A802593.5080004@sissa.it> Just one additional note of caution: kpoints.x reduces the number of k-points (and compute weights) according to the symmetry of the bravais lattice only, while the subroutine kpoint_grid in PW/ used by pw.x takes into account the crystal symmetry (which can be lower than the lattice symmetry if you have more than one atom per cell or non-collinear magnetism) HTH GS Manoj Srivastava wrote: > Dear Lorenzo, > Thanks a lot. I will look into the code. In the mean time I found a paper > which talks about generation of special k points and evaluation of their > weight. Its by Chadi & Cohen, Phys. Rev. B, 8,5747-5753 (1973). They have > some examples in it too. > > Regards, > Manoj Srivastava > University of Florida, > Gainesville, FL > > On Mon, 3 Aug 2009, Lorenzo Paulatto wrote: > >> In data 31 luglio 2009 alle ore 16:25:39, Manoj Srivastava >> ha scritto: >> >>> Dear All, >>> I was wondering if someone can tell me, how to generate k point weights >>> in the BZ. Reference of a paper would be great! >> Dear Manoj, >> you can find the algorithm tha tgenerates points and weights in >> pwtools/kpoints.f >> The obvious reference is the original article from Monkhorst and Pack: >> Phys. Rev. B 13, 5188 - 5192 (1976), although I don't know if they give an >> explicit formulation for the weights there (weights depend on how many >> symmetry-equivalent copies of a point are present in the set, not on the >> generation algorithm). >> >> cheers >> >> >> -- >> Lorenzo Paulatto >> SISSA & DEMOCRITOS (Trieste) >> phone: +39 040 3787 511 >> skype: paulatz >> www: http://people.sissa.it/~paulatto/ >> >> *** save italian brains *** >> http://saveitalianbrains.wordpress.com/ >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ferretti at MIT.EDU Mon Aug 10 15:57:39 2009 From: ferretti at MIT.EDU (Andrea Ferretti) Date: Mon, 10 Aug 2009 09:57:39 -0400 (EDT) Subject: [Pw_forum] Problem in parallel execution, please help In-Reply-To: Message-ID: As Lorenzo wrote, the problem is with your mpich installation... it seems you have to run mpdboot (one of the suggestion by th error message)... create a file .mpd.hosts (eg in you home dir) add the word "localhost" in one line and type mpdboot -f ~/.mpd.hosts then you should be able to run... remember that if you do not include the above command in the startup of your machine, you have to run it manually every time you reboot it. andrea > > Hope so that all of you will be fine, I am new to linux and I tried to > install PWscf in parallel on a quad core machine but still facing problems . > What I did sequentially, i am writing here > > 1) i download mpich2-1.0.4p1 from internet and install it. > 2) then i installed espresso4.0.2 using the following two commands > > (a) env MPIF90=mpif77 ./configure (after this command finally it gave mssg, > parallel envoirnment successful) > (b) make all > > after that when i tried any example it is giving mssg as: > > Program PWSCF v.4.0.2 starts ... > Today is 10Aug2009 at 18:51:21 > > Parallel version (MPI) > > Number of processors in use: 1 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > Iterative solution of the eigenvalue problem > Too few procs for parallel algorithm > we need at least 4 procs per pool > > a serial algorithm will be used > > > Planes per process (thick) : nr3 = 15 npp = 15 ncplane = 225 > > Proc/ planes cols G planes cols G columns G > Pool (dense grid) (smooth grid) (wavefct grid) > 1 15 121 869 15 121 869 31 113 > > > AND when i tried to execute my files using the command > mpirun -np 4 /home/sushil/espresso-4.0.2/bin/pw.x -in yvo.inp> scf.out1 > > it is giving in output as: > > piexec_localhost.localdomain: cannot connect to local mpd > (/tmp/mpd2.console_sushil); possible causes: > 1. no mpd is running on this host > 2. an mpd is running but was started without a "console" (-n option) > In case 1, you can start an mpd on this host with: > mpd & > and you will be able to run jobs just on this host. > For more details on starting mpds on a set of hosts, see > the MPICH2 Installation Guide. > > please help me and guide me . > > Thanks > > Yours sincerly, > > Dev Sharma > University of Delhi, > India > -- Andrea Ferretti MIT, Dept Material Science & Engineering bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA Tel: +1 617-452-2455; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From matteo at umn.edu Mon Aug 10 16:22:29 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 10 Aug 2009 09:22:29 -0500 Subject: [Pw_forum] about U In-Reply-To: <13488300.515861249891521624.JavaMail.coremail@bj126app82.126.com> References: <13488300.515861249891521624.JavaMail.coremail@bj126app82.126.com> Message-ID: <4A802D25.8000807@umn.edu> Dear Q. J. Wang on the wiki web page of quantum-espresso you should be able to find a tutorial on how to do this. the latest version of necessary scripts and codes to construct the response matrices can be found in http://www.quantum-espresso.org/wiki/index.php/QESB09#First_week the instructions you find in there should be sufficient for you to understand how to use the files. regards, Matteo wangqj1 wrote: > ---------- ???????????? ---------- > ????????"wangqj1 " > ??????????2009-07-22 12:42:56 > ????????pw_forum > ?????? about U > > Dear pwscf users > I want to compute the value of U,in the paper PRB 71, 035105 > (2005),the Eq.(18),(19),but I don't know how to construct the response > matrices. matrices \chi and \chi_0,I want to construct the matrices > manually instead of programe pack like the example. And how do I > extract the the date from the out file of unperturbed self-consistent > calculation and the files of perturbed calculations(like pert-0.1.out > ,pert-0.2.out and so on ) to construct the matrices of \chi and \chi_0 > as in Eq.(18) ? > Beat regards > Q J Wang > XiangTan University > > > ????YEAH.NET?????????????????????????? > > ??????????????????????,www.yeah.net > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From manoj at phys.ufl.edu Mon Aug 10 16:30:23 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Mon, 10 Aug 2009 10:30:23 -0400 (EDT) Subject: [Pw_forum] generating k point weights In-Reply-To: <4A802593.5080004@sissa.it> Message-ID: Dear All, Thank you very much for all the help :) Regards, Manoj Srivastava University of Florida Gainesville, FL On Mon, 10 Aug 2009, Gabriele Sclauzero wrote: > Just one additional note of caution: kpoints.x reduces the number of k-points (and compute > weights) according to the symmetry of the bravais lattice only, while the subroutine > kpoint_grid in PW/ used by pw.x takes into account the crystal symmetry (which can be > lower than the lattice symmetry if you have more than one atom per cell or non-collinear > magnetism) > > HTH > > GS > > Manoj Srivastava wrote: > > Dear Lorenzo, > > Thanks a lot. I will look into the code. In the mean time I found a paper > > which talks about generation of special k points and evaluation of their > > weight. Its by Chadi & Cohen, Phys. Rev. B, 8,5747-5753 (1973). They have > > some examples in it too. > > > > Regards, > > Manoj Srivastava > > University of Florida, > > Gainesville, FL > > > > On Mon, 3 Aug 2009, Lorenzo Paulatto wrote: > > > >> In data 31 luglio 2009 alle ore 16:25:39, Manoj Srivastava > >> ha scritto: > >> > >>> Dear All, > >>> I was wondering if someone can tell me, how to generate k point weights > >>> in the BZ. Reference of a paper would be great! > >> Dear Manoj, > >> you can find the algorithm tha tgenerates points and weights in > >> pwtools/kpoints.f > >> The obvious reference is the original article from Monkhorst and Pack: > >> Phys. Rev. B 13, 5188 - 5192 (1976), although I don't know if they give an > >> explicit formulation for the weights there (weights depend on how many > >> symmetry-equivalent copies of a point are present in the set, not on the > >> generation algorithm). > >> > >> cheers > >> > >> > >> -- > >> Lorenzo Paulatto > >> SISSA & DEMOCRITOS (Trieste) > >> phone: +39 040 3787 511 > >> skype: paulatz > >> www: http://people.sissa.it/~paulatto/ > >> > >> *** save italian brains *** > >> http://saveitalianbrains.wordpress.com/ > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From nkxirainbow at gmail.com Mon Aug 10 16:41:39 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 10 Aug 2009 22:41:39 +0800 Subject: [Pw_forum] generating k point weights In-Reply-To: <4A802593.5080004@sissa.it> References: <4A802593.5080004@sissa.it> Message-ID: <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> Dear Gabriele Sclauzero: >Just one additional note of caution: kpoints.x reduces the number of k-points (and compute >weights) according to the symmetry of the bravais lattice only, while the subroutine >kpoint_grid in PW/ used by pw.x takes into account the crystal symmetry (which can be >lower than the lattice symmetry if you have more than one atom per cell or non-collinear >magnetism) I am confused with your statement:"crystal symmetry can be lower than the lattice symmetry if you have more than one atom per cell". Could you explain it more clearly? Or could you give me a simple example? Thank you ?? ____________________________________ 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/20090810/531940cb/attachment-0001.htm From baroni at sissa.it Mon Aug 10 17:47:45 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 10 Aug 2009 17:47:45 +0200 Subject: [Pw_forum] generating k point weights In-Reply-To: <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> References: <4A802593.5080004@sissa.it> <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> Message-ID: More precisely: the point symmetry of the bravais lattive can be higher than the maximum symmetry of any lattie site in the crystal. For example, the point symmetry of the bravais lattice of the diamond structure is cubic, but no lattice site in the diamond structure has cubic symmetry (actually, each atomic site has tetrahedral symmetry). In this case, cubic symmetry s recovered by associating a fractional lattice translation to certain operation of the cubic group (it is said the the space group of the structure is "non symmorphic" in this case). More generally, it may happen that you simulate a system of low symmetry (a molecule, for instance) with a supercell of higher symmetry (think of using a cubic supercell for symulating an isolated water molecule, for instance) ... SB On Aug 10, 2009, at 4:41 PM, xirainbow wrote: > Dear Gabriele Sclauzero: > > >Just one additional note of caution: kpoints.x reduces the number > of k-points (and compute > >weights) according to the symmetry of the bravais lattice only, > while the subroutine > >kpoint_grid in PW/ used by pw.x takes into account the crystal > symmetry (which can be > >lower than the lattice symmetry if you have more than one atom per > cell or non-collinear > >magnetism) > > I am confused with your statement:"crystal symmetry can be lower > than the lattice symmetry if you have more than one atom per cell". > Could you explain it more clearly? > Or could you give me a simple example? > Thank you ?? > > ____________________________________ > 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 --- 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/20090810/bf370681/attachment.htm From sclauzer at sissa.it Mon Aug 10 18:09:21 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 10 Aug 2009 18:09:21 +0200 Subject: [Pw_forum] generating k point weights In-Reply-To: <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> References: <4A802593.5080004@sissa.it> <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> Message-ID: <4A804631.8090809@sissa.it> xirainbow wrote: > Dear Gabriele Sclauzero: > > >Just one additional note of caution: kpoints.x reduces the number of > k-points (and compute > >weights) according to the symmetry of the bravais lattice only, while > the subroutine > >kpoint_grid in PW/ used by pw.x takes into account the crystal > symmetry (which can be > >lower than the lattice symmetry if you have more than one atom per > cell or non-collinear > >magnetism) > > I am confused with your statement:"crystal symmetry can be lower than > the lattice symmetry if you have more than one atom per cell". Maybe I misused the standard terminology. > Could you explain it more clearly? Every periodic system can be described by one among the 14 Bravais lattices plus a so-called "basis", i.e. a set of atomic position within the unit cell of that lattice. The symmetry point group of the lattice is the set of all rotations which leave the lattice invariant (which means that it can be mapped to itself with the application of a translation of a l.c. of the basis vectors, if needed). This is the symmetry group given by kpoints.x (which in fact does not ask anything about the basis of atoms). To determine the symmetry of a crystallographic system you have to check which symmetry operations leave the system invariant, which means that, after a rotation, each atom overlaps with itself or with an equivalent atom (again, modulus a translation by a lattice vector). If you have more than one atom, or your atom is not in the origin an operation with transform the lattice into itself may not send all the atoms on top of equivalent atoms, hence it is not a symmetry operation. For some systems (e.g. diamond), you may recover some rotations by applying a translation by a fraction of a lattice vector after the rotation. > Or could you give me a simple example? Sorry, I don't have a crystallographic example in mind right now, but I can give you a practical example of what I've got my hands on at the moment. In order to simulate monatomic nanowires I use a tetragonal cell (ibrav=6) with one atom per cell (along the z axis). The lattice symmetry (point group D_4d) is maintained also after checking the atomic basis (although this system in reality as D_{\inf h} point group, but this is another story...). If you adsorb an impurity aside of the wire, e.g. a molecule lying in the xz plane, the symmetry of the system will be lowered (C_2v in this case). In fact you will lose the inversion symmetry (this halves the number of symmetry operations) and the rotations along z. I hope I've not confused you further... GS > Thank you ?? > > ____________________________________ > 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 -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Aug 10 18:27:38 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 10 Aug 2009 18:27:38 +0200 Subject: [Pw_forum] davico error while calculating projected density of states In-Reply-To: <3a749910908100325u624af2a1ra9c745c4759a848b@mail.gmail.com> References: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> <4A7FED64.8060308@sissa.it> <3a749910908100325u624af2a1ra9c745c4759a848b@mail.gmail.com> Message-ID: <4A804A7A.4070709@sissa.it> Dear Bipul, Bipul Rakshit wrote: > Dear Gabriele Sclauzero, > thanks for your kind reply. > Since I am sending you the input, so i send you to your private mail. > Please see the input and suggest me if there is anything wrong. I don't see any reason of sending the input files privately to me (unless you have specific reasons), since this is not in the open-source spirit of the forum and you will prevent other users from helping you. In your input files: &system occupations='smearing', smearing='methfessel-paxton', degauss=0.000073498 This value of degauss seems very low to me. Are you sure that you need it, and most important, have you converged w.r.t the number of k-points? &electrons conv_thr = 1.0d-5 this is too high, use the default or something lower. Anyway, I don't see any problem related to the I/O issue in your input files. You have to check if the nscf run completed successfully and wrote the wavefunctions to disk. The files may be corrupted due to an interrupted run or an hardware failure. You should also be careful when running on clusters with local scratch area (does it apply to your case?). Please provide more information about your compilation/HW-SW configuration and a full output file from DOS or PDOS calculation. GS > > > > On Mon, Aug 10, 2009 at 3:20 PM, Gabriele Sclauzero > wrote: > > > > Bipul Rakshit wrote: > > Dear PWSCF users, > > I am doing calculation of LaMnO3. When I try to do the projected > density > > of states, then it shows the error > > > > Calling projwave .... > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from davcio : error # 10 > > error while reading from file > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > I have first done the scf, > > nscf > > dos.x > > then projwfc.x > > > > kindly help me in this regard > > First check if all the files containing the wavefunctions > (outdir/prefix.wfc*) are present > and are not corrupted. > If so, please give more details (i.e. input files). If not, rerun > scf and nscf steps. > > Regards > > GS > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From baroni at sissa.it Mon Aug 10 19:56:01 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 10 Aug 2009 19:56:01 +0200 Subject: [Pw_forum] davico error while calculating projected density of states In-Reply-To: <4A804A7A.4070709@sissa.it> References: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> <4A7FED64.8060308@sissa.it> <3a749910908100325u624af2a1ra9c745c4759a848b@mail.gmail.com> <4A804A7A.4070709@sissa.it> Message-ID: <58C9821B-4F4D-4C2A-AF74-2C7426242CC3@sissa.it> Dear Bipul, dear all: please always consider that none of the people posting to this mailing list belong to any kind of "customer service". all of us are pleased to help when we can / feel like that ... none of us has to. so, please, refrain from sending private emails to members of the list, unless you have a specific reason to do so ... also, even if/when you get assistance precisely from exactlyy the same person you would address privately, when you address him/her on the mailing list, instead, you give others the possibility of learning at the same time you are learning. in conclusion, do use the list as much as possible ... SB On Aug 10, 2009, at 6:27 PM, Gabriele Sclauzero wrote: > Dear Bipul, > > > > Bipul Rakshit wrote: >> Dear Gabriele Sclauzero, >> thanks for your kind reply. >> Since I am sending you the input, so i send you to your private mail. >> Please see the input and suggest me if there is anything wrong. > > I don't see any reason of sending the input files privately to me > (unless you have > specific reasons), since this is not in the open-source spirit of > the forum and you will > prevent other users from helping you. > > In your input files: > > &system > occupations='smearing', smearing='methfessel-paxton', > degauss=0.000073498 > > This value of degauss seems very low to me. Are you sure that you > need it, and most > important, have you converged w.r.t the number of k-points? > > > &electrons > conv_thr = 1.0d-5 > > this is too high, use the default or something lower. > > Anyway, I don't see any problem related to the I/O issue in your > input files. You have to > check if the nscf run completed successfully and wrote the > wavefunctions to disk. The > files may be corrupted due to an interrupted run or an hardware > failure. You should also > be careful when running on clusters with local scratch area (does it > apply to your case?). > Please provide more information about your compilation/HW-SW > configuration and a full > output file from DOS or PDOS calculation. > > GS > >> >> >> >> On Mon, Aug 10, 2009 at 3:20 PM, Gabriele Sclauzero >> > > wrote: >> >> >> >> Bipul Rakshit wrote: >>> Dear PWSCF users, >>> I am doing calculation of LaMnO3. When I try to do the projected >> density >>> of states, then it shows the error >>> >>> Calling projwave .... >>> >>> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%%%%%%%%%%%%% >>> from davcio : error # 10 >>> error while reading from file >>> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%%%%%%%%%%%%% >>> >>> stopping ... >>> >>> I have first done the scf, >>> nscf >>> dos.x >>> then projwfc.x >>> >>> kindly help me in this regard >> >> First check if all the files containing the wavefunctions >> (outdir/prefix.wfc*) are present >> and are not corrupted. >> If so, please give more details (i.e. input files). If not, rerun >> scf and nscf steps. >> >> Regards >> >> GS >> > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum 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/20090810/11f586ab/attachment-0001.htm From shruba at gmail.com Mon Aug 10 20:18:14 2009 From: shruba at gmail.com (shruba at gmail.com) Date: Mon, 10 Aug 2009 14:18:14 -0400 Subject: [Pw_forum] davico error while calculating projected density of states In-Reply-To: <58C9821B-4F4D-4C2A-AF74-2C7426242CC3@sissa.it> References: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> <4A7FED64.8060308@sissa.it> <3a749910908100325u624af2a1ra9c745c4759a848b@mail.gmail.com> <4A804A7A.4070709@sissa.it> <58C9821B-4F4D-4C2A-AF74-2C7426242CC3@sissa.it> Message-ID: <822f4ec80908101118w221d78d5g3cafb5c0bb6218f1@mail.gmail.com> Hi Bipul, I had similar problem with PDOS, after using wf_collect=.true. PDOS was working fine, you might try it, see if it helps. Regards shruba gangopadhyay On Mon, Aug 10, 2009 at 1:56 PM, Stefano Baroni wrote: > Dear Bipul, dear all: > please always consider that none of the people posting to this mailing list > belong to any kind of "customer service". all of us are pleased to help when > we can / feel like that ... none of us has to. so, please, refrain from > sending private emails to members of the list, unless you have a specific > reason to do so ... also, even if/when you get assistance precisely from > exactlyy the same person you would address privately, when you address > him/her on the mailing list, instead, you give others the possibility of > learning at the same time you are learning. in conclusion, do use the list > as much as possible ... > > SB > > > > On Aug 10, 2009, at 6:27 PM, Gabriele Sclauzero wrote: > > Dear Bipul, > > > > Bipul Rakshit wrote: > > Dear Gabriele Sclauzero, > > thanks for your kind reply. > > Since I am sending you the input, so i send you to your private mail. > > Please see the input and suggest me if there is anything wrong. > > > I don't see any reason of sending the input files privately to me (unless > you have > specific reasons), since this is not in the open-source spirit of the forum > and you will > prevent other users from helping you. > > In your input files: > > &system > occupations='smearing', smearing='methfessel-paxton', > degauss=0.000073498 > > This value of degauss seems very low to me. Are you sure that you need it, > and most > important, have you converged w.r.t the number of k-points? > > > &electrons > conv_thr = 1.0d-5 > > this is too high, use the default or something lower. > > Anyway, I don't see any problem related to the I/O issue in your input > files. You have to > check if the nscf run completed successfully and wrote the wavefunctions to > disk. The > files may be corrupted due to an interrupted run or an hardware failure. > You should also > be careful when running on clusters with local scratch area (does it apply > to your case?). > Please provide more information about your compilation/HW-SW configuration > and a full > output file from DOS or PDOS calculation. > > GS > > > > > On Mon, Aug 10, 2009 at 3:20 PM, Gabriele Sclauzero > >> wrote: > > > > > Bipul Rakshit wrote: > > Dear PWSCF users, > > I am doing calculation of LaMnO3. When I try to do the projected > > density > > of states, then it shows the error > > > Calling projwave .... > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from davcio : error # 10 > > error while reading from file > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > > I have first done the scf, > > nscf > > dos.x > > then projwfc.x > > > kindly help me in this regard > > > First check if all the files containing the wavefunctions > > (outdir/prefix.wfc*) are present > > and are not corrupted. > > If so, please give more details (i.e. input files). If not, rerun > > scf and nscf steps. > > > Regards > > > GS > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum 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 > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- shruba gangopadhyay graduate student department of chemistry university of central florida orlando, FL-32826 'friendship doubles joys and reduces sorrows by half' (Francis Bacon). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090810/2aa7c977/attachment.htm From nkxirainbow at gmail.com Tue Aug 11 04:02:10 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 11 Aug 2009 10:02:10 +0800 Subject: [Pw_forum] generating k point weights In-Reply-To: References: <4A802593.5080004@sissa.it> <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> Message-ID: <21fbc4790908101902g3103efb3g52ba515e6b9fc22f@mail.gmail.com> Dear Stefano Baroni and Gabriele Sclauzero: First of all, thank you very much for your detailed explanation :? I think I fully undertand it. First, the "kpoints.x" reduces the number of k-points according to parameter "ibrav". That means kpoints.x chooses the symmetry among 14 Bravais lattices. Second, the "pw.x" checkes all symmetry operations within a given Bravais lattice determined by kpoints.x. That means pw.x determines the symmetry among 7 crystal systems. But, now I have a another question about bands.x. In the instruction of bands.x, it says: Presently it can calculate: (a) The expectation value of the spin operator on each spinor wave-function. (b) *The symmetry properties of each wavefunction*. The instruction of parameter "lsym" says: If .true. the bands are classified according to the irreducible representations of the small group of k. A file "filband".rap with the same format of "filband" is written. I want to know the symmetry properties obatained by "band.x" is based on 7 crystal systems, 14 Bravais lattices or 32 point groups. Once again, thank you very much ?? ____________________________________ 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/20090811/e6e05ad2/attachment.htm From bipulrr at gmail.com Tue Aug 11 06:12:30 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 11 Aug 2009 09:42:30 +0530 Subject: [Pw_forum] davico error while calculating projected density of states In-Reply-To: <58C9821B-4F4D-4C2A-AF74-2C7426242CC3@sissa.it> References: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> <4A7FED64.8060308@sissa.it> <3a749910908100325u624af2a1ra9c745c4759a848b@mail.gmail.com> <4A804A7A.4070709@sissa.it> <58C9821B-4F4D-4C2A-AF74-2C7426242CC3@sissa.it> Message-ID: <3a749910908102112m696a7ee6s18567594d732df5d@mail.gmail.com> Dear SB and GB, thanks for your kind advice. Now and onwards I will remember the things and will send the message to all of the forum people (unless there is some specific reason) And sorry for act. regards On Mon, Aug 10, 2009 at 11:26 PM, Stefano Baroni wrote: > Dear Bipul, dear all: > please always consider that none of the people posting to this mailing list > belong to any kind of "customer service". all of us are pleased to help when > we can / feel like that ... none of us has to. so, please, refrain from > sending private emails to members of the list, unless you have a specific > reason to do so ... also, even if/when you get assistance precisely from > exactlyy the same person you would address privately, when you address > him/her on the mailing list, instead, you give others the possibility of > learning at the same time you are learning. in conclusion, do use the list > as much as possible ... > > SB > > > > On Aug 10, 2009, at 6:27 PM, Gabriele Sclauzero wrote: > > Dear Bipul, > > > > Bipul Rakshit wrote: > > Dear Gabriele Sclauzero, > > thanks for your kind reply. > > Since I am sending you the input, so i send you to your private mail. > > Please see the input and suggest me if there is anything wrong. > > > I don't see any reason of sending the input files privately to me (unless > you have > specific reasons), since this is not in the open-source spirit of the forum > and you will > prevent other users from helping you. > > In your input files: > > &system > occupations='smearing', smearing='methfessel-paxton', > degauss=0.000073498 > > This value of degauss seems very low to me. Are you sure that you need it, > and most > important, have you converged w.r.t the number of k-points? > > > &electrons > conv_thr = 1.0d-5 > > this is too high, use the default or something lower. > > Anyway, I don't see any problem related to the I/O issue in your input > files. You have to > check if the nscf run completed successfully and wrote the wavefunctions to > disk. The > files may be corrupted due to an interrupted run or an hardware failure. > You should also > be careful when running on clusters with local scratch area (does it apply > to your case?). > Please provide more information about your compilation/HW-SW configuration > and a full > output file from DOS or PDOS calculation. > > GS > > > > > On Mon, Aug 10, 2009 at 3:20 PM, Gabriele Sclauzero > >> wrote: > > > > > Bipul Rakshit wrote: > > Dear PWSCF users, > > I am doing calculation of LaMnO3. When I try to do the projected > > density > > of states, then it shows the error > > > Calling projwave .... > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from davcio : error # 10 > > error while reading from file > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > > I have first done the scf, > > nscf > > dos.x > > then projwfc.x > > > kindly help me in this regard > > > First check if all the files containing the wavefunctions > > (outdir/prefix.wfc*) are present > > and are not corrupted. > > If so, please give more details (i.e. input files). If not, rerun > > scf and nscf steps. > > > Regards > > > GS > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum 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 > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/ac400819/attachment-0001.htm From bipulrr at gmail.com Tue Aug 11 07:50:39 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 11 Aug 2009 11:20:39 +0530 Subject: [Pw_forum] davico error while calculating projected density of states In-Reply-To: <3a749910908102112m696a7ee6s18567594d732df5d@mail.gmail.com> References: <3a749910908100112h5a38a55bu3688cc50c2560d73@mail.gmail.com> <4A7FED64.8060308@sissa.it> <3a749910908100325u624af2a1ra9c745c4759a848b@mail.gmail.com> <4A804A7A.4070709@sissa.it> <58C9821B-4F4D-4C2A-AF74-2C7426242CC3@sissa.it> <3a749910908102112m696a7ee6s18567594d732df5d@mail.gmail.com> Message-ID: <3a749910908102250n6a400d85n80bc5b80ff5b09f7@mail.gmail.com> Dear Shruba, using wf_collect=.true., really solves this problem. thanks for your help On Tue, Aug 11, 2009 at 9:42 AM, Bipul Rakshit wrote: > Dear SB and GB, > thanks for your kind advice. Now and onwards I will remember the things and > will send the message to all of the forum people (unless there is some > specific reason) > > And sorry for act. > regards > > > On Mon, Aug 10, 2009 at 11:26 PM, Stefano Baroni wrote: > >> Dear Bipul, dear all: >> please always consider that none of the people posting to this mailing >> list belong to any kind of "customer service". all of us are pleased to help >> when we can / feel like that ... none of us has to. so, please, refrain from >> sending private emails to members of the list, unless you have a specific >> reason to do so ... also, even if/when you get assistance precisely from >> exactlyy the same person you would address privately, when you address >> him/her on the mailing list, instead, you give others the possibility of >> learning at the same time you are learning. in conclusion, do use the list >> as much as possible ... >> >> SB >> >> >> >> On Aug 10, 2009, at 6:27 PM, Gabriele Sclauzero wrote: >> >> Dear Bipul, >> >> >> >> Bipul Rakshit wrote: >> >> Dear Gabriele Sclauzero, >> >> thanks for your kind reply. >> >> Since I am sending you the input, so i send you to your private mail. >> >> Please see the input and suggest me if there is anything wrong. >> >> >> I don't see any reason of sending the input files privately to me (unless >> you have >> specific reasons), since this is not in the open-source spirit of the >> forum and you will >> prevent other users from helping you. >> >> In your input files: >> >> &system >> occupations='smearing', smearing='methfessel-paxton', >> degauss=0.000073498 >> >> This value of degauss seems very low to me. Are you sure that you need it, >> and most >> important, have you converged w.r.t the number of k-points? >> >> >> &electrons >> conv_thr = 1.0d-5 >> >> this is too high, use the default or something lower. >> >> Anyway, I don't see any problem related to the I/O issue in your input >> files. You have to >> check if the nscf run completed successfully and wrote the wavefunctions >> to disk. The >> files may be corrupted due to an interrupted run or an hardware failure. >> You should also >> be careful when running on clusters with local scratch area (does it apply >> to your case?). >> Please provide more information about your compilation/HW-SW configuration >> and a full >> output file from DOS or PDOS calculation. >> >> GS >> >> >> >> >> On Mon, Aug 10, 2009 at 3:20 PM, Gabriele Sclauzero > >> >> wrote: >> >> >> >> >> Bipul Rakshit wrote: >> >> Dear PWSCF users, >> >> I am doing calculation of LaMnO3. When I try to do the projected >> >> density >> >> of states, then it shows the error >> >> >> Calling projwave .... >> >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> from davcio : error # 10 >> >> error while reading from file >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> stopping ... >> >> >> I have first done the scf, >> >> nscf >> >> dos.x >> >> then projwfc.x >> >> >> kindly help me in this regard >> >> >> First check if all the files containing the wavefunctions >> >> (outdir/prefix.wfc*) are present >> >> and are not corrupted. >> >> If so, please give more details (i.e. input files). If not, rerun >> >> scf and nscf steps. >> >> >> Regards >> >> >> GS >> >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum 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 >> >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/688d5cb9/attachment.htm From baroni at sissa.it Tue Aug 11 10:10:52 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 11 Aug 2009 10:10:52 +0200 Subject: [Pw_forum] generating k point weights In-Reply-To: <21fbc4790908101902g3103efb3g52ba515e6b9fc22f@mail.gmail.com> References: <4A802593.5080004@sissa.it> <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> <21fbc4790908101902g3103efb3g52ba515e6b9fc22f@mail.gmail.com> Message-ID: <5E60B11C-C950-48FA-A781-FC117B3EED06@sissa.it> YOU have written the answer to your question "If .true. the bands are classified according to the irreducible representations of the small group of k" (which is the only sensible thing to do) Stefano Baroni - SISSA Trieste --- swift text written and sent on the go On 11/ago/2009, at 04.02, xirainbow wrote: > Dear Stefano Baroni and Gabriele Sclauzero: > > First of all, thank you very much for your detailed explanation :? > I think I fully undertand it. > First, the "kpoints.x" reduces the number of k-points according to > parameter "ibrav". That means kpoints.x chooses the symmetry among > 14 Bravais lattices. > Second, the "pw.x" checkes all symmetry operations within a given > Bravais lattice determined by kpoints.x. That means pw.x determines > the symmetry among 7 crystal systems. > > But, now I have a another question about bands.x. > In the instruction of bands.x, it says: > Presently it can calculate: > (a) The expectation value of the spin operator on each spinor > wave-function. > (b) The symmetry properties of each wavefunction. > The instruction of parameter "lsym" says: > If .true. the bands are classified according to the irreducible > representations of the small group of k. A file "filband".rap with > the same format of "filband" is written. > > I want to know the symmetry properties obatained by "band.x" is > based on 7 crystal systems, 14 Bravais lattices or 32 point groups. > > Once again, thank you very much ?? > > ____________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/444e9e73/attachment.htm From nkxirainbow at gmail.com Tue Aug 11 10:28:06 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 11 Aug 2009 16:28:06 +0800 Subject: [Pw_forum] generating k point weights In-Reply-To: <5E60B11C-C950-48FA-A781-FC117B3EED06@sissa.it> References: <4A802593.5080004@sissa.it> <21fbc4790908100741w3808661fkc39a4ec78fa528cb@mail.gmail.com> <21fbc4790908101902g3103efb3g52ba515e6b9fc22f@mail.gmail.com> <5E60B11C-C950-48FA-A781-FC117B3EED06@sissa.it> Message-ID: <21fbc4790908110128m1407479h86629f33ca9be122@mail.gmail.com> Dear Stefano Baroni: >YOU have written the answer to your question >"If .true. the bands are classified according to the irreducible representations of the small group >of k" (which is the only sensible thing to do) Sorry, I almost forgot the definition of "small group". I refered to text book and found the answer ?? Thank you for your concise reply ?? ____________________________________ 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/20090811/f9c371a6/attachment.htm From dimpy.sharma at tyndall.ie Tue Aug 11 10:44:25 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 11 Aug 2009 09:44:25 +0100 Subject: [Pw_forum] Error in output file Message-ID: Hi Quantum espresso users, I have tried to set up calculation in quantum espresso , however in the output file, it is showing as %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 1 wrong number of columns in ATOMIC_POSITIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I have given the coordinates directly from my structure as I got in Material studio, Can anybody please help me? Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/d8668080/attachment.htm From paulatto at sissa.it Tue Aug 11 11:16:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 11 Aug 2009 11:16:41 +0200 Subject: [Pw_forum] Error in output file In-Reply-To: References: Message-ID: In data 11 agosto 2009 alle ore 10:44:25, Dimpy Sharma ha scritto: > I have given the coordinates directly from my structure as I got in > Material studio, Can anybody please help me? Dis usually means that nat is smaller than it should be, or you've forgot to include some atom in the list. Please recheck. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From lanhaiping at gmail.com Tue Aug 11 11:18:10 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 11 Aug 2009 17:18:10 +0800 Subject: [Pw_forum] Error in output file In-Reply-To: References: Message-ID: Hi, Dimpy! It is clear that you have done some typos in your input file for atomic postions as the error information indicates. Therefore, You should check your file again , to find whether your atoms are consistent with ' nat' you set for . And without your input , no body can help . regards On Tue, Aug 11, 2009 at 4:44 PM, Dimpy Sharma wrote: > > Hi Quantum espresso users, > > I have tried to set up calculation in quantum espresso , however in the > output file, it is showing as > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_cards : error # 1 > wrong number of columns in ATOMIC_POSITIONS > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > I have given the coordinates directly from my structure as I got in > Material studio, Can anybody please help me? > > Dimpy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/8bb22a96/attachment.htm From stenuit at sissa.it Tue Aug 11 11:32:35 2009 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Tue, 11 Aug 2009 11:32:35 +0200 Subject: [Pw_forum] TDDFT and GW In-Reply-To: <449616990.04837@nudt.edu.cn> References: <449616990.04837@nudt.edu.cn> Message-ID: <4A813AB3.7000508@sissa.it> Dear Jiayu and Pwscf Users, It is our pleasure to inform you that a GW code is now implemented in the CVS version of Q.E. . This code (GWW) is based on the used of Wannier-like orbitals [see PRB 79, 201104(R) (2009) ] for evaluating the polarization propagator. It allows to address large systems (a few hundreds of atoms). Examples for using the code can be found either in the examples/GWW_examples directory from the main QE directory, or on our webpage (still under construction...): http://gww.qe-forge.org/ For its installation: "./configure" and "make gww" will generate the GWW binaries. Regards, Joe and Paolo Jiayu Dai wrote: > Dear all, > > It's so exciting to see the new release of espresso-4.1, and a lot of new parts in > the code. But i would like to know if it includes the parts of TDDFT and GW? They > have been discussed a lot before, and expected to be done soon? > > By the way, if we want change something about the exchange-correction functions in > the code, what's the step to do it? It should be a big job? > > Best wishes. > > Jiayu > > > > > ------------------------------ > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------------------------- Geoffrey Stenuit Theory at Elettra Group CNR-INFM DEMOCRITOS National Simulation Center c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE email: stenuit at sissa.it tel: +39 040 375-8713 fax: -8776 From bipulrr at gmail.com Tue Aug 11 14:48:20 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 11 Aug 2009 18:18:20 +0530 Subject: [Pw_forum] Doubt in Phonon calculations Message-ID: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> Dear PWSCF users, I am doing phonon of LaMnO3, which is having 20 atoms in the unit cell (After finishing the electronic part) I am just calculating the phonon at Gamma point for this compound. I have send the relevant input files also. My doubt is if you see the O/P of phonon (phonon.out) file, it seems it is going to calculate all the 60 modes. But as far as I know at gamma atleast few modes are degenerate and acoustic is zero. So kindly look at the input files and tell the possible error regards -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/9da52394/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.ph.in Type: application/octet-stream Size: 316 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090811/9da52394/attachment-0004.obj -------------- next part -------------- A non-text attachment was scrubbed... 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Name: phonon.out Type: application/octet-stream Size: 16484 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090811/9da52394/attachment-0007.obj From eyvaz_isaev at yahoo.com Tue Aug 11 15:27:02 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 11 Aug 2009 06:27:02 -0700 (PDT) Subject: [Pw_forum] Doubt in Phonon calculations In-Reply-To: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> Message-ID: <768087.680.qm@web65712.mail.ac4.yahoo.com> Dear Bipul, Is it OK that you have only 2 symmetry operations? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 8/11/09, Bipul Rakshit wrote: > From: Bipul Rakshit > Subject: [Pw_forum] Doubt in Phonon calculations > To: "PWSCF Forum" > Date: Tuesday, August 11, 2009, 4:48 PM > Dear PWSCF users, > I am doing phonon of LaMnO3, which is having 20 atoms in > the unit cell (After finishing the electronic part) > I am just calculating the phonon at Gamma point > for this compound. I have send the relevant input files > also. > > My doubt is if you see the O/P of phonon (phonon.out) file, > it seems it is going to calculate all the 60 modes. > But as far as I know at gamma atleast few modes are > degenerate and acoustic is zero. > > So kindly look at the input files and tell the possible > error > > regards > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Tue Aug 11 15:33:02 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 11 Aug 2009 15:33:02 +0200 Subject: [Pw_forum] Doubt in Phonon calculations In-Reply-To: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> References: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> Message-ID: All the modes are cakculated. Degenerate modes are calculated because all of the partners of irreps are needed to properly symmtetrize the dynamical matrix (or else, one should use more k-points than actually used in ph.x). Acoustic modes are calculated for the sake of it (actually, the amount of violation of the acoustic sum rule tells something about the overall convergence of the calculation). Stefano Baroni - Trieste --- swift text written and sent on the go On 11/ago/2009, at 14.48, Bipul Rakshit wrote: > Dear PWSCF users, > I am doing phonon of LaMnO3, which is having 20 atoms in the unit > cell (After finishing the electronic part) > I am just calculating the phonon at Gamma point for this compound. I > have send the relevant input files also. > My doubt is if you see the O/P of phonon (phonon.out) file, it seems > it is going to calculate all the 60 modes. > But as far as I know at gamma atleast few modes are degenerate and > acoustic is zero. > > So kindly look at the input files and tell the possible error > regards > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From nkxirainbow at gmail.com Tue Aug 11 15:39:36 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 11 Aug 2009 21:39:36 +0800 Subject: [Pw_forum] Doubt in Phonon calculations In-Reply-To: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> References: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> Message-ID: <21fbc4790908110639s7d3c6b29k5790d44dcc1f1698@mail.gmail.com> Dear Bipul Rakshit: >My doubt is if you see the O/P of phonon (phonon.out) file, it seems it is going to calculate all >the 60 modes. >But as far as I know at gamma atleast few modes are degenerate and acoustic is zero. I look at your uploaded files and found the following content: " ibrav= 0, celldm(1) =14.62476638, nat= 20, ntyp= 4, CELL_PARAMETERS cubic 0.73727 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.71933" The symmetry of your system is very low. I think you can do certain symmetry analysis for your system, determine how many degenerated mode are before calculation. ____________________________________ 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/20090811/7185631e/attachment.htm From eyvaz_isaev at yahoo.com Tue Aug 11 16:20:31 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 11 Aug 2009 07:20:31 -0700 (PDT) Subject: [Pw_forum] Doubt in Phonon calculations In-Reply-To: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> Message-ID: <171231.34314.qm@web65701.mail.ac4.yahoo.com> Well, most likely, low symmetry comes from inconsistent CELL_PARAMETERS which are limited by 5 digits, and the ATOMIC_POSITIONS angstrom defined with more digits. As it is known in QE atomic positions are equivalent with the tolerance of 1.d-6 (i.e. 6 digits). To me, the use of "crystal" is more safe. >degauss=0.000073498 How could you obtain such kind "exact" broadening width? > conv_thr = 1.0d-5 Too high threshold, default is 1.d-6. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 8/11/09, Bipul Rakshit wrote: > From: Bipul Rakshit > Subject: [Pw_forum] Doubt in Phonon calculations > To: "PWSCF Forum" > Date: Tuesday, August 11, 2009, 4:48 PM > Dear PWSCF users, > I am doing phonon of LaMnO3, which is having 20 atoms in > the unit cell (After finishing the electronic part) > I am just calculating the phonon at Gamma point > for this compound. I have send the relevant input files > also. > > My doubt is if you see the O/P of phonon (phonon.out) file, > it seems it is going to calculate all the 60 modes. > But as far as I know at gamma atleast few modes are > degenerate and acoustic is zero. > > So kindly look at the input files and tell the possible > error > > regards > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From kazempoor2000 at yahoo.com Tue Aug 11 16:45:00 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 11 Aug 2009 07:45:00 -0700 (PDT) Subject: [Pw_forum] affinity Message-ID: <341176.96851.qm@web112511.mail.gq1.yahoo.com> Hi Some people take this formula to compute U for their material. E(d_n+1)+E(d_n-1)-2E(d_n)==U For isolated atom(Ti), the HOMO and LUMO is d orbital. On the other hand the affinity and ionization energy is like this: A = E(n)-E(n+1) I = E(n-1)-E(n) So can I compute A and I and then U=A-I. Is is correct? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/e94b56d7/attachment.htm From dimpy.sharma at tyndall.ie Tue Aug 11 17:19:09 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 11 Aug 2009 16:19:09 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 26, Issue 34 References: Message-ID: Thanks for your advice, however as per the information given in the output, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 691 species H in ATOMIC_POSITIONS is nonexistent %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% At this position the Hydrogen atom has got coordiantes a 0.000000 in all the three axes. Thus any other suggestions?? Thanks Dimpy -----Original Message----- From: pw_forum-bounces at pwscf.org on behalf of pw_forum-request at pwscf.org Sent: Tue 8/11/2009 1:48 PM To: pw_forum at pwscf.org Subject: Pw_forum Digest, Vol 26, Issue 34 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: generating k point weights (Stefano Baroni) 2. Re: generating k point weights (xirainbow) 3. Error in output file (Dimpy Sharma) 4. Re: Error in output file (Lorenzo Paulatto) 5. Re: Error in output file (lan haiping) 6. Re: TDDFT and GW (Geoffrey Stenuit) 7. Doubt in Phonon calculations (Bipul Rakshit) ---------------------------------------------------------------------- Message: 1 Date: Tue, 11 Aug 2009 10:10:52 +0200 From: Stefano Baroni Subject: Re: [Pw_forum] generating k point weights To: PWSCF Forum Message-ID: <5E60B11C-C950-48FA-A781-FC117B3EED06 at sissa.it> Content-Type: text/plain; charset="utf-8" YOU have written the answer to your question "If .true. the bands are classified according to the irreducible representations of the small group of k" (which is the only sensible thing to do) Stefano Baroni - SISSA Trieste --- swift text written and sent on the go On 11/ago/2009, at 04.02, xirainbow wrote: > Dear Stefano Baroni and Gabriele Sclauzero: > > First of all, thank you very much for your detailed explanation :? > I think I fully undertand it. > First, the "kpoints.x" reduces the number of k-points according to > parameter "ibrav". That means kpoints.x chooses the symmetry among > 14 Bravais lattices. > Second, the "pw.x" checkes all symmetry operations within a given > Bravais lattice determined by kpoints.x. That means pw.x determines > the symmetry among 7 crystal systems. > > But, now I have a another question about bands.x. > In the instruction of bands.x, it says: > Presently it can calculate: > (a) The expectation value of the spin operator on each spinor > wave-function. > (b) The symmetry properties of each wavefunction. > The instruction of parameter "lsym" says: > If .true. the bands are classified according to the irreducible > representations of the small group of k. A file "filband".rap with > the same format of "filband" is written. > > I want to know the symmetry properties obatained by "band.x" is > based on 7 crystal systems, 14 Bravais lattices or 32 point groups. > > Once again, thank you very much ?? > > ____________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/444e9e73/attachment-0001.htm ------------------------------ Message: 2 Date: Tue, 11 Aug 2009 16:28:06 +0800 From: xirainbow Subject: Re: [Pw_forum] generating k point weights To: PWSCF Forum Message-ID: <21fbc4790908110128m1407479h86629f33ca9be122 at mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Stefano Baroni: >YOU have written the answer to your question >"If .true. the bands are classified according to the irreducible representations of the small group >of k" (which is the only sensible thing to do) Sorry, I almost forgot the definition of "small group". I refered to text book and found the answer ?? Thank you for your concise reply ?? ____________________________________ 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/20090811/f9c371a6/attachment-0001.htm ------------------------------ Message: 3 Date: Tue, 11 Aug 2009 09:44:25 +0100 From: "Dimpy Sharma" Subject: [Pw_forum] Error in output file To: Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Quantum espresso users, I have tried to set up calculation in quantum espresso , however in the output file, it is showing as %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 1 wrong number of columns in ATOMIC_POSITIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I have given the coordinates directly from my structure as I got in Material studio, Can anybody please help me? Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/d8668080/attachment-0001.htm ------------------------------ Message: 4 Date: Tue, 11 Aug 2009 11:16:41 +0200 From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] Error in output file To: "PWSCF Forum" Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes In data 11 agosto 2009 alle ore 10:44:25, Dimpy Sharma ha scritto: > I have given the coordinates directly from my structure as I got in > Material studio, Can anybody please help me? Dis usually means that nat is smaller than it should be, or you've forgot to include some atom in the list. Please recheck. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ ------------------------------ Message: 5 Date: Tue, 11 Aug 2009 17:18:10 +0800 From: lan haiping Subject: Re: [Pw_forum] Error in output file To: PWSCF Forum Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, Dimpy! It is clear that you have done some typos in your input file for atomic postions as the error information indicates. Therefore, You should check your file again , to find whether your atoms are consistent with ' nat' you set for . And without your input , no body can help . regards On Tue, Aug 11, 2009 at 4:44 PM, Dimpy Sharma wrote: > > Hi Quantum espresso users, > > I have tried to set up calculation in quantum espresso , however in the > output file, it is showing as > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_cards : error # 1 > wrong number of columns in ATOMIC_POSITIONS > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > I have given the coordinates directly from my structure as I got in > Material studio, Can anybody please help me? > > Dimpy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/8bb22a96/attachment-0001.htm ------------------------------ Message: 6 Date: Tue, 11 Aug 2009 11:32:35 +0200 From: Geoffrey Stenuit Subject: Re: [Pw_forum] TDDFT and GW To: Jiayu Dai , PWSCF Forum , q-e-users at qe-forge.org Message-ID: <4A813AB3.7000508 at sissa.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Jiayu and Pwscf Users, It is our pleasure to inform you that a GW code is now implemented in the CVS version of Q.E. . This code (GWW) is based on the used of Wannier-like orbitals [see PRB 79, 201104(R) (2009) ] for evaluating the polarization propagator. It allows to address large systems (a few hundreds of atoms). Examples for using the code can be found either in the examples/GWW_examples directory from the main QE directory, or on our webpage (still under construction...): http://gww.qe-forge.org/ For its installation: "./configure" and "make gww" will generate the GWW binaries. Regards, Joe and Paolo Jiayu Dai wrote: > Dear all, > > It's so exciting to see the new release of espresso-4.1, and a lot of new parts in > the code. But i would like to know if it includes the parts of TDDFT and GW? They > have been discussed a lot before, and expected to be done soon? > > By the way, if we want change something about the exchange-correction functions in > the code, what's the step to do it? It should be a big job? > > Best wishes. > > Jiayu > > > > > ------------------------------ > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------------------------- Geoffrey Stenuit Theory at Elettra Group CNR-INFM DEMOCRITOS National Simulation Center c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE email: stenuit at sissa.it tel: +39 040 375-8713 fax: -8776 ------------------------------ Message: 7 Date: Tue, 11 Aug 2009 18:18:20 +0530 From: Bipul Rakshit Subject: [Pw_forum] Doubt in Phonon calculations To: PWSCF Forum Message-ID: <3a749910908110548n25ff5e44p172985c4ba217e02 at mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear PWSCF users, I am doing phonon of LaMnO3, which is having 20 atoms in the unit cell (After finishing the electronic part) I am just calculating the phonon at Gamma point for this compound. I have send the relevant input files also. My doubt is if you see the O/P of phonon (phonon.out) file, it seems it is going to calculate all the 60 modes. But as far as I know at gamma atleast few modes are degenerate and acoustic is zero. So kindly look at the input files and tell the possible error regards -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/9da52394/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.ph.in Type: application/octet-stream Size: 316 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090811/9da52394/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... 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Name: phonon.out Type: application/octet-stream Size: 16484 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090811/9da52394/attachment-0003.obj ------------------------------ _______________________________________________ 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 34 **************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8330 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090811/92cce395/attachment-0001.bin From paulatto at sissa.it Tue Aug 11 17:29:53 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 11 Aug 2009 17:29:53 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 26, Issue 34 In-Reply-To: References: Message-ID: In data 11 agosto 2009 alle ore 17:19:09, Dimpy Sharma ha scritto: > At this position the Hydrogen atom has got coordiantes a 0.000000 in all > the three axes. Thus any other suggestions?? Dear Dimpy, probably you have set ntyp to the wrong value (smaller then it should be). You may have noticed that, in the first few of lines of output, the code issued a warning, saying that it had ignored one input line. I've noticed that it is the second question you've asked in two days regarding some trivial syntactical inconsistence (btw, was yesterday solution correct?). Please take some time and recheck your input file carefully; after writing it, relax take a cup of coffee and recheck it. It takes some time, but saves times in the end. Finally, provide your input file when asking for help, it is much more difficult to find an error in a file without being able to read it. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From bipulrr at gmail.com Tue Aug 11 17:51:32 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 11 Aug 2009 21:21:32 +0530 Subject: [Pw_forum] Doubt in Phonon calculations In-Reply-To: <21fbc4790908110639s7d3c6b29k5790d44dcc1f1698@mail.gmail.com> References: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> <21fbc4790908110639s7d3c6b29k5790d44dcc1f1698@mail.gmail.com> Message-ID: <3a749910908110851u71b71fcj1567e49c75f13874@mail.gmail.com> Dear Hui Wang, THanks for you kind advice. Just tell me I have to do the symmetry analysis manually, or there is some simple method to do so? thanks On 8/11/09, xirainbow wrote: > Dear Bipul Rakshit: > >>My doubt is if you see the O/P of phonon (phonon.out) file, it seems it is > going to calculate all >the 60 modes. >>But as far as I know at gamma atleast few modes are degenerate and acoustic > is zero. > I look at your uploaded files and found the following content: > " ibrav= 0, celldm(1) =14.62476638, nat= 20, ntyp= 4, > CELL_PARAMETERS cubic > 0.73727 0.00000 0.00000 > 0.00000 1.00000 0.00000 > 0.00000 0.00000 0.71933" > The symmetry of your system is very low. > I think you can do certain symmetry analysis for your system, determine how > many degenerated mode are before calculation. > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From dimpy.sharma at tyndall.ie Tue Aug 11 18:49:53 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 11 Aug 2009 17:49:53 +0100 Subject: [Pw_forum] (no subject) Message-ID: Hi there, I have tried to perform scf alculation in my system, however the result is not converged,It stopped after first few iterations. Instead the output shows following error p4_16508: p4_error: interrupt SIGx: 13 rm_l_23_24807: (392.835938) net_send: could not write to fd=5, errno = 32 rm_l_5_16527: (398.265625) net_send: could not write to fd=5, errno = 32 mpirun: got sig, my pid is 17869 childs pid is 18462 mpirun My input file is as follows &CONTROL calculation ='scf' restart_mode ='from_scratch' outdir = '/sfiwork/dsharma/test/ pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = 'dsh' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =14.895468 nat = 780 ntyp = 2 ecutwfc = 35 ecutrho = 120 nbnd =1700 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.000000000 0.000000000 0.000000000 0.000000000 1.000000000 0.000000000 0.000000000 0.000000000 6.000000000 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H 1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 4.428658922 8.103176805 29.794371687 Si 4.336832871 18.551141820 20.425720839 Si 3.983248480 19.970914222 26.328297321 ...... Kindly advice me! Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/126ed455/attachment.htm From dimpy.sharma at tyndall.ie Tue Aug 11 19:10:02 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 11 Aug 2009 18:10:02 +0100 Subject: [Pw_forum] Charge is wrong ...in the output file Message-ID: Hi QEs users, I got an error in my output file as follows %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% However from my previous survey in PW_forum, I have found that this problem may be due to not doing spin polarized calculation with an odd number of electrons, what does it mean? My input file is &CONTROL calculation ='scf' restart_mode ='from_scratch' outdir = '/sfihome/dsharma/Pscf/test' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = 'Pscf1' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =20.40066 nat = 94 ntyp = 3 ecutwfc = 30 ecutrho = 120 nbnd = 220 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.000000000 0.000000000 0.000000000 0.000000000 1.000000000 0.000000000 0.000000000 0.000000000 5.000000000 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H 1.00800 H.pz-vbc.UPF O 15.9994 O.pz-rrkjus.UPF ATOMIC_POSITIONS angstroms O 7.0781 6.9497 27.1761 O 4.3952 6.9992 27.2391 H 7.4599 6.0212 27.1358 H 5.3921 7.0051 27.1349 H 1.5615 4.4933 27.1304 Si 3.4277 0.5123 26.6794 Si 7.2634 3.3235 26.6750 Si 0.4470 0.4413 26.6627 ........ K_POINTS automatic 2 2 1 0 0 0 Can anyboy please help? DS. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/8208bef7/attachment.htm From eyvaz_isaev at yahoo.com Tue Aug 11 19:24:37 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 11 Aug 2009 10:24:37 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: Message-ID: <45161.25679.qm@web65713.mail.ac4.yahoo.com> Dear Sharma, --- On Tue, 8/11/09, Dimpy Sharma wrote: > I have tried to perform scf alculation in my system, > however the result is not converged,It stopped after first > few iterations. Instead the output shows following error You are incorrect, as "not converged" and "stopped" are inequivalent. > rm_l_23_24807: (392.835938) net_send: could not write to > fd=5, errno = 32 May be your disk is full, did you check? Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From eyvaz_isaev at yahoo.com Tue Aug 11 19:35:20 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 11 Aug 2009 10:35:20 -0700 (PDT) Subject: [Pw_forum] Charge is wrong ...in the output file In-Reply-To: Message-ID: <64342.93742.qm@web65714.mail.ac4.yahoo.com> > ???? charge is wrong Did you any search in PW forum archive? You will be surprized how many times this question has been asked. Then see your scf.out file how many electrons you have. Most likely you have odd number. Besides, I would recommend to start with a simple system to learn the code (using examples provided) and then start with a complex system. > Charge is wrong ...in the output file No, charge is wrong due to your incorrect input data. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From wangqj1 at 126.com Wed Aug 12 04:20:07 2009 From: wangqj1 at 126.com (wangqj1) Date: Wed, 12 Aug 2009 10:20:07 +0800 (CST) Subject: [Pw_forum] GW Message-ID: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> Dear Joe and Paolo In Pw_forum Digest, Vol 26, Issue 34 you said that the code (GWW) which allows to address large systems (a few hundreds of atoms). But on the webpage http://gww.qe-forge.org/ ,I don't which flag control the number of atoms in the namelist,it looks as a postprograme and read the information from the PW scf . Thanks for your help . Best wishes Q J Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090812/b4577d30/attachment-0001.htm From baroni at sissa.it Wed Aug 12 08:30:45 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 12 Aug 2009 08:30:45 +0200 Subject: [Pw_forum] GW In-Reply-To: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> References: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> Message-ID: <93FD48A7-2055-4BBA-8D53-2B8091D99976@sissa.it> You got it. Stefano Baroni SISSA - Trieste --- swift text written and sent on the go On 12/ago/2009, at 04.20, wangqj1 wrote: > > Dear Joe and Paolo > In Pw_forum Digest, Vol 26, Issue 34 you said that the code > (GWW) which allows to address large systems (a few hundreds of > atoms). But on the webpage http://gww.qe-forge.org/ ,I don't which > flag control the number of atoms in the namelist,it looks as a > postprograme and read the information from the PW scf . > Thanks for your help . > Best wishes > Q J Wang > XiangTan University > > > > > > > ???????????,www.yeah.net > _______________________________________________ > 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/20090812/0a1051f0/attachment.htm From baroni at sissa.it Wed Aug 12 08:30:45 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 12 Aug 2009 08:30:45 +0200 Subject: [Pw_forum] GW In-Reply-To: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> References: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> Message-ID: <93FD48A7-2055-4BBA-8D53-2B8091D99976@sissa.it> You got it. Stefano Baroni SISSA - Trieste --- swift text written and sent on the go On 12/ago/2009, at 04.20, wangqj1 wrote: > > Dear Joe and Paolo > In Pw_forum Digest, Vol 26, Issue 34 you said that the code > (GWW) which allows to address large systems (a few hundreds of > atoms). But on the webpage http://gww.qe-forge.org/ ,I don't which > flag control the number of atoms in the namelist,it looks as a > postprograme and read the information from the PW scf . > Thanks for your help . > Best wishes > Q J Wang > XiangTan University > > > > > > > ???????????,www.yeah.net > _______________________________________________ > 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/20090812/0a1051f0/attachment-0001.htm From sclauzer at sissa.it Wed Aug 12 10:18:14 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 12 Aug 2009 10:18:14 +0200 Subject: [Pw_forum] inter_pool_comm In-Reply-To: <166cd7c60908050513m670080d2hc358a4df5ecb1bb1@mail.gmail.com> References: <166cd7c60908050513m670080d2hc358a4df5ecb1bb1@mail.gmail.com> Message-ID: <4A827AC6.5040003@sissa.it> Dear Dmitry, Dmitry Korotin wrote: > Dear QE developers, > could anyone explain to me in a few words a difference between > inter_pool_comm and intra_pool_comm variables. I am not really These variables specify a so-called MPI communicator. Very briefly, they define a subset of mpi processes among which the MPI communication will take place. If you have no pools, at the basic level you have only parallelization over G vectors (plane-waves) and you need to call mp_sum with inter_pool_comm as communicator (which will coincide with the full set of mpi processes if no other parallelization schemes are active) every time you are summing over G vectors (or real space grid). If you use more than one pool, when you sum over k-points you have to take into account that each pool is working on a subset of all k-points, therefore you have to collect the partial results from each pool. This is done by calling mp_sum with inter_pool_comm as communicator. Summarizing, after a summation over G vectors, call: CALL mp_sum ( ???, intra_pool_comm ) and after a summation over k-points call CALL mp_sum ( ???, inter_pool_comm ) where in place of ??? you put the name of the variable in which you accumulate the partial result. BTW, for those not familiar with italian/latin, intra means "within", inter means "among", more or less. > familiar with MPI, but I need to sum some variable over k-points. > Should I use mp_sum(variable_name,inter_pool_comm) or > mp_sum(variable_name,intra_pool_comm)? > > Does mp_sum take into account k-point weights? (As I understood from No, I think it's a general purpose interface for mpi reduce subroutines. You have include weights explicitly before summing. > the source this routine is used for summation over k-points?) Not only, also G-vectors or other things, depending on the value of the communicator. As a simple example, take a look at PW/new_ns.f90, which computes what written on the top comment lines. There is a summation over G vectors (written as a scalar product of two wavefunctions) proj (i, ibnd) = ZDOTC (npw, swfcatom (1, i), 1, evc (1, ibnd), 1) which needs CALL mp_sum ( proj, intra_pool_comm ) and after the summation over k-points you find: CALL mp_sum( nr, inter_pool_comm ) > > Thank you in advance. HTH GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From stenuit at sissa.it Wed Aug 12 10:25:30 2009 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Wed, 12 Aug 2009 10:25:30 +0200 Subject: [Pw_forum] GW In-Reply-To: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> References: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> Message-ID: <20090812102530.besnex8qm840sowk@webmail.sissa.it> Dear XiangTan, It is exactly this. The general sequence of binaries for computing the GW quasi-particle energies is the following (in a molecule): 1. pw.x 2. pw4gww.x 3. gww.x Actually, the pw4gww.x binary will read the prefix.save directory and the prefix.wfc files generated in the first step by pw.x. It is the .save directory that control for example the number of atoms,... for pw4gww.x . The gww.x binary will then act as a post-processing of pw4gww.x... This is the overall approach of "how to use this GW code". Thanks for your remark, Regards, Joe Quoting wangqj1 : > > Dear Joe and Paolo > In Pw_forum Digest, Vol 26, Issue 34 you said that the code > (GWW) which allows to address large systems (a few hundreds of > atoms). But on the webpage http://gww.qe-forge.org/ ,I don't which > flag control the number of atoms in the namelist,it looks as a > postprograme and read the information from the PW scf . > Thanks for your help . > Best wishes > Q J Wang > XiangTan University > > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From stenuit at sissa.it Wed Aug 12 10:31:30 2009 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Wed, 12 Aug 2009 10:31:30 +0200 Subject: [Pw_forum] GW In-Reply-To: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> References: <24367123.95841250043607989.JavaMail.coremail@bj126app103.126.com> Message-ID: <20090812103130.8tgn7zwr2800w0c8@webmail.sissa.it> Dear Q J Wang, It is exactly this. The general sequence of binaries for computing the GW quasi-particle energies is the following (in a molecule): 1. pw.x 2. pw4gww.x 3. gww.x Actually, the pw4gww.x binary will read the prefix.save directory and the prefix.wfc files generated in the first step by pw.x. It is the .save directory that control for example the number of atoms,... for pw4gww.x . The gww.x binary will then act as a post-processing of pw4gww.x... This is the overall approach of "how to use this GW code". Thanks for your remark, Regards, Joe Quoting wangqj1 : > > Dear Joe and Paolo > In Pw_forum Digest, Vol 26, Issue 34 you said that the code > (GWW) which allows to address large systems (a few hundreds of > atoms). But on the webpage http://gww.qe-forge.org/ ,I don't which > flag control the number of atoms in the namelist,it looks as a > postprograme and read the information from the PW scf . > Thanks for your help . > Best wishes > Q J Wang > XiangTan University > > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From daijiayu at nudt.edu.cn Wed Aug 12 16:09:37 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Wed, 12 Aug 2009 22:09:37 +0800 Subject: [Pw_forum] TDDFT and GW Message-ID: <450086177.19985@nudt.edu.cn> Oh, it'so exciting. I will try it, and i hope everyone like me can enjoy it. Thanks very much. Jiayu In your mail: >From: Geoffrey Stenuit >Reply-To: >To: Jiayu Dai , PWSCF Forum , q-e-users at qe-forge.org >Subject: Re: [Pw_forum] TDDFT and GW >Date:Tue, 11 Aug 2009 11:32:35 +0200 > >Dear Jiayu and Pwscf Users, > > It is our pleasure to inform you that a GW code is now implemented in > the CVS version of Q.E. . > This code (GWW) is based on the used of Wannier-like orbitals [see PRB > 79, 201104(R) (2009) ] for evaluating the polarization propagator. It > allows to address large systems (a few hundreds of atoms). > > Examples for using the code can be found either in the > examples/GWW_examples directory from the main QE directory, or on our > webpage (still under construction...): > > http://gww.qe-forge.org/ > > For its installation: "./configure" and "make gww" will generate the GWW > binaries. > > Regards, > > Joe and Paolo > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From sclauzer at sissa.it Wed Aug 12 16:44:01 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 12 Aug 2009 16:44:01 +0200 Subject: [Pw_forum] Difinition of V_bare and electric field potential In-Reply-To: <105892.39138.qm@web38804.mail.mud.yahoo.com> References: <105892.39138.qm@web38804.mail.mud.yahoo.com> Message-ID: <4A82D531.70306@sissa.it> Dear ding, the question about V_bare falls within the FAQs of this forum. Please have a look at this thread, for instance: http://www.democritos.it/pipermail/pw_forum/2006-October/005053.html Honestly I don't understand completely the second part of your question. Anyway, I think that the potential due to an external electric field (the one you switch on with tefield) is added to the local potential, so that it is already included in V_bare (it should be called vltot in pwscf code). Cheers, GS loc duong ding wrote: > Dear all, > > I wonder what is definition of V_bare and electric field potential in PWscf code. The > electric field potential in Pwscf is the same as electrostatic potential? > > It may be a stupid question but I can not find the consistence in the name of potential > as usual call. > > I appreciate your explaination! > > Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D > Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, > Suwon, 440-746, Korea Email: mambom1902 at yahoo.com > > > > _______________________________________________ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From madhura at jncasr.ac.in Wed Aug 12 19:47:28 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Wed, 12 Aug 2009 23:17:28 +0530 (IST) Subject: [Pw_forum] DOS and pDOS parallelization Message-ID: <58439.172.16.1.8.1250099248.squirrel@172.16.1.8> Dear all, There have been many discussions in this forum about parallelization of DOS and projected DOS codes. However, some of the points were not clear to me, so I have performed some scf calculations for a very simple system using 8 processors and with flag wf_collect 'false'. I have performed same calculations once without use of pools (A) and then using 2 pools (B). Then using theses wavefunctions I have performed DOS and PDOS calculations. Following is the summary of results and my interpretation: i) Pool parallelization is not implemented for both these codes. ii) DOS calculations: for both the cases A and B, one can calculate DOS with the same no. of processors (= 8) and the results match within numerical errors; even though for case B, the wavefunctions were obtained with pooling and DOS without it. For case A, even if I use 4 processors I get identical results as when I use 8 processors. (Note, I have not checked with less no. of proc.s for B). => The condition that we need the same no. of processors and pools as were used in scf calculations is not necessary; and it is possible to get DOS results even with wavefunctions generated with pool parallelization. iii) PDOS calculations: This can be calculated only in case of A and using the same no. of processors. If I use wavefunctions generated in case B or less no. of processors (= 4) with A wavefn.s then I get "davcio" error. => For PDOS calculations, one cannot use wavefunctions generated with pool parallelization unless wf_collect flag is set to 'true' for scf calc.s; also one has to use the same no. of proc.s as were used for scf calc.s to get projected DOS. Now my question is are these interpretations correct? Or they may change for some other system?? Do I need to do some more checks to ascertain these? If yes, what sort of tests? Thanks for reading this long mail patiently, but I need to clarify on these points before I can start with bigger systems. Sincerely, Madhura. -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From ferretti at MIT.EDU Thu Aug 13 00:11:19 2009 From: ferretti at MIT.EDU (Andrea Ferretti) Date: Wed, 12 Aug 2009 18:11:19 -0400 (EDT) Subject: [Pw_forum] DOS and pDOS parallelization In-Reply-To: <58439.172.16.1.8.1250099248.squirrel@172.16.1.8> Message-ID: Dear Madhura, the issue of using the same parallelism scheme (# of processors, # of pools, etc) in postprocessing calculations is mainly concerned with the need to read wfcs. As you wrote, if you specify wf_collect = .TRUE. you completely remove this issue (you can read wfcs whatever the parallelization scheme you used to produce them). >From this point of view, the main difference between DOS and pDOS calculations is that the former does not need to read wfcs, while the latter does. Moreover, the taks the DOS program has to perform is so inexpensive that it is performed by a single processor even if the code is run in parallel. This is consistent with your observation at (ii). In the case of pDOS (i.e. when running projwfc.x) if you do not collect wfcs you should run with the same # of processors and the same pool parallelism. Otherwise, as you experienced, you get a davcio error (some of the wfcs files were not found). According to me, anyway, projwfc should work with pools if the above conditions are fulfilled. hope it helps andrea > > There have been many discussions in this forum about parallelization of > DOS and projected DOS codes. However, some of the points were not clear to > me, so I have performed some scf calculations for a very simple system > using 8 processors and with flag wf_collect 'false'. I have performed same > calculations once without use of pools (A) and then using 2 pools (B). > Then using theses wavefunctions I have performed DOS and PDOS > calculations. Following is the summary of results and my interpretation: > > i) Pool parallelization is not implemented for both these codes. > > ii) DOS calculations: for both the cases A and B, one can calculate DOS > with the same no. of processors (= 8) and the results match within > numerical errors; even though for case B, the wavefunctions were obtained > with pooling and DOS without it. > For case A, even if I use 4 processors I get identical results as when I > use 8 processors. (Note, I have not checked with less no. of proc.s for B). > => The condition that we need the same no. of processors and pools as were > used in scf calculations is not necessary; and it is possible to get DOS > results even with wavefunctions generated with pool parallelization. > > iii) PDOS calculations: This can be calculated only in case of A and using > the same no. of processors. If I use wavefunctions generated in case B or > less no. of processors (= 4) with A wavefn.s then I get "davcio" error. => > For PDOS calculations, one cannot use wavefunctions generated with pool > parallelization unless wf_collect flag is set to 'true' for scf calc.s; > also one has to use the same no. of proc.s as were used for scf calc.s to > get projected DOS. > > Now my question is are these interpretations correct? Or they may change > for some other system?? Do I need to do some more checks to ascertain > these? If yes, what sort of tests? > > Thanks for reading this long mail patiently, but I need to clarify on > these points before I can start with bigger systems. > Sincerely, > Madhura. > > > -- Andrea Ferretti MIT, Dept Material Science & Engineering bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA Tel: +1 617-452-2455; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From madhura at jncasr.ac.in Thu Aug 13 06:56:15 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Thu, 13 Aug 2009 10:26:15 +0530 (IST) Subject: [Pw_forum] DOS and pDOS parallelization In-Reply-To: References: <58439.172.16.1.8.1250099248.squirrel@172.16.1.8> Message-ID: <34236.172.16.1.8.1250139375.squirrel@172.16.1.8> Dear Andrea, Thanks for the explanation. I had always thought that DOS code also requires wavefunction files; and that is why one needs to give the same prefix and outdir path as in scf calculations. If code does not need wavefunctions, which files it uses for DOS calc.s? As per suggestion, I have run PDOS calc.s with the same number of pools and processors (in case of B) and got results. That means PDOS code is parallelized with pool implementation, but not DOS. Thanks once again, Madhura. > > Dear Madhura, > > the issue of using the same parallelism scheme (# of processors, # of > pools, etc) in postprocessing calculations is mainly concerned with the > need to read wfcs. As you wrote, if you specify wf_collect = .TRUE. you > completely remove this issue (you can read wfcs whatever the > parallelization > scheme you used to produce them). > >>From this point of view, the main difference between DOS and pDOS > calculations is that the former does not need to read wfcs, while the > latter does. > > Moreover, the taks the DOS program has to perform is so inexpensive that > it is performed by a single processor even if the code is run in parallel. > This is consistent with your observation at (ii). > > In the case of pDOS (i.e. when running projwfc.x) if you do not collect > wfcs you should run with the same # of processors and the same pool > parallelism. Otherwise, as you experienced, you get a davcio error > (some of the wfcs files were not found). > According to me, anyway, projwfc should work with pools if the above > conditions are fulfilled. > > hope it helps > andrea > > >> >> There have been many discussions in this forum about parallelization of >> DOS and projected DOS codes. However, some of the points were not clear >> to >> me, so I have performed some scf calculations for a very simple system >> using 8 processors and with flag wf_collect 'false'. I have performed >> same >> calculations once without use of pools (A) and then using 2 pools (B). >> Then using theses wavefunctions I have performed DOS and PDOS >> calculations. Following is the summary of results and my interpretation: >> >> i) Pool parallelization is not implemented for both these codes. >> >> ii) DOS calculations: for both the cases A and B, one can calculate DOS >> with the same no. of processors (= 8) and the results match within >> numerical errors; even though for case B, the wavefunctions were >> obtained >> with pooling and DOS without it. >> For case A, even if I use 4 processors I get identical results as when >> I >> use 8 processors. (Note, I have not checked with less no. of proc.s for >> B). >> => The condition that we need the same no. of processors and pools as >> were >> used in scf calculations is not necessary; and it is possible to get DOS >> results even with wavefunctions generated with pool parallelization. >> >> iii) PDOS calculations: This can be calculated only in case of A and >> using >> the same no. of processors. If I use wavefunctions generated in case B >> or >> less no. of processors (= 4) with A wavefn.s then I get "davcio" error. >> => >> For PDOS calculations, one cannot use wavefunctions generated with pool >> parallelization unless wf_collect flag is set to 'true' for scf calc.s; >> also one has to use the same no. of proc.s as were used for scf calc.s >> to >> get projected DOS. >> >> Now my question is are these interpretations correct? Or they may change >> for some other system?? Do I need to do some more checks to ascertain >> these? If yes, what sort of tests? >> >> Thanks for reading this long mail patiently, but I need to clarify on >> these points before I can start with bigger systems. >> Sincerely, >> Madhura. >> >> >> > > -- > Andrea Ferretti > MIT, Dept Material Science & Engineering > bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA > Tel: +1 617-452-2455; Skype: andrea_ferretti > URL: http://quasiamore.mit.edu > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From anavat_ila at yahoo.com Thu Aug 13 11:00:27 2009 From: anavat_ila at yahoo.com (Ali Tavana) Date: Thu, 13 Aug 2009 02:00:27 -0700 (PDT) Subject: [Pw_forum] negative (alpha)^2*F(w) In-Reply-To: Message-ID: <3423.40785.qm@web51808.mail.re2.yahoo.com> Dear QE users, I have a question about e-ph lambda, calculated by "matdyn" program. I've found that for some frequencies the quantity "(alpha)^2*F(w)/w" or "dos_a2F(w)/w" can be negative, most probably because of the negative (imaginary) frequencies (I can't believe a2F(w) become negative!). In "matdyn" program these negative values are considered in lambda calculations. Should one remove these negative values as these imaginary frequency modes can never exist in the system? then where are those phonon branches? I think negative values of frequency can show in some manner more strong electron structure interaction, so what do you suggest one should do? regards, Ali From bipulrr at gmail.com Thu Aug 13 11:43:28 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 13 Aug 2009 15:13:28 +0530 Subject: [Pw_forum] difference in vc-relax and relax calculations Message-ID: <3a749910908130243g3fff97b2g386f66af0ca82909@mail.gmail.com> Dear PWSCF users, I I am doing calculation of LaMnO3. First I take the experimental lattice constant and atomic positions, and then run first vc-relax. After the system is relaxed. I use those lattice parameters and atomic position to do a relax calculation. But after running the vc-relax calculation i got appreciable very less pressure(~ -0.69 kbar), but as soon as I run the relax calculation, I am getting pressure of about -152.0 kbar. I didnt understand the error. Please have a look at my files and suggest me. regards -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090813/830f52ea/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.vc-relax.in Type: application/octet-stream Size: 3809 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090813/830f52ea/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.vc-relax.out Type: application/octet-stream Size: 2323 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090813/830f52ea/attachment-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: lamno3.relax.in Type: application/octet-stream Size: 4303 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090813/830f52ea/attachment-0002.obj From oulihui666 at 126.com Thu Aug 13 11:37:14 2009 From: oulihui666 at 126.com (oulihui666) Date: Thu, 13 Aug 2009 17:37:14 +0800 (CST) Subject: [Pw_forum] Frequency and zero point energy calculations Message-ID: <26935521.319391250156234372.JavaMail.coremail@bj126app81.126.com> Dear all, Recently, I have been performing calulation of frequency and zero point energy of CO2 molecule. However, unfortunately, I have obtained negative frequency. According to the manual, there are several possible reseaons: (1) wrong data file read. (2) wrong atomic masses given in input will yield wrong frequencies (but the content of file fildyn should be valid, since the force constants, not the dynamical matrix, are written to file). (3) convergence threshold for either SCF (conv thr) or phonon calculation (tr2 ph) too large: try to reduce them. (4) maybe your system does have negative or strange phonon frequencies, with the approximations you used. A negative frequency signals a mechanical instability of the chosen structure. Check that the structure is reasonable, and check the following parameters: ? The cutoff for wavefunctions, ecutwfc ? For US PP: the cutoff for the charge density, ecutrho ? The k-point grid, especially for metallic systems! My calculated process as follows: (1) Optimizing CO2 structure(input file as follows); &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/olh/tmp/' , pseudo_dir = '/home/olh/pseudo/' , prefix = 'CO2' , / &SYSTEM ibrav = 1, celldm(1) = 15.11781502, nat = 3, ntyp = 2, ecutwfc = 26 , ecutrho = 260 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 0.5, starting_magnetization(2) = 0.5, / &ELECTRONS conv_thr = 1.D-12 , mixing_beta = 0.4D0 , / &IONS ion_dynamics = 'bfgs' , / ATOMIC_SPECIES C 12.01100 C.pbe-rrkjus.UPF O 15.99940 O.pbe-rrkjus.UPF ATOMIC_POSITIONS angstrom C 4.000000000 4.000000000 4.000000000 1 1 1 O 5.160000000 4.000000000 4.000000000 1 1 1 O 2.840000000 4.000000000 4.000000000 1 1 1 K_POINTS gamma (2) Performing scf calculations: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/olh/tmp/' , pseudo_dir = '/home/olh/pseudo/' , prefix = 'CO2' , / &SYSTEM ibrav = 1, celldm(1) = 15.11781502, nat = 3, ntyp = 2, ecutwfc = 26 , ecutrho = 260 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 0.5, starting_magnetization(2) = 0.5, / &ELECTRONS conv_thr = 1.D-12 , mixing_beta = 0.4D0 , / ATOMIC_SPECIES C 12.01100 C.pbe-rrkjus.UPF O 15.99940 O.pbe-rrkjus.UPF ATOMIC_POSITIONS angstrom C 4.000000000 4.000000000 4.000000000 0 0 0 O 5.172018724 4.000000000 4.000000000 0 0 0 O 2.827981276 4.000000000 4.000000000 0 0 0 K_POINTS automatic 16 16 16 1 1 1 (3) Performing frequency calculation using PHONOS codes: phonons of CO2 at Gamma &inputph tr2_ph=1.0d-20, prefix='CO2', epsil=.false., amass(1)=12.0110, amass(2)=15.9994, outdir='/home/olh/tmp/', fildyn='CO2.dynG', / 0.0 0.0 0.0 Finally, I obtained the frequency of CO2 molecule, output file as follows: Convergence has been achieved Number of q in the star = 1 List of q in the star: 1 0.000000000 0.000000000 0.000000000 Diagonalizing the dynamical matrix q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -3.661345 [THz] = -122.130124 [cm-1] omega( 2) = -3.661345 [THz] = -122.130124 [cm-1] omega( 3) = 3.659957 [THz] = 122.083850 [cm-1] omega( 4) = 7.879986 [THz] = 262.849774 [cm-1] omega( 5) = 7.879986 [THz] = 262.849774 [cm-1] omega( 6) = 19.746862 [THz] = 658.688787 [cm-1] omega( 7) = 19.746862 [THz] = 658.688787 [cm-1] omega( 8) = 38.945041 [THz] = 1299.075383 [cm-1] omega( 9) = 70.000609 [THz] = 2334.984491 [cm-1] ************************************************************************** Mode symmetry, D_4h(4/mmm) point group: omega( 1 - 2) = -122.1 [cm-1] --> E_g X_5 M_5 R omega( 3 - 3) = 122.1 [cm-1] --> A_2u X_4' M_4' I omega( 4 - 5) = 262.8 [cm-1] --> E_u X_5' M_5' I omega( 6 - 7) = 658.7 [cm-1] --> E_u X_5' M_5' I omega( 8 - 8) = 1299.1 [cm-1] --> A_1g X_1 M_1 R omega( 9 - 9) = 2335.0 [cm-1] --> A_2u X_4' M_4' I ************************************************************************** PHONON : 1h48m CPU time, 2h25m wall time ...... There are still negative frequency in output file by increasing K_POINTS and reducing tr2_ph, anyone who help me will be appreciated. In addition, I intend to calculate the zero point energy of system by PHNONS code, but it does not give the zero point energy and other thermodynamics properties in output file. How could I do? I need your help urgently. Thanks in advance Best regards Lihui -- ====================================== Lihui Ou PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:oulihui666 at 126.com ====================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090813/265ef2f1/attachment-0001.htm From giannozz at democritos.it Thu Aug 13 13:15:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Aug 2009 13:15:10 +0200 Subject: [Pw_forum] IBM-AIX vs ifort In-Reply-To: <3a749910908050320x7c3c9f49i157300089f548e81@mail.gmail.com> References: <3a749910908050320x7c3c9f49i157300089f548e81@mail.gmail.com> Message-ID: <200908131315.11068.giannozz@democritos.it> On Wednesday 05 August 2009 12:20, Bipul Rakshit wrote: > I am doing a relax calculation of LaMnO3, the linux doing > Entering Dynamics: iteration =2 > > while the AIX-IBM is doing > Entering Dynamics: iteration =12 > > Can any body suggest why it is happening? no, nobody can suggest anything, on the basis of such a confused and obscure message Paolo -- Paolo Giannozzi, Democritos and Udine University From ferretti at MIT.EDU Thu Aug 13 15:00:49 2009 From: ferretti at MIT.EDU (Andrea Ferretti) Date: Thu, 13 Aug 2009 09:00:49 -0400 (EDT) Subject: [Pw_forum] DOS and pDOS parallelization In-Reply-To: <34236.172.16.1.8.1250139375.squirrel@172.16.1.8> Message-ID: Dear Madhura, > > Thanks for the explanation. > I had always thought that DOS code also requires wavefunction files; and > that is why one needs to give the same prefix and outdir path as in scf > calculations. If code does not need wavefunctions, which files it uses > for DOS calc.s? the code needs mainly the eigenvalues, which are stored in $prefix.save/K?????/eigenval.xml files, where K????? (i.e. K00001, K00002, etc ) correspond to each kpt. > As per suggestion, I have run PDOS calc.s with the same number of pools > and processors (in case of B) and got results. That means PDOS code is > parallelized with pool implementation, but not DOS. > yes you are right, this means that pDOS is parallelized over G vectors and pools, while DOS calculation is not parallelized but is anyway compatible with the parallel environment (i.e. it does not crash if run parallel) andrea > Thanks once again, > Madhura. > > > > > Dear Madhura, > > > > the issue of using the same parallelism scheme (# of processors, # of > > pools, etc) in postprocessing calculations is mainly concerned with the > > need to read wfcs. As you wrote, if you specify wf_collect = .TRUE. you > > completely remove this issue (you can read wfcs whatever the > > parallelization > > scheme you used to produce them). > > > >>From this point of view, the main difference between DOS and pDOS > > calculations is that the former does not need to read wfcs, while the > > latter does. > > > > Moreover, the taks the DOS program has to perform is so inexpensive that > > it is performed by a single processor even if the code is run in parallel. > > This is consistent with your observation at (ii). > > > > In the case of pDOS (i.e. when running projwfc.x) if you do not collect > > wfcs you should run with the same # of processors and the same pool > > parallelism. Otherwise, as you experienced, you get a davcio error > > (some of the wfcs files were not found). > > According to me, anyway, projwfc should work with pools if the above > > conditions are fulfilled. > > > > hope it helps > > andrea > > > > > >> > >> There have been many discussions in this forum about parallelization of > >> DOS and projected DOS codes. However, some of the points were not clear > >> to > >> me, so I have performed some scf calculations for a very simple system > >> using 8 processors and with flag wf_collect 'false'. I have performed > >> same > >> calculations once without use of pools (A) and then using 2 pools (B). > >> Then using theses wavefunctions I have performed DOS and PDOS > >> calculations. Following is the summary of results and my interpretation: > >> > >> i) Pool parallelization is not implemented for both these codes. > >> > >> ii) DOS calculations: for both the cases A and B, one can calculate DOS > >> with the same no. of processors (= 8) and the results match within > >> numerical errors; even though for case B, the wavefunctions were > >> obtained > >> with pooling and DOS without it. > >> For case A, even if I use 4 processors I get identical results as when > >> I > >> use 8 processors. (Note, I have not checked with less no. of proc.s for > >> B). > >> => The condition that we need the same no. of processors and pools as > >> were > >> used in scf calculations is not necessary; and it is possible to get DOS > >> results even with wavefunctions generated with pool parallelization. > >> > >> iii) PDOS calculations: This can be calculated only in case of A and > >> using > >> the same no. of processors. If I use wavefunctions generated in case B > >> or > >> less no. of processors (= 4) with A wavefn.s then I get "davcio" error. > >> => > >> For PDOS calculations, one cannot use wavefunctions generated with pool > >> parallelization unless wf_collect flag is set to 'true' for scf calc.s; > >> also one has to use the same no. of proc.s as were used for scf calc.s > >> to > >> get projected DOS. > >> > >> Now my question is are these interpretations correct? Or they may change > >> for some other system?? Do I need to do some more checks to ascertain > >> these? If yes, what sort of tests? > >> > >> Thanks for reading this long mail patiently, but I need to clarify on > >> these points before I can start with bigger systems. > >> Sincerely, > >> Madhura. > >> > >> > >> > > > > -- > > Andrea Ferretti > > MIT, Dept Material Science & Engineering > > bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA > > Tel: +1 617-452-2455; Skype: andrea_ferretti > > URL: http://quasiamore.mit.edu > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- Andrea Ferretti MIT, Dept Material Science & Engineering bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA Tel: +1 617-452-2455; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Thu Aug 13 15:03:07 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Aug 2009 15:03:07 +0200 Subject: [Pw_forum] References for damped dynamics structural minimization? In-Reply-To: <835044.69547.qm@web50905.mail.re2.yahoo.com> References: <835044.69547.qm@web50905.mail.re2.yahoo.com> Message-ID: <200908131503.07998.giannozz@democritos.it> On Tuesday 04 August 2009 16:14, J. J. Ramsey wrote: > I've been trying to find references for the damped quick-min Verlet > algorithm used by PWscf in structural relaxation (when calculation = > 'relax' and ion_dynamics = 'damp') if you find anything, please let us know P. -- Paolo Giannozzi, Democritos and Udine University From giannozz at democritos.it Thu Aug 13 15:08:58 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Aug 2009 15:08:58 +0200 Subject: [Pw_forum] runtime error In-Reply-To: References: Message-ID: <200908131508.58482.giannozz@democritos.it> On Saturday 08 August 2009 19:41, Aritz Leonardo wrote: > Any idea where to look for solutions? first of all you should look into the output, preferrably by running interactively (no redirection to a file). If no indication comes from the output: there is something wrong in your compiler/librararies. Since g95 is very good and very reliable, I would say that there is something wrong with your mpi libraries Paolo -- Paolo Giannozzi, Democritos and Udine University From giannozz at democritos.it Thu Aug 13 15:17:20 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Aug 2009 15:17:20 +0200 Subject: [Pw_forum] running the parallel code In-Reply-To: <84ff69170908081040g53f305ffuca050bfc497ff8bc@mail.gmail.com> References: <84ff69170908081040g53f305ffuca050bfc497ff8bc@mail.gmail.com> Message-ID: <200908131517.20959.giannozz@democritos.it> On Saturday 08 August 2009 19:40, vamsi kv wrote: > I want to know how to run pwscf on parallel systems with shared memory. > what type of libraries has to be used. use MPI -- Paolo Giannozzi, Democritos and Udine University From sh.shapt at gmail.com Thu Aug 13 16:10:21 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Thu, 13 Aug 2009 15:10:21 +0100 Subject: [Pw_forum] Calculation of spin polarisation in odd electrons in PWscf Message-ID: Hi QES user I want to know how does thecalculation ofspin polarisation in odd number of electrons been done in Quantum espresso, as I have odd number of eelctrons in my system which is semiconductor. Thanks Shaptarishi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090813/16c69a41/attachment.htm From degironc at sissa.it Thu Aug 13 17:59:14 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 13 Aug 2009 17:59:14 +0200 Subject: [Pw_forum] Trying to clarify the dipole correction (again!) In-Reply-To: <96033.30039.qm@web50909.mail.re2.yahoo.com> References: <96033.30039.qm@web50909.mail.re2.yahoo.com> Message-ID: <4A843852.4080303@sissa.it> Dear J.J. Ramsey at variance with what is defined in Bengtsson's paper the dipole potential is not discontinuous in QE but is defined by periodically alternating an increasing slope (associate to the "physical" electric field present in the cell) and a rapidly decreasing slope that should be located in a region of negligibly small charge density. This is done to avoid too sharp features in the calculation. The definition is also generalized so that the region where the dipole correction operates can be centered in an arbitrary point of the cell and not just in the center of it as defined in the paper. the regression region (the region with a rapidly decreasing slope) occupies a fraction eopreg of the cell size while the maximum of the increasing slope occurs at a fraction emaxpos. so if emaxpos = 0.45 and eopreg=0.1 the region where the correction is physically meaningful goes from -45% to +45% of the cell and the regression region (that should contains no charge density) occupies the central 10% of the cell. This is a good setting if you center your slab around the origin. if instead emaxpos=0.95 and eopreg=0.1 the the dipole correction is applied for +5% to +95% of the cell while in the rest one have the regression region. this is OK if you put your slab in the center of the cell. Stefano de Gironcoli - SISSA and DEMOCRITOS J. J. Ramsey wrote: > In the reference on the dipole correction used in QE, L. Bengtsson, PRB 59, 12301 (1999), the dipole potential is given as > > V_dip(z) = 4*pi*m*(z/z_m - 0.5), 0 < z < z_m > > where z_m is the height of the box, and there is a discontinuity in the potential at z = 0,z_m. I'm not sure how this fits into the QE documentation on the dipole correction. Is V_dip in QE supposed to be something like this?: > > V_dip(z) = 4*pi*m*[z/z_m - (emaxpos + eopreg -1)], emaxpos + eopreg -1 < z/z_m < emaxpos; > = something with a steep but finite slope, otherwise > > My guess is probably wrong, but the explanations in the documentation of the roles of emaxpos and eopreg appear to be tied to the case where eamp is nonzero. I'm not sure if the documentation for the dipfield variable is supposed to indicate that the actual slope of the potential is supposed to be eamp + 4*pi*m/z_m. > > University of Akron > Civil Engineering (!) Dept. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From madhura at jncasr.ac.in Thu Aug 13 19:06:02 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Thu, 13 Aug 2009 22:36:02 +0530 (IST) Subject: [Pw_forum] DOS and pDOS parallelization In-Reply-To: References: <34236.172.16.1.8.1250139375.squirrel@172.16.1.8> Message-ID: <43260.172.16.1.8.1250183162.squirrel@172.16.1.8> Thanks for the explanation. That was really helpful. -Madhura > > Dear Madhura, > >> >> Thanks for the explanation. >> I had always thought that DOS code also requires wavefunction files; >> and >> that is why one needs to give the same prefix and outdir path as in scf >> calculations. If code does not need wavefunctions, which files it uses >> for DOS calc.s? > > the code needs mainly the eigenvalues, which are stored in > $prefix.save/K?????/eigenval.xml files, > where K????? (i.e. K00001, K00002, etc ) correspond to each kpt. > > >> As per suggestion, I have run PDOS calc.s with the same number of pools >> and processors (in case of B) and got results. That means PDOS code is >> parallelized with pool implementation, but not DOS. >> > > yes you are right, > this means that pDOS is parallelized over G vectors and pools, while > DOS calculation is not parallelized but is anyway compatible with > the parallel environment (i.e. it does not crash if run parallel) > > andrea > >> Thanks once again, >> Madhura. >> >> > >> > Dear Madhura, >> > >> > the issue of using the same parallelism scheme (# of processors, # of >> > pools, etc) in postprocessing calculations is mainly concerned with >> the >> > need to read wfcs. As you wrote, if you specify wf_collect = .TRUE. >> you >> > completely remove this issue (you can read wfcs whatever the >> > parallelization >> > scheme you used to produce them). >> > >> >>From this point of view, the main difference between DOS and pDOS >> > calculations is that the former does not need to read wfcs, while the >> > latter does. >> > >> > Moreover, the taks the DOS program has to perform is so inexpensive >> that >> > it is performed by a single processor even if the code is run in >> parallel. >> > This is consistent with your observation at (ii). >> > >> > In the case of pDOS (i.e. when running projwfc.x) if you do not >> collect >> > wfcs you should run with the same # of processors and the same pool >> > parallelism. Otherwise, as you experienced, you get a davcio error >> > (some of the wfcs files were not found). >> > According to me, anyway, projwfc should work with pools if the above >> > conditions are fulfilled. >> > >> > hope it helps >> > andrea >> > >> > >> >> >> >> There have been many discussions in this forum about parallelization >> of >> >> DOS and projected DOS codes. However, some of the points were not >> clear >> >> to >> >> me, so I have performed some scf calculations for a very simple >> system >> >> using 8 processors and with flag wf_collect 'false'. I have performed >> >> same >> >> calculations once without use of pools (A) and then using 2 pools >> (B). >> >> Then using theses wavefunctions I have performed DOS and PDOS >> >> calculations. Following is the summary of results and my >> interpretation: >> >> >> >> i) Pool parallelization is not implemented for both these codes. >> >> >> >> ii) DOS calculations: for both the cases A and B, one can calculate >> DOS >> >> with the same no. of processors (= 8) and the results match within >> >> numerical errors; even though for case B, the wavefunctions were >> >> obtained >> >> with pooling and DOS without it. >> >> For case A, even if I use 4 processors I get identical results as >> when >> >> I >> >> use 8 processors. (Note, I have not checked with less no. of proc.s >> for >> >> B). >> >> => The condition that we need the same no. of processors and pools as >> >> were >> >> used in scf calculations is not necessary; and it is possible to get >> DOS >> >> results even with wavefunctions generated with pool parallelization. >> >> >> >> iii) PDOS calculations: This can be calculated only in case of A and >> >> using >> >> the same no. of processors. If I use wavefunctions generated in case >> B >> >> or >> >> less no. of processors (= 4) with A wavefn.s then I get "davcio" >> error. >> >> => >> >> For PDOS calculations, one cannot use wavefunctions generated with >> pool >> >> parallelization unless wf_collect flag is set to 'true' for scf >> calc.s; >> >> also one has to use the same no. of proc.s as were used for scf >> calc.s >> >> to >> >> get projected DOS. >> >> >> >> Now my question is are these interpretations correct? Or they may >> change >> >> for some other system?? Do I need to do some more checks to ascertain >> >> these? If yes, what sort of tests? >> >> >> >> Thanks for reading this long mail patiently, but I need to clarify on >> >> these points before I can start with bigger systems. >> >> Sincerely, >> >> Madhura. >> >> >> >> >> >> >> > >> > -- >> > Andrea Ferretti >> > MIT, Dept Material Science & Engineering >> > bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA >> > Tel: +1 617-452-2455; Skype: andrea_ferretti >> > URL: http://quasiamore.mit.edu >> > >> > Please, if possible, don't send me MS Word or PowerPoint attachments >> > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> > > -- > Andrea Ferretti > MIT, Dept Material Science & Engineering > bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA > Tel: +1 617-452-2455; Skype: andrea_ferretti > URL: http://quasiamore.mit.edu > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From kondor.jess at gmail.com Thu Aug 13 20:18:23 2009 From: kondor.jess at gmail.com (Jess Kondor) Date: Thu, 13 Aug 2009 14:18:23 -0400 Subject: [Pw_forum] compile error, pathscale compiler Message-ID: <1d9d5d9d0908131118p120fadd0k8a139669a13a604c@mail.gmail.com> hello all, I use pathscale compiler (3.2) to compiler q-e, v.4.1. I got this error message: mpif90 -O2 -OPT:Olimit=0 -ftpp -march=opteron -D__EKO -D__FFTW3 -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c mp_base.f90 CALL synchronize( gid ) ^ pathf95-700 pathf90: ERROR BCAST_REAL, File = mp_base.f90, Line = 62, Column = 14 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( gid ) ^ pathf95-700 pathf90: ERROR BCAST_INTEGER, File = mp_base.f90, Line = 111, Column = 14 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( gid ) ^ pathf95-700 pathf90: ERROR BCAST_LOGICAL, File = mp_base.f90, Line = 157, Column = 14 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR REDUCE_BASE_REAL, File = mp_base.f90, Line = 252, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR REDUCE_BASE_INTEGER, File = mp_base.f90, Line = 383, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR REDUCE_BASE_REAL_TO, File = mp_base.f90, Line = 484, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR REDUCE_BASE_INTEGER_TO, File = mp_base.f90, Line = 572, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR PARALLEL_MIN_INTEGER, File = mp_base.f90, Line = 660, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR PARALLEL_MAX_INTEGER, File = mp_base.f90, Line = 756, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR PARALLEL_MIN_REAL, File = mp_base.f90, Line = 851, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. CALL synchronize( comm ) ^ pathf95-700 pathf90: ERROR PARALLEL_MAX_REAL, File = mp_base.f90, Line = 947, Column = 8 The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. pathf95: PathScale(TM) Fortran Version 3.2 (f14) Thu Aug 13, 2009 10:14:01 pathf95: 1277 source lines pathf95: 11 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) pathf95: "explain pathf95-message number" gives more information about each message make[1]: *** [mp_base.o] Error 2 Unfortunately, I don't know fortran very well, so I cannot figure it out what is wrong. BTW, pgi compiler can compile this module. -- ===================================== Jess Kondor NSTI, PhD ===================================== From giannozz at democritos.it Thu Aug 13 21:31:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Aug 2009 21:31:57 +0200 Subject: [Pw_forum] compile error, pathscale compiler In-Reply-To: <1d9d5d9d0908131118p120fadd0k8a139669a13a604c@mail.gmail.com> References: <1d9d5d9d0908131118p120fadd0k8a139669a13a604c@mail.gmail.com> Message-ID: <200908132131.57035.giannozz@democritos.it> On Thursday 13 August 2009 20:18, Jess Kondor wrote: > CALL synchronize( gid ) > ^ > pathf95-700 pathf90: ERROR BCAST_REAL, File = mp_base.f90, Line = 62, > Column = 14 > The intrinsic call "SYNCHRONIZE" is being made with illegal arguments. apparently some genius working at pathscale has decided that "synchronize" is a nice name for an intrinsic function. Define it external or change the routine name. P. -- Paolo Giannozzi, Democritos and Udine University From baroni at sissa.it Thu Aug 13 21:04:17 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 13 Aug 2009 21:04:17 +0200 Subject: [Pw_forum] negative (alpha)^2*F(w) In-Reply-To: <3423.40785.qm@web51808.mail.re2.yahoo.com> References: <3423.40785.qm@web51808.mail.re2.yahoo.com> Message-ID: <6ACB7B0F-ED4A-461F-90E0-6D2054827EDE@sissa.it> As discussed, many times in this forum, as well as in many textbooks, negative squared ferquencies are a signal of a mechanical instability. Are you sure that you want to spend a lot of computer resources calculating the supercondictive properties of an instable (and, hence, non-existent unless very special conditions occur) system? SB --- swift text written and sent on the go On 13/ago/2009, at 11.00, Ali Tavana wrote: > Dear QE users, > > I have a question about e-ph lambda, calculated by "matdyn" program. > I've found that for some frequencies the quantity "(alpha)^2*F(w)/w" > or "dos_a2F(w)/w" can be negative, most probably because of the > negative (imaginary) frequencies (I can't believe a2F(w) become > negative!). In "matdyn" program these negative values are considered > in lambda calculations. Should one remove these negative values as > these imaginary frequency modes can never exist in the system? then > where are those phonon branches? I think negative values of > frequency can show in some manner more strong electron structure > interaction, so what do you suggest one should do? > > regards, > Ali > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From asafis at yahoo.com.br Thu Aug 13 22:30:41 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Thu, 13 Aug 2009 13:30:41 -0700 (PDT) Subject: [Pw_forum] scf Message-ID: <51554.45053.qm@web52301.mail.re2.yahoo.com> Hello I am doing a scf calculation system and uses degauss = 0.003 and needed change it paar 0001. With this new value, the calculation does not converge. What may be happening? Regards, Alvaro ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090813/883fbee6/attachment.htm From spmmal at gmail.com Thu Aug 13 22:38:06 2009 From: spmmal at gmail.com (spmmal) Date: Thu, 13 Aug 2009 16:38:06 -0400 Subject: [Pw_forum] scf In-Reply-To: <51554.45053.qm@web52301.mail.re2.yahoo.com> References: <51554.45053.qm@web52301.mail.re2.yahoo.com> Message-ID: <4A8479AE.5040901@gmail.com> ?lvaro Alves wrote: > Hello I am doing a scf calculation system and uses degauss = 0.003 and > needed change it paar 0001. With this new value, the calculation does > not converge. What may be happening? > > Regards, Alvaro > > > > ------------------------------------------------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 > > - Celebridades > > - M?sica > > - Esportes > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Is there any general rule of setting parameters to make the SCF calculation converge. Thanks. From asafis at yahoo.com.br Thu Aug 13 23:43:15 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Thu, 13 Aug 2009 14:43:15 -0700 (PDT) Subject: [Pw_forum] scf In-Reply-To: <51554.45053.qm@web52301.mail.re2.yahoo.com> Message-ID: <762020.77023.qm@web52307.mail.re2.yahoo.com> Hello. I am doing a scf calculation system and uses degauss = 0.003 and needed change it? for 0001. With this new value, the calculation does not converge. What may be happening?? Regards, Alvaro A. S. Santos --- Em qui, 13/8/09, ?lvaro Alves escreveu: De: ?lvaro Alves Assunto: [Pw_forum] scf Para: "pw" Data: Quinta-feira, 13 de Agosto de 2009, 17:30 Hello I am doing a scf calculation system and uses degauss = 0.003 and needed change it paar 0001. With this new value, the calculation does not converge. What may be happening? Regards, Alvaro Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes -----Anexo incorporado----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090813/5b6243c3/attachment.htm From eyvaz_isaev at yahoo.com Thu Aug 13 23:45:33 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 13 Aug 2009 14:45:33 -0700 (PDT) Subject: [Pw_forum] scf Message-ID: <575265.89108.qm@web65715.mail.ac4.yahoo.com> Dear Alvaro, --- On Fri, 8/14/09, spmmal wrote: >> Hello I am doing a scf calculation system and uses? degauss = 0.003 >> and? needed change it paar 0001. With this new value, the calculation >> does? not converge. What may be happening? ? > Is there any general rule of setting parameters to make the > SCF calculation? converge. Thanks. First of all, you shoud follow general Netiquette accepted in this forum: provide your affiliation. Then the best choice (or a general rule) is the use of default parameters. See /Doc/PW.txt file and example files. Change default value if you know what you are doing. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From eyvaz_isaev at yahoo.com Thu Aug 13 23:54:46 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 13 Aug 2009 14:54:46 -0700 (PDT) Subject: [Pw_forum] scf In-Reply-To: <762020.77023.qm@web52307.mail.re2.yahoo.com> Message-ID: <410482.51897.qm@web65704.mail.ac4.yahoo.com> I am not sure convergence may depend on degauss value. To avoid this choice you can use "tetrahedra' method. Did you check your system by XCrysDen? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/14/09, ?lvaro Alves wrote: > From: ?lvaro Alves > Subject: Re: [Pw_forum] scf > To: "PWSCF Forum" > Date: Friday, August 14, 2009, 1:43 AM > Hello. > I am doing a scf calculation system and uses degauss = 0.003 > and > needed change it? for 0001. With this new value, the > calculation does > not converge. What may be happening?? > > > Regards, Alvaro > > A. S. Santos > > --- Em qui, 13/8/09, ?lvaro Alves > escreveu: > > De: ?lvaro Alves > Assunto: [Pw_forum] scf > Para: "pw" > Data: Quinta-feira, 13 de Agosto de 2009, 17:30 > > Hello I am doing a scf calculation system and > uses degauss = 0.003 and > needed change it paar 0001. With this new value, the > calculation does > not converge. What may be happening? > > > Regards, Alvaro > > > > > > > Veja quais s?o os assuntos do momento > no Yahoo! + Buscados: Top > 10 - Celebridades > - M?sica > - Esportes > -----Anexo incorporado----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > Veja quais s?o os assuntos do momento > no Yahoo! + Buscados: Top > 10 - Celebridades > - M?sica > - Esportes > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Fri Aug 14 02:35:22 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 13 Aug 2009 17:35:22 -0700 (PDT) Subject: [Pw_forum] Frequency and zero point energy calculations In-Reply-To: <26935521.319391250156234372.JavaMail.coremail@bj126app81.126.com> Message-ID: <12078.70190.qm@web65709.mail.ac4.yahoo.com> Dear Lihui, >?performing calulation of frequency and zero point > energy of CO2 molecule. However, unfortunately, I have > obtained?negative frequency. > there are several possible reseaons: Well, you did not include one more reason counting them: there is a physical reason for this as you consider CO2 molecule (the linear chain). Obviously, its physical properties do not change if you rotate it fixing C atom in the cell center. This might lead to negative frequencies. If you like to consider CO2 as a molecule you should use the Gamma point only (i.e. you consider CO2 in a big box). > In addition, I intend to calculate the zero point > energy of system by PHNONS code, but it does not give the > zero point energy and other thermodynamics properties in > output file. How could I do? I need your help > urgently. PH code itself does not calculate these properties. You can try download the QHA code from qe-forge.org. If some troubles with this, please let me know. > I need your help urgently. Please keep in mind our forum consists of volunteers and nobody is oblidged to give you urgent reply. Bests, Eyvaz. P.S. Can you please show eigendisplacements? ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From jjr19 at uakron.edu Fri Aug 14 03:53:24 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Thu, 13 Aug 2009 18:53:24 -0700 (PDT) Subject: [Pw_forum] Trying to clarify the dipole correction (again!) In-Reply-To: <4A843852.4080303@sissa.it> References: <96033.30039.qm@web50909.mail.re2.yahoo.com> <4A843852.4080303@sissa.it> Message-ID: <802446.63063.qm@web50904.mail.re2.yahoo.com> ----- Original Message ---- > From: Stefano de Gironcoli > To: PWSCF Forum > Sent: Thursday, August 13, 2009 11:59:14 AM > Subject: Re: [Pw_forum] Trying to clarify the dipole correction (again!) > > Dear J.J. Ramsey > > at variance with what is defined in Bengtsson's paper the dipole > potential is not discontinuous in QE but is defined by periodically > alternating an increasing slope (associate to the "physical" electric > field present in the cell) and a rapidly decreasing slope that should > be located in a region of negligibly small charge density. This is done > to avoid too sharp features in the calculation. In other words, the discontinuity in Bengtsson's paper, where the slope is infinite, is replaced by a large but finite slope. > so if emaxpos = 0.45 and eopreg=0.1 the region where the correction > is physically meaningful goes from -45% to +45% of the cell and the > regression region (that should contains no charge density) occupies > the central 10% of the cell. This is a good setting if you center your > slab around the origin. I gather you mean the case where the slab is near the bottom of the unit cell. From baroni at sissa.it Fri Aug 14 07:48:28 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 14 Aug 2009 07:48:28 +0200 Subject: [Pw_forum] scf In-Reply-To: <51554.45053.qm@web52301.mail.re2.yahoo.com> References: <51554.45053.qm@web52301.mail.re2.yahoo.com> Message-ID: <95177CEB-E10F-4818-A4BA-966771674BA2@sissa.it> Alvaro: > Hello I am doing a scf calculation system and uses degauss = 0.003 i.e. 40 mev > and needed change it paar 0001. i.e. 1.3 mev, very small indeed > With this new value, the calculation does not converge. What may be > happening? I can only imagine you are using Gaussian smearing for an isolated molecule with a degenerate HOMO. the degeneracy is split by the low summetry imposed by the supercell, and the electronic structure oscillates between the two (or more) states corresponding to each partner of the multiplet. when you use a decent gaussian smearing, the code makes an average among the degenerate states and it converges. when the smearing is instead indecently small, it does not ... As you see, from the poor information you are providing, I can only guess. Why don't you provide a few bits of imformation, rather than trusting our clairvoyance? > Regards, Alvaro I understand that you think we can read your thoughts, but we cannot ... and, as you know, we would also like to know the identity of those we correspon to in this forum. In the future, please provide your complete identity, including your affiliation. Thanks - Stefano --- 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 From baroni at sissa.it Fri Aug 14 07:49:26 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 14 Aug 2009 07:49:26 +0200 Subject: [Pw_forum] scf In-Reply-To: <4A8479AE.5040901@gmail.com> References: <51554.45053.qm@web52301.mail.re2.yahoo.com> <4A8479AE.5040901@gmail.com> Message-ID: <3599A3E8-FD92-4795-BDE4-2F3C3C11DD41@sissa.it> On Aug 13, 2009, at 10:38 PM, spmmal wrote: > Is there any general rule of setting parameters to make the SCF > calculation converge. Thanks. experience, hard work, common sense 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/20090814/0600f411/attachment.htm From bipulrr at gmail.com Fri Aug 14 07:55:23 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Fri, 14 Aug 2009 11:25:23 +0530 Subject: [Pw_forum] matdyn error Message-ID: <3a749910908132255x13311317j4eb55858c46affe0@mail.gmail.com> Dear pwscf users, I am doing Gamma point phonon analysis for LaMnO3, after running matdyn.x i am getting the following, error. Norm of the difference between old and new effective charges: 0.00000000000000000000 Norm of the difference between old and new force-constants: 0.20461738165775616993 0.833333333333333 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from frc_blk : error # 1 wrong total_weight %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... 2 Since at gamma point i am getting some -ve freq. the sum rule i want to apply. And to see the final frequencies after applying sum rule. Kindly guide me and suggest for the possible reason for this error. -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... 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Name: matdyn.in Type: application/octet-stream Size: 280 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0002.obj From hqzhou at nju.edu.cn Fri Aug 14 07:50:16 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Fri, 14 Aug 2009 13:50:16 +0800 Subject: [Pw_forum] scf References: <762020.77023.qm@web52307.mail.re2.yahoo.com> Message-ID: <81E29F70776F4174900188380550A47A@solarflare> Alvaro, I think you need to test total energy or total magnetization against degauss, the value of degauss should be small enough to make total energy converge. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: ?lvaro Alves To: PWSCF Forum Sent: Friday, August 14, 2009 5:43 AM Subject: Re: [Pw_forum] scf Hello. I am doing a scf calculation system and uses degauss = 0.003 and needed change it for 0001. With this new value, the calculation does not converge. What may be happening? Regards, Alvaro A. S. Santos --- Em qui, 13/8/09, ?lvaro Alves escreveu: De: ?lvaro Alves Assunto: [Pw_forum] scf Para: "pw" Data: Quinta-feira, 13 de Agosto de 2009, 17:30 Hello I am doing a scf calculation system and uses degauss = 0.003 and needed change it paar 0001. With this new value, the calculation does not converge. What may be happening? Regards, Alvaro ---------------------------------------------------------------------- Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes -----Anexo incorporado----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ------------------------------------------------------------------------------ Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes ------------------------------------------------------------------------------ _______________________________________________ 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/20090814/e9a7e156/attachment.htm From anavat_ila at yahoo.com Fri Aug 14 08:53:44 2009 From: anavat_ila at yahoo.com (Ali Tavana) Date: Thu, 13 Aug 2009 23:53:44 -0700 (PDT) Subject: [Pw_forum] negative a2F(w)/w In-Reply-To: Message-ID: <396384.6019.qm@web51805.mail.re2.yahoo.com> I know my system is instable, but calculation for the stable systems takes 160 days for each q point on a 8 core machine!! In the other hand some people have published a Nature article about the superconductive properties calculation of that instable system with your code. Any way, thank you for your answer. > > As discussed, many times in this forum, as well as in many > textbooks,? > negative squared ferquencies are a signal of a mechanical > instability.? > Are you sure that you want to spend a lot of computer > resources? > calculating the supercondictive properties of an instable > (and, hence,? > non-existent unless very special conditions occur) system? > SB > From sclauzer at sissa.it Fri Aug 14 10:26:09 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 14 Aug 2009 10:26:09 +0200 Subject: [Pw_forum] Frequency and zero point energy calculations In-Reply-To: <26935521.319391250156234372.JavaMail.coremail@bj126app81.126.com> References: <26935521.319391250156234372.JavaMail.coremail@bj126app81.126.com> Message-ID: <4A851FA1.6050708@sissa.it> Dear Lihui Ou, oulihui666 wrote: > Dear all, > Recently, I have been performing calulation of frequency and zero > point energy of CO2 molecule. However, unfortunately, I have > obtained negative frequency. According to the manual, there are several > ibrav = 1, > celldm(1) = 15.11781502, This seems too small. You want to avoid spurious interactions between periodic replicas of the molecule. > nat = 3, > ntyp = 2, > ecutwfc = 26 , > ecutrho = 260 , These cut-offs may also be too small. C and O have 2p electrons which are hard to deal with PWs, even with US PPs. > occupations = 'smearing' , > degauss = 0.02 , This is too large for a molecule, you can use much smaller values. > &ELECTRONS > conv_thr = 1.D-12 , This requirement may be too strict. Anyway, if you don't have problems in convergence you can keep it as it is. > (2) Performing scf calculations: > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/olh/tmp/' , > pseudo_dir = '/home/olh/pseudo/' , > prefix = 'CO2' , > / > &SYSTEM > ibrav = 1, > celldm(1) = 15.11781502, > nat = 3, > ntyp = 2, > ecutwfc = 26 , > ecutrho = 260 , > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'methfessel-paxton' , > nspin = 2 , > starting_magnetization(1) = 0.5, > starting_magnetization(2) = 0.5, > / > &ELECTRONS > conv_thr = 1.D-12 , > mixing_beta = 0.4D0 , > / > ATOMIC_SPECIES > C 12.01100 C.pbe-rrkjus.UPF > O 15.99940 O.pbe-rrkjus.UPF > ATOMIC_POSITIONS angstrom > C 4.000000000 4.000000000 4.000000000 0 0 0 > O 5.172018724 4.000000000 4.000000000 0 0 0 > O 2.827981276 4.000000000 4.000000000 0 0 0 > K_POINTS automatic > 16 16 16 1 1 1 Maybe I don't understand what you want to calculate, but I don't see any need of a k-point sampling when computing an isolated molecule. Why don't you use gamma as in the relax calculation? > > (3) Performing frequency calculation using PHONOS codes: > phonons of CO2 at Gamma > &inputph > tr2_ph=1.0d-20, This is very strict! > prefix='CO2', > epsil=.false., > amass(1)=12.0110, > amass(2)=15.9994, > outdir='/home/olh/tmp/', > fildyn='CO2.dynG', > / > 0.0 0.0 0.0 > Finally, I obtained the frequency of CO2 molecule, output file as follows: > Convergence has been achieved > Number of q in the star = 1 > List of q in the star: > 1 0.000000000 0.000000000 0.000000000 > Diagonalizing the dynamical matrix > q = ( 0.000000000 0.000000000 0.000000000 ) > ************************************************************************** > omega( 1) = -3.661345 [THz] = -122.130124 [cm-1] > omega( 2) = -3.661345 [THz] = -122.130124 [cm-1] > omega( 3) = 3.659957 [THz] = 122.083850 [cm-1] > omega( 4) = 7.879986 [THz] = 262.849774 [cm-1] > omega( 5) = 7.879986 [THz] = 262.849774 [cm-1] > omega( 6) = 19.746862 [THz] = 658.688787 [cm-1] > omega( 7) = 19.746862 [THz] = 658.688787 [cm-1] > omega( 8) = 38.945041 [THz] = 1299.075383 [cm-1] > omega( 9) = 70.000609 [THz] = 2334.984491 [cm-1] > ************************************************************************** > Mode symmetry, D_4h(4/mmm) point group: > omega( 1 - 2) = -122.1 [cm-1] --> E_g X_5 M_5 R > omega( 3 - 3) = 122.1 [cm-1] --> A_2u X_4' M_4' I > omega( 4 - 5) = 262.8 [cm-1] --> E_u X_5' M_5' I > omega( 6 - 7) = 658.7 [cm-1] --> E_u X_5' M_5' I > omega( 8 - 8) = 1299.1 [cm-1] --> A_1g X_1 M_1 R > omega( 9 - 9) = 2335.0 [cm-1] --> A_2u X_4' M_4' I > ************************************************************************** > PHONON : 1h48m CPU time, 2h25m wall time > ...... > There are still negative frequency in output file by increasing K_POINTS > and reducing tr2_ph, anyone who help me will be appreciated. Increasing the number of k-points won't help you, obviously... the first three frequencies should be zero, since they are associated to translational modes of the barycenter of the molecule. They come out non-zero for the convergence issues you mentioned in your mail. You can enforce acoustic sum rules with the appropriate flags in the input (see Doc/INPUT_PH.txt). Anyway, I don't think you need a phonon calculation to compute the energy associated to the translational motion. You should pay attention only at the other frequencies. > In addition, I intend to calculate the zero point energy of system by > PHNONS code, but it does not give the zero point energy and other > thermodynamics properties in output file. How could I do? I need your > help urgently. No comment... Cheers, GS > > Thanks in advance > Best regards > Lihui > > -- > ====================================== > Lihui Ou > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,/430072/,Hubei Province,China > /E-mail:oulihui666 at 126.com / > ====================================== > > > ------------------------------------------------------------------------ > ???????????,www.yeah.net > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ntcuong at jaist.ac.jp Fri Aug 14 10:44:40 2009 From: ntcuong at jaist.ac.jp (Nguyen Thanh Cuong) Date: Fri, 14 Aug 2009 17:44:40 +0900 Subject: [Pw_forum] PAW pseudo-potential for Al and Ni References: <51554.45053.qm@web52301.mail.re2.yahoo.com> <95177CEB-E10F-4818-A4BA-966771674BA2@sissa.it> Message-ID: <9D7727CF644140E58D63C9B187A343BD@hjkc> Dear pwscf users, Does anyone have generated the paw pseudo-potentials for Al and Ni with ld1 code? Would you share the ld1 input files? Thank you in advance for your helps. Best regards, Nguyen Thanh Cuong Phd student School of Materials Science Japan Advanced Institute of Science and Technology From degironc at sissa.it Fri Aug 14 11:08:25 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 14 Aug 2009 11:08:25 +0200 Subject: [Pw_forum] scf In-Reply-To: <51554.45053.qm@web52301.mail.re2.yahoo.com> References: <51554.45053.qm@web52301.mail.re2.yahoo.com> Message-ID: <4A852989.2050603@sissa.it> dear Alvaro 0.003 Ry is about 50 meV ... a very small value, and 0.001 is even smaller. this will require almost and infinity of k-points in order to obtain converged results... and such a small value may make scf convergence very difficult (unless very many k-points are used) because from one iteration to the next the occupation of levels can suddenly change in a non-linear way making the mixing scheme ineffective... are you sure you need such a small value of degauss ? stefano de Gironcoli - SISSA and DEMOCRITOS ?lvaro Alves wrote: > Hello I am doing a scf calculation system and uses degauss = 0.003 and > needed change it paar 0001. With this new value, the calculation does > not converge. What may be happening? > > Regards, Alvaro > > > > ------------------------------------------------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 > > - Celebridades > > - M?sica > > - Esportes > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From dimpy.sharma at tyndall.ie Fri Aug 14 11:43:26 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Fri, 14 Aug 2009 10:43:26 +0100 Subject: [Pw_forum] Calculation of spin polarisation from PWscf Message-ID: Hi there, I want to know how do we perform calculation for spin polarisation in PWscf, as I have odd number of electrons in my system. However I have one more thing to ask, in my previous system as I already wrote charge is wrong apperedin the output, but in that system there are even number of electrons, so is their any other probable reason? Can anybody help? Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/fab6c3db/attachment.htm From decboy9 at gmail.com Fri Aug 14 13:15:44 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 14 Aug 2009 16:45:44 +0530 Subject: [Pw_forum] ban band number Message-ID: Hi 2 All, I was trying to calculate optical properties of my system using Epsilon.x. After Scf, when i run espilon it gave error Performing eps calculation... %%%%%%%%%%%%%%%%%%%%%%%% from epsilon : error # 1 ban band number %%%%%%%%%%%%%%%%%%%%%%%% stopping .. Please help and guide me , what does at mean and what is the possible solution. ??? Thanks in advance Dev sharma, University of Delhi, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/633105b9/attachment.htm From degironc at sissa.it Fri Aug 14 13:32:12 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 14 Aug 2009 13:32:12 +0200 Subject: [Pw_forum] ban band number In-Reply-To: References: Message-ID: <4A854B3C.7040708@sissa.it> grep -e "ban band" */*.f90 returns the following: PP/epsilon.f90: IF ( REAL(nbnd, DP) <= nelec / 2.0_DP ) CALL errore('epsilon', 'ban band number', 1) I guess that this means you specified a too small value for nbnd. I also guess that "ban" is a mispelling for "bad" stefano dev sharma wrote: > Hi 2 All, > > I was trying to calculate optical properties of my system using > Epsilon.x. After Scf, when i run espilon it gave error > Performing eps calculation... > > %%%%%%%%%%%%%%%%%%%%%%%% > from epsilon : error # 1 > ban band number > %%%%%%%%%%%%%%%%%%%%%%%% > > stopping .. > > Please help and guide me , what does at mean and what is the possible > solution. ??? > Thanks in advance > > Dev sharma, > University of Delhi, > India > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From lanhaiping at gmail.com Fri Aug 14 13:33:51 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 14 Aug 2009 19:33:51 +0800 Subject: [Pw_forum] Calculation of spin polarisation from PWscf In-Reply-To: References: Message-ID: Hi, Dimpy! I think it is a well repeated question if you pay more attention to previous messages or userguide. As described in $QE/Doc/INPUT_PW.html: ' nspin INTEGER *Default:* 1 nspin = 1 : non-polarized calculation (default) nspin = 2 : spin-polarized calculation, LSDA (magnetization along z axis) nspin = 4 : spin-polarized calculation, noncollinear (magnetization in generic direction) DO NOT specify nspin in this case; specify "noncolin=.TRUE." instead Hope it helps P.S. Please provide your affiliation as it is the basic Netiquette of QE community . Regards On Fri, Aug 14, 2009 at 5:43 PM, Dimpy Sharma wrote: > > Hi there, > > I want to know how do we perform calculation for spin polarisation in > PWscf, as I have odd number of electrons in my system. However I have one > more thing to ask, in my previous system as I already wrote charge is wrong > apperedin the output, but in that system there are even number of electrons, > so is their any other probable reason? > > Can anybody help? > > Dimpy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/ad128d8c/attachment.htm From degironc at sissa.it Fri Aug 14 15:36:51 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 14 Aug 2009 15:36:51 +0200 Subject: [Pw_forum] Trying to clarify the dipole correction (again!) In-Reply-To: <802446.63063.qm@web50904.mail.re2.yahoo.com> References: <96033.30039.qm@web50909.mail.re2.yahoo.com> <4A843852.4080303@sissa.it> <802446.63063.qm@web50904.mail.re2.yahoo.com> Message-ID: <4A856873.3010500@sissa.it> J. J. Ramsey wrote: > ----- Original Message ---- > > >> From: Stefano de Gironcoli >> To: PWSCF Forum >> Sent: Thursday, August 13, 2009 11:59:14 AM >> Subject: Re: [Pw_forum] Trying to clarify the dipole correction (again!) >> >> Dear J.J. Ramsey >> >> at variance with what is defined in Bengtsson's paper the dipole >> potential is not discontinuous in QE but is defined by periodically >> alternating an increasing slope (associate to the "physical" electric >> field present in the cell) and a rapidly decreasing slope that should >> be located in a region of negligibly small charge density. This is done >> to avoid too sharp features in the calculation. >> > > In other words, the discontinuity in Bengtsson's paper, where the slope is infinite, is replaced by a large but finite slope. > yes >> so if emaxpos = 0.45 and eopreg=0.1 the region where the correction >> is physically meaningful goes from -45% to +45% of the cell and the >> regression region (that should contains no charge density) occupies >> the central 10% of the cell. This is a good setting if you center your >> slab around the origin. >> > > I gather you mean the case where the slab is near the bottom of the unit cell. > or centered around the origin like in the the Al(001) surface of example03.. remember that we have periodic boundary conditions and the origin does not have any special meaning. stefano From mastermik at gmail.com Fri Aug 14 16:13:46 2009 From: mastermik at gmail.com (Mikiyas Tsegaye) Date: Fri, 14 Aug 2009 10:13:46 -0400 Subject: [Pw_forum] matdyn error In-Reply-To: References: Message-ID: Dear Rakshit, I'm just copy pasting from a previous answer in the forum to the same question: it might help, it might not. Hello, Assuming that there are no problems of numerical inaccuracy or inadequate convergence thresholds, negative frequencies at gamma point in a geometry-relaxed system usually mean that (within the system and the calculation method used) there is some distortion (decreasing the symmetry of the system) which leads to lower energy, i.e. you are at a saddle point in the energy hypersurface. You must move some atom out of the initial symmetry and optimize geometry again starting from that modified situation. If you can obtain the vector coordinates for the normal mode of vibration corresponding to the negative frequency, a displacement of the involved atoms, proportional to that normal mode, by e.g. a maximum of 0.2 angstrom will give to you a starting displaced geometry closer to the true energy minimum. Sometimes you need to do this several times if not all of the negative frequencies disappear after the first attempt. If, after obtaining a new geometry with no negative frequencies at the gamma point, you still have negative frequencies at other BZ points, this means that your system is unstable against some atomic displacements that multiply some of the primitive cell vectors by e.g. 2 or 3, leading to a supercell. Curing this situation may be more tedious. Good luck, Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 > > > Message: 3 > Date: Fri, 14 Aug 2009 11:25:23 +0530 > From: Bipul Rakshit > Subject: [Pw_forum] matdyn error > To: PWSCF Forum > Message-ID: > <3a749910908132255x13311317j4eb55858c46affe0 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear pwscf users, > > I am doing Gamma point phonon analysis for LaMnO3, after running > matdyn.x i > am getting the following, error. > > Norm of the difference between old and new effective charges: > 0.00000000000000000000 > Norm of the difference between old and new force-constants: > 0.20461738165775616993 > 0.833333333333333 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > from frc_blk : error # 1 > wrong total_weight > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > stopping ... > 2 > > Since at gamma point i am getting some -ve freq. the sum rule i want > to > apply. And to see the final frequencies after applying sum rule. > > Kindly guide me and suggest for the possible reason for this error. > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0001.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: lamno3.ph.in > Type: application/octet-stream > Size: 316 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0003.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: q2r.in > Type: application/octet-stream > Size: 71 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0004.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: matdyn.in > Type: application/octet-stream > Size: 280 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0005.obj > > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/0d9b7726/attachment.htm From giannozz at democritos.it Fri Aug 14 17:36:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Aug 2009 17:36:53 +0200 Subject: [Pw_forum] matdyn error In-Reply-To: <3a749910908132255x13311317j4eb55858c46affe0@mail.gmail.com> References: <3a749910908132255x13311317j4eb55858c46affe0@mail.gmail.com> Message-ID: <200908141736.53374.giannozz@democritos.it> On Friday 14 August 2009 07:55, Bipul Rakshit wrote: > I am doing Gamma point phonon analysis for LaMnO3, > after running matdyn.x i am getting the following, error. you calculated phonons at q=0 only, so all you can and should do is to run dynmat.x (not matdyn.x) to apply the acoustic sum rule and to calculate lo-to splitting. Paolo -- Paolo Giannozzi, Democritos and Udine University From giannozz at democritos.it Fri Aug 14 17:57:01 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Aug 2009 17:57:01 +0200 Subject: [Pw_forum] line crossing Valance bands (VB) & CB In-Reply-To: References: Message-ID: <200908141757.01327.giannozz@democritos.it> On Thursday 06 August 2009 18:31, dev sharma wrote: > I have successfully calculated the band structure of my system. It is also > matching the results. But when I plot my band structure in ps format only > one line from conduction band and valance band is showing fluctuations. > Means one line ,in ps output, from conduction band has apparently come down > to valance band and vice versa. And this fluctuation is just at the end > of graph. (means i have given 41 k points in calculations= 'bands' and in > only last 3 there is some fluctuations, the whole other graphs is smooth > otherwsie). I am not sure I understand what you mean. One possibility is the following: when one calculates bands, a few high-lying states may not be the correct ones because of the way iterative diagonalization works (it starts from an initial guess). This is a rather normal behavior. The highest states in a band calculation should be discarded. Paolo -- Paolo Giannozzi, Democritos and Udine University From sh.shapt at gmail.com Fri Aug 14 21:29:18 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Fri, 14 Aug 2009 20:29:18 +0100 Subject: [Pw_forum] Request for Pseudopotentials Si and H Message-ID: Hi Quantum espresso users, I need the following pseudopotential file for my simulation Si.vbc.UPF and H.vbc.UPF . Howeevr I could not find them in PWScf, so can anybody suggest me from where can I download these pseudopotentials. Please help me!! Thanks Shaptarishi. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/68f0f0e3/attachment.htm From manoj at phys.ufl.edu Fri Aug 14 22:53:01 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 14 Aug 2009 16:53:01 -0400 (EDT) Subject: [Pw_forum] Request for Pseudopotentials Si and H In-Reply-To: Message-ID: Hey SaptariBshi, You can find them in /pseudo directory under espresso, e.g. espresso-4.0.4/pseudo -Manoj Srivastava University of Florida Gainesville, FL On Fri, 14 Aug 2009, Shaptrishi Sharma wrote: > Hi Quantum espresso users, > > I need the following pseudopotential file for my simulation Si.vbc.UPF and > H.vbc.UPF . Howeevr I could not find them in PWScf, so can anybody suggest > me from where can I download these pseudopotentials. Please help me!! > Thanks > > Shaptarishi. > From baroni at sissa.it Sat Aug 15 08:35:17 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 15 Aug 2009 08:35:17 +0200 Subject: [Pw_forum] Request for Pseudopotentials Si and H In-Reply-To: References: Message-ID: <74720C20-4C1B-483C-8421-F8AA2F292C52@sissa.it> On Aug 14, 2009, at 9:29 PM, Shaptrishi Sharma wrote: > Hi Quantum espresso users, > > I need the following pseudopotential file for my simulation > Si.vbc.UPF and H.vbc.UPF . Howeevr I could not find them in PWScf, > so can anybody suggest me from where can I download these > pseudopotentials. Please help me!! http://www.quantum-espresso.org/pseudo/1.3/UPF/Si.pz-vbc.UPF http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz-vbc.UPF 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/20090815/4ae8319d/attachment-0001.htm From vtmtrinh at caltech.edu Sat Aug 15 22:42:56 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Sat, 15 Aug 2009 13:42:56 -0700 (PDT) Subject: [Pw_forum] spin splitting Message-ID: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> Dear PWSCF Users, Does any of you know how to calculate spin splitting using QE? More clearly, if I have 2 structures (Si 8-atom cell), one at equilibrium and the other one with atoms being displced according to phonon mode. I would like calculate the energies of the spin up and down. There are 2 concerns that I have: (i) The difference in eneries for these 2 states is too small. Can we get to that level of accuracy by using QE. (ii) how to do it (how to fix spin up and down). Any suggestion would be appreciated. Thank you, MyTrinh Vo Computation group JPL/CalTech From oulihui666 at 126.com Sun Aug 16 03:44:19 2009 From: oulihui666 at 126.com (oulihui666) Date: Sun, 16 Aug 2009 09:44:19 +0800 (CST) Subject: [Pw_forum] About zero point energy Message-ID: <3903308.318351250387059965.JavaMail.coremail@bj126app26.126.com> Dear all, I have a question about zero point energy calculation. According to a article called "Tutorial on calculating phonons: comparing the linear response and the small displacement methods", author states that we can calculate zero point energy use the results obtained with linear response method, i.e phonon code in pwscf. Calculated steps as follows(for example Al): (1) > pw.x < Al.scf (This generates the self-consistent wave-function) (2) > ph.x < Al.ph.in (This generate the dynamic matrices) (3) > q2r.x < q2r.in (Obtaining force constant matrix) (4) > matdyn.x < matdyn.in (Calculating the phonon dispersions) (5) > matdyn.x < phdos.in (Calculating phonon density of states) and this will produce a file called "Al.phdos" which contains the phonon density of states. Now by typing: awk '{e=e+2*1/2}END{print e/33.357*4.1357/1000}' Al.phdos and you should see that the zero point energy. The question is, I do not understand the meaning of "{e=e+2*1/2}END{print e/33.357*4.1357/1000}", is this appropriate for the calculation of zero point energy? In addition, In mail list, by calculating phonons all over the Brillouin zone (in practice, on a regular grid), and zero point energy by calculating {\hbar\over 2} \sum_{{\bf q},\nu} \omega_{{\bf q},\nu}. I do not understand the meaning of {\hbar\over 2} \sum_{{\bf q},\nu} \omega_{{\bf q},\nu} well. Anyone who help me will be appreciated. Many thanks Best regards Lihui -- ====================================== Lihui Ou PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:oulihui666 at 126.com ====================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090816/a3e20a7e/attachment.htm From baroni at sissa.it Sun Aug 16 10:45:13 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 16 Aug 2009 10:45:13 +0200 Subject: [Pw_forum] About zero point energy In-Reply-To: <3903308.318351250387059965.JavaMail.coremail@bj126app26.126.com> References: <3903308.318351250387059965.JavaMail.coremail@bj126app26.126.com> Message-ID: > Dear all, Hi Lihui: > I have a question about zero point energy calculation. According > to a article called "Tutorial on calculating phonons: comparing the > linear response and the small displacement methods", author states > that we can calculate zero point energy use the results obtained > with linear response method, i.e phonon code in pwscf. Calculated > steps as follows(for example Al): > (1) > pw.x < Al.scf (This generates the self-consistent wave-function) > (2) > ph.x < Al.ph.in (This generate the dynamic matrices) > (3) > q2r.x < q2r.in (Obtaining force constant matrix) > (4) > matdyn.x < matdyn.in (Calculating the phonon dispersions) > (5) > matdyn.x < phdos.in (Calculating phonon density of states) > and this will produce a file called "Al.phdos" which contains the > phonon density of states. Now by typing: > awk '{e=e+2*1/2}END{print e/33.357*4.1357/1000}' Al.phdos I am close to null in AWK, nor did I know anything about ".phdos" files and it took me a while to understand what's going on here. 1) I see that ".phdos" files contain two columns of data, both starting from zero, both positive, data in the first column equally spaced. Let's assume the first column is a table of frequencies, the second the corresponding dos. 2) You did not say what article you are referring to. You could have, but in any case GOOGLE helps. Here is, I think, the source of your troubles ... http://www.mcc.uiuc.edu/summerschool/2007/qmc/tutorials/Tutorial_phonons_alfe.pdf 3) AWK parses text files line by line: "$1" and "$2" is the name that AWK givs to the first and second text fields it encounters (I did not remember this: I re-learn AWK once every 5 years, the last time was 5 mins ago here: http://www.gnu.org/software/gawk/manual/gawk.html > and you should see that the zero point energy. The question is, I do > not understand the meaning of "{e=e+2*1/2}END{print e/ > 33.357*4.1357/1000}", is this appropriate for the calculation of > zero point energy? the awk line reported in the lecture notes you are reading is supposed to make an integral (sum) over frequency of the product of the frequency (first column, "$1"), and dos (second column, "$2"). (see Eq. 7 in the lecture notes and take the T->0 limit). can you see now what happened? (HINT the lecture notes contain a typo: dollars "$" are not displayed ...; the instruction in curly brackets following "print" must be a change of variables / normalization ... > In addition, In mail list, by calculating phonons all over the > Brillouin zone (in practice, on a regular grid), and zero point > energy by calculating {\hbar\over 2} \sum_{{\bf q},\nu} \omega_{{\bf > q},\nu}. I do not understand the meaning of {\hbar\over 2} > \sum_{{\bf q},\nu} \omega_{{\bf q},\nu} well. Anyone who help me > will be appreciated. I do not understand if what you do not understand are basic concepts (how the zero-point energy is related to the dos, how BZ integrals are related to frequency integrals ...) or details, such as the syntax of AWK/LaTeX ... Please, try to clarify this to yourself in the frst place. If it is physics concepts that you do not understand, make an effort to formulate a specific question for each specific point you do not understand, and then revert to us with a specific question. If it is AWK/LaTeX, do like me: browse the net with google and/or take a walk to the nearest library and learn the tools you need (occasionally, we would also be pleased to help for such matters, but the help is in this case even less guaranteed the with physics). 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/20090816/18958a92/attachment.htm From paulatto at sissa.it Sun Aug 16 23:37:05 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 16 Aug 2009 23:37:05 +0200 (CEST) Subject: [Pw_forum] Request for Pseudopotentials Si and H In-Reply-To: <74720C20-4C1B-483C-8421-F8AA2F292C52@sissa.it> References: <74720C20-4C1B-483C-8421-F8AA2F292C52@sissa.it> Message-ID: <39363.78.12.159.112.1250458625.squirrel@webmail.sissa.it> On Sat, August 15, 2009 08:35, Stefano Baroni wrote: > http://www.quantum-espresso.org/pseudo/1.3/UPF/Si.pz-vbc.UPF > http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz-vbc.UPF > > SB > As a more general hint: habe a look here: -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ quantu ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From manoj at phys.ufl.edu Mon Aug 17 01:52:08 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Sun, 16 Aug 2009 19:52:08 -0400 (EDT) Subject: [Pw_forum] question about PWCOND Message-ID: Dear Alexander and PWSCF users, I have a question about an expression in the scatter_forw.f90 subroutine, specifically about the following expression - IF (ABS(AIMAG(zk(lam, kp))).LT.eps) THEN f1(lam,iorb)=-ezk(lam)*CONJG(di(iorb,lam))*zk2(lam) f2(lam,iorb)=-ezk(lam)*CONJG(ci(iorb,lam))*zk2(lam) ELSE f1(lam,iorb)=-CONJG(ci(iorb,lam))*zk2(lam) f2(lam,iorb)=-CONJG(di(iorb,lam))*zk2(lam) ENDIF Why does this expression have if/else statement depending on imaginary part of zk? I did some algebra and realized that f1 for (ABS(AIMAG(zk(lam, kp))).LT.eps) is related with f1 for (ABS(AIMAG(zk(lam, kp))).GT.eps) by changing zk to -zk. Same is true for f2. It is defined in previous subroutine that zk=sqrt(E-E_lambda) where E is given energy and E_lambda is eigenvalue of 2D problem. Square root gives us two solution, one would be zk and another -zk, and I dont understand how do you choose which solution to use in the expression for f1 and f2, depending on imaginary part of zk. Would anyone mind to explain? Regards, Manoj From manoj at phys.ufl.edu Mon Aug 17 06:35:41 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Mon, 17 Aug 2009 00:35:41 -0400 (EDT) Subject: [Pw_forum] question about PWCOND In-Reply-To: Message-ID: I am sorry I forgot to mention the value of 'eps', it is 1.d-8. Thanks, Manoj Srivastava University of Florida Gainesville, FL On Sun, 16 Aug 2009, Manoj Srivastava wrote: > Dear Alexander and PWSCF users, > I have a question about an expression in the scatter_forw.f90 subroutine, > specifically about the following expression - > IF (ABS(AIMAG(zk(lam, kp))).LT.eps) THEN > f1(lam,iorb)=-ezk(lam)*CONJG(di(iorb,lam))*zk2(lam) > f2(lam,iorb)=-ezk(lam)*CONJG(ci(iorb,lam))*zk2(lam) > ELSE > f1(lam,iorb)=-CONJG(ci(iorb,lam))*zk2(lam) > f2(lam,iorb)=-CONJG(di(iorb,lam))*zk2(lam) > ENDIF > Why does this expression have if/else statement depending on imaginary > part of zk? I did some algebra and realized that f1 for (ABS(AIMAG(zk(lam, > kp))).LT.eps) is related with f1 for (ABS(AIMAG(zk(lam, kp))).GT.eps) by > changing zk to -zk. Same is true for f2. It is defined in previous > subroutine that > zk=sqrt(E-E_lambda) > where E is given energy and E_lambda is eigenvalue of 2D problem. > Square root gives us two solution, one would be zk and > another -zk, and I dont understand how do you choose which solution to use > in the expression for f1 and f2, depending on imaginary part of zk. > Would anyone mind to explain? > > Regards, > Manoj > > From sclauzer at sissa.it Mon Aug 17 08:46:52 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 17 Aug 2009 08:46:52 +0200 Subject: [Pw_forum] Reply (was Frequency and zero point energy calculations) In-Reply-To: <5014682.21451250296629355.JavaMail.coremail@bj126app103.126.com> References: <5014682.21451250296629355.JavaMail.coremail@bj126app103.126.com> Message-ID: <4A88FCDC.5010802@sissa.it> Dear Lihui, oulihui666 wrote: > Dear Gabriele Sclauzero, > I am intend to calculate the frequency of CO2 molecule, so I should > perform scf calculation at first, when setting k points as gamma, it > will appear a error in the process of calculating frequency, as follows: > *********************************************************************** > from phq_readin. error #1 > cannot start from pw.x data file using Gamma-point tricks > *********************************************************************** From what I can understand, this does not mean that you cannot do the calculation for the Gamma point only, but rather that the calculation cannot be done using Gamma point-specific algorithms (which are much faster than the general ones). You should anyway be allowed to do the calculation using K_POINTS AUTOMATIC 1 1 1 0 0 0 which builds a k-point grid containing the Gamma point only, but does not use Gamma-point tricks. You can do the relaxations (and all other expensive pw calculations) using K_POINTS GAMMA and then, starting from the optimized atomic positions, do a nscf run using K_POINTS AUTOMATIC 1 1 1 0 0 0 before the phonon run. Cheers GS P.S: please avoid private mails and stick to the thread you started in the forum, so that anyone can help and know when your problem has been solved. Thanks! > So I do not set k point as gamma in scf calculation. > > Best regards > Lihui > > -- > ====================================== > Lihui Ou > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,/430072/,Hubei Province,China > /E-mail:oulihui666 at 126.com / > ====================================== > > > ------------------------------------------------------------------------ > ???????????,www.yeah.net -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Aug 17 09:09:48 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 17 Aug 2009 09:09:48 +0200 Subject: [Pw_forum] spin splitting In-Reply-To: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> Message-ID: <4A89023C.80808@sissa.it> Dear user, vtmtrinh at caltech.edu wrote: > Dear PWSCF Users, > > Does any of you know how to calculate spin splitting using QE? More > clearly, if I have 2 structures (Si 8-atom cell), one at equilibrium and > the other one with atoms being displced according to phonon mode. I would > like calculate the energies of the spin up and down. There are 2 concerns You did not clarify much, in my poor understanding. What do you want to calculate? The splittings between the spin up/spin down eigenvalues? That should be easy, you do a calculation with nspin=2 and a guess for the starting magnetization and, if your system stays magnetic, you can easily compute the splittings from the list of eigenvalues given on output at the end of the calculation. Or maybe you want to compute total energy difference between an AF and a FM configuration? Why do you mention two configurations that differ by atomic displacements and ask about computing spin up/spin down splittings? Does magnetism arise in the second case due to the displacement from equilibrium configuration? > that I have: (i) The difference in eneries for these 2 states is too > small. Can we get to that level of accuracy by using QE. It depends what is the accuracy you need. In principle you can increase it by increasing PW/charge-density cutoffs, number of k-points, and decreasing degauss (you may also need to decrease conv_thr or other things that did not come in my mind in this moment...). Then you probably have to face with the error due to the use of pseudo-potentials, but generally the error in energy differences can be believed to be lower than absolute error on the total energies. (ii) how to do > it (how to fix spin up and down). I don't understand exactly what you want to fix. You can for instance fix the total spin magnetization of your system using the tot_magnetization or multiplicity variables. HTH GS > > Any suggestion would be appreciated. > > Thank you, > > MyTrinh Vo > > Computation group > JPL/CalTech > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Mon Aug 17 10:05:30 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 17 Aug 2009 10:05:30 +0200 Subject: [Pw_forum] PAW pseudo-potential for Al and Ni In-Reply-To: <9D7727CF644140E58D63C9B187A343BD@hjkc> References: <51554.45053.qm@web52301.mail.re2.yahoo.com> <95177CEB-E10F-4818-A4BA-966771674BA2@sissa.it> <9D7727CF644140E58D63C9B187A343BD@hjkc> Message-ID: In data 14 agosto 2009 alle ore 10:44:40, Nguyen Thanh Cuong ha scritto: > Does anyone have generated the paw pseudo-potentials for Al and Ni with > ld1 code? Would you share the ld1 input files? Dear Nguyen, I'm sending you an input file for Aluminium, it is not very tested it (I've only checked basic Al structure and 2 AlN structures). I don't have one for Ni, but I think it could be adapted from a Palladium input you can find in atomic_doc/paw_library/input good luck! -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ -------------- next part -------------- A non-text attachment was scrubbed... Name: Al.in Type: application/octet-stream Size: 746 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090817/88a95320/attachment.obj From dimpy.sharma at tyndall.ie Mon Aug 17 10:27:21 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 17 Aug 2009 09:27:21 +0100 Subject: [Pw_forum] Request for Pseudopotentials for Si and H References: Message-ID: Hi There, Thanks for your help, however I did not need these Pseudopotentials as I already have these ( Si.pz-vbc.UPF and H.pz-vbc.UPF ). I need the following or else if I use these values my calculations did not run. The one which I need are as follows. Si 28.08600 Si.vbc.UPF and H 1.00800 H.vbc.UPF Thanks Shapta. -----Original Message----- From: pw_forum-bounces at pwscf.org on behalf of pw_forum-request at pwscf.org Sent: Sat 8/15/2009 7:35 AM To: pw_forum at pwscf.org Subject: Pw_forum Digest, Vol 26, Issue 44 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: matdyn error (Mikiyas Tsegaye) 2. Re: matdyn error (Paolo Giannozzi) 3. Re: line crossing Valance bands (VB) & CB (Paolo Giannozzi) 4. Request for Pseudopotentials Si and H (Shaptrishi Sharma) 5. Re: Request for Pseudopotentials Si and H (Manoj Srivastava) 6. Re: Request for Pseudopotentials Si and H (Stefano Baroni) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Aug 2009 10:13:46 -0400 From: Mikiyas Tsegaye Subject: Re: [Pw_forum] matdyn error To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="us-ascii" Dear Rakshit, I'm just copy pasting from a previous answer in the forum to the same question: it might help, it might not. Hello, Assuming that there are no problems of numerical inaccuracy or inadequate convergence thresholds, negative frequencies at gamma point in a geometry-relaxed system usually mean that (within the system and the calculation method used) there is some distortion (decreasing the symmetry of the system) which leads to lower energy, i.e. you are at a saddle point in the energy hypersurface. You must move some atom out of the initial symmetry and optimize geometry again starting from that modified situation. If you can obtain the vector coordinates for the normal mode of vibration corresponding to the negative frequency, a displacement of the involved atoms, proportional to that normal mode, by e.g. a maximum of 0.2 angstrom will give to you a starting displaced geometry closer to the true energy minimum. Sometimes you need to do this several times if not all of the negative frequencies disappear after the first attempt. If, after obtaining a new geometry with no negative frequencies at the gamma point, you still have negative frequencies at other BZ points, this means that your system is unstable against some atomic displacements that multiply some of the primitive cell vectors by e.g. 2 or 3, leading to a supercell. Curing this situation may be more tedious. Good luck, Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 > > > Message: 3 > Date: Fri, 14 Aug 2009 11:25:23 +0530 > From: Bipul Rakshit > Subject: [Pw_forum] matdyn error > To: PWSCF Forum > Message-ID: > <3a749910908132255x13311317j4eb55858c46affe0 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear pwscf users, > > I am doing Gamma point phonon analysis for LaMnO3, after running > matdyn.x i > am getting the following, error. > > Norm of the difference between old and new effective charges: > 0.00000000000000000000 > Norm of the difference between old and new force-constants: > 0.20461738165775616993 > 0.833333333333333 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > from frc_blk : error # 1 > wrong total_weight > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > stopping ... > 2 > > Since at gamma point i am getting some -ve freq. the sum rule i want > to > apply. And to see the final frequencies after applying sum rule. > > Kindly guide me and suggest for the possible reason for this error. > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0001.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: lamno3.ph.in > Type: application/octet-stream > Size: 316 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0003.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: q2r.in > Type: application/octet-stream > Size: 71 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0004.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: matdyn.in > Type: application/octet-stream > Size: 280 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0005.obj > > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/0d9b7726/attachment-0001.htm ------------------------------ Message: 2 Date: Fri, 14 Aug 2009 17:36:53 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] matdyn error To: PWSCF Forum Message-ID: <200908141736.53374.giannozz at democritos.it> Content-Type: text/plain; charset="iso-8859-1" On Friday 14 August 2009 07:55, Bipul Rakshit wrote: > I am doing Gamma point phonon analysis for LaMnO3, > after running matdyn.x i am getting the following, error. you calculated phonons at q=0 only, so all you can and should do is to run dynmat.x (not matdyn.x) to apply the acoustic sum rule and to calculate lo-to splitting. Paolo -- Paolo Giannozzi, Democritos and Udine University ------------------------------ Message: 3 Date: Fri, 14 Aug 2009 17:57:01 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] line crossing Valance bands (VB) & CB To: PWSCF Forum Message-ID: <200908141757.01327.giannozz at democritos.it> Content-Type: text/plain; charset="iso-8859-1" On Thursday 06 August 2009 18:31, dev sharma wrote: > I have successfully calculated the band structure of my system. It is also > matching the results. But when I plot my band structure in ps format only > one line from conduction band and valance band is showing fluctuations. > Means one line ,in ps output, from conduction band has apparently come down > to valance band and vice versa. And this fluctuation is just at the end > of graph. (means i have given 41 k points in calculations= 'bands' and in > only last 3 there is some fluctuations, the whole other graphs is smooth > otherwsie). I am not sure I understand what you mean. One possibility is the following: when one calculates bands, a few high-lying states may not be the correct ones because of the way iterative diagonalization works (it starts from an initial guess). This is a rather normal behavior. The highest states in a band calculation should be discarded. Paolo -- Paolo Giannozzi, Democritos and Udine University ------------------------------ Message: 4 Date: Fri, 14 Aug 2009 20:29:18 +0100 From: Shaptrishi Sharma Subject: [Pw_forum] Request for Pseudopotentials Si and H To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Quantum espresso users, I need the following pseudopotential file for my simulation Si.vbc.UPF and H.vbc.UPF . Howeevr I could not find them in PWScf, so can anybody suggest me from where can I download these pseudopotentials. Please help me!! Thanks Shaptarishi. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/68f0f0e3/attachment-0001.htm ------------------------------ Message: 5 Date: Fri, 14 Aug 2009 16:53:01 -0400 (EDT) From: Manoj Srivastava Subject: Re: [Pw_forum] Request for Pseudopotentials Si and H To: PWSCF Forum Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hey SaptariBshi, You can find them in /pseudo directory under espresso, e.g. espresso-4.0.4/pseudo -Manoj Srivastava University of Florida Gainesville, FL On Fri, 14 Aug 2009, Shaptrishi Sharma wrote: > Hi Quantum espresso users, > > I need the following pseudopotential file for my simulation Si.vbc.UPF and > H.vbc.UPF . Howeevr I could not find them in PWScf, so can anybody suggest > me from where can I download these pseudopotentials. Please help me!! > Thanks > > Shaptarishi. > ------------------------------ Message: 6 Date: Sat, 15 Aug 2009 08:35:17 +0200 From: Stefano Baroni Subject: Re: [Pw_forum] Request for Pseudopotentials Si and H To: PWSCF Forum Message-ID: <74720C20-4C1B-483C-8421-F8AA2F292C52 at sissa.it> Content-Type: text/plain; charset="iso-8859-1" On Aug 14, 2009, at 9:29 PM, Shaptrishi Sharma wrote: > Hi Quantum espresso users, > > I need the following pseudopotential file for my simulation > Si.vbc.UPF and H.vbc.UPF . Howeevr I could not find them in PWScf, > so can anybody suggest me from where can I download these > pseudopotentials. Please help me!! http://www.quantum-espresso.org/pseudo/1.3/UPF/Si.pz-vbc.UPF http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz-vbc.UPF 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/20090815/4ae8319d/attachment.htm ------------------------------ _______________________________________________ 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 44 **************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 7890 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090817/a8dbd767/attachment-0001.bin From paulatto at sissa.it Mon Aug 17 10:28:52 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 17 Aug 2009 10:28:52 +0200 Subject: [Pw_forum] Request for Pseudopotentials for Si and H In-Reply-To: References: Message-ID: In data 17 agosto 2009 alle ore 10:27:21, Dimpy Sharma ha scritto: > Si 28.08600 Si.vbc.UPF > H 1.00800 H.vbc.UPF You can just rename the file, or change the input. The name of the pseudopotential does not matter, what matter is what's inside (and results should be pseudopotential-independent, as long as you use the same functional). regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Mon Aug 17 10:40:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Aug 2009 10:40:50 +0200 Subject: [Pw_forum] Request for Pseudopotentials for Si and H In-Reply-To: References: Message-ID: <200908171040.50749.giannozz@democritos.it> On Monday 17 August 2009 10:27, Dimpy Sharma wrote: > Thanks for your help, however I did not need these Pseudopotentials as I > already have these ( Si.pz-vbc.UPF and H.pz-vbc.UPF ). they are EXACTLY THE SAME as those you need. *.pz-vbc.UPF is the correct naming convention. > I need the following or else if I use these values my calculations > did not run this is impossible -- Paolo Giannozzi, Democritos and Udine University From neelphysics at yahoo.in Mon Aug 17 11:36:08 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Mon, 17 Aug 2009 15:06:08 +0530 (IST) Subject: [Pw_forum] Doubt in computation time Message-ID: <513181.94341.qm@web95012.mail.in2.yahoo.com> HI 2 all, I have a doubt. Please help me, i will be very thankful to all of you. When we define our system in terms of atomic positions, we have four option like bohr, angstrom etc. I want to know weather the computational time will be less when we describe any crystal structure in option crystal (atomic positions {crystal}) as compared to angstrom/bohr(atomic positions {angstrom}) as the parameters nat (number of atoms) in &system will less in crystal option as compared to angstrom/bohr 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/20090817/4bb42d40/attachment.htm From marzari at MIT.EDU Mon Aug 17 11:45:47 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 17 Aug 2009 05:45:47 -0400 Subject: [Pw_forum] Doubt in computation time In-Reply-To: <513181.94341.qm@web95012.mail.in2.yahoo.com> References: <513181.94341.qm@web95012.mail.in2.yahoo.com> Message-ID: <4A8926CB.5090601@mit.edu> Dear Neel, there is no difference. You can specify the size of your unit cell using different units of measure, but provided you convert your units correctly, you will of course have the same unit cell, and same computational cost. Of course you can use larger cells that contain multiples of the primitive unit cell, and this a larger "nat" and a larger computational cost. Suggestion - before proceeding further with the code, try to study silicon using a 2-atom fcc unit cell, specifying atomic positions in any of the possible modes, and checking that the results and the computational time does not change. nicola Neel Singh wrote: > HI 2 all, > > I have a doubt. Please help me, i will be very thankful to all of you. > When we define our system in terms of atomic positions, we have four > option like bohr, angstrom etc. I want to know weather the > computational time will be less when we describe any crystal structure > in option crystal (atomic positions {crystal}) as compared to > angstrom/bohr(atomic positions {angstrom}) as the parameters nat > (number of atoms) in &system will less in crystal option as compared > to angstrom/bohr option. > > Thanks > > Neel Singh > University of Delhi, > India > > > ------------------------------------------------------------------------ > Love Cricket? Check out live scores, photos, video highlights and > more. Click here > . > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From quantumdft at gmail.com Mon Aug 17 11:50:38 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 17 Aug 2009 17:50:38 +0800 Subject: [Pw_forum] Doubt in computation time In-Reply-To: <513181.94341.qm@web95012.mail.in2.yahoo.com> References: <513181.94341.qm@web95012.mail.in2.yahoo.com> Message-ID: <412f6c680908170250q4a6f8794y131bbfd2e3ac942e@mail.gmail.com> you could perform a small test job. In the test job, you could do two single point energy calculations: one with absolute coordinates, the other with fractional coordinates. For small system, the test would be finish in a minute. then you could compare the wall time reported by the output files. vega On Mon, Aug 17, 2009 at 5:36 PM, Neel Singh wrote: > HI 2 all, > > I have a doubt. Please help me, i will be very thankful to all of you. When > we define our system in terms of atomic positions, we have four option like > bohr, angstrom etc. I want to know weather the computational time will be > less when we describe any crystal structure in option crystal (atomic > positions {crystal}) as compared to angstrom/bohr(atomic positions > {angstrom}) as the parameters nat (number of atoms) in &system will less in > crystal option as compared to angstrom/bohr option. > > Thanks > > Neel Singh > University of Delhi, > India > > ------------------------------ > Love Cricket? Check out live scores, photos, video highlights and more. Click > here . > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090817/9d2c2164/attachment.htm From marzari at MIT.EDU Mon Aug 17 12:53:50 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 17 Aug 2009 06:53:50 -0400 Subject: [Pw_forum] About zero point energy In-Reply-To: <3903308.318351250387059965.JavaMail.coremail@bj126app26.126.com> References: <3903308.318351250387059965.JavaMail.coremail@bj126app26.126.com> Message-ID: <4A8936BE.5090807@mit.edu> > (5) > matdyn.x < phdos.in (Calculating phonon density of states) > and this will produce a file called "Al.phdos" which contains the > phonon density of states. Now by typing: > awk '{e=e+2*1/2}END{print e/33.357*4.1357/1000}' Al.phdos Dear Lihui, I would be careful in getting quantities via the integration of densities of states (by the way, is it only me with this bias ?). Every time an electronic or a phononic band goes flat you have a van hove singularity in the density of states - to me it seems that integrating that carefully requires a lot of diligence in sampling, while it would be straightforward to obtain if you were doing a k-point integral. Question for Eyvaz - does the qha code do the integrals in reciprocal space, or via the pdos ? nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From eyvaz_isaev at yahoo.com Mon Aug 17 15:00:48 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 17 Aug 2009 06:00:48 -0700 (PDT) Subject: [Pw_forum] About zero point energy In-Reply-To: <4A8936BE.5090807@mit.edu> Message-ID: <423688.9393.qm@web65707.mail.ac4.yahoo.com> Hi Nicola, > --- On Mon, 8/17/09, Nicola Marzari wrote: > Question for Eyvaz - does the qha code do the integrals in > reciprocal space, or via the pdos ? QHA calculates zero point energy (and others, too) via pdos. It is rather straightforward, and I did not see any considerable deviation from available calculations for metals. By default the frequency step is 0,75cm-1. I suggest, the same way is accepted in PHONON by Parlinski. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From jarodriguezm at bt.unal.edu.co Mon Aug 17 18:48:38 2009 From: jarodriguezm at bt.unal.edu.co (Jairo Arbey Rodriguez Martinez) Date: Mon, 17 Aug 2009 11:48:38 -0500 Subject: [Pw_forum] cp.x: interpolation tables recalculation Message-ID: <74d8a4ef0908170948l52043ae5s267c67d796fd49e9@mail.gmail.com> Dear users of quantum espresso I ask you any help about the next error message: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0 4429 23.54842 ****** 37.4 -3407.45376 -3407.45376 -3406.10550 -3382.55708 0.0000 0.0000 -0.0005 -0.1518 Delta V(G=0): 0.041783Ry, 1.136964eV application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1[cli_1]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from newnlinit : error # 1 interpolation tables recalculation, not implemented yet %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- The antecedents ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- I wish to calculate GaAs with defects (volume calculation). In order to do, I have begun with a supercell 2x2x2 of 64 atoms, 32 of Ga and 32 of As in their ideal positions. My first objective is to do a variable cell calculation (vc-cp) in order to apply to the cell with defects later, and to obtain the new volume and the relax positions. The task was divided in minor task, as following: (all is executed using cp.x, of espresso-4.0.4, ultrasoft pbe pseudos) i) electronic minimization # relax_0.in--> electron_dynamics='damp', electron_damping=0.2 ion_dynamics='none' relax_1.in--> electron_dynamics='damp', electron_damping=0.2 ion_dynamics='none' # ii) ion dynamics # relax_2.in--> electron_dynamics='damp', electron_damping=1.0 ion_dynamics='damp',ion_damping=0.5 , relax_3.in--> electron_dynamics='damp', electron_damping=0.5 ion_dynamics='damp',ion_damping=0.1 , relax_4.in--> electron_dynamics='damp', electron_damping=0.2 ion_dynamics='damp',ion_damping=0.05 , relax_5.in--> electron_dynamics='damp', electron_damping=0.2 ion_dynamics='damp',ion_damping=0.002 , # iii) ion dynamics with thermostat # relax_16.in--> electron_dynamics='damp',electron_damping=0.2,grease=0.999,ion_dynamics='damp',ion_damping=0.002,greasp=0.999,ion_temperature='nose',tempw=300.,fnosep=9.00, # iv) Parrinello-Rahman Dynamics # relax_18.in--> electron_dynamics='damp',electron_damping=0.5,grease=0.999, ion_dynamics='damp',ion_damping=0.5,greasp=0.999, cell_dynamics='pr',cell_damping=0.9,greash=0.9999,press=0.0D0,wmass=2.50D0,cell_temperature='nose',temph=300.,fnoseh=4.00,cell_dofree='xyz' # ------------------------------------------------------------------------------------------------------ In the last step I got the message I have pasted at the beginning of this e-mail. I am very grateful with any light about it. -- Jairo Arbey Rodr?guez M. Dept. of Physics, Universidad Nacional de Colombia, Bogota From vtmtrinh at caltech.edu Mon Aug 17 21:36:25 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Mon, 17 Aug 2009 12:36:25 -0700 (PDT) Subject: [Pw_forum] spin splitting In-Reply-To: <4A89023C.80808@sissa.it> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> <4A89023C.80808@sissa.it> Message-ID: <2688.137.78.73.28.1250537785.squirrel@webmail.caltech.edu> Hi Gabriele, Thanks for your reply. I am sorry for the unclear question. The question is to calculate the splitting between the spin up and spin down states in the conduction band (CB) of Si. For equlibrium Si bulk, there should be no spin splitting. Therefore, the splitting can be induced by moving the atoms a long phonon modes. The spin splitting is probably of the order ~1e-7eV. Yes, you are right. I need to set nspin=2. Since I also need to include the spin-orbit coupling in this calculation, I have to use noncolinear=.true. I run a calculation yesterday, in which I set lspinorb=.true. and noncolinear=.true. By setting this I think that spin-polarized calculation was aslo done. However, in the output, I don't see the eigen values for spin up and spin down, but only one (like for the non-polarization case). I am not sure if I did not set the right parameters. Attached is my input. Could you let me know what wrong with it. Thanks, MyTrinh > Dear user, > > vtmtrinh at caltech.edu wrote: >> Dear PWSCF Users, >> >> Does any of you know how to calculate spin splitting using QE? More >> clearly, if I have 2 structures (Si 8-atom cell), one at equilibrium and >> the other one with atoms being displced according to phonon mode. I >> would >> like calculate the energies of the spin up and down. There are 2 >> concerns > > You did not clarify much, in my poor understanding. What do you want to > calculate? The > splittings between the spin up/spin down eigenvalues? > That should be easy, you do a calculation with nspin=2 and a guess for the > starting > magnetization and, if your system stays magnetic, you can easily compute > the splittings > from the list of eigenvalues given on output at the end of the > calculation. > > Or maybe you want to compute total energy difference between an AF and a > FM configuration? > > Why do you mention two configurations that differ by atomic displacements > and ask about > computing spin up/spin down splittings? Does magnetism arise in the second > case due to the > displacement from equilibrium configuration? > > >> that I have: (i) The difference in eneries for these 2 states is too >> small. Can we get to that level of accuracy by using QE. > > It depends what is the accuracy you need. In principle you can increase it > by increasing > PW/charge-density cutoffs, number of k-points, and decreasing degauss (you > may also need > to decrease conv_thr or other things that did not come in my mind in this > moment...). Then > you probably have to face with the error due to the use of > pseudo-potentials, but > generally the error in energy differences can be believed to be lower than > absolute error > on the total energies. > > (ii) how to do >> it (how to fix spin up and down). > > I don't understand exactly what you want to fix. You can for instance fix > the total spin > magnetization of your system using the tot_magnetization or multiplicity > variables. > > HTH > > GS > > >> >> Any suggestion would be appreciated. >> >> Thank you, >> >> MyTrinh Vo >> >> Computation group >> JPL/CalTech >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- A non-text attachment was scrubbed... Name: si.in Type: application/octet-stream Size: 1089 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090817/055b6107/attachment-0001.obj From vtmtrinh at caltech.edu Mon Aug 17 21:49:56 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Mon, 17 Aug 2009 12:49:56 -0700 (PDT) Subject: [Pw_forum] spin splitting In-Reply-To: <4A89023C.80808@sissa.it> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> <4A89023C.80808@sissa.it> Message-ID: <2719.137.78.73.28.1250538596.squirrel@webmail.caltech.edu> Hi Gabriele, I am sorry. Before, there are usually the words "spin up" and "spin down" in the spin polarization cases. I did not see it this time, so I thought something was wrong here. When I looked at the band data again, I saw the number of eigen values are double there, which means one for each spin state. So I saw it now. I am sorry for my bad. Thanks, Trinh > Dear user, > > vtmtrinh at caltech.edu wrote: >> Dear PWSCF Users, >> >> Does any of you know how to calculate spin splitting using QE? More >> clearly, if I have 2 structures (Si 8-atom cell), one at equilibrium and >> the other one with atoms being displced according to phonon mode. I >> would >> like calculate the energies of the spin up and down. There are 2 >> concerns > > You did not clarify much, in my poor understanding. What do you want to > calculate? The > splittings between the spin up/spin down eigenvalues? > That should be easy, you do a calculation with nspin=2 and a guess for the > starting > magnetization and, if your system stays magnetic, you can easily compute > the splittings > from the list of eigenvalues given on output at the end of the > calculation. > > Or maybe you want to compute total energy difference between an AF and a > FM configuration? > > Why do you mention two configurations that differ by atomic displacements > and ask about > computing spin up/spin down splittings? Does magnetism arise in the second > case due to the > displacement from equilibrium configuration? > > >> that I have: (i) The difference in eneries for these 2 states is too >> small. Can we get to that level of accuracy by using QE. > > It depends what is the accuracy you need. In principle you can increase it > by increasing > PW/charge-density cutoffs, number of k-points, and decreasing degauss (you > may also need > to decrease conv_thr or other things that did not come in my mind in this > moment...). Then > you probably have to face with the error due to the use of > pseudo-potentials, but > generally the error in energy differences can be believed to be lower than > absolute error > on the total energies. > > (ii) how to do >> it (how to fix spin up and down). > > I don't understand exactly what you want to fix. You can for instance fix > the total spin > magnetization of your system using the tot_magnetization or multiplicity > variables. > > HTH > > GS > > >> >> Any suggestion would be appreciated. >> >> Thank you, >> >> MyTrinh Vo >> >> Computation group >> JPL/CalTech >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Aug 18 09:00:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 18 Aug 2009 09:00:25 +0200 Subject: [Pw_forum] spin splitting In-Reply-To: <2688.137.78.73.28.1250537785.squirrel@webmail.caltech.edu> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> <4A89023C.80808@sissa.it> <2688.137.78.73.28.1250537785.squirrel@webmail.caltech.edu> Message-ID: <4A8A5189.6050704@sissa.it> vtmtrinh at caltech.edu wrote: > Hi Gabriele, > > Thanks for your reply. I am sorry for the unclear question. > The question is to calculate the splitting between the spin up and spin > down states in the conduction band (CB) of Si. For equlibrium Si bulk, > there should be no spin splitting. Therefore, the splitting can be induced > by moving the atoms a long phonon modes. The spin splitting is probably of > the order ~1e-7eV. > > Yes, you are right. I need to set nspin=2. Since I also need to include > the spin-orbit coupling in this calculation, I have to use > noncolinear=.true. Now the situation is much more clear :-) > > I run a calculation yesterday, in which I set lspinorb=.true. and > noncolinear=.true. By setting this I think that spin-polarized calculation > was aslo done. However, in the output, I don't see the eigen values for > spin up and spin down, but only one (like for the non-polarization case). You're right, in a noncolinear calculation you don't see SPIN UP and SPIN DOWN bands as in a LSD calculation. Anyway, as you also noticed, the number of bands is doubled when you set noncolin=.true. If you don't include SO coupling, you should get (for each band of the non spin-polarized calculation) a spin up and a spin down band which coincide with those obtained with a collinear LSD calculation (i.e. with noncolin=.false., nspin=2). Also the final total magnetization should be the same (you can check from the output). You can plot the bands (for instance using bands.x and then plotband.x) and compare the splittings. When you include SO the situation is more complicated (you should label your bands with the irreps of the (magnetic) double group of the system), but in principle more close to reality. You can plot bands also in this case and see what changes and how much (tyr lsym=.true. when running bands: it can label bands according to the irreps and it may be very useful). The SO splitting would be small, though. In the Si atom the SO splitting of 3p electrons should be of the order of few mRy (which is only slightly larger than the error from PPs, so be careful...), and in the bulk they are usually lower. Cheers, GS > I am not sure if I did not set the right parameters. Attached is my > input. Could you let me know what wrong with it. > > Thanks, > > MyTrinh > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From degironc at sissa.it Tue Aug 18 09:35:32 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 18 Aug 2009 09:35:32 +0200 Subject: [Pw_forum] cp.x: interpolation tables recalculation In-Reply-To: <74d8a4ef0908170948l52043ae5s267c67d796fd49e9@mail.gmail.com> References: <74d8a4ef0908170948l52043ae5s267c67d796fd49e9@mail.gmail.com> Message-ID: <4A8A59C4.5000100@sissa.it> I think the proble mis that you started from a volume that is too small and the cell tends to expand thus requiring longer arrays in order to describe the same cutoff and since the recalculation of arrays is not implemented the code stops. try to start from a larger volume. stefano de Gironcoli Jairo Arbey Rodriguez Martinez wrote: > Dear users of quantum espresso > > I ask you any help about the next error message: > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > nfi ekinc temph tempp etot enthal econs > econt vnhh xnhh0 vnhp xnhp0 > 4429 23.54842 ****** 37.4 -3407.45376 -3407.45376 -3406.10550 > -3382.55708 0.0000 0.0000 -0.0005 -0.1518 > Delta V(G=0): 0.041783Ry, 1.136964eV > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1[cli_1]: > aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from newnlinit : error # 1 > interpolation tables recalculation, not implemented yet > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > The antecedents > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > I wish to calculate GaAs with defects (volume calculation). In order > to do, I have begun with a supercell 2x2x2 of 64 atoms, 32 of Ga and > 32 of As in their ideal positions. My first objective is to do a > variable cell calculation (vc-cp) in order to apply to the cell with > defects later, and to obtain the new volume and the relax positions. > The task was divided in minor task, as following: (all is executed > using cp.x, of espresso-4.0.4, ultrasoft pbe pseudos) > > i) electronic minimization > # > relax_0.in--> electron_dynamics='damp', electron_damping=0.2 > ion_dynamics='none' > relax_1.in--> electron_dynamics='damp', electron_damping=0.2 > ion_dynamics='none' > # > ii) ion dynamics > # > relax_2.in--> electron_dynamics='damp', electron_damping=1.0 > ion_dynamics='damp',ion_damping=0.5 , > relax_3.in--> electron_dynamics='damp', electron_damping=0.5 > ion_dynamics='damp',ion_damping=0.1 , > relax_4.in--> electron_dynamics='damp', electron_damping=0.2 > ion_dynamics='damp',ion_damping=0.05 , > relax_5.in--> electron_dynamics='damp', electron_damping=0.2 > ion_dynamics='damp',ion_damping=0.002 , > # > iii) ion dynamics with thermostat > # > relax_16.in--> electron_dynamics='damp',electron_damping=0.2,grease=0.999,ion_dynamics='damp',ion_damping=0.002,greasp=0.999,ion_temperature='nose',tempw=300.,fnosep=9.00, > # > iv) Parrinello-Rahman Dynamics > # > relax_18.in--> > electron_dynamics='damp',electron_damping=0.5,grease=0.999, > ion_dynamics='damp',ion_damping=0.5,greasp=0.999, > cell_dynamics='pr',cell_damping=0.9,greash=0.9999,press=0.0D0,wmass=2.50D0,cell_temperature='nose',temph=300.,fnoseh=4.00,cell_dofree='xyz' > # > ------------------------------------------------------------------------------------------------------ > In the last step I got the message I have pasted at the beginning of > this e-mail. I am very grateful with any light about it. > -- > Jairo Arbey Rodr?guez M. > Dept. of Physics, Universidad Nacional de Colombia, Bogota > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From samirmeher at gmail.com Tue Aug 18 11:39:31 2009 From: samirmeher at gmail.com (Samir Ranjan Meher) Date: Tue, 18 Aug 2009 15:09:31 +0530 Subject: [Pw_forum] Eigenvalues not converging Message-ID: <8a4c6de60908180239l4b9c0e17r76f6805b57a8088b@mail.gmail.com> Dear All, I am doing the SCF calculation for GaN using TM Pesudopotentials for Ga and N. But my SCF calculation is not converging. I have tried changing the "mixing-beta" parameter from 0.7 to 0.1.......still does not work. Any suggestions??? My SCF input file is as follows:- &control calculation = 'scf' restart_mode='from_scratch', prefix='test', tstress = .true. tprnfor = .true. pseudo_dir = '/home/samirmeher/espresso-4.0.5/pseudo/', outdir='/home/samirmeher/tmp/' / &system ibrav= 4, celldm(1) =3.23, celldm(3) =5.2078, nat= 4, ntyp= 2, ecutwfc = 50.0, ecutrho = 300.0, / &electrons diagonalization='cg' mixing_mode = 'plain' mixing_beta = 0.6 conv_thr = 1.0d-8 / ATOMIC_SPECIES Ga 69.723 Ga.rel.TM.UPF N 14.007 N.rel.TM.UPF ATOMIC_POSITIONS Ga 0.000000000 0.000000000 0.000000000 Ga 0.333000000 0.666000000 0.500000000 N 0.000000000 0.000000000 0.375000000 N 0.333000000 0.666000000 0.875000000 K_POINTS (automatic) 6 6 6 0 0 0 Thanks in advance. Samir Ranjan Meher. IIT Madras. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090818/8e6e9b3f/attachment.htm From paulatto at sissa.it Tue Aug 18 11:48:19 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 18 Aug 2009 11:48:19 +0200 Subject: [Pw_forum] Eigenvalues not converging In-Reply-To: <8a4c6de60908180239l4b9c0e17r76f6805b57a8088b@mail.gmail.com> References: <8a4c6de60908180239l4b9c0e17r76f6805b57a8088b@mail.gmail.com> Message-ID: In data 18 agosto 2009 alle ore 11:39:31, Samir Ranjan Meher ha scritto: > Any suggestions??? My SCF input file is as follows:- Dear Samir, I've had look at your input file: it looks like you've put the atoms very close together. For example, Nitrogen and Gallium atoms are only 0.6 Angstrom apart. Furthermore, it looks like a surface slab geometry, which is not what you said you're doing. I suspect you've done some simple mistake in your input file: celldm(1) must be in *bohr* units, while celldm(3) is in units of celldm(1) (celldm(3)*celldm(1) is in bohr). If the atoms are overlapping too much the ultrasoft generalized orthogonality conditions breaks down, often causing problem during diagonalization. My advice is to recheck and fix your input. You can use xcrysden to visualize it. Remember reset the diagonalization method to davidson, using conjugate-gradient is probably unnecessary once the input is correct. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From eyvaz_isaev at yahoo.com Tue Aug 18 12:48:55 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 18 Aug 2009 03:48:55 -0700 (PDT) Subject: [Pw_forum] Eigenvalues not converging In-Reply-To: <8a4c6de60908180239l4b9c0e17r76f6805b57a8088b@mail.gmail.com> Message-ID: <676546.3151.qm@web65715.mail.ac4.yahoo.com> Dear Samir, In addition to Lorenzo's reply: 1. change celldm(*) variables to simply a=XYZ1, and c=XYZ2, as lattice parameters you specified are in Angstrom. 2. add {crystal} to ATOMIC_POSITIONS, otherwise they are in cartesian and in units of "alat" i.e. lattice parameter "a" Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 8/18/09, Samir Ranjan Meher wrote: > From: Samir Ranjan Meher > Subject: [Pw_forum] Eigenvalues not converging > To: pw_forum at pwscf.org > Date: Tuesday, August 18, 2009, 1:39 PM > Dear All, > I am doing the SCF calculation for GaN using TM > Pesudopotentials for Ga and N. But my SCF calculation is not > converging. I have tried changing the > "mixing-beta" parameter from 0.7 to > 0.1.......still does not work. Any suggestions??? My SCF > input file is as follows:- > > ?&control > ??? calculation = 'scf' > ??? restart_mode='from_scratch', > ??? prefix='test', > ??? tstress = .true. > ??? tprnfor = .true. > ??? pseudo_dir = > '/home/samirmeher/espresso-4.0.5/pseudo/', > > ??? outdir='/home/samirmeher/tmp/' > ?/ > ?&system > ??? ibrav=? 4, celldm(1) =3.23, celldm(3) =5.2078, > nat=? 4, ntyp= 2, > ??? ecutwfc = 50.0, > ??? ecutrho = 300.0, > ?/ > ?&electrons > ??? diagonalization='cg' > > ??? mixing_mode = 'plain' > ??? mixing_beta = 0.6 > ??? conv_thr =? 1.0d-8 > ?/ > ATOMIC_SPECIES > ?Ga? 69.723? Ga.rel.TM.UPF > ?N?? 14.007? N.rel.TM.UPF > ATOMIC_POSITIONS > ?? Ga????? 0.000000000??? 0.000000000??? > 0.000000000??? > > ?? Ga????? 0.333000000??? 0.666000000??? > 0.500000000??? > ??? N????? 0.000000000??? 0.000000000??? > 0.375000000??? > ??? N????? 0.333000000??? 0.666000000??? > 0.875000000 > K_POINTS (automatic) > ?6 6 6 0 0 0 > > Thanks in advance. > > Samir Ranjan Meher. > IIT Madras. > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From nkxirainbow at gmail.com Tue Aug 18 13:27:01 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 18 Aug 2009 19:27:01 +0800 Subject: [Pw_forum] Doubt in Phonon calculations In-Reply-To: <3a749910908110851u71b71fcj1567e49c75f13874@mail.gmail.com> References: <3a749910908110548n25ff5e44p172985c4ba217e02@mail.gmail.com> <21fbc4790908110639s7d3c6b29k5790d44dcc1f1698@mail.gmail.com> <3a749910908110851u71b71fcj1567e49c75f13874@mail.gmail.com> Message-ID: <21fbc4790908180427jc93414bp22c862ec12b69df6@mail.gmail.com> Dear Bipul Rakshit: > Dear Hui Wang, > THanks for you kind advice. Just tell me I have to do the symmetry > analysis manually, or there is some simple method to do so? > thanks I am sorry for not replying you timely. I think you should do the symmetry analysis manually, which is the method I take ?? ____________________________________ > 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/20090818/d8346932/attachment.htm From sumanta.bhandary at fysik.uu.se Tue Aug 18 17:18:25 2009 From: sumanta.bhandary at fysik.uu.se (Sumanta Bhandary) Date: Tue, 18 Aug 2009 17:18:25 +0200 Subject: [Pw_forum] Band Character Message-ID: <20090818171825.8jqyqqr3kosc4gc4@webmail6.uu.se> Dear Users, Is it possible to know the character of each band (i.e which orbital & atom is contributing ) from band structure calculation ? Best Regards Sumanta Bhandary Uppsala University From paulatto at sissa.it Tue Aug 18 17:45:48 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 18 Aug 2009 17:45:48 +0200 Subject: [Pw_forum] Band Character In-Reply-To: <20090818171825.8jqyqqr3kosc4gc4@webmail6.uu.se> References: <20090818171825.8jqyqqr3kosc4gc4@webmail6.uu.se> Message-ID: In data 18 agosto 2009 alle ore 17:18:25, Sumanta Bhandary ha scritto: > Dear Users, > Is it possible to know the character of each band (i.e > which orbital & atom is contributing ) from band structure calculation ? Dear Sumanta, you can have this sort of information studying the density of states projected on atomic orbitals. Please see the example08 and the input description (Doc/INPUT_PROJWFC.html) for further details. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Tue Aug 18 17:59:35 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 18 Aug 2009 17:59:35 +0200 Subject: [Pw_forum] Band Character In-Reply-To: <20090818171825.8jqyqqr3kosc4gc4@webmail6.uu.se> References: <20090818171825.8jqyqqr3kosc4gc4@webmail6.uu.se> Message-ID: <4A8ACFE7.2050309@sissa.it> Dear Sumanta, Sumanta Bhandary wrote: > Dear Users, > Is it possible to know the character of each band (i.e > which orbital & atom is contributing ) from band structure calculation ? Yes it is possible. You can use projwfc.x after running pw.x (either a scf or an nscf calculation, but with k-point set giving a correct sampling of the full BZ) and specify a name for the variable filproj. In that file you will find the projections of all the KS eigenstates onto the atomic wavefunctions (which are obtained by multiplying the radial atomic wavefunctions in the pseudopotential by spherical harmonics). Part of the same information is given as standard output from projwfc.x: each KS state is written as a weighted sum of atomic states (but only the atomic states with weight higher than a threshold are written). HTH GS > > Best Regards > Sumanta Bhandary > Uppsala University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From vaskarpour at yahoo.com Tue Aug 18 18:38:37 2009 From: vaskarpour at yahoo.com (Vahid Askarpour) Date: Tue, 18 Aug 2009 09:38:37 -0700 (PDT) Subject: [Pw_forum] Invalid lattice parameters error Message-ID: <38223.77242.qm@web51507.mail.re2.yahoo.com> Dear?forum members,??? The unit cell I'm using is triclinic (a=9.127 angstrom, b=5.519 angstrom, c=7.310 angstrom, alpha=89.99, beta=89.97, gamma=53.22). From the INPUT_PW file, I have set up the following input file but upon running, I get the error message?[?from? iosys? : error #??????1?????? invalid lattice parameters ( celldm or a ) : ] HI P1 &control ??? calculation='scf' ??? restart_mode='from_scratch', ??? prefix='HI' ??? pseudo_dir='./' ??? tprnfor=.true. / &system ??? ibrav = 14, celldm(2) = 0.5988224025, ?????????????????? ?celldm(3) = 0.8010074809, ?????????????????? ?celldm(4) = 0.0000614269, ?????????????????? ?celldm(5) = 0.0003768014, ?????????????????? ?celldm(6) = 0.5987680123, ??? nat= 16, ntyp= 2, ??? ecutwfc = 25, ecutrho=100 / &electrons !??? startingwfc='file' !??? startingpot='file' ??? conv_thr = 1.0e-8 ??? mixing_beta = 0.7 ??? mixing_mode = 'plain' / ATOMIC_SPECIES ?H?? 1.008 H.pbe-van_bm.UPF ?I?? 126.9045 I.pbe-met-bw.UPF ATOMIC_POSITIONS { crystal } H? 0.5410207170436070? 0.2731428788748004? 0.9812405064657934 H? 0.2703280018862530? 0.0318734311508943? 0.9811470399403316 H? 0.2966381896088398? 0.5428274133060331? 0.9813688770166042 H? 0.0305193255654289? 0.2972402363284921? 0.9812162736639934 H? 0.5240191380861352? 0.2821804440402000? 0.4810349452297299 H? 0.7901457291072584? 0.5278026483551734? 0.4809733355175832 H? 0.5503375668794302? 0.7931413098225334? 0.4809973787092623 H? 0.2796395683865633? 0.5518707364781123? 0.4810673549134845 I? 0.0287228720900162? 0.0281729883454607? 0.9810579054121011 I? 0.5468852020128577? 0.0307440392015779? 0.9811054652563451 I? 0.5421524600906093? 0.5489875444131580? 0.9811619723365439 I? 0.0254587527869568? 0.5437654990654623? 0.9811359888414298 I? 0.2785043683854438? 0.2760237825195679? 0.4811252184426305 I? 0.7951973666149109? 0.2812631211428072? 0.4811251339825996 I? 0.7919429686844875? 0.7968531100249291? 0.4811360286455067 I? 0.2737842053792243? 0.7942598243358985? 0.4811316491123244 K_POINTS {automatic} ?4 4 4? 0 0 0 CELL_PARAMETERS {?cubic } 9.12786342452????? 0.00000000000???? 0.00000000000 3.27213632473????? 4.37713934806???? 0.00000000000 0.00382822633???? -0.00126841112???? 7.31099888769 I appreciate any suggestions you may have. Regards, Vahid Dalhousie University, Halifax From paulatto at sissa.it Tue Aug 18 18:49:21 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 18 Aug 2009 18:49:21 +0200 Subject: [Pw_forum] Invalid lattice parameters error In-Reply-To: <38223.77242.qm@web51507.mail.re2.yahoo.com> References: <38223.77242.qm@web51507.mail.re2.yahoo.com> Message-ID: In data 18 agosto 2009 alle ore 18:38:37, Vahid Askarpour ha scritto: > invalid lattice parameters ( celldm or a ) : ] > ... > ibrav = 14, celldm(2) = 0.5988224025, > celldm(3) = 0.8010074809, > celldm(4) = 0.0000614269, > celldm(5) = 0.0003768014, > celldm(6) = 0.5987680123, Dear Vahid, the code is suggesting you what you have to: you forgot to specify celldm(1), i.e. the main lattice parameter. Which, in your case will be 9.127/.529177 bohr. Furthermore, I've noticed you've specified the cell also using the CELL_PARAMETERS card; keep in mind that they will are ignored, unless ibrav=0. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From positronium at gmail.com Tue Aug 18 18:49:25 2009 From: positronium at gmail.com (Lex Kemper) Date: Tue, 18 Aug 2009 12:49:25 -0400 Subject: [Pw_forum] Invalid lattice parameters error In-Reply-To: <38223.77242.qm@web51507.mail.re2.yahoo.com> References: <38223.77242.qm@web51507.mail.re2.yahoo.com> Message-ID: <4A8ADB95.7070807@phys.ufl.edu> Hi Vahid, Please read the manual carefully. You should specify either a combination of celldm(i)s (including celldm(1) !), or the CELL_PARAMETERS block. Not both. Lex Kemper Department of Physics University of Florida Vahid Askarpour wrote: > Dear forum members, > > The unit cell I'm using is triclinic (a=9.127 angstrom, b=5.519 angstrom, c=7.310 angstrom, alpha=89.99, beta=89.97, gamma=53.22). From the INPUT_PW file, I have set up the following input file but upon running, I get the error message [ from iosys : error # 1 invalid lattice parameters ( celldm or a ) : ] > > HI > P1 > &control > calculation='scf' > restart_mode='from_scratch', > prefix='HI' > pseudo_dir='./' > tprnfor=.true. > / > &system > ibrav = 14, celldm(2) = 0.5988224025, > celldm(3) = 0.8010074809, > celldm(4) = 0.0000614269, > celldm(5) = 0.0003768014, > celldm(6) = 0.5987680123, > nat= 16, ntyp= 2, > ecutwfc = 25, ecutrho=100 > / > &electrons > ! startingwfc='file' > ! startingpot='file' > conv_thr = 1.0e-8 > mixing_beta = 0.7 > mixing_mode = 'plain' > / > ATOMIC_SPECIES > H 1.008 H.pbe-van_bm.UPF > I 126.9045 I.pbe-met-bw.UPF > ATOMIC_POSITIONS { crystal } > H 0.5410207170436070 0.2731428788748004 0.9812405064657934 > H 0.2703280018862530 0.0318734311508943 0.9811470399403316 > H 0.2966381896088398 0.5428274133060331 0.9813688770166042 > H 0.0305193255654289 0.2972402363284921 0.9812162736639934 > H 0.5240191380861352 0.2821804440402000 0.4810349452297299 > H 0.7901457291072584 0.5278026483551734 0.4809733355175832 > H 0.5503375668794302 0.7931413098225334 0.4809973787092623 > H 0.2796395683865633 0.5518707364781123 0.4810673549134845 > I 0.0287228720900162 0.0281729883454607 0.9810579054121011 > I 0.5468852020128577 0.0307440392015779 0.9811054652563451 > I 0.5421524600906093 0.5489875444131580 0.9811619723365439 > I 0.0254587527869568 0.5437654990654623 0.9811359888414298 > I 0.2785043683854438 0.2760237825195679 0.4811252184426305 > I 0.7951973666149109 0.2812631211428072 0.4811251339825996 > I 0.7919429686844875 0.7968531100249291 0.4811360286455067 > I 0.2737842053792243 0.7942598243358985 0.4811316491123244 > K_POINTS {automatic} > 4 4 4 0 0 0 > CELL_PARAMETERS { cubic } > 9.12786342452 0.00000000000 0.00000000000 > 3.27213632473 4.37713934806 0.00000000000 > 0.00382822633 -0.00126841112 7.31099888769 > > I appreciate any suggestions you may have. > > Regards, > > Vahid > Dalhousie University, Halifax > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From ttduyle at gmail.com Tue Aug 18 23:31:51 2009 From: ttduyle at gmail.com (Duy Le) Date: Tue, 18 Aug 2009 17:31:51 -0400 Subject: [Pw_forum] ld1.x: Generate pseudo potential for Co Message-ID: <8974d3b20908181431k3489bf92xbcc71b96c79b7b65@mail.gmail.com> Dear all, I wonder if anyone has generated PBE (or any others) pseudo potential for Co with including 3P (and/or 3S)? If you did, and if you don't mind to share, please tell me some hints or just share the potential (input of ld1.x code is good enough). I've spend quite sometime to do this task, however, I always got the polite message "Errors in PS-KS equation". Any other suggestion is appreciated. Best regards, D. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090818/ad457a36/attachment.htm From jarodriguezm at bt.unal.edu.co Wed Aug 19 00:33:22 2009 From: jarodriguezm at bt.unal.edu.co (Jairo Arbey Rodriguez Martinez) Date: Tue, 18 Aug 2009 17:33:22 -0500 Subject: [Pw_forum] cp.x: interpolation tables recalculation In-Reply-To: <4A8A59C4.5000100@sissa.it> References: <74d8a4ef0908170948l52043ae5s267c67d796fd49e9@mail.gmail.com> <4A8A59C4.5000100@sissa.it> Message-ID: <74d8a4ef0908181533yac61a45xc6973142ee203ff2@mail.gmail.com> Dear Stefano Thanks for the clue. I go to try, but the calculation must be restart from the begining. 2009/8/18 Stefano de Gironcoli : > I think the proble mis that you started from a volume that is too small > and the cell tends to expand thus requiring longer arrays in order to > describe the same cutoff ?and since the recalculation of arrays is not > implemented the code stops. > try to start from a larger volume. > stefano de Gironcoli > > > Jairo Arbey Rodriguez Martinez wrote: >> Dear users of quantum espresso >> >> I ask you any help about the next error message: >> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> ?nfi ? ?ekinc ?temph ?tempp ? ? ? ?etot ? ? ?enthal ? ? ? econs >> econt ? ?vnhh ? xnhh0 ? ?vnhp ? xnhp0 >> ?4429 23.54842 ****** ? 37.4 -3407.45376 -3407.45376 -3406.10550 >> -3382.55708 ?0.0000 ?0.0000 -0.0005 -0.1518 >> ? Delta V(G=0): ? 0.041783Ry, ? ?1.136964eV >> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1[cli_1]: >> aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 >> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> ? ? from ?newnlinit : error # ? ? ? ? 1 >> ? ? interpolation tables recalculation, not implemented yet >> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> ? ? stopping ... >> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> The antecedents >> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> I wish to calculate GaAs with defects (volume calculation). In order >> to do, I have begun with a supercell 2x2x2 of 64 atoms, 32 of Ga and >> 32 of As in their ideal positions. My first objective is to do a >> variable cell calculation (vc-cp) in order to apply to the cell with >> defects later, and to obtain the new volume and the relax positions. >> The task was divided in minor task, as following: (all is executed >> using cp.x, of espresso-4.0.4, ultrasoft pbe pseudos) >> >> i) electronic minimization >> ? # >> ?relax_0.in--> electron_dynamics='damp', electron_damping=0.2 >> ion_dynamics='none' >> ?relax_1.in--> electron_dynamics='damp', electron_damping=0.2 >> ion_dynamics='none' >> ?# >> ii) ion dynamics >> ?# >> ?relax_2.in--> electron_dynamics='damp', electron_damping=1.0 >> ion_dynamics='damp',ion_damping=0.5 , >> ?relax_3.in--> electron_dynamics='damp', electron_damping=0.5 >> ion_dynamics='damp',ion_damping=0.1 , >> ?relax_4.in--> electron_dynamics='damp', electron_damping=0.2 >> ion_dynamics='damp',ion_damping=0.05 , >> ?relax_5.in--> electron_dynamics='damp', electron_damping=0.2 >> ion_dynamics='damp',ion_damping=0.002 , >> ?# >> iii) ion dynamics with thermostat >> ?# >> relax_16.in--> electron_dynamics='damp',electron_damping=0.2,grease=0.999,ion_dynamics='damp',ion_damping=0.002,greasp=0.999,ion_temperature='nose',tempw=300.,fnosep=9.00, >> ?# >> iv) Parrinello-Rahman Dynamics >> ?# >> relax_18.in--> >> electron_dynamics='damp',electron_damping=0.5,grease=0.999, >> ion_dynamics='damp',ion_damping=0.5,greasp=0.999, >> cell_dynamics='pr',cell_damping=0.9,greash=0.9999,press=0.0D0,wmass=2.50D0,cell_temperature='nose',temph=300.,fnoseh=4.00,cell_dofree='xyz' >> ?# >> ------------------------------------------------------------------------------------------------------ >> In the last step I got the message I have pasted at the beginning of >> this e-mail. I am very grateful with any light about it. >> -- >> Jairo Arbey Rodr?guez M. >> Dept. of Physics, Universidad Nacional de Colombia, Bogota >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Jairo Arbey Rodr?guez M. From ttduyle at gmail.com Wed Aug 19 06:48:39 2009 From: ttduyle at gmail.com (Duy Le) Date: Wed, 19 Aug 2009 00:48:39 -0400 Subject: [Pw_forum] ld1.x: Generate pseudo potential for Co In-Reply-To: <8974d3b20908181431k3489bf92xbcc71b96c79b7b65@mail.gmail.com> References: <8974d3b20908181431k3489bf92xbcc71b96c79b7b65@mail.gmail.com> Message-ID: <8974d3b20908182148u4d584ab4q60278a8151ff081c@mail.gmail.com> Dear all, I wonder if anyone has generated PBE (or any others) pseudo potential for Co with including 3P (and/or 3S)? If you did, and if you don't mind to share, please tell me some hints or just share the potential (input of ld1.x code is good enough). I've spend quite sometime to do this task, however, I always got the polite message "Errors in PS-KS equation". Any other suggestion is appreciated. Best regards, D. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/a0ab5c2f/attachment.htm From decboy9 at gmail.com Wed Aug 19 07:31:45 2009 From: decboy9 at gmail.com (dev sharma) Date: Wed, 19 Aug 2009 11:01:45 +0530 Subject: [Pw_forum] Request for Er pseudo potential Message-ID: hi all, I would be very thankful , if someone can provide (Er) Erbium pseudo-potential, as i dont know how to make pseudo-potentiall and it is also not present on PWscf pseudo list. I will be very thankful. With regards, Dev Sharma, University of Delhi India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/4d87aa6c/attachment.htm From kazempoor2000 at yahoo.com Wed Aug 19 10:39:24 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 19 Aug 2009 01:39:24 -0700 (PDT) Subject: [Pw_forum] point charge Message-ID: <803817.29744.qm@web112507.mail.gq1.yahoo.com> Hi I want to know if? espresso? can do charged vacancy calculation or not? I know about isolated atoms but I am not sure about big bulk supercell? If it can, how we can put the charge on the right position of the vacancy(which constraint should we introduced)? another question, Could anyone introduced me some reference about screening effect around the point defect? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/8c907b73/attachment.htm From nkxirainbow at gmail.com Wed Aug 19 10:48:42 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 19 Aug 2009 16:48:42 +0800 Subject: [Pw_forum] point charge In-Reply-To: <803817.29744.qm@web112507.mail.gq1.yahoo.com> References: <803817.29744.qm@web112507.mail.gq1.yahoo.com> Message-ID: <21fbc4790908190148v7afdf9c0s612602204d1e0b17@mail.gmail.com> Dear Ali Kazempour: I want to know if espresso can do charged vacancy calculation or not? I > know about isolated atoms but I am not sure about big bulk supercell? > I found the following content at http://ammin.geoscienceworld.org/cgi/content/full/91/4/511 "First-principles calculations within the local density and pseudopotential approximations were performed to investigate the effects of pressure on the energetics and structural behavior of *charged vacancy* defects in MgO. The simulations were *performed for a supercell* containing 216 atoms with their positions being fully optimized.Calculations were performed using the parallel code *PWscf *" As I never did this kind of calculation, I can not give you more advice :) ____________________________________ 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/20090819/fa06de9c/attachment.htm From neelphysics at yahoo.in Wed Aug 19 10:50:15 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Wed, 19 Aug 2009 14:20:15 +0530 (IST) Subject: [Pw_forum] PseudoPotential for Ce? Message-ID: <357431.92353.qm@web95006.mail.in2.yahoo.com> hi all, I want to study Ce and its compound, but I don't have any PP of Ce, I don't know about PP generation or convert PP. I have searched the forum that Stefano Fabris Sir has provided this PP to some people. Could anyone of you send me a copy of PP for Ce? Thanks With regards. 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/20090819/965d98e0/attachment.htm From fabris at democritos.it Wed Aug 19 10:57:08 2009 From: fabris at democritos.it (Stefano Fabris) Date: Wed, 19 Aug 2009 10:57:08 +0200 Subject: [Pw_forum] PseudoPotential for Ce? In-Reply-To: <357431.92353.qm@web95006.mail.in2.yahoo.com> References: <357431.92353.qm@web95006.mail.in2.yahoo.com> Message-ID: <29DC7B82-EF20-4B92-A33F-CF8D331BD446@democritos.it> Dear Neel, here is a link to my previous post concerning this issue. http://www.democritos.it/pipermail/pw_forum/2009-March/012235.html Hope it helps. Yours sincerely, Stefano On 19 Aug 2009, at 10:50, Neel Singh wrote: > hi all, > I want to study Ce and its compound, but I don't have any PP of Ce, > I don't know about PP > generation or convert PP. I have searched the forum that Stefano > Fabris Sir has provided this PP to some people. > Could anyone of you send me a copy of PP for Ce? > Thanks > With regards. > Neel singh , > University of Delhi, > India > > > Love Cricket? Check out live scores, photos, video highlights and > more. Click here._______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Fabris Theory at Elettra Group CNR-INFM DEMOCRITOS National Simulation Center c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE website: www.democritos.it/the-group email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776 --- From sh.shapt at gmail.com Wed Aug 19 11:13:28 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Wed, 19 Aug 2009 10:13:28 +0100 Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had not been converged Message-ID: Hi , I have submitted one relax calculation for 56 atoms in quantum espresso , however after 39 iterations it stops without any further informations, nor even a CRASH file. So any body can suggest me what the possible reason? Thanks SS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/ebdd6803/attachment.htm From paulatto at sissa.it Wed Aug 19 11:20:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 19 Aug 2009 11:20:35 +0200 Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had not been converged In-Reply-To: References: Message-ID: In data 19 agosto 2009 alle ore 11:13:28, Shaptrishi Sharma ha scritto: > even a CRASH file. So any body can suggest me what the possible reason? Dear Shaptrishi, you need to provide more detail if you want a meaningful answer. At least the last 500 lines of job's output. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Wed Aug 19 11:35:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 19 Aug 2009 11:35:55 +0200 Subject: [Pw_forum] point charge In-Reply-To: <803817.29744.qm@web112507.mail.gq1.yahoo.com> References: <803817.29744.qm@web112507.mail.gq1.yahoo.com> Message-ID: <200908191135.55936.giannozz@democritos.it> On Wednesday 19 August 2009 10:39, ali kazempour wrote: > I want to know if? espresso? can do charged vacancy calculation or not? it can > how we can put the charge on the right position of the vacancy we cannot. The additional charge will go where it will like to go. Paolo -- Paolo Giannozzi, Democritos and Udine University From fabris at democritos.it Wed Aug 19 11:37:32 2009 From: fabris at democritos.it (Stefano Fabris) Date: Wed, 19 Aug 2009 11:37:32 +0200 Subject: [Pw_forum] point charge In-Reply-To: <803817.29744.qm@web112507.mail.gq1.yahoo.com> References: <803817.29744.qm@web112507.mail.gq1.yahoo.com> Message-ID: Dear Ali, you have to give a deeper thought on your concept of "putting the charge in the right position". In standard calculations this is a result not an input. As a specific example in the defects you mention, think at ionic systems where the charge localization around a given defect is mainly (but not only) controlled by the Madelung potential. Note that in these systems a charged defect does not necessarily imply a charged supercell. But you are right, there are cases in which different charges can be associated to a given defect (think for example at F centers that can exists in several charge states), and here you do need charged supercells. QE can deals with these cases by specifying the number of electrons in the system, and adding a compensating uniform background. Note that in these cases, thermodynamic arguments allow for predicting which is the most stable defect in given environment conditions. There are several studies about this issues (including the screening), the first ones I found in my records are these for ionic systems PRB 68, 085110 (2003) and PRB 59, 797 (1999); and this one for semiconductors: PRL 67, 2339 (1991). These, and the references in within, should give you enough concepts (and keywords) to performs more focused literature research. Yours sincerely, Stefano On 19 Aug 2009, at 10:39, ali kazempour wrote: > Hi > I want to know if espresso can do charged vacancy calculation or > not? I know about isolated atoms but I am not sure about big bulk > supercell? > If it can, how we can put the charge on the right position of the > vacancy(which constraint should we introduced)? > another question, Could anyone introduced me some reference about > screening effect around the point defect? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Fabris Theory at Elettra Group CNR-INFM DEMOCRITOS National Simulation Center c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE website: www.democritos.it/the-group email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776 --- From Michael at ihpc.a-star.edu.sg Wed Aug 19 11:29:04 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Wed, 19 Aug 2009 17:29:04 +0800 Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had not been converged In-Reply-To: References: Message-ID: My two guesses are: (1) Ran out of time in the queue. (2) Only allowed 40 optimization steps. That said, we need more information. Usually something will show up in the error file that will give us a hint. Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Shaptrishi Sharma Sent: Wednesday, August 19, 2009 5:13 PM To: pw_forum at pwscf.org Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had not been converged Hi , I have submitted one relax calculation for 56 atoms in quantum espresso , however after 39 iterations it stops without any further informations, nor even a CRASH file. So any body can suggest me what the possible reason? Thanks SS This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From tunderaji at gmail.com Wed Aug 19 15:15:55 2009 From: tunderaji at gmail.com (Raji Abdulrafiu) Date: Wed, 19 Aug 2009 15:15:55 +0200 Subject: [Pw_forum] insufficient virtual memory Message-ID: <306556ed0908190615v460ee058ja0c27a2605e1a833@mail.gmail.com> Dear all, I am doing PDOS calculation for system ( 776 electrons ) using the 'projwfc.x'. After some time, the error message below was written in my output error file. ..... forrtl: severe (41): insufficient virtual memory Image PC Routine Line Source projwfc.x 0000000000BF9C3A Unknown Unknown Unknown projwfc.x 0000000000BF8E3A Unknown Unknown Unknown projwfc.x 0000000000BAD71A Unknown Unknown Unknown I read through the responses to similar problem from the pwscf forum. Following the recommended steps (by Profs. Eyvaz and Giannozzi), I reduced the 'ecutwfc' and 'ecutrho' from 35Ry & 450 to 30Ry and 350, respectively. The 'nbnd' was also reduced from 700 to 500. I set 'diagonalization = david', to save the CPU time. Also "startingwfc"= ''atomic' (default). Despite all these steps, the error persists, and I am just not sure of what to do again. I need help please!. I am using ver.4.0 of QE, and the calculation is being done using the CINECA parallel computers. Thank you Raji Abdulrafiu Tunde, Solid state and Material Physics Group, Department of Physics, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Cell: +27722668228 Fax: +27216503342 From sh.shapt at gmail.com Wed Aug 19 15:54:44 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Wed, 19 Aug 2009 14:54:44 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 26, Issue 52 In-Reply-To: References: Message-ID: Hi Mike, Thansk for your help, well I cannot understand your this point "Only allowed 40 optimization steps." How do we know that the optimisation steps are 40 and why?? Thanks SS On 8/19/09, pw_forum-request at pwscf.org wrote: > > 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. point charge (ali kazempour) > 2. Re: point charge (xirainbow) > 3. PseudoPotential for Ce? (Neel Singh) > 4. Re: PseudoPotential for Ce? (Stefano Fabris) > 5. Relax calculation in quantum espresso with 56 atoms had not > been converged (Shaptrishi Sharma) > 6. Re: Relax calculation in quantum espresso with 56 atoms had > not been converged (Lorenzo Paulatto) > 7. Re: point charge (Paolo Giannozzi) > 8. Re: point charge (Stefano Fabris) > 9. Re: Relax calculation in quantum espresso with 56 atoms had > not been converged (Michael Sullivan) > 10. insufficient virtual memory (Raji Abdulrafiu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Aug 2009 01:39:24 -0700 (PDT) > From: ali kazempour > Subject: [Pw_forum] point charge > To: pw > Message-ID: <803817.29744.qm at web112507.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi > I want to know if? espresso? can do charged vacancy calculation or not? I > know about isolated atoms but I am not sure about big bulk supercell? > If it can, how we can put the charge on the right position of the > vacancy(which constraint should we introduced)? > another question, Could anyone introduced me some reference about screening > effect around the point defect? > thanks a lot > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090819/8c907b73/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Wed, 19 Aug 2009 16:48:42 +0800 > From: xirainbow > Subject: Re: [Pw_forum] point charge > To: PWSCF Forum > Message-ID: > <21fbc4790908190148v7afdf9c0s612602204d1e0b17 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Ali Kazempour: > > I want to know if espresso can do charged vacancy calculation or not? > I > > know about isolated atoms but I am not sure about big bulk supercell? > > > I found the following content at > http://ammin.geoscienceworld.org/cgi/content/full/91/4/511 > "First-principles calculations within the local density and > pseudopotential approximations > were performed to investigate the effects of pressure on the energetics and > structural behavior of *charged vacancy* defects in MgO. The simulations > were *performed for a supercell* containing 216 atoms with their positions > being fully optimized.Calculations were performed using the parallel > code *PWscf > *" > As I never did this kind of calculation, I can not give you more advice :) > > ____________________________________ > 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/20090819/fa06de9c/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Wed, 19 Aug 2009 14:20:15 +0530 (IST) > From: Neel Singh > Subject: [Pw_forum] PseudoPotential for Ce? > To: pw_forum at pwscf.org > Message-ID: <357431.92353.qm at web95006.mail.in2.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > hi all, > I want to study Ce and its compound, but I don't have any PP of Ce, I > don't know about PP > generation or convert PP. I have searched the forum that Stefano Fabris Sir > has provided this PP to some people. > Could anyone of you send me a copy of PP for Ce? > Thanks > With regards. > 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/20090819/965d98e0/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Wed, 19 Aug 2009 10:57:08 +0200 > From: Stefano Fabris > Subject: Re: [Pw_forum] PseudoPotential for Ce? > To: PWSCF Forum > Message-ID: <29DC7B82-EF20-4B92-A33F-CF8D331BD446 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Dear Neel, > > here is a link to my previous post concerning this issue. > > http://www.democritos.it/pipermail/pw_forum/2009-March/012235.html > > Hope it helps. > > Yours sincerely, > Stefano > > On 19 Aug 2009, at 10:50, Neel Singh wrote: > > > hi all, > > I want to study Ce and its compound, but I don't have any PP of Ce, > > I don't know about PP > > generation or convert PP. I have searched the forum that Stefano > > Fabris Sir has provided this PP to some people. > > Could anyone of you send me a copy of PP for Ce? > > Thanks > > With regards. > > Neel singh , > > University of Delhi, > > India > > > > > > Love Cricket? Check out live scores, photos, video highlights and > > more. Click here._______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Fabris > Theory at Elettra Group > CNR-INFM DEMOCRITOS National Simulation Center > c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE > website: www.democritos.it/the-group > email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776 > --- > > > > > > > > > > > > > > > ------------------------------ > > Message: 5 > Date: Wed, 19 Aug 2009 10:13:28 +0100 > From: Shaptrishi Sharma > Subject: [Pw_forum] Relax calculation in quantum espresso with 56 > atoms had not been converged > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi , > > I have submitted one relax calculation for 56 atoms in quantum espresso , > however after 39 iterations it stops without any further informations, nor > even a CRASH file. So any body can suggest me what the possible reason? > > Thanks > SS > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090819/ebdd6803/attachment-0001.htm > > ------------------------------ > > Message: 6 > Date: Wed, 19 Aug 2009 11:20:35 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Relax calculation in quantum espresso with 56 > atoms had not been converged > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 19 agosto 2009 alle ore 11:13:28, Shaptrishi Sharma > ha scritto: > > even a CRASH file. So any body can suggest me what the possible reason? > > Dear Shaptrishi, > you need to provide more detail if you want a meaningful answer. At least > the last 500 lines of job's output. > > best regards > > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 7 > Date: Wed, 19 Aug 2009 11:35:55 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] point charge > To: PWSCF Forum > Message-ID: <200908191135.55936.giannozz at democritos.it> > Content-Type: text/plain; charset="iso-8859-1" > > On Wednesday 19 August 2009 10:39, ali kazempour wrote: > > > I want to know if? espresso? can do charged vacancy calculation or not? > > it can > > > how we can put the charge on the right position of the vacancy > > we cannot. The additional charge will go where it will like to go. > > Paolo > -- > Paolo Giannozzi, Democritos and Udine University > > > ------------------------------ > > Message: 8 > Date: Wed, 19 Aug 2009 11:37:32 +0200 > From: Stefano Fabris > Subject: Re: [Pw_forum] point charge > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > Dear Ali, > > you have to give a deeper thought on your concept of "putting the > charge in the right position". In standard calculations this is a > result not an input. As a specific example in the defects you mention, > think at ionic systems where the charge localization around a given > defect is mainly (but not only) controlled by the Madelung potential. > Note that in these systems a charged defect does not necessarily imply > a charged supercell. But you are right, there are cases in which > different charges can be associated to a given defect (think for > example at F centers that can exists in several charge states), and > here you do need charged supercells. QE can deals with these cases by > specifying the number of electrons in the system, and adding a > compensating uniform background. Note that in these cases, > thermodynamic arguments allow for predicting which is the most stable > defect in given environment conditions. There are several studies > about this issues (including the screening), the first ones I found in > my records are these for ionic systems PRB 68, 085110 (2003) and PRB > 59, 797 (1999); and this one for semiconductors: PRL 67, 2339 (1991). > These, and the references in within, should give you enough concepts > (and keywords) to performs more focused literature research. > > Yours sincerely, > Stefano > On 19 Aug 2009, at 10:39, ali kazempour wrote: > > > Hi > > I want to know if espresso can do charged vacancy calculation or > > not? I know about isolated atoms but I am not sure about big bulk > > supercell? > > If it can, how we can put the charge on the right position of the > > vacancy(which constraint should we introduced)? > > another question, Could anyone introduced me some reference about > > screening effect around the point defect? > > thanks a lot > > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Fabris > Theory at Elettra Group > CNR-INFM DEMOCRITOS National Simulation Center > c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE > website: www.democritos.it/the-group > email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776 > --- > > > > > > > > > > > > > > > ------------------------------ > > Message: 9 > Date: Wed, 19 Aug 2009 17:29:04 +0800 > From: Michael Sullivan > Subject: Re: [Pw_forum] Relax calculation in quantum espresso with 56 > atoms had not been converged > To: PWSCF Forum > Message-ID: > > > > > Content-Type: text/plain; charset="us-ascii" > > My two guesses are: > > (1) Ran out of time in the queue. > (2) Only allowed 40 optimization steps. > > That said, we need more information. Usually something will show up in the > error file that will give us a hint. > > Mike > michael at ihpc.a-star.edu.sg > http://www.sullivan.sg/ > > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Shaptrishi Sharma > Sent: Wednesday, August 19, 2009 5:13 PM > To: pw_forum at pwscf.org > Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had > not been converged > > Hi , > > I have submitted one relax calculation for 56 atoms in quantum espresso , > however after 39 iterations it stops without any further informations, nor > even a CRASH file. So any body can suggest me what the possible reason? > > Thanks > SS > > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please do > not copy or use it for any purpose, or disclose its contents to any other > person. Thank you. > > > ------------------------------ > > Message: 10 > Date: Wed, 19 Aug 2009 15:15:55 +0200 > From: Raji Abdulrafiu > Subject: [Pw_forum] insufficient virtual memory > To: pw_forum at pwscf.org > Message-ID: > <306556ed0908190615v460ee058ja0c27a2605e1a833 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear all, > > I am doing PDOS calculation for system ( 776 electrons ) using the > 'projwfc.x'. After some time, the error message below was written in > my output error file. > ..... > forrtl: severe (41): insufficient virtual memory > Image PC Routine Line > Source > projwfc.x 0000000000BF9C3A Unknown Unknown Unknown > projwfc.x 0000000000BF8E3A Unknown Unknown Unknown > projwfc.x 0000000000BAD71A Unknown Unknown Unknown > > I read through the responses to similar problem from the pwscf forum. > Following the recommended steps (by Profs. Eyvaz and Giannozzi), I > reduced the 'ecutwfc' and 'ecutrho' from 35Ry & 450 to 30Ry and > 350, respectively. The 'nbnd' was also reduced from 700 to 500. I set > 'diagonalization = david', to save the CPU time. Also "startingwfc"= > ''atomic' (default). Despite all these steps, the error persists, and > I am just not sure of what to do again. I need help please!. I am > using ver.4.0 of QE, and the calculation is being done using the > CINECA parallel computers. > > > Thank you > > Raji Abdulrafiu Tunde, > Solid state and Material Physics Group, > Department of Physics, > University of Cape Town, > Private Bag X3, > Rondebosch 7701, > Cape Town. South Africa. > Cell: +27722668228 > Fax: +27216503342 > > > ------------------------------ > > _______________________________________________ > 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 52 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/46f21d61/attachment-0001.htm From paulatto at sissa.it Wed Aug 19 16:08:04 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 19 Aug 2009 16:08:04 +0200 Subject: [Pw_forum] insufficient virtual memory In-Reply-To: <306556ed0908190615v460ee058ja0c27a2605e1a833@mail.gmail.com> References: <306556ed0908190615v460ee058ja0c27a2605e1a833@mail.gmail.com> Message-ID: In data 19 agosto 2009 alle ore 15:15:55, Raji Abdulrafiu ha scritto: > Despite all these steps, the error persists, and > I am just not sure of what to do again. I need help please!. I am > using ver.4.0 of QE, and the calculation is being done using the > CINECA parallel computers. Dear Raji, the memory usage of projwfc.x only depends on the wfc cutoff, all the other chages were probably irrelevant. The code loads the wavefunctions for all bands from one k point at a time, and for all atomic wavefunctions at the same time. The amount of required memory can increase fast with the number of atoms and with the number of bands. Furthermore that code is not parallelized (at the moment), this could cause some problem. I would advice you to request an entire node (4 processors) for the calculation and than only use one processor, in this way you'll have 8GB of RAM all for yourself. If it still does not work, please ask again providing more detail about your system, and *important* the version of QE you are using. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From yccheng.nju at gmail.com Wed Aug 19 16:15:13 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 19 Aug 2009 22:15:13 +0800 Subject: [Pw_forum] LDA+U for noncollinear Message-ID: Dear pwscf users, LDA+U method can work with spin polarized case as example 25. However, it seems that LDA+U can not work with noncollinear calculation. A previous link mentioned this problem http://www.democritos.it/pipermail/pw_forum/2005-May/002552.html. Has this problem been solved in V4.1? Thank you in advance. sincerely, -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/1f06db92/attachment.htm From asafis at yahoo.com.br Wed Aug 19 16:41:07 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Wed, 19 Aug 2009 07:41:07 -0700 (PDT) Subject: [Pw_forum] magnetic coupling Message-ID: <975251.21172.qm@web52306.mail.re2.yahoo.com> Hello everyone. I'm trying to calculate the magnetic coupling in a dinuclear compound of copper. Compared with the experimental results, we find that the magnitude of the magnetic moments are not good. What can I try to change parameters to get a better result? Regards, A. S. Santos ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/5c0df722/attachment.htm From asafis at yahoo.com.br Wed Aug 19 17:27:27 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Wed, 19 Aug 2009 08:27:27 -0700 (PDT) Subject: [Pw_forum] magnetic coupling Message-ID: <522927.95962.qm@web52310.mail.re2.yahoo.com> ? Hello everyone. I'm trying to calculate the magnetic coupling in a dinuclear compound of copper. Compared with the experimental results, we find that the magnitude of the magnetic moments are not good. What can I try to change parameters to get a better result? Regards, A. S. Santos __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/840b07ef/attachment.htm From asafis at yahoo.com.br Wed Aug 19 19:19:08 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Wed, 19 Aug 2009 10:19:08 -0700 (PDT) Subject: [Pw_forum] magnetic coupling Message-ID: <214325.78074.qm@web52303.mail.re2.yahoo.com> Hello everyone. I'm trying to calculate the magnetic coupling in a dinuclear compound of copper. Compared with the experimental results, we find that the magnitude of the magnetic moments are not good. What can I try to change parameters to get a better result? Regards, A. S. Alves __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/6362f30f/attachment.htm From asafis at yahoo.com.br Wed Aug 19 19:36:15 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Wed, 19 Aug 2009 10:36:15 -0700 (PDT) Subject: [Pw_forum] magnetic coupling Message-ID: <756194.88880.qm@web52302.mail.re2.yahoo.com> Hello everyone. I'm trying to calculate the magnetic coupling in a dinuclear compound of copper. Compared with the experimental results, we find that the magnitude of the magnetic moments are not good. What can I try to change parameters to get a better result? Regards, A. S. Alves ----- Mensagem encaminhada ---- De: ?lvaro Alves Para: pw_forum at pwscf.org Enviadas: Quarta-feira, 19 de Agosto de 2009 12:27:27 Assunto: [Pw_forum] magnetic coupling __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/0566679b/attachment.htm From nab83 at cornell.edu Wed Aug 19 20:28:11 2009 From: nab83 at cornell.edu (Nicole Benedek) Date: Wed, 19 Aug 2009 14:28:11 -0400 Subject: [Pw_forum] More ncpp2upf and fhi2upf Message-ID: <4A8C443B.7090209@cornell.edu> Dear All, I am trying to convert from opium's ncpp (or fhi) format to upf and have been following the recent discussions here. The advice (from Eric Walter) seems to be to use fhi2upf instead of ncpp2upf, since ncpp2upf seems to be broken if you have augmentation operators (which I do). However, fhi2upf will not convert potentials with semi-core states, which I also have. Are there any hacks or workarounds, either in espresso or opium, for psps that have both augmentation operators and semi-core states? I have tried modifying fhi2upf to deal with semi-core states, but without much success. Cheers, Nicole Dr Nicole Benedek Research Associate Cornell Center for Materials Research Cornell University From lanhaiping at gmail.com Wed Aug 19 21:08:11 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 20 Aug 2009 03:08:11 +0800 Subject: [Pw_forum] More ncpp2upf and fhi2upf In-Reply-To: <4A8C443B.7090209@cornell.edu> References: <4A8C443B.7090209@cornell.edu> Message-ID: Hi, Nicole: Would you like to give me some advices on generating semi-core pseudopotential with Opium ? I always find it is quite difficult to have a proper configurations and related cut-off radius for semi-core PPs. If possible, please share some of your experience. About fhi2upf, from my previous experience, i didnot come to this problem with semicore-PPs generated by fhi98pp, since I donot succeed in generating any proper semicore PPs with opium. Regards, On Thu, Aug 20, 2009 at 2:28 AM, Nicole Benedek wrote: > Dear All, > > I am trying to convert from opium's ncpp (or fhi) format to upf and have > been following the recent discussions here. The advice (from Eric Walter) > seems to be to use fhi2upf instead of ncpp2upf, since ncpp2upf seems to be > broken if you have augmentation operators (which I do). However, fhi2upf > will not convert potentials with semi-core states, which I also have. Are > there any hacks or workarounds, either in espresso or opium, for psps that > have both augmentation operators and semi-core states? I have tried > modifying fhi2upf to deal with semi-core states, but without much success. > > Cheers, > Nicole > > Dr Nicole Benedek > Research Associate > Cornell Center for Materials Research > Cornell University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090820/f0230227/attachment.htm From ejwalt at wm.edu Wed Aug 19 21:25:03 2009 From: ejwalt at wm.edu (Eric J. Walter) Date: Wed, 19 Aug 2009 15:25:03 -0400 Subject: [Pw_forum] More ncpp2upf and fhi2upf In-Reply-To: <4A8C443B.7090209@cornell.edu> References: <4A8C443B.7090209@cornell.edu> Message-ID: <4A8C518F.4050400@wm.edu> Hi, I have used fhi2upf.x for conversion of an fhi psp with both semicore and augmentation operators. Perhaps you could send me your output from fhi2upf? Also, I would like to state publicly that it is OPIUM's fault NOT ncpp2upf that the conversion you are discussing fails. Perhaps it is better to send questions like these to the OPIUM mailing list? opium-talk at sourceforge.net Regards, Eric Nicole Benedek wrote: > Dear All, > > I am trying to convert from opium's ncpp (or fhi) format to upf and have been following the recent discussions here. The advice (from Eric Walter) seems to be to use fhi2upf instead of ncpp2upf, since ncpp2upf seems to be broken if you have augmentation operators (which I do). However, fhi2upf will not convert potentials with semi-core states, which I also have. Are there any hacks or workarounds, either in espresso or opium, for psps that have both augmentation operators and semi-core states? I have tried modifying fhi2upf to deal with semi-core states, but without much success. > > Cheers, > Nicole > > Dr Nicole Benedek > Research Associate > Cornell Center for Materials Research > Cornell University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Wed Aug 19 22:14:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 19 Aug 2009 22:14:53 +0200 Subject: [Pw_forum] More ncpp2upf and fhi2upf In-Reply-To: <4A8C443B.7090209@cornell.edu> References: <4A8C443B.7090209@cornell.edu> Message-ID: <200908192214.54683.giannozz@democritos.it> On Wednesday 19 August 2009 20:28, Nicole Benedek wrote: > [...] ncpp2upf seems to be broken if you have augmentation operators I beg your pardon: "augmentation operators" in norm conserving pseudopotentials? and how can a converter from an obsolete format be broken? it hasn't changed since a long time paolo -- Paolo Giannozzi, Democritos and Udine University From jjr19 at uakron.edu Wed Aug 19 22:49:23 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Wed, 19 Aug 2009 13:49:23 -0700 (PDT) Subject: [Pw_forum] More ncpp2upf and fhi2upf In-Reply-To: <4A8C518F.4050400@wm.edu> References: <4A8C443B.7090209@cornell.edu> <4A8C518F.4050400@wm.edu> Message-ID: <903450.79785.qm@web50909.mail.re2.yahoo.com> ----- Original Message ---- > From: Eric J. Walter > To: PWSCF Forum > Cc: opium-talk at lists.sourceforge.net > Sent: Wednesday, August 19, 2009 3:25:03 PM > Subject: Re: [Pw_forum] More ncpp2upf and fhi2upf > > > Hi, > > I have used fhi2upf.x for conversion of an fhi psp with both semicore > and augmentation operators. Perhaps you could send me your output from > fhi2upf? How do you get it to handle semicore? The documentation at the top of fhi2upf.f90 lists "no semicore states" as one of the restrictions of the program. From ejwalt at wm.edu Wed Aug 19 23:49:38 2009 From: ejwalt at wm.edu (Eric J. Walter) Date: Wed, 19 Aug 2009 17:49:38 -0400 Subject: [Pw_forum] More ncpp2upf and fhi2upf In-Reply-To: <903450.79785.qm@web50909.mail.re2.yahoo.com> References: <4A8C443B.7090209@cornell.edu> <4A8C518F.4050400@wm.edu> <903450.79785.qm@web50909.mail.re2.yahoo.com> Message-ID: <4A8C7372.4090605@wm.edu> J. J. Ramsey wrote: > ----- Original Message ---- > > >> From: Eric J. Walter >> To: PWSCF Forum >> Cc: opium-talk at lists.sourceforge.net >> Sent: Wednesday, August 19, 2009 3:25:03 PM >> Subject: Re: [Pw_forum] More ncpp2upf and fhi2upf >> >> >> Hi, >> >> I have used fhi2upf.x for conversion of an fhi psp with both semicore >> and augmentation operators. Perhaps you could send me your output from >> fhi2upf? >> > > How do you get it to handle semicore? The documentation at the top of fhi2upf.f90 lists "no semicore states" as one of the restrictions of the program. > > > > OPIUM generates single projector pseudopotentials. The term "semicore" pseudopotential means, in this case, for Ti, that 3s and 3p are used for the 's' and 'p' semilocal potentials instead of 4s and 4p. As long as there is only one potential per ang. mom., the fhi2psp code seems to work fine for this case. Is this clear? Regards, Eric > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From Michael at ihpc.a-star.edu.sg Thu Aug 20 03:15:29 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Thu, 20 Aug 2009 09:15:29 +0800 Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had not been converged In-Reply-To: References: Message-ID: You may have set nstep to 40. If you are using BFGS, it could be that it actually took 50 steps (the default, I think) but it only used the last 39 steps. Have a look at the energies and see how it looks by using a grep command like this: grep "! total energy " If you add -c to grep then it should give you the number of optimization steps it took. If this isn't the case, then you'll need to share more information and it could be an issue with your computer. Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Shaptrishi Sharma Sent: Wednesday, August 19, 2009 9:55 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Pw_forum Digest, Vol 26, Issue 52 Hi Mike, Thansk for your help, well I cannot understand your this point "Only allowed 40 optimization steps." How do we know that the optimisation steps are 40 and why?? Thanks SS My two guesses are: (1) Ran out of time in the queue. (2) Only allowed 40 optimization steps. That said, we need more information. Usually something will show up in the error file that will give us a hint. Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Shaptrishi Sharma Sent: Wednesday, August 19, 2009 5:13 PM To: pw_forum at pwscf.org Subject: [Pw_forum] Relax calculation in quantum espresso with 56 atoms had not been converged Hi , I have submitted one relax calculation for 56 atoms in quantum espresso , however after 39 iterations it stops without any further informations, nor even a CRASH file. So any body can suggest me what the possible reason? Thanks SS This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From lfhuang at theory.issp.ac.cn Thu Aug 20 05:50:10 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 20 Aug 2009 11:50:10 +0800 Subject: [Pw_forum] =?utf-8?q?magnetic_coupling?= Message-ID: <20090820035010.32013.qmail@ms.hfcas.ac.cn> Dear A.S.Santos: First, please attach your affiliation at the bottom of your letter, because it is a nettiquette; Second, please give more detailed information/data on your work if you want anyone to answer your question; Third, please do not send FOUR letters on the same title at one time! Just one is enough. Best Wishes! Yours Sincerely > From: ?lvaro Alves > Subject: [Pw_forum] magnetic coupling > To: pw > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone. I'm trying to calculate the magnetic coupling in a dinuclear compound of copper. Compared with the experimental results, we find that the magnitude of the magnetic moments are not good. What can I try to change parameters to get a better result? > > Regards, > > A. S. Santos > Subject: [Pw_forum] magnetic coupling > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > ? Hello everyone. I'm trying to calculate the magnetic coupling in a > dinuclear compound of copper. Compared with the experimental results, > we find that the magnitude of the magnetic moments are not good. What > can I try to change parameters to get a better result? > > Regards, > > A. S. Santos > > > > __________________________________________________ > Fale com seus amigos de gra?a com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090819/840b07ef/attachment-0001.htm > > Subject: [Pw_forum] magnetic coupling > To: pw > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone. I'm trying to calculate the magnetic coupling in a > dinuclear compound of copper. Compared with the experimental results, > we find that the magnitude of the magnetic moments are not good. What > can I try to change parameters to get a better result? > > Regards, > > A. S. Alves > > Subject: [Pw_forum] magnetic coupling > To: pw > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone. I'm trying to calculate the magnetic coupling in a > dinuclear compound of copper. Compared with the experimental results, > we find that the magnitude of the magnetic moments are not good. What > can I try to change parameters to get a better result? > > Regards, > > A. S. Alves > ------ ====================================================================== L.F.Huang(???) ph.D candidate ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090820/178143f4/attachment.htm From sclauzer at sissa.it Thu Aug 20 08:40:48 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 20 Aug 2009 08:40:48 +0200 Subject: [Pw_forum] Request for Er pseudo potential In-Reply-To: References: Message-ID: <4A8CEFF0.6050607@sissa.it> If you are interested in PAW, please give a look at this post from the forum archives: http://www.democritos.it/pipermail/pw_forum/2009-May/012897.html GS dev sharma wrote: > hi all, > I would be very thankful , if someone can provide (Er) Erbium > pseudo-potential, as i dont know how to make pseudo-potentiall and it is > also not present on PWscf pseudo list. > I will be very thankful. > > With regards, > Dev Sharma, > University of Delhi > India > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Aug 20 09:01:10 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 20 Aug 2009 09:01:10 +0200 Subject: [Pw_forum] insufficient virtual memory In-Reply-To: References: <306556ed0908190615v460ee058ja0c27a2605e1a833@mail.gmail.com> Message-ID: <4A8CF4B6.8020307@sissa.it> Lorenzo Paulatto wrote: > In data 19 agosto 2009 alle ore 15:15:55, Raji Abdulrafiu > ha scritto: >> Despite all these steps, the error persists, and >> I am just not sure of what to do again. I need help please!. I am >> using ver.4.0 of QE, and the calculation is being done using the >> CINECA parallel computers. > > Dear Raji, > the memory usage of projwfc.x only depends on the wfc cutoff, all the > other chages were probably irrelevant. > > The code loads the wavefunctions for all bands from one k point at a time, > and for all atomic wavefunctions at the same time. The amount of required > memory can increase fast with the number of atoms and with the number of > bands. Furthermore that code is not parallelized (at the moment), this > could cause some problem. I agree with all above, but I'm pretty sure that projwfc has been parallelized over G vectors and even over pools (although the latter does not distribute memory). It has not been parallelized with tasks, so that each pool works on all the bands. If the problem is actually a memory issue (but in my experience if the scf/nscf run worked on the same number of nodes, the PDOS calculations should work as well, since I believe it uses less memory than the corresponding pw.x calculation), you can specify wf_collect=.TRUE. in the pw.x run (in scf you don't need to repeat the self-consistency cycle, simply do a restart calculation) and then run projwfc.x on a larger number of processors (at fixed number of pools!), larger than whatever used for the pw.x run. In this was you can distribute more memory via R&G space parallelization. > > I would advice you to request an entire node (4 processors) for the > calculation and than only use one processor, in this way you'll have 8GB > of RAM all for yourself. This is also a good solution. Anyway, if you still want to run parallel and need more than one node, you have to be sure that the MPI implementation is distributing one process per node. HTH GS If it still does not work, please ask again > providing more detail about your system, and *important* the version of QE > you are using. > > best regards > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Aug 20 09:08:35 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 20 Aug 2009 09:08:35 +0200 Subject: [Pw_forum] magnetic coupling In-Reply-To: <756194.88880.qm@web52302.mail.re2.yahoo.com> References: <756194.88880.qm@web52302.mail.re2.yahoo.com> Message-ID: <4A8CF673.4090504@sissa.it> Dear Alvaro, You would have more change to get a reply if you put a reward to your question, rather than sending many times the same mail :-) ?lvaro Alves wrote: > Hello everyone. I'm trying to calculate the magnetic coupling in a > dinuclear compound of copper. Compared with the experimental results, we > find that the magnitude of the magnetic moments are not good. What can I > try to change parameters to get a better result? You would have more change to get a meaningful reply if you gave us more details on your system. What I can suggest from guessing your problem is to either to try DFT+U or to force magnetization/magnetic moments to a desired value using constrained magnetization (see Doc/INPUT_PW.txt). Cheers GS > > Regards, > > A. S. Alves > > > ----- Mensagem encaminhada ---- > *De:* ?lvaro Alves > *Para:* pw_forum at pwscf.org > *Enviadas:* Quarta-feira, 19 de Agosto de 2009 12:27:27 > *Assunto:* [Pw_forum] magnetic coupling > > > > > __________________________________________________ > Fale com seus amigos de gra?a com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ > > __________________________________________________ > Fale com seus amigos de gra?a com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ouuing at gmail.com Thu Aug 20 11:07:42 2009 From: ouuing at gmail.com (liu hanyu) Date: Thu, 20 Aug 2009 17:07:42 +0800 Subject: [Pw_forum] Lo-To spliting Message-ID: hello: i want to ask a question that I want to calculate Lo-To spliting whether or not I only calculate the G point frequency. can that get result what i want ? thank you ! -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), MS. State key Laboratory of Superhard Materials, Jilin University, China Email: ouuing at email.jlu.edu.cn ouuing at gmail.com From paguado at gmail.com Thu Aug 20 12:52:05 2009 From: paguado at gmail.com (Pablo Aguado) Date: Thu, 20 Aug 2009 12:52:05 +0200 Subject: [Pw_forum] meaning of delgep & cutplot Message-ID: Dear all, I'm learning how to compute complex band structures following example 12 in Espresso package. One of the inputs for PWCOND provided in this example is as follows: &inputcond outdir='/home/xxxxxxx/tmp/' prefixl='al' band_file ='bands.al' ikind=0 energy0=10.d0 denergy=-0.4d0 ewind=1.d0 epsproj=1.d-3 delgep = 1.d-12 cutplot = 3.d0 / 1 0.0 0.0 1.0 60 My question is, what are the meanings of the variables delgep and cutplot? Because I can't find them in the input file description. Thank you in advance Pablo From eyvaz_isaev at yahoo.com Thu Aug 20 12:53:50 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 20 Aug 2009 03:53:50 -0700 (PDT) Subject: [Pw_forum] Lo-To spliting In-Reply-To: Message-ID: <452422.84458.qm@web65708.mail.ac4.yahoo.com> Dear Liu, In order to get LO-TO splitting you have to calculate phonons at the Gamma point (why?) and then apply dynmat.x. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/20/09, liu hanyu wrote: > From: liu hanyu > Subject: [Pw_forum] Lo-To spliting > To: Pw_forum at pwscf.org > Date: Thursday, August 20, 2009, 1:07 PM > hello: > ? ? i? want to ask a question > that???I want to calculate Lo-To > spliting whether or not I only calculate the G > point frequency. can that get result what i want ? > ? thank you ! > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > MS. > State key? Laboratory of Superhard Materials, Jilin > University, China > Email: ouuing at email.jlu.edu.cn? > ? ? ouuing at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Thu Aug 20 14:18:46 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 20 Aug 2009 14:18:46 +0200 Subject: [Pw_forum] meaning of delgep & cutplot In-Reply-To: References: Message-ID: <4A8D3F26.9080804@sissa.it> Hi Pablo, Pablo Aguado wrote: > > My question is, what are the meanings of the variables delgep and > cutplot? Because I can't find them in the input file description. About the first question, please follow the thread: http://www.democritos.it/pipermail/pw_forum/2008-December/010899.html Quick answer: delgep is used to fix a problem with a LAPACK subroutine. In general you don't need to specify a value for it, you may need to increase if that specific problem arises with your copy of the LAPACK. About the second, from what I see in the code cutplot should be a cutoff on the imaginary part of a k_z vector used when writing complex bands to a separate output file. It does not modify the results of the transmission calculation by any means. I think this option should be documented in Doc/INPUT_PWCOND.def, but presently it is not. GS > > Thank you in advance > > Pablo > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From kazempoor2000 at yahoo.com Thu Aug 20 14:27:40 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 20 Aug 2009 05:27:40 -0700 (PDT) Subject: [Pw_forum] vc-relax or relax Message-ID: <314186.7829.qm@web112508.mail.gq1.yahoo.com> Dear All I make 72 atom supercell to study the effect of vacancy on defect formation energy. If I remove one atom do I run vc-relax or relax calculation only? I mean is this concentratio(1/72=0.013) high that affect? the lattice constant also or not? thanks a lot ? Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090820/b90d10f8/attachment.htm From paulatto at sissa.it Thu Aug 20 14:32:19 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 20 Aug 2009 14:32:19 +0200 Subject: [Pw_forum] vc-relax or relax In-Reply-To: <314186.7829.qm@web112508.mail.gq1.yahoo.com> References: <314186.7829.qm@web112508.mail.gq1.yahoo.com> Message-ID: In data 20 agosto 2009 alle ore 14:27:40, ali kazempour ha scritto: > I make 72 atom supercell to study the effect of vacancy on defect > formation energy. If I remove one atom do I run vc-relax or relax > calculation only? I mean is this concentratio(1/72=0.013) high that > affect the lattice constant also or not? Dear Ali, it is difficult to say, you can do a normal relax and print the pressure in order to see if it is low enough. It would also be interesting to know which is the vacancy concentration in the real system you are trying to simulate: is it 1/72 or is it much lower? In the latter case, you should definitely keep the cell parameter fixed. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From ttduyle at gmail.com Thu Aug 20 14:38:24 2009 From: ttduyle at gmail.com (Duy Le) Date: Thu, 20 Aug 2009 08:38:24 -0400 Subject: [Pw_forum] vc-relax or relax In-Reply-To: <314186.7829.qm@web112508.mail.gq1.yahoo.com> References: <314186.7829.qm@web112508.mail.gq1.yahoo.com> Message-ID: <8974d3b20908200538w6be0b167r4ba8d34fd48a250d@mail.gmail.com> Hi, It's not easy to tell unless you do your own test. Try to do your calculation with many different concentration (increase the size of cell) and compare the properties that are well-known (bondlength, formation energy...). In practice, the concentration of vacancies maybe about ZERO, my point is the large the cell is, the better. Best, D. On Thu, Aug 20, 2009 at 8:27 AM, ali kazempour wrote: > > Dear All > I make 72 atom supercell to study the effect of vacancy on defect formation > energy. If I remove one atom do I run vc-relax or relax calculation only? I > mean is this concentratio(1/72=0.013) high that affect the lattice constant > also or not? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Men don't need hands to do things! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090820/84d4d740/attachment.htm From lanhaiping at gmail.com Thu Aug 20 15:00:41 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 20 Aug 2009 21:00:41 +0800 Subject: [Pw_forum] vc-relax or relax In-Reply-To: <314186.7829.qm@web112508.mail.gq1.yahoo.com> References: <314186.7829.qm@web112508.mail.gq1.yahoo.com> Message-ID: Hi, Ali. I learned from some literature that Only ion-relaxation should be done if you want to examine defects' properties. You can find a book " Theory of Defects in Semiconductors" which has thorough discussion over this issue . Hope help. Regards On Thu, Aug 20, 2009 at 8:27 PM, ali kazempour wrote: > > Dear All > I make 72 atom supercell to study the effect of vacancy on defect formation > energy. If I remove one atom do I run vc-relax or relax calculation only? I > mean is this concentratio(1/72=0.013) high that affect the lattice constant > also or not? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090820/3497a4a0/attachment.htm From marcello.rosini at unimore.it Thu Aug 20 16:01:58 2009 From: marcello.rosini at unimore.it (Marcello Rosini) Date: Thu, 20 Aug 2009 16:01:58 +0200 Subject: [Pw_forum] average potential Message-ID: <4A8D5756.3040803@unimore.it> Hallo everybody I am now extracting the average potential from some structures... The procedure used is the following: I run pw.x, then I run pp.x with plot_num=1 and plot_num=2, finally average.x, with the sum of the two files obtained from pp.x Here the questions: 1. In pp.x, what is the V_bare? 2. when summing and averaging the total local potential I expect to find a zero average. This does not happen, is my procedure wrong? 3. Is pw.x able to print somewhere the total local potential in k-space, V(G)? how should I do? 4. Is it true for pw.x V(G=0)=0? I am trying to find some answer by reading the source code, but any help will be greatly appreciated. Thanks Marcello -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dipartimento di Fisica, Universit? di Modena e Reggio Emilia and S3 National Research Centre of CNR-INFM via campi 213/a - 41125 Modena - Italy tel: +39 059.205.5067 email: marcello.rosini at unimore.it www.nanomodelling.unimore.it ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From kazempoor2000 at yahoo.com Thu Aug 20 17:11:48 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 20 Aug 2009 08:11:48 -0700 (PDT) Subject: [Pw_forum] force Message-ID: <887803.65890.qm@web112517.mail.gq1.yahoo.com> Dear I use vc-relax to optimize the lattice constant and also the position for bulk. After I make supercell with these optimized value and run a scf with similar value as bulk. But the force as I listed below for some atom is relatively more than other. Is it good for force or should I do again vc-relax for supercell? Forces acting on atoms (Ry/au): ???? atom?? 1 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00000000 ???? atom?? 2 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00000000 ???? atom?? 3 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00000000 ???? atom?? 4 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00000000 ???? atom?? 5 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00020439 ???? atom?? 6 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00020567 ???? atom?? 7 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00020567 ???? atom?? 8 type? 1?? force =???? 0.00000000??? 0.00000000??? 0.00020315 ???? atom?? 9 type? 1?? force =???? 0.00000000??? 0.00000000?? -0.00020439 ???? atom? 10 type? 1?? force =???? 0.00000000??? 0.00000000?? -0.00020567 ???? atom? 11 type? 1?? force =???? 0.00000000??? 0.00000000?? -0.00020567 ???? atom? 12 type? 1?? force =???? 0.00000000??? 0.00000000?? -0.00020315 ???? atom? 13 type? 1?? force =??? -0.00000152?? -0.00000152?? -0.00019723 ???? atom? 14 type? 1?? force =???? 0.00000136?? -0.00000136?? -0.00019719 ???? atom? 15 type? 1?? force =??? -0.00000136??? 0.00000136?? -0.00019719 ???? atom? 16 type? 1?? force =???? 0.00000152??? 0.00000152?? -0.00019723 ???? atom? 17 type? 1?? force =??? -0.00000186?? -0.00000186??? 0.00000000 ???? atom? 18 type? 1?? force =???? 0.00000137?? -0.00000137??? 0.00000000 ???? atom? 19 type? 1?? force =??? -0.00000137??? 0.00000137??? 0.00000000 ???? atom? 20 type? 1?? force =???? 0.00000186??? 0.00000186??? 0.00000000 ???? atom? 21 type? 1?? force =??? -0.00000152?? -0.00000152??? 0.00019723 ???? atom? 22 type? 1?? force =???? 0.00000136?? -0.00000136??? 0.00019719 ???? atom? 23 type? 1?? force =??? -0.00000136??? 0.00000136??? 0.00019719 ???? atom? 24 type? 1?? force =???? 0.00000152??? 0.00000152??? 0.00019723 ???? atom? 25 type? 2?? force =??? -0.00126659?? -0.00126659??? 0.00000000 ???? atom? 26 type? 2?? force =??? -0.00126600?? -0.00126594??? 0.00000000 ???? atom? 27 type? 2?? force =??? -0.00126594?? -0.00126600??? 0.00000000 ???? atom? 28 type? 2?? force =??? -0.00126811?? -0.00126811??? 0.00000000 ???? atom? 29 type? 2?? force =??? -0.00120604?? -0.00120604??? 0.00011420 ???? atom? 30 type? 2?? force =??? -0.00120546?? -0.00120538??? 0.00011547 ???? atom? 31 type? 2?? force =??? -0.00120538?? -0.00120546??? 0.00011547 ???? atom? 32 type? 2?? force =??? -0.00120536?? -0.00120536??? 0.00011440 ???? atom? 33 type? 2?? force =??? -0.00120604?? -0.00120604?? -0.00011420 ???? atom? 34 type? 2?? force =??? -0.00120546?? -0.00120538?? -0.00011547 ???? atom? 35 type? 2?? force =??? -0.00120538?? -0.00120546?? -0.00011547 ???? atom? 36 type? 2?? force =??? -0.00120536?? -0.00120536?? -0.00011440 ???? atom? 37 type? 2?? force =???? 0.00126811??? 0.00126811??? 0.00000000 ???? atom? 38 type? 2?? force =???? 0.00126594??? 0.00126600??? 0.00000000 ???? atom? 39 type? 2?? force =???? 0.00126600??? 0.00126594??? 0.00000000 ???? atom? 40 type? 2?? force =???? 0.00126659??? 0.00126659??? 0.00000000 ???? atom? 41 type? 2?? force =???? 0.00120536??? 0.00120536??? 0.00011440 ???? atom? 42 type? 2?? force =???? 0.00120538??? 0.00120546??? 0.00011547 ???? atom? 43 type? 2?? force =???? 0.00120546??? 0.00120538??? 0.00011547 ???? atom? 44 type? 2?? force =???? 0.00120604??? 0.00120604??? 0.00011420 ???? atom? 45 type? 2?? force =???? 0.00120536??? 0.00120536?? -0.00011440 ???? atom? 46 type? 2?? force =???? 0.00120538??? 0.00120546?? -0.00011547 ???? atom? 47 type? 2?? force =???? 0.00120546??? 0.00120538?? -0.00011547 ???? atom? 48 type? 2?? force =???? 0.00120604??? 0.00120604?? -0.00011420 ???? atom? 49 type? 2?? force =??? -0.00120811??? 0.00120812?? -0.00010994 ???? atom? 50 type? 2?? force =??? -0.00120609??? 0.00120609?? -0.00011010 ???? atom? 51 type? 2?? force =??? -0.00120474??? 0.00120474?? -0.00011334 ???? atom? 52 type? 2?? force =??? -0.00120812??? 0.00120811?? -0.00010994 ???? atom? 53 type? 2?? force =??? -0.00126901??? 0.00126929??? 0.00000000 ???? atom? 54 type? 2?? force =??? -0.00126831??? 0.00126831??? 0.00000000 ???? atom? 55 type? 2?? force =??? -0.00126875??? 0.00126875??? 0.00000000 ???? atom? 56 type? 2?? force =??? -0.00126929??? 0.00126901??? 0.00000000 ???? atom? 57 type? 2?? force =??? -0.00120811??? 0.00120812??? 0.00010994 ???? atom? 58 type? 2?? force =??? -0.00120609??? 0.00120609??? 0.00011010 ???? atom? 59 type? 2?? force =??? -0.00120474??? 0.00120474??? 0.00011334 ???? atom? 60 type? 2?? force =??? -0.00120812??? 0.00120811??? 0.00010994 ???? atom? 61 type? 2?? force =???? 0.00120812?? -0.00120811?? -0.00010994 ???? atom? 62 type? 2?? force =???? 0.00120474?? -0.00120474?? -0.00011334 ???? atom? 63 type? 2?? force =???? 0.00120609?? -0.00120609?? -0.00011010 ???? atom? 64 type? 2?? force =???? 0.00120811?? -0.00120812?? -0.00010994 ???? atom? 65 type? 2?? force =???? 0.00126929?? -0.00126901??? 0.00000000 ???? atom? 66 type? 2?? force =???? 0.00126875?? -0.00126875??? 0.00000000 ???? atom? 67 type? 2?? force =???? 0.00126831?? -0.00126831??? 0.00000000 ???? atom? 68 type? 2?? force =???? 0.00126901?? -0.00126929??? 0.00000000 ???? atom? 69 type? 2?? force =???? 0.00120812?? -0.00120811??? 0.00010994 ???? atom? 70 type? 2?? force =???? 0.00120474?? -0.00120474??? 0.00011334 ???? atom? 71 type? 2?? force =???? 0.00120609?? -0.00120609??? 0.00011010 ???? atom? 72 type? 2?? force =???? 0.00120811?? -0.00120812??? 0.00010994 ???? Total force =???? 0.012066???? Total SCF correction =???? 0.000257 ???? entering subroutine stress ... ????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=? -90.60 ? -0.00062585?? 0.00000003?? 0.00000000??????? -92.07????? 0.00????? 0.00 ?? 0.00000003? -0.00062585?? 0.00000000????????? 0.00??? -92.07????? 0.00 ?? 0.00000000?? 0.00000000? -0.00059589????????? 0.00????? 0.00??? -87.66 thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090820/e42130bb/attachment.htm From paulatto at sissa.it Thu Aug 20 17:38:52 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 20 Aug 2009 17:38:52 +0200 Subject: [Pw_forum] average potential In-Reply-To: <4A8D5756.3040803@unimore.it> References: <4A8D5756.3040803@unimore.it> Message-ID: Dear Marcello, I'll try to answer as correctly as possible, but I'm not checking the code for each point, so there could be some minor discrepancy with reality. In data 20 agosto 2009 alle ore 16:01:58, Marcello Rosini ha scritto: > 1. In pp.x, what is the V_bare? the superposition of the local potentials from the pseudopotentials. I.e. the descreened potential of the ions. It may contain some other piece, though, in some specific case (maybe the jigsaw potential, but that's easy to spot). > 2. when summing and averaging the total local potential I expect to find > a zero average. This does not happen, is my procedure wrong? Not really, the average of the *total* potential has to be zero. But this is only enforced when the total potential is computed. Actually, I'm not even sure that's what happening, see point 4. > 3. Is pw.x able to print somewhere the total local potential in k-space, > V(G)? how should I do? In module scf there is the object "v" which is a derived type. rho%of_g(ngm,nspin) is what you are looking for. You can also grab it from v_of_rho.f90 as soon as it is computed. > 4. Is it true for pw.x V(G=0)=0? I'm not sure, there is a variable called v_of_0 that is set to the G=0 component of the local potential, and used to offset the bands. I think this is an equivalent approach, but I don't know the details. > I am trying to find some answer by reading the source code, but any help > will be greatly appreciated. you're welcome -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nkxirainbow at gmail.com Thu Aug 20 17:48:12 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 20 Aug 2009 23:48:12 +0800 Subject: [Pw_forum] force In-Reply-To: <887803.65890.qm@web112517.mail.gq1.yahoo.com> References: <887803.65890.qm@web112517.mail.gq1.yahoo.com> Message-ID: <21fbc4790908200848g335cdc8oe18845574b2aee89@mail.gmail.com> Dear ali kazempour: > entering subroutine stress ... > > total stress (Ry/bohr**3) (kbar) P= > -90.60 > -0.00062585 0.00000003 0.00000000 -92.07 0.00 0.00 > 0.00000003 -0.00062585 0.00000000 0.00 -92.07 0.00 > 0.00000000 0.00000000 -0.00059589 0.00 0.00 -87.66 I notice that the stress is "*P= -90.60*". I think this value indicates that your structure do not find equilibrium. What is the value of "*press_conv_thr*" when you use vc-relax to optimize the lattice constant? What is the value of "*K_POINTS*" for your different calculations? I think you need to give input and output files for your calculations. ____________________________________ 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/20090820/16abcf77/attachment-0001.htm From lanhaiping at gmail.com Thu Aug 20 20:35:19 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 21 Aug 2009 02:35:19 +0800 Subject: [Pw_forum] force In-Reply-To: <887803.65890.qm@web112517.mail.gq1.yahoo.com> References: <887803.65890.qm@web112517.mail.gq1.yahoo.com> Message-ID: Dear Ali : What the force thread you set for the unit cell ? i.e, forc_conv_thr . The values you posted here are quite close to the default setting , 1.0D-3. Therefore, You can run ion-relaxation to satisfy yourself, whichi i think is not a computation burden. If you have built your unitcell system with satisfied accuaray, there is no reason to make cell relation for a supercell. Regards, On Thu, Aug 20, 2009 at 11:11 PM, ali kazempour wrote: > Dear > I use vc-relax to optimize the lattice constant and also the position for > bulk. After I make supercell with these optimized value and run a scf with > similar value as bulk. But the force as I listed below for some atom is > relatively more than other. Is it good for force or should I do again > vc-relax for supercell? > Forces acting on atoms (Ry/au): > > atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 > atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 > atom 3 type 1 force = 0.00000000 0.00000000 0.00000000 > atom 4 type 1 force = 0.00000000 0.00000000 0.00000000 > atom 5 type 1 force = 0.00000000 0.00000000 0.00020439 > atom 6 type 1 force = 0.00000000 0.00000000 0.00020567 > atom 7 type 1 force = 0.00000000 0.00000000 0.00020567 > atom 8 type 1 force = 0.00000000 0.00000000 0.00020315 > atom 9 type 1 force = 0.00000000 0.00000000 -0.00020439 > atom 10 type 1 force = 0.00000000 0.00000000 -0.00020567 > atom 11 type 1 force = 0.00000000 0.00000000 -0.00020567 > atom 12 type 1 force = 0.00000000 0.00000000 -0.00020315 > atom 13 type 1 force = -0.00000152 -0.00000152 -0.00019723 > atom 14 type 1 force = 0.00000136 -0.00000136 -0.00019719 > atom 15 type 1 force = -0.00000136 0.00000136 -0.00019719 > atom 16 type 1 force = 0.00000152 0.00000152 -0.00019723 > atom 17 type 1 force = -0.00000186 -0.00000186 0.00000000 > atom 18 type 1 force = 0.00000137 -0.00000137 0.00000000 > atom 19 type 1 force = -0.00000137 0.00000137 0.00000000 > atom 20 type 1 force = 0.00000186 0.00000186 0.00000000 > atom 21 type 1 force = -0.00000152 -0.00000152 0.00019723 > atom 22 type 1 force = 0.00000136 -0.00000136 0.00019719 > atom 23 type 1 force = -0.00000136 0.00000136 0.00019719 > atom 24 type 1 force = 0.00000152 0.00000152 0.00019723 > atom 25 type 2 force = -0.00126659 -0.00126659 0.00000000 > atom 26 type 2 force = -0.00126600 -0.00126594 0.00000000 > atom 27 type 2 force = -0.00126594 -0.00126600 0.00000000 > atom 28 type 2 force = -0.00126811 -0.00126811 0.00000000 > atom 29 type 2 force = -0.00120604 -0.00120604 0.00011420 > atom 30 type 2 force = -0.00120546 -0.00120538 0.00011547 > atom 31 type 2 force = -0.00120538 -0.00120546 0.00011547 > atom 32 type 2 force = -0.00120536 -0.00120536 0.00011440 > atom 33 type 2 force = -0.00120604 -0.00120604 -0.00011420 > atom 34 type 2 force = -0.00120546 -0.00120538 -0.00011547 > atom 35 type 2 force = -0.00120538 -0.00120546 -0.00011547 > atom 36 type 2 force = -0.00120536 -0.00120536 -0.00011440 > atom 37 type 2 force = 0.00126811 0.00126811 0.00000000 > atom 38 type 2 force = 0.00126594 0.00126600 0.00000000 > atom 39 type 2 force = 0.00126600 0.00126594 0.00000000 > atom 40 type 2 force = 0.00126659 0.00126659 0.00000000 > atom 41 type 2 force = 0.00120536 0.00120536 0.00011440 > atom 42 type 2 force = 0.00120538 0.00120546 0.00011547 > atom 43 type 2 force = 0.00120546 0.00120538 0.00011547 > atom 44 type 2 force = 0.00120604 0.00120604 0.00011420 > atom 45 type 2 force = 0.00120536 0.00120536 -0.00011440 > atom 46 type 2 force = 0.00120538 0.00120546 -0.00011547 > atom 47 type 2 force = 0.00120546 0.00120538 -0.00011547 > atom 48 type 2 force = 0.00120604 0.00120604 -0.00011420 > atom 49 type 2 force = -0.00120811 0.00120812 -0.00010994 > atom 50 type 2 force = -0.00120609 0.00120609 -0.00011010 > atom 51 type 2 force = -0.00120474 0.00120474 -0.00011334 > atom 52 type 2 force = -0.00120812 0.00120811 -0.00010994 > atom 53 type 2 force = -0.00126901 0.00126929 0.00000000 > atom 54 type 2 force = -0.00126831 0.00126831 0.00000000 > atom 55 type 2 force = -0.00126875 0.00126875 0.00000000 > atom 56 type 2 force = -0.00126929 0.00126901 0.00000000 > atom 57 type 2 force = -0.00120811 0.00120812 0.00010994 > atom 58 type 2 force = -0.00120609 0.00120609 0.00011010 > atom 59 type 2 force = -0.00120474 0.00120474 0.00011334 > atom 60 type 2 force = -0.00120812 0.00120811 0.00010994 > atom 61 type 2 force = 0.00120812 -0.00120811 -0.00010994 > atom 62 type 2 force = 0.00120474 -0.00120474 -0.00011334 > atom 63 type 2 force = 0.00120609 -0.00120609 -0.00011010 > atom 64 type 2 force = 0.00120811 -0.00120812 -0.00010994 > atom 65 type 2 force = 0.00126929 -0.00126901 0.00000000 > atom 66 type 2 force = 0.00126875 -0.00126875 0.00000000 > atom 67 type 2 force = 0.00126831 -0.00126831 0.00000000 > atom 68 type 2 force = 0.00126901 -0.00126929 0.00000000 > atom 69 type 2 force = 0.00120812 -0.00120811 0.00010994 > atom 70 type 2 force = 0.00120474 -0.00120474 0.00011334 > atom 71 type 2 force = 0.00120609 -0.00120609 0.00011010 > atom 72 type 2 force = 0.00120811 -0.00120812 0.00010994 > > Total force = 0.012066 Total SCF correction = 0.000257 > > > entering subroutine stress ... > > total stress (Ry/bohr**3) (kbar) P= > -90.60 > -0.00062585 0.00000003 0.00000000 -92.07 0.00 0.00 > 0.00000003 -0.00062585 0.00000000 0.00 -92.07 0.00 > 0.00000000 0.00000000 -0.00059589 0.00 0.00 -87.66 > > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090821/295f3092/attachment.htm From mastermik at gmail.com Thu Aug 20 21:03:37 2009 From: mastermik at gmail.com (Mikiyas Tsegaye) Date: Thu, 20 Aug 2009 15:03:37 -0400 Subject: [Pw_forum] matdyn.x warning message Message-ID: <1690C53E-35D0-4D9F-A7F3-52759B1BF71E@gmail.com> Dear Friends, I'm trying to plot the phonon dispersion of graphene. I have done the dispersions for Silicon, and Germanium, and also for Diamond. All of which worked out well. Graphene, however, is giving me the following error in the second-to-last matdyn.x step: -------------------------------------------------------------------- message from routine matdyn Z* not found in file graphene.fc, TO-LO splitting at q=0 will be absent A direction for q was not specified: TO-LO splitting will be absent -------------------------------------------------------------------- The dispersion that it then produces looks very jagged and the numbers are off. For examples, the acoustic modes don't go to zero at the gamma point, and the acoustic and optical branches don't touch at the K-point like they're supposed to. I would really appreciate any help on this matter. My input file is as follows: ----------------------------------------------- # SCF step &control calculation='scf', restart_mode='from_scratch', prefix='graph', tstress=.true., tprnfor=.true., pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav = 0, nat=2, ntyp= 1, ecutwfc = 40.0, ecutrho = 480.0, occupations = 'smearing', smearing = 'gaussian', degauss = 0.02, / &electrons diagonalization = 'cg', conv_thr = 1.0d-6 / CELL_PARAMETERS {hexagonal} 4.02 2.321 0.00 4.02 -2.321 0.00 0.00 0.00 69.75 ATOMIC_SPECIES C 12.01 C.pz-vbc.UPF ATOMIC_POSITIONS {bohr} C 0.0 0.0 0.0 C 2.68 0.0 0.0 K_POINTS automatic 16 16 1 0 0 0 $PW_COMMAND < graphene.scf.in > graphene.scf.out # calculate phonons phonons of graphene &INPUTPH amass(1) = 12.01, outdir = '$TMP_DIR/', prefix = 'graph', tr2_ph = 1.0d-12, fildyn = 'graph.dyn', fildrho = 'graph.rho', ldisp = .true., lnscf = .true., nq1 = 16, nq2 = 16, nq3 = 1 ------------------------------------------------------- Am I missing something in my inputs? thank you! - Mikiyas Tsegaye University of Virginia, ECE Charlottesville, VA, USA mst3c at virginia.edu From eyvaz_isaev at yahoo.com Thu Aug 20 22:49:31 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 20 Aug 2009 13:49:31 -0700 (PDT) Subject: [Pw_forum] matdyn.x warning message In-Reply-To: <1690C53E-35D0-4D9F-A7F3-52759B1BF71E@gmail.com> Message-ID: <707183.40234.qm@web65704.mail.ac4.yahoo.com> Dear Mikiyas, > Z* not found in file graphene.fc, TO-LO splitting at q=0 > will be absent > A direction for q was not specified: TO-LO splitting will > be absent The first message is just stating that you consider graphene as a metallic system for which there is no LO-TO splitting, of course. The second message: may be your q-path does not contain Gamma point. Anyway, it is harmless in your (metallic) case If you send me your fc-file and q-path, I will try to have a look at. > ? ???ecutrho = 480.0, You do not need such high ecutrho as you use norm-conserving PsP. Use default value (4*ecutwfc). By the way, did you specify zasr in q2r.in and matdyin.in files? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/20/09, Mikiyas Tsegaye wrote: > > I'm trying to plot the phonon dispersion of graphene. I > have done the? > dispersions for Silicon, and Germanium, and also for > Diamond. All of? > which worked out well. Graphene, however, is giving me the > following? > error in the second-to-last matdyn.x step: > > -------------------------------------------------------------------- > message from routine matdyn > > Z* not found in file graphene.fc, TO-LO splitting at q=0 > will be absent > A direction for q was not specified: TO-LO splitting will > be absent > > -------------------------------------------------------------------- > > The dispersion that it then produces looks very jagged and > the numbers? > are off. For examples, the acoustic modes don't go to zero > at the? > gamma point, and the acoustic and optical branches don't > touch at the? > K-point like they're supposed to. I would really appreciate > any help? > on this matter. My input file is as follows: > > ----------------------------------------------- > # SCF step > > ? &control > ? ???calculation='scf', > ? ???restart_mode='from_scratch', > ? ???prefix='graph', > ? ???tstress=.true., > ? ???tprnfor=.true., > ? ???pseudo_dir = '$PSEUDO_DIR/', > ? ???outdir='$TMP_DIR/' > ? / > ? &system > ? ???ibrav = 0, nat=2, ntyp= 1, > ? ???ecutwfc = 40.0, > ? ???ecutrho = 480.0, > ? ???occupations = 'smearing', > ? ???smearing = 'gaussian', > ? ???degauss = 0.02, > ? / > ? &electrons > ? ???diagonalization = 'cg', > ? ???conv_thr =? 1.0d-6 > ? / > CELL_PARAMETERS {hexagonal} > 4.02? 2.321? 0.00 > 4.02 -2.321? 0.00 > 0.00? 0.00???69.75 > ATOMIC_SPECIES > C 12.01 C.pz-vbc.UPF > ATOMIC_POSITIONS {bohr} > C? 0.0? 0.0? 0.0 > C? 2.68 0.0? 0.0 > K_POINTS automatic > 16 16 1 0 0 0 > > $PW_COMMAND < graphene.scf.in > graphene.scf.out > > # calculate phonons > > phonons of graphene > &INPUTPH > ? amass(1) = 12.01, > ? outdir = '$TMP_DIR/', > ? prefix = 'graph', > ? tr2_ph = 1.0d-12, > ? fildyn = 'graph.dyn', > ? fildrho = 'graph.rho', > ? ldisp = .true., > ? lnscf = .true., > ? nq1 = 16, > ? nq2 = 16, > ? nq3 = 1 > ? > ------------------------------------------------------- > > Am I missing something in my inputs? > > thank you! > > - Mikiyas Tsegaye > University of Virginia, ECE > Charlottesville, VA, USA > mst3c at virginia.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From vtmtrinh at caltech.edu Fri Aug 21 02:25:23 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Thu, 20 Aug 2009 17:25:23 -0700 (PDT) Subject: [Pw_forum] spin splitting In-Reply-To: <4A8A5189.6050704@sissa.it> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> <4A89023C.80808@sissa.it> <2688.137.78.73.28.1250537785.squirrel@webmail.caltech.edu> <4A8A5189.6050704@sissa.it> Message-ID: <1719.137.78.73.28.1250814323.squirrel@webmail.caltech.edu> Thanks a lot for your help. Also, I have another question. How is the spin-orbit implemented in QE, i.e. is there any approximation. In other words, could you give me the ref that QE is based on (if any). I am looking for the part of the code that ralted to the spin-orbit, but so far, I still could not locate it. I appreciate if you could let me know. Best, MyTrinh > > > vtmtrinh at caltech.edu wrote: >> Hi Gabriele, >> >> Thanks for your reply. I am sorry for the unclear question. >> The question is to calculate the splitting between the spin up and spin >> down states in the conduction band (CB) of Si. For equlibrium Si bulk, >> there should be no spin splitting. Therefore, the splitting can be >> induced >> by moving the atoms a long phonon modes. The spin splitting is probably >> of >> the order ~1e-7eV. >> >> Yes, you are right. I need to set nspin=2. Since I also need to >> include >> the spin-orbit coupling in this calculation, I have to use >> noncolinear=.true. > > Now the situation is much more clear :-) > > >> >> I run a calculation yesterday, in which I set lspinorb=.true. and >> noncolinear=.true. By setting this I think that spin-polarized >> calculation >> was aslo done. However, in the output, I don't see the eigen values for >> spin up and spin down, but only one (like for the non-polarization >> case). > > You're right, in a noncolinear calculation you don't see SPIN UP and SPIN > DOWN bands as in > a LSD calculation. > Anyway, as you also noticed, the number of bands is doubled when you set > noncolin=.true. > If you don't include SO coupling, you should get (for each band of the non > spin-polarized > calculation) a spin up and a spin down band which coincide with those > obtained with a > collinear LSD calculation (i.e. with noncolin=.false., nspin=2). Also the > final total > magnetization should be the same (you can check from the output). > You can plot the bands (for instance using bands.x and then plotband.x) > and compare the > splittings. > When you include SO the situation is more complicated (you should label > your bands with > the irreps of the (magnetic) double group of the system), but in principle > more close to > reality. > You can plot bands also in this case and see what changes and how much > (tyr lsym=.true. > when running bands: it can label bands according to the irreps and it may > be very useful). > The SO splitting would be small, though. In the Si atom the SO splitting > of 3p electrons > should be of the order of few mRy (which is only slightly larger than the > error from PPs, > so be careful...), and in the bulk they are usually lower. > > > Cheers, > > GS > > >> I am not sure if I did not set the right parameters. Attached is my >> input. Could you let me know what wrong with it. >> >> Thanks, >> >> MyTrinh >> > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Fri Aug 21 09:02:27 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 21 Aug 2009 09:02:27 +0200 Subject: [Pw_forum] spin splitting In-Reply-To: <1719.137.78.73.28.1250814323.squirrel@webmail.caltech.edu> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> <4A89023C.80808@sissa.it> <2688.137.78.73.28.1250537785.squirrel@webmail.caltech.edu> <4A8A5189.6050704@sissa.it> <1719.137.78.73.28.1250814323.squirrel@webmail.caltech.edu> Message-ID: <4A8E4683.4060705@sissa.it> vtmtrinh at caltech.edu wrote: > Thanks a lot for your help. > > Also, I have another question. How is the spin-orbit implemented in QE, > i.e. is there any approximation. In other words, could you give me the > ref that QE is based on (if any). I am looking for the part of the code > that ralted to the spin-orbit, but so far, I still could not locate it. I > appreciate if you could let me know. The SO coupling is dealt with through the use of special pseudopotentials (called "fully-relativistic"), hence only contributions in the core regions are retained (since they are by far the most important). The way these PPs are built is described in Phys. Rev. B 71, 115106 (2005) If you want deeper details about all the theory beyond noncollinear and SO in QE, I can point you to Andrea Dal Corso's webpage http://people.sissa.it/~dalcorso/ who is the main developer of that part of the code. You'll find detailed lecture notes and a list of references therein. Regards, GS > > Best, > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Fri Aug 21 09:28:26 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Aug 2009 09:28:26 +0200 Subject: [Pw_forum] matdyn.x warning message In-Reply-To: <1690C53E-35D0-4D9F-A7F3-52759B1BF71E@gmail.com> References: <1690C53E-35D0-4D9F-A7F3-52759B1BF71E@gmail.com> Message-ID: <63C6AA79-CD57-4F24-8FDD-8622807503B4@democritos.it> On Aug 20, 2009, at 21:03 , Mikiyas Tsegaye wrote: > For examples, the acoustic modes don't go to zero at the gamma point you need to enforce acoustic sum rule > and the acoustic and optical branches don't touch at the K-point they do. Some time ago I heard a similar claim. I verified that they touch at K. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From marcello.rosini at unimore.it Fri Aug 21 09:51:59 2009 From: marcello.rosini at unimore.it (Marcello Rosini) Date: Fri, 21 Aug 2009 09:51:59 +0200 Subject: [Pw_forum] symmetry operations Message-ID: <4A8E521F.3000804@unimore.it> Hallo everybody, I noticed this apparent inconsistency with pw.x: when I start a relax calculation the output says 6 symmetry operations and point group C_3v when restarting the same calculation, the output says 2 symmetry operations and point group C_s How can it be possible? Thanks for help Marcello -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dipartimento di Fisica, Universit? di Modena e Reggio Emilia and S3 National Research Centre of CNR-INFM via campi 213/a - 41125 Modena - Italy tel: +39 059.205.5067 email: marcello.rosini at unimore.it www.nanomodelling.unimore.it ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From giannozz at democritos.it Fri Aug 21 10:26:01 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Aug 2009 10:26:01 +0200 Subject: [Pw_forum] average potential In-Reply-To: <4A8D5756.3040803@unimore.it> References: <4A8D5756.3040803@unimore.it> Message-ID: On Aug 20, 2009, at 16:01 , Marcello Rosini wrote: > 4. Is it true for pw.x V(G=0)=0? no. Please have a look at this: www.fisica.uniud.it/~giannozz/public/plane_waves.pdf P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 21 10:27:28 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Aug 2009 10:27:28 +0200 Subject: [Pw_forum] symmetry operations In-Reply-To: <4A8E521F.3000804@unimore.it> References: <4A8E521F.3000804@unimore.it> Message-ID: On Aug 21, 2009, at 9:51 , Marcello Rosini wrote: > I noticed this apparent inconsistency with pw.x: when I start a relax > calculation the output says > 6 symmetry operations and point group C_3v > when restarting the same calculation, the output says > 2 symmetry operations and point group C_s please provide an example that can be re-run and a description of the procedure you followed Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 21 10:30:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Aug 2009 10:30:12 +0200 Subject: [Pw_forum] force In-Reply-To: <887803.65890.qm@web112517.mail.gq1.yahoo.com> References: <887803.65890.qm@web112517.mail.gq1.yahoo.com> Message-ID: <72438188-FBEB-4817-8B66-8BD9CD267822@democritos.it> On Aug 20, 2009, at 17:11 , ali kazempour wrote: > I use vc-relax to optimize the lattice constant and also the > position for bulk. > After I make supercell with these optimized value and run a scf > with similar > value as bulk. But the force as I listed below for some atom is > relatively more > than other I see quite small forces. If you do a supercell, do not forget that you will not get exactly the same values as for the original cell, unless the k- point grid of the unit cell refolds into the k-point grid of the supercell Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From kazempoor2000 at yahoo.com Fri Aug 21 11:22:20 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 21 Aug 2009 02:22:20 -0700 (PDT) Subject: [Pw_forum] shift kpoint Message-ID: <276727.58352.qm@web112508.mail.gq1.yahoo.com> Dear all In principle ,where the shift of kpoints is important? I mean which information should we loose when we don't use from shift in our kpoint mesh? I read in some references that for supercell calculation in defect studies ,they shifts kpoints from the origin to avoid picking up the gamma point as one of the sampling points). does it mean that symmetry reduces this set to a set of points in the irreducible part of BZ? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090821/45933cfb/attachment.htm From paulatto at sissa.it Fri Aug 21 11:28:30 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 21 Aug 2009 11:28:30 +0200 Subject: [Pw_forum] shift kpoint In-Reply-To: <276727.58352.qm@web112508.mail.gq1.yahoo.com> References: <276727.58352.qm@web112508.mail.gq1.yahoo.com> Message-ID: In data 21 agosto 2009 alle ore 11:22:20, ali kazempour ha scritto: > Dear all > In principle ,where the shift of kpoints is important? I mean which > information should we loose when we don't use from shift in our kpoint > mesh? You don't loose any information, it's just that a shifted grid makes the calculation converge faster w.r.t the number of kpoints. This is normally only true after applying symmetry operation to reduce the number of kpoints. > [...] does it mean that symmetry reduces this set to a set of points in > the irreducible part of BZ? Exactly. There are some exceptions though, e.g. using Gamma point (and only Gamma point) is the only meaningful choice for isolated systems. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From decboy9 at gmail.com Fri Aug 21 13:00:00 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 21 Aug 2009 16:30:00 +0530 Subject: [Pw_forum] Request for Er pseudo potential In-Reply-To: <4A8CEFF0.6050607@sissa.it> References: <4A8CEFF0.6050607@sissa.it> Message-ID: Sir, It is your wish. If u want to test it first , it is ok otherwise if you can give Er pseudo potential then i will test it for my system and will back to you for the discussion. I will be thankful sir, if you can provide the requested pseudo-potential and have a look on the results produced using it. Thank You, With regards, Dev On Thu, Aug 20, 2009 at 12:10 PM, Gabriele Sclauzero wrote: > If you are interested in PAW, please give a look at this post from the > forum archives: > > http://www.democritos.it/pipermail/pw_forum/2009-May/012897.html > > GS > > dev sharma wrote: > > hi all, > > I would be very thankful , if someone can provide (Er) Erbium > > pseudo-potential, as i dont know how to make pseudo-potentiall and it is > > also not present on PWscf pseudo list. > > I will be very thankful. > > > > With regards, > > Dev Sharma, > > University of Delhi > > India > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum 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/20090821/5eaad202/attachment.htm From paulatto at sissa.it Fri Aug 21 16:02:09 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 21 Aug 2009 16:02:09 +0200 Subject: [Pw_forum] Request for Er pseudo potential In-Reply-To: References: <4A8CEFF0.6050607@sissa.it> Message-ID: In data 21 agosto 2009 alle ore 13:00:00, dev sharma ha scritto: > It is your wish. If u want to test it first , it is ok otherwise if you > can give Er pseudo potential then i will test it for my system and will > back to you for the discussion. I will be thankful sir, if you can > provide the > requested pseudo-potential and have a look on the results produced using > it. Dear Sharma, it is not Gabriele that right person to ask, but Chao Chao, at qtp.ufl.edu best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mastermik at gmail.com Fri Aug 21 21:40:02 2009 From: mastermik at gmail.com (Mikiyas Tsegaye) Date: Fri, 21 Aug 2009 15:40:02 -0400 Subject: [Pw_forum] matdyn.x warning message (Mikiyas Tsegaye) In-Reply-To: References: Message-ID: <5E8C9D92-53D7-4956-B5F9-DD4CC9E997E5@gmail.com> Dear Eyvaz, My q-path is the following: (from matdyn.in input file) ----------------------------------- &input asr='simple', amass(1)= 12.01, flfrc='graphene.fc', flfrq='graphene.freq', / 14 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.3 0.0 0.0 0.0 0.4 0.0 0.0 0.0 0.5 0.0 0.0 0.1 0.1 0.0 0.0 0.2 0.2 0.0 0.0 0.3 0.3 0.0 0.0 0.33 0.33 0.0 0.0 0.3 0.3 0.0 0.0 0.2 0.2 0.0 0.0 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 ------------------------------------ How do you want me to send you my force constant file? It is quite large (6 X 6 X 1 grid). Is it OK to email such large number of lines to the public forum. Or perhaps a private email? thank you for your help. > Dear Friends, > > I'm trying to plot the phonon dispersion of graphene. I have done the > dispersions for Silicon, and Germanium, and also for Diamond. All of > which worked out well. Graphene, however, is giving me the following > error in the second-to-last matdyn.x step: > > -------------------------------------------------------------------- > message from routine matdyn > > Z* not found in file graphene.fc, TO-LO splitting at q=0 will be > absent > A direction for q was not specified: TO-LO splitting will be absent > > -------------------------------------------------------------------- > > The dispersion that it then produces looks very jagged and the numbers > are off. For examples, the acoustic modes don't go to zero at the > gamma point, and the acoustic and optical branches don't touch at the > K-point like they're supposed to. I would really appreciate any help > on this matter. My input file is as follows: > > ----------------------------------------------- > # SCF step > > &control > calculation='scf', > restart_mode='from_scratch', > prefix='graph', > tstress=.true., > tprnfor=.true., > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav = 0, nat=2, ntyp= 1, > ecutwfc = 40.0, > ecutrho = 480.0, > occupations = 'smearing', > smearing = 'gaussian', > degauss = 0.02, > / > &electrons > diagonalization = 'cg', > conv_thr = 1.0d-6 > / > CELL_PARAMETERS {hexagonal} > 4.02 2.321 0.00 > 4.02 -2.321 0.00 > 0.00 0.00 69.75 > ATOMIC_SPECIES > C 12.01 C.pz-vbc.UPF > ATOMIC_POSITIONS {bohr} > C 0.0 0.0 0.0 > C 2.68 0.0 0.0 > K_POINTS automatic > 16 16 1 0 0 0 > > $PW_COMMAND < graphene.scf.in > graphene.scf.out > > # calculate phonons > > phonons of graphene > &INPUTPH > amass(1) = 12.01, > outdir = '$TMP_DIR/', > prefix = 'graph', > tr2_ph = 1.0d-12, > fildyn = 'graph.dyn', > fildrho = 'graph.rho', > ldisp = .true., > lnscf = .true., > nq1 = 16, > nq2 = 16, > nq3 = 1 > ------------------------------------------------------- > > Am I missing something in my inputs? > > thank you! > > - Mikiyas Tsegaye > University of Virginia, ECE > Charlottesville, VA, USA > mst3c at virginia.edu > > > ------------------------------ > > Message: 3 > Date: Thu, 20 Aug 2009 13:49:31 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] matdyn.x warning message > To: PWSCF Forum > Message-ID: <707183.40234.qm at web65704.mail.ac4.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Mikiyas, > >> Z* not found in file graphene.fc, TO-LO splitting at q=0 >> will be absent >> A direction for q was not specified: TO-LO splitting will >> be absent > > The first message is just stating that you consider graphene as a > metallic system for which there is no LO-TO splitting, of course. > > The second message: may be your q-path does not contain Gamma point. > Anyway, it is harmless in your (metallic) case > > If you send me your fc-file and q-path, I will try to have a look > at. > >> ? ???ecutrho = 480.0, > You do not need such high ecutrho as you use norm-conserving PsP. > Use default value (4*ecutwfc). > > By the way, did you specify zasr in q2r.in and matdyin.in files? > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & > Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping > University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Thu, 8/20/09, Mikiyas Tsegaye wrote: > > >> >> I'm trying to plot the phonon dispersion of graphene. I >> have done the? >> dispersions for Silicon, and Germanium, and also for >> Diamond. All of? >> which worked out well. Graphene, however, is giving me the >> following? >> error in the second-to-last matdyn.x step: >> >> -------------------------------------------------------------------- >> message from routine matdyn >> >> Z* not found in file graphene.fc, TO-LO splitting at q=0 >> will be absent >> A direction for q was not specified: TO-LO splitting will >> be absent >> >> -------------------------------------------------------------------- >> >> The dispersion that it then produces looks very jagged and >> the numbers? >> are off. For examples, the acoustic modes don't go to zero >> at the? >> gamma point, and the acoustic and optical branches don't >> touch at the? >> K-point like they're supposed to. I would really appreciate >> any help? >> on this matter. My input file is as follows: >> >> ----------------------------------------------- >> # SCF step >> >> ? &control >> ? ???calculation='scf', >> ? ???restart_mode='from_scratch', >> ? ???prefix='graph', >> ? ???tstress=.true., >> ? ???tprnfor=.true., >> ? ???pseudo_dir = '$PSEUDO_DIR/', >> ? ???outdir='$TMP_DIR/' >> ? / >> ? &system >> ? ???ibrav = 0, nat=2, ntyp= 1, >> ? ???ecutwfc = 40.0, >> ? ???ecutrho = 480.0, >> ? ???occupations = 'smearing', >> ? ???smearing = 'gaussian', >> ? ???degauss = 0.02, >> ? / >> ? &electrons >> ? ???diagonalization = 'cg', >> ? ???conv_thr =? 1.0d-6 >> ? / >> CELL_PARAMETERS {hexagonal} >> 4.02? 2.321? 0.00 >> 4.02 -2.321? 0.00 >> 0.00? 0.00???69.75 >> ATOMIC_SPECIES >> C 12.01 C.pz-vbc.UPF >> ATOMIC_POSITIONS {bohr} >> C? 0.0? 0.0? 0.0 >> C? 2.68 0.0? 0.0 >> K_POINTS automatic >> 16 16 1 0 0 0 >> >> $PW_COMMAND < graphene.scf.in > graphene.scf.out >> >> # calculate phonons >> >> phonons of graphene >> &INPUTPH >> ? amass(1) = 12.01, >> ? outdir = '$TMP_DIR/', >> ? prefix = 'graph', >> ? tr2_ph = 1.0d-12, >> ? fildyn = 'graph.dyn', >> ? fildrho = 'graph.rho', >> ? ldisp = .true., >> ? lnscf = .true., >> ? nq1 = 16, >> ? nq2 = 16, >> ? nq3 = 1 >> ? >> ------------------------------------------------------- >> >> Am I missing something in my inputs? >> >> thank you! >> >> - Mikiyas Tsegaye >> University of Virginia, ECE >> Charlottesville, VA, USA >> mst3c at virginia.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > > > ------------------------------ > > _______________________________________________ > 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 58 > **************************************** From mastermik at gmail.com Fri Aug 21 21:54:58 2009 From: mastermik at gmail.com (Mikiyas Tsegaye) Date: Fri, 21 Aug 2009 15:54:58 -0400 Subject: [Pw_forum] matdyn.x warning message In-Reply-To: References: Message-ID: <7D5867DA-AD68-4E84-94FF-069673970257@gmail.com> Dear Giannozzi, As you can see in the reply I sent to Eyvaz (see below), I specified ASR = 'simple' in my matdyn input file. I also specify the same thing in my q2r.x input file. But for some reason, this is not happening. I tried a separate single point calculation just for gamma, and then ran dynmat.x with ASR = simple, and the acoustic frequencies did go to 0. So, does this mean that matdyn.x is not enforcing the sum rule appropriately? As I have said, the same type of code has worked beautifully with Si, Ge, and diamond so far. I don't know what the hiccup is with my graphene runs. thank you > On Aug 20, 2009, at 21:03 , Mikiyas Tsegaye wrote: > >> For examples, the acoustic modes don't go to zero at the gamma point > > you need to enforce acoustic sum rule > >> and the acoustic and optical branches don't touch at the K-point > > they do. Some time ago I heard a similar claim. I verified that they > touch at K. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > Dear Eyvaz, > > My q-path is the following: (from matdyn.in input file) > ----------------------------------- > &input > asr='simple', > amass(1)= 12.01, > flfrc='graphene.fc', > flfrq='graphene.freq', > / > 14 > 0.0 0.0 0.0 0.0 > 0.0 0.1 0.0 0.0 > 0.0 0.2 0.0 0.0 > 0.0 0.3 0.0 0.0 > 0.0 0.4 0.0 0.0 > 0.0 0.5 0.0 0.0 > 0.1 0.1 0.0 0.0 > 0.2 0.2 0.0 0.0 > 0.3 0.3 0.0 0.0 > 0.33 0.33 0.0 0.0 > 0.3 0.3 0.0 0.0 > 0.2 0.2 0.0 0.0 > 0.1 0.1 0.0 0.0 > 0.0 0.0 0.0 0.0 > > ------------------------------------ From eyvaz_isaev at yahoo.com Fri Aug 21 23:04:58 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 21 Aug 2009 14:04:58 -0700 (PDT) Subject: [Pw_forum] matdyn.x warning message (Mikiyas Tsegaye) In-Reply-To: <5E8C9D92-53D7-4956-B5F9-DD4CC9E997E5@gmail.com> Message-ID: <339400.99979.qm@web65704.mail.ac4.yahoo.com> Hi Mikiyas, > It is quite? large (6 X 6 X 1 grid). Is it OK to email such large number > of lines? to the public forum. Or perhaps a private email? Please send it to my private mail to keep the forum clean. Bests, Eyvaz. --- On Fri, 8/21/09, Mikiyas Tsegaye wrote: > From: Mikiyas Tsegaye > Subject: Re: [Pw_forum] matdyn.x warning message (Mikiyas Tsegaye) > To: pw_forum at pwscf.org > Date: Friday, August 21, 2009, 11:40 PM > Dear Eyvaz, > > My q-path is the following: (from matdyn.in input file) > ----------------------------------- > &input > asr='simple', > amass(1)= 12.01, > flfrc='graphene.fc', > flfrq='graphene.freq', > / > 14 > 0.0 0.0 0.0???0.0 > 0.0 0.1 0.0???0.0 > 0.0 0.2 0.0???0.0 > 0.0 0.3 0.0???0.0 > 0.0 0.4 0.0???0.0 > 0.0 0.5 0.0???0.0 > 0.1 0.1 0.0???0.0 > 0.2 0.2 0.0???0.0 > 0.3 0.3 0.0???0.0 > 0.33 0.33 0.0 0.0 > 0.3 0.3 0.0???0.0 > 0.2 0.2 0.0???0.0 > 0.1 0.1 0.0???0.0 > 0.0 0.0 0.0???0.0 > > ------------------------------------ > > How do you want me to send you my force constant file? It > is quite? > large (6 X 6 X 1 grid). Is it OK to email such large number > of lines? > to the public forum. Or perhaps a private email? > > thank you for your help. > > > Dear Friends, > > > > I'm trying to plot the phonon dispersion of graphene. > I have done the > > dispersions for Silicon, and Germanium, and also for > Diamond. All of > > which worked out well. Graphene, however, is giving me > the following > > error in the second-to-last matdyn.x step: > > > > > -------------------------------------------------------------------- > > message from routine matdyn > > > > Z* not found in file graphene.fc, TO-LO splitting at > q=0 will be? > > absent > > A direction for q was not specified: TO-LO splitting > will be absent > > > > > -------------------------------------------------------------------- > > > > The dispersion that it then produces looks very jagged > and the numbers > > are off. For examples, the acoustic modes don't go to > zero at the > > gamma point, and the acoustic and optical branches > don't touch at the > > K-point like they're supposed to. I would really > appreciate any help > > on this matter. My input file is as follows: > > > > ----------------------------------------------- > > # SCF step > > > >? &control > >? ???calculation='scf', > >? ???restart_mode='from_scratch', > >? ???prefix='graph', > >? ???tstress=.true., > >? ???tprnfor=.true., > >? ???pseudo_dir = '$PSEUDO_DIR/', > >? ???outdir='$TMP_DIR/' > >? / > >? &system > >? ???ibrav = 0, nat=2, ntyp= 1, > >? ???ecutwfc = 40.0, > >? ???ecutrho = 480.0, > >? ???occupations = 'smearing', > >? ???smearing = 'gaussian', > >? ???degauss = 0.02, > >? / > >? &electrons > >? ???diagonalization = 'cg', > >? ???conv_thr =? 1.0d-6 > >? / > > CELL_PARAMETERS {hexagonal} > > 4.02? 2.321? 0.00 > > 4.02 -2.321? 0.00 > > 0.00? 0.00???69.75 > > ATOMIC_SPECIES > > C 12.01 C.pz-vbc.UPF > > ATOMIC_POSITIONS {bohr} > > C? 0.0? 0.0? 0.0 > > C? 2.68 0.0? 0.0 > > K_POINTS automatic > > 16 16 1 0 0 0 > > > > $PW_COMMAND < graphene.scf.in > > graphene.scf.out > > > > # calculate phonons > > > > phonons of graphene > > &INPUTPH > >? amass(1) = 12.01, > >? outdir = '$TMP_DIR/', > >? prefix = 'graph', > >? tr2_ph = 1.0d-12, > >? fildyn = 'graph.dyn', > >? fildrho = 'graph.rho', > >? ldisp = .true., > >? lnscf = .true., > >? nq1 = 16, > >? nq2 = 16, > >? nq3 = 1 > >? > ------------------------------------------------------- > > > > Am I missing something in my inputs? > > > > thank you! > > > > - Mikiyas Tsegaye > > University of Virginia, ECE > > Charlottesville, VA, USA > > mst3c at virginia.edu > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 20 Aug 2009 13:49:31 -0700 (PDT) > > From: Eyvaz Isaev > > Subject: Re: [Pw_forum] matdyn.x warning message > > To: PWSCF Forum > > Message-ID: <707183.40234.qm at web65704.mail.ac4.yahoo.com> > > Content-Type: text/plain; charset=iso-8859-1 > > > > Dear Mikiyas, > > > >> Z* not found in file graphene.fc, TO-LO splitting > at q=0 > >> will be absent > >> A direction for q was not specified: TO-LO > splitting will > >> be absent > > > > The first message is just stating that you consider > graphene as a? > > metallic system for which there is no LO-TO splitting, > of course. > > > > The second message: may be your q-path does not > contain Gamma point.? > > Anyway, it is harmless in your (metallic) case > > > > If you send me your fc-file and? q-path,? I > will try to have a look? > > at. > > > >> ? ???ecutrho = 480.0, > > You do not need such high ecutrho as you use > norm-conserving PsP. > > Use default value (4*ecutwfc). > > > > By the way, did you specify zasr in q2r.in and > matdyin.in files? > > > > Bests, > > Eyvaz. > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State Institute > of Steel &? > > Alloys, Russia, > > Department of Physics, Chemistry, and Biology (IFM), > Linkoping? > > University, Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, > isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > > > > --- On Thu, 8/20/09, Mikiyas Tsegaye > wrote: > > > > > >> > >> I'm trying to plot the phonon dispersion of > graphene. I > >> have done the? > >> dispersions for Silicon, and Germanium, and also > for > >> Diamond. All of? > >> which worked out well. Graphene, however, is > giving me the > >> following? > >> error in the second-to-last matdyn.x step: > >> > >> > -------------------------------------------------------------------- > >> message from routine matdyn > >> > >> Z* not found in file graphene.fc, TO-LO splitting > at q=0 > >> will be absent > >> A direction for q was not specified: TO-LO > splitting will > >> be absent > >> > >> > -------------------------------------------------------------------- > >> > >> The dispersion that it then produces looks very > jagged and > >> the numbers? > >> are off. For examples, the acoustic modes don't go > to zero > >> at the? > >> gamma point, and the acoustic and optical branches > don't > >> touch at the? > >> K-point like they're supposed to. I would really > appreciate > >> any help? > >> on this matter. My input file is as follows: > >> > >> ----------------------------------------------- > >> # SCF step > >> > >> ? &control > >> ? ???calculation='scf', > >> ? ???restart_mode='from_scratch', > >> ? ???prefix='graph', > >> ? ???tstress=.true., > >> ? ???tprnfor=.true., > >> ? ???pseudo_dir = '$PSEUDO_DIR/', > >> ? ???outdir='$TMP_DIR/' > >> ? / > >> ? &system > >> ? ???ibrav = 0, nat=2, ntyp= 1, > >> ? ???ecutwfc = 40.0, > >> ? ???ecutrho = 480.0, > >> ? ???occupations = 'smearing', > >> ? ???smearing = 'gaussian', > >> ? ???degauss = 0.02, > >> ? / > >> ? &electrons > >> ? ???diagonalization = 'cg', > >> ? ???conv_thr =? 1.0d-6 > >> ? / > >> CELL_PARAMETERS {hexagonal} > >> 4.02? 2.321? 0.00 > >> 4.02 -2.321? 0.00 > >> 0.00? 0.00???69.75 > >> ATOMIC_SPECIES > >> C 12.01 C.pz-vbc.UPF > >> ATOMIC_POSITIONS {bohr} > >> C? 0.0? 0.0? 0.0 > >> C? 2.68 0.0? 0.0 > >> K_POINTS automatic > >> 16 16 1 0 0 0 > >> > >> $PW_COMMAND < graphene.scf.in > > graphene.scf.out > >> > >> # calculate phonons > >> > >> phonons of graphene > >> &INPUTPH > >> ? amass(1) = 12.01, > >> ? outdir = '$TMP_DIR/', > >> ? prefix = 'graph', > >> ? tr2_ph = 1.0d-12, > >> ? fildyn = 'graph.dyn', > >> ? fildrho = 'graph.rho', > >> ? ldisp = .true., > >> ? lnscf = .true., > >> ? nq1 = 16, > >> ? nq2 = 16, > >> ? nq3 = 1 > >> ? > >> > ------------------------------------------------------- > >> > >> Am I missing something in my inputs? > >> > >> thank you! > >> > >> - Mikiyas Tsegaye > >> University of Virginia, ECE > >> Charlottesville, VA, USA > >> mst3c at virginia.edu > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > > > > > > > > ------------------------------ > > > > _______________________________________________ > > 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 58 > > **************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From vtmtrinh at caltech.edu Sat Aug 22 02:39:32 2009 From: vtmtrinh at caltech.edu (vtmtrinh at caltech.edu) Date: Fri, 21 Aug 2009 17:39:32 -0700 (PDT) Subject: [Pw_forum] spin splitting In-Reply-To: <4A8E4683.4060705@sissa.it> References: <2916.137.78.73.28.1250368976.squirrel@webmail.caltech.edu> <4A89023C.80808@sissa.it> <2688.137.78.73.28.1250537785.squirrel@webmail.caltech.edu> <4A8A5189.6050704@sissa.it> <1719.137.78.73.28.1250814323.squirrel@webmail.caltech.edu> <4A8E4683.4060705@sissa.it> Message-ID: <1925.137.78.73.28.1250901572.squirrel@webmail.caltech.edu> Thanks a lot Grabiele. My Trinh > > > vtmtrinh at caltech.edu wrote: >> Thanks a lot for your help. >> >> Also, I have another question. How is the spin-orbit implemented in QE, >> i.e. is there any approximation. In other words, could you give me the >> ref that QE is based on (if any). I am looking for the part of the code >> that ralted to the spin-orbit, but so far, I still could not locate it. >> I >> appreciate if you could let me know. > > The SO coupling is dealt with through the use of special pseudopotentials > (called > "fully-relativistic"), hence only contributions in the core regions are > retained (since > they are by far the most important). > The way these PPs are built is described in > Phys. Rev. B 71, 115106 (2005) > > If you want deeper details about all the theory beyond noncollinear and SO > in QE, I can > point you to Andrea Dal Corso's webpage > http://people.sissa.it/~dalcorso/ > who is the main developer of that part of the code. You'll find detailed > lecture notes and > a list of references therein. > > Regards, > > GS > >> >> Best, >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Sat Aug 22 12:54:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 22 Aug 2009 12:54:05 +0200 Subject: [Pw_forum] matdyn.x warning message In-Reply-To: <7D5867DA-AD68-4E84-94FF-069673970257@gmail.com> References: <7D5867DA-AD68-4E84-94FF-069673970257@gmail.com> Message-ID: On Aug 21, 2009, at 21:54 , Mikiyas Tsegaye wrote: > As I have said, the same type of code has worked beautifully with Si, > Ge, and diamond so far. I don't know what the hiccup is with my > graphene runs. nor do I, and unfortunately I cannot find any longer the input data I wrote some time ago, but be assured that there is some hiccup somewhere Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From bipulrr at gmail.com Sat Aug 22 20:42:15 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sun, 23 Aug 2009 00:12:15 +0530 Subject: [Pw_forum] LDA+U and phonon Message-ID: <3a749910908221142u61cd93dfnccd079c957a70b9c@mail.gmail.com> Dear PWSCF users, Is LDA+U, in phonon code is not implimented? Because for LaMnO3 i have done scf with lda+u, then i try to run phonon at Gamma point only and it shows an error from phq_readin : error # 1 The phonon code with LDA+U is not yet available So is there any additional flag i have to use in *.ph.in file? or its not possible to cal. phonon with U? -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From giannozz at democritos.it Sat Aug 22 23:12:45 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 22 Aug 2009 23:12:45 +0200 Subject: [Pw_forum] LDA+U and phonon In-Reply-To: <3a749910908221142u61cd93dfnccd079c957a70b9c@mail.gmail.com> References: <3a749910908221142u61cd93dfnccd079c957a70b9c@mail.gmail.com> Message-ID: On Aug 22, 2009, at 20:42 , Bipul Rakshit wrote: > Is LDA+U, in phonon code is not implimented? it isn't. You didn't search the archives of the mailing list for "LDA+U phonon", did you? P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Aug 23 10:43:28 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 23 Aug 2009 10:43:28 +0200 Subject: [Pw_forum] matdyn.x warning message In-Reply-To: <63C6AA79-CD57-4F24-8FDD-8622807503B4@democritos.it> References: <1690C53E-35D0-4D9F-A7F3-52759B1BF71E@gmail.com> <63C6AA79-CD57-4F24-8FDD-8622807503B4@democritos.it> Message-ID: On Aug 21, 2009, at 9:28 , Paolo Giannozzi wrote: > On Aug 20, 2009, at 21:03 , Mikiyas Tsegaye wrote: > >> and the acoustic and optical branches don't touch at the K-point > > they do. Some time ago I heard a similar claim. I verified that they > touch at K. correcting myself: actually I verified that valence and conduction bands touch at K, not the behavior of phonon branches. Anyway: in http://www.fisica/uniud/it/~giannozz/public/ there are two files, graph0.tar.gz and graph1.tar.gz, containing a reduced version of your data (c/a=10, default ecutrho, smaller k- and q-point grids), with two equivalent cell descriptions (graph1 has all symmetries, graph0 is missing some) and what I think are the respective Gamma-K-M-Gamma lines (you know that they depend upon your lattice description, don't you?). I don't see anything wrong. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From bipulrr at gmail.com Sun Aug 23 18:46:26 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sun, 23 Aug 2009 22:16:26 +0530 Subject: [Pw_forum] Question about K-points Message-ID: <3a749910908230946u41b6c56nabfeb827ad62fa8@mail.gmail.com> Dear Pwscf users, I have a question about phonon calculation. I am doing phonon of K2S (antifluorite structure), using 10x10x10 k-points mesh. In that calculations i find -ve frequencies. But then on increasing the mesh 14x14x14 and also the kinetic energy cutoff from 32 to 38 Ry, now i am getting all the +ve freq. Can you please tell me the reason or give me some reference, so that by reading that i can understand the things. regards -- Bipul Rakshit Research Fellow, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From ttduyle at gmail.com Sun Aug 23 20:07:36 2009 From: ttduyle at gmail.com (Duy Le) Date: Sun, 23 Aug 2009 14:07:36 -0400 Subject: [Pw_forum] Question about K-points In-Reply-To: <3a749910908230946u41b6c56nabfeb827ad62fa8@mail.gmail.com> References: <3a749910908230946u41b6c56nabfeb827ad62fa8@mail.gmail.com> Message-ID: <8974d3b20908231107i709ea652w59bcf0bd2db8254a@mail.gmail.com> Dear Bipul, I haven't done such kind of calculation. However, when reading your question, there are couple of questions that may help you: 1. Did you perform the STRUCTURE convergence test for K-point mesh and/or energy cutoff? 2. Did you use the relaxed equilibrium structure which was obtained by using 10x10x10 mesh and 32Ry cutoff to perform 14x14x14 mesh and 38Ry cutoff phonon calculation? 3. How about the forces acting on the atoms in 2 cases? Are they too different? Hope those help! ------------------------------------------------- Duy Le PhD Student. University of Central Florida. On Sun, Aug 23, 2009 at 12:46 PM, Bipul Rakshit wrote: > Dear Pwscf users, > I have a question about phonon calculation. > I am doing phonon of K2S (antifluorite structure), using 10x10x10 > k-points mesh. In that calculations i find -ve frequencies. > > But then on increasing the mesh 14x14x14 and also the kinetic energy > cutoff from 32 to 38 Ry, now i am getting all the +ve freq. > > Can you please tell me the reason or give me some reference, so that > by reading that i can understand the things. > > regards > -- > Bipul Rakshit > Research Fellow, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Men don't need hands to do things! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090823/9414b0f5/attachment.htm From sclauzer at sissa.it Mon Aug 24 08:45:32 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 24 Aug 2009 08:45:32 +0200 Subject: [Pw_forum] Reply (was Frequency and zero point energy calculations) In-Reply-To: <4A88FCDC.5010802@sissa.it> References: <5014682.21451250296629355.JavaMail.coremail@bj126app103.126.com> <4A88FCDC.5010802@sissa.it> Message-ID: <4A92370C.6040106@sissa.it> Dear Lihui, I have an update to this answer: for phonon calculations based on data produced by pw.x using gamma point tricks (i.e. K_POINTS GAMMA), you should use the code phcg.x in the Gamma/ directory, not ph.x. regards, GS Gabriele Sclauzero wrote: > Dear Lihui, > > oulihui666 wrote: >> Dear Gabriele Sclauzero, >> I am intend to calculate the frequency of CO2 molecule, so I should >> perform scf calculation at first, when setting k points as gamma, it >> will appear a error in the process of calculating frequency, as follows: >> *********************************************************************** >> from phq_readin. error #1 >> cannot start from pw.x data file using Gamma-point tricks >> *********************************************************************** > > From what I can understand, this does not mean that you cannot do the calculation for the > Gamma point only, but rather that the calculation cannot be done using Gamma > point-specific algorithms (which are much faster than the general ones). > You should anyway be allowed to do the calculation using > K_POINTS AUTOMATIC > 1 1 1 0 0 0 > which builds a k-point grid containing the Gamma point only, but does not use Gamma-point > tricks. > > You can do the relaxations (and all other expensive pw calculations) using > K_POINTS GAMMA > and then, starting from the optimized atomic positions, do a nscf run using > K_POINTS AUTOMATIC > 1 1 1 0 0 0 > before the phonon run. > > Cheers > > GS > > P.S: please avoid private mails and stick to the thread you started in the forum, so that > anyone can help and know when your problem has been solved. Thanks! > > > >> So I do not set k point as gamma in scf calculation. >> >> Best regards >> Lihui >> >> -- >> ====================================== >> Lihui Ou >> PH.D Candidate in Electrochemistry >> College of Chemistry and Molecular Science >> Wuhan University,/430072/,Hubei Province,China >> /E-mail:oulihui666 at 126.com / >> ====================================== >> >> >> ------------------------------------------------------------------------ >> ???????????,www.yeah.net > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From bipulrr at gmail.com Mon Aug 24 08:59:38 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 24 Aug 2009 12:29:38 +0530 Subject: [Pw_forum] about kvec In-Reply-To: <3a749910908232319s763af6e2u4f9469495cc98f2@mail.gmail.com> References: <3a749910908232319s763af6e2u4f9469495cc98f2@mail.gmail.com> Message-ID: <3a749910908232359i64511644n17bdcceae6ad7ed6@mail.gmail.com> Dear Pwscf users For band structure plotting, I use the Brillouin zone points from the site http://www.cryst.ehu.es/ and then in KVEC option. I just want to know in KVEC, the brillouine zone points are given in reciprocal or cartesian co-ordinates system. regards -- Bipul Rakshit Research Fellow, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/512a3c5b/attachment.htm From miguel.martinez at ehu.es Mon Aug 24 09:59:44 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Mon, 24 Aug 2009 09:59:44 +0200 Subject: [Pw_forum] about kvec In-Reply-To: <3a749910908232359i64511644n17bdcceae6ad7ed6@mail.gmail.com> References: <3a749910908232319s763af6e2u4f9469495cc98f2@mail.gmail.com> <3a749910908232359i64511644n17bdcceae6ad7ed6@mail.gmail.com> Message-ID: <20090824095944.05ee5b2d@lcpybm> Dear Bipul, The server already specifies the coordinates. CDML means that the coordinate system is taken from the Cracknell Davis Miller Love book [1]. ITA refers to the conventional cell coordinate system as in the International Tables of Crystallography, vol A. In case you wonder, sometimes one of these will match the ones in espresso. If your system is base-centered monoclinic, though, then you're on your own. Regards, Miguel [1] Cracknell, A. P., Davies, B. L., Miller, S. C., and Love, W. F. (1979). Kronecker Product Tables. Vol. 1. On Mon, 24 Aug 2009 12:29:38 +0530 Bipul Rakshit wrote: > Dear Pwscf users > > For band structure plotting, I use the Brillouin zone points from the > site > > http://www.cryst.ehu.es/ > > and then in KVEC option. I just want to know in KVEC, the brillouine > zone points are given in reciprocal or cartesian co-ordinates system. > > regards > -- ---------------------------------------- Miguel Mart?nez Canales Condensed Matter Physics Dpt. UPV/EHU Faculty of Science and Technology Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From decboy9 at gmail.com Mon Aug 24 10:20:23 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 24 Aug 2009 13:50:23 +0530 Subject: [Pw_forum] problem in parallel running Message-ID: Hi 2 all, I have installed QE 4.0.2 on cluster with openMPI but when i am running my jobscript with the command mpirun -np 4 /home/devsharma/espresso-4.0.2/bin/pw.x -in yvo.inp> scf.out i am getting an error massage in the terminal MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 0. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 2 with PID 7437 on node headnode.du.ac.in exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [headnode.du.ac.in:07434] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [headnode.du.ac.in:07434] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [1]+ Exit 1 sh submit.sh ========================================================== and also the scf Output is Program PWSCF v.4.0.2 starts ... Today is 24Aug2009 at 13:37: 5 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Warning: card &IONS ignored Warning: card / ignored %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readpp : error # 29 file /home/devshama/pseudo/Y.pbe-nsp-van.UPF not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readpp : error # 29 file /home/devshama/pseudo/Y.pbe-nsp-van.UPF not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readpp : error # 29 file /home/devshama/pseudo/Y.pbe-nsp-van.UPF not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Please help me, as i am not very much expert in Linux. what does this error means?? Please guide, Thanks in Advance, With regards, Dev Sharma, University of Delhi, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/1c359253/attachment.htm From paulatto at sissa.it Mon Aug 24 10:31:57 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 24 Aug 2009 10:31:57 +0200 Subject: [Pw_forum] problem in parallel running In-Reply-To: References: Message-ID: In data 24 agosto 2009 alle ore 10:20:23, dev sharma ha scritto: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from readpp : error # 29 > file /home/devshama/pseudo/Y.pbe-nsp-van.UPF not found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Please help me, as i am not very much expert in Linux. what does this > error means?? Dear Dev, the error message looks quite clear to me: the code cannot find the pseudopotential file. Please check if the file is actually there, and if it's there check that it is readable on the nodes where quantum espresso is running. best regards. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Mon Aug 24 10:37:40 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 24 Aug 2009 10:37:40 +0200 Subject: [Pw_forum] Question about K-points In-Reply-To: <3a749910908230946u41b6c56nabfeb827ad62fa8@mail.gmail.com> References: <3a749910908230946u41b6c56nabfeb827ad62fa8@mail.gmail.com> Message-ID: In data 23 agosto 2009 alle ore 18:46:26, Bipul Rakshit ha scritto: > I have a question about phonon calculation. > I am doing phonon of K2S (antifluorite structure), using 10x10x10 > k-points mesh. In that calculations i find -ve frequencies. > > But then on increasing the mesh 14x14x14 and also the kinetic energy > cutoff from 32 to 38 Ry, now i am getting all the +ve freq. Dear Bipul, unluckily convergence of physical quantities is not variational with the number of k-points; i.e. if you increase the number of k-points you will go toward convergence, but not necessarily in a monotone way. Notwithstanding that, if I had to bet, I would say that the problem was the cutoff too low: if the Potassium pseudopotential includes semi-core electrons it may be quite hard. Without knowing the detail of your calculation there is little more I can honestly say. You could try to perform two more calculation: one increasing only the number of k-points and one only the cutoff. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nkxirainbow at gmail.com Mon Aug 24 10:42:13 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 24 Aug 2009 16:42:13 +0800 Subject: [Pw_forum] problem in parallel running In-Reply-To: References: Message-ID: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> Dear dev sharma: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from readpp : error # 29 > file /home/devshama/pseudo/Y.pbe-nsp-van.UPF not found Is there *Y.pbe-nsp-van.UPF* pseudo potential file in you * /home/devshama/pseudo/* directory? ____________________________________ 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/20090824/94e4af25/attachment.htm From decboy9 at gmail.com Mon Aug 24 10:47:51 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 24 Aug 2009 14:17:51 +0530 Subject: [Pw_forum] problem in parallel running In-Reply-To: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> Message-ID: Dear Sir, Yes, *Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. I had already checked it before pasting the problem. * On Mon, Aug 24, 2009 at 2:12 PM, xirainbow wrote: > Dear dev sharma: > > >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from readpp : error # 29 >> file /home/devshama/pseudo/Y.pbe-nsp-van.UPF not found > > Is there *Y.pbe-nsp-van.UPF* pseudo potential file in you * > /home/devshama/pseudo/* directory? > > ____________________________________ > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/def79d5f/attachment.htm From nkxirainbow at gmail.com Mon Aug 24 10:52:50 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 24 Aug 2009 16:52:50 +0800 Subject: [Pw_forum] problem in parallel running In-Reply-To: References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> Message-ID: <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> Dear dev sharma: On 8/24/09, dev sharma wrote: > > Dear Sir, > Yes, *Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. I had > already checked it before pasting the problem.* Can you give the input file? ?? ____________________________________ 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/20090824/be687a32/attachment-0001.htm From giannozz at democritos.it Mon Aug 24 10:54:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 24 Aug 2009 10:54:44 +0200 Subject: [Pw_forum] problem in parallel running In-Reply-To: References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> Message-ID: <4A925554.1070406@democritos.it> dev sharma wrote: > Yes, /Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. if the code says it isn't there, it isn't there. Remember that ALL processes must be able to access that file DURING PARALLEL EXECUTION P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From decboy9 at gmail.com Mon Aug 24 11:10:42 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 24 Aug 2009 14:40:42 +0530 Subject: [Pw_forum] problem in parallel running In-Reply-To: <4A925554.1070406@democritos.it> References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> <4A925554.1070406@democritos.it> Message-ID: Dear Sir, I am sending all the terminal commands to you. Please guide me., [devsharma at headnode ~]$ ls espresso-4.0.2 pseudo tmp work [devsharma at headnode ~]$ cd pseudo/ [devsharma at headnode pseudo]$ ls 0710.pdf Cr.pw91-sp-van.info Li.pz-n-vbc.UPF Pt.pw91-n-van.info Ag.pbe-d-rrkjus.info Cr.pw91-sp-van.UPF Li.pz-s-mt.UPF Pt.pw91-n-van.UPF Ag.pbe-d-rrkjus.UPF Cs.pbe-mt_bw.info Li.pz-s-van_ak.info Pt.pz-nd-rrkjus.UPF Ag.pz-d-rrkjus.UPF Cs.pbe-mt_bw.UPF Li.pz-s-van_ak.UPF Pt.pz-rrkjus.UPF Al.blyp-n-van_ak.info C.tpss-mt.UPF Mg.pw91-np-van.info Pt.rel-pz-n-rrkjus.UPF Al.blyp-n-van_ak.UPF Cu.blyp-n-van_ak.info Mg.pw91-np-van.UPF Re.pw91-n-van.info Al.bp-n-van_ak.info Cu.blyp-n-van_ak.UPF Mg.pz-bhs.UPF Re.pw91-n-van.UPF Al.bp-n-van_ak.UPF Cu.pbe-d-rrkjus.info Mg.pz-n-vbc.info Rh.pbe-nd-rrkjus.UPF Al.pbe-n-van.info Cu.pbe-d-rrkjus.UPF Mg.pz-n-vbc.UPF Rh.pbe-rrkjus.UPF Al.pbe-n-van.UPF Cu.pbe-n-van_ak.info Mn.pbe-sp-van.info Rh.pz-rrkjus.UPF Al.pbe-rrkj.UPF Cu.pbe-n-van_ak.UPF Mn.pbe-sp-van.UPF Ru.pbe-n-van.info Al.pw91-n-van.info Cu.pw91-n-van_ak.info Mo.pw91-n-van.info Ru.pbe-n-van.UPF Al.pw91-n-van.UPF Cu.pw91-n-van_ak.UPF Mo.pw91-n-van.UPF Ru.pw91-n-van.info Al.pz-vbc.UPF Cu.pz-d-rrkjus.UPF Na.blyp-sp-van_ak.info Ru.pw91-n-van.UPF Ar.pz-rrkj.info Cu.pz-n-van_ak.info Na.blyp-sp-van_ak.UPF S.blyp-mt.info Ar.pz-rrkj.UPF Cu.pz-n-van_ak.UPF Na.bp-sp-van_ak.info S.blyp-mt.UPF As.pbe-n-van.info Fe.blyp-sp-van_ak.info Na.bp-sp-van_ak.UPF S.blyp-van_ak.info As.pbe-n-van.UPF Fe.blyp-sp-van_ak.UPF Na.pbe-n-mt_bw.info S.blyp-van_ak.UPF As.pw91-n-van.info Fe.blyp-sp-van.info Na.pbe-n-mt_bw.UPF S.bp-van_ak.info As.pw91-n-van.UPF Fe.blyp-sp-van.UPF Na.pbe-n-van.UPF S.bp-van_ak.UPF As.pz-bhs.info Fe.bp-sp-van_ak.info Na.pbe-sp-van_ak.info Sb.pw91-n-van.info As.pz-bhs.UPF Fe.bp-sp-van_ak.UPF Na.pbe-sp-van_ak.UPF Sb.pw91-n-van.UPF Au.blyp-van_ak.info Fe.pbe-nd-rrkjus.UPF Na.pw91-n-mt.UPF Sb.pz-bhs.info Au.blyp-van_ak.UPF Fe.pbe-sp-van_ak.info Na.pw91-n-van.UPF Sb.pz-bhs.UPF Au.bp-van_ak.info Fe.pbe-sp-van_ak.UPF Na.pw91-sp-van_ak.info Sc.pbe-nsp-van.info Au.bp-van_ak.UPF Fe.pbe-sp-van.info Na.pw91-sp-van_ak.UPF Sc.pbe-nsp-van.UPF Au.pbe-nd-rrkjus.UPF Fe.pbe-sp-van_mit.info Na.pz-n-vbc.info Sc.pw91-nsp-van.info Au.pbe-nd-van.info Fe.pbe-sp-van_mit.UPF Na.pz-n-vbc.UPF Sc.pw91-nsp-van.UPF Au.pbe-nd-van.UPF Fe.pbe-sp-van.UPF Na.pz-sp-van_ak.info Se.pbe-van.info Au.pbe-van_ak.info Fe.pw91-sp-van_ak.info Na.pz-sp-van_ak.UPF Se.pbe-van.UPF Au.pbe-van_ak.UPF Fe.pw91-sp-van_ak.UPF Nb.elastic_constant_tests.pdf Se.pz-bhs.info Au.pw91-d-van.UPF Fe.pz-nd-rrkjus.UPF N.blyp-mt.info Se.pz-bhs.UPF Au.pw91-van_ak.info Fe.pz-sp-van_ak.info N.blyp-mt.UPF Si.pbe-n-van.info Au.pw91-van_ak.UPF Fe.pz-sp-van_ak.UPF N.blyp-van_ak.info Si.pbe-n-van.UPF Au.pz-d-rrkjus.UPF filename.upf N.blyp-van_ak.UPF Si.pbe-rrkj.UPF Au.pz-d-van.UPF F.pbe-n-van.info Nb.pbe-nsp-van.info Si.pw91-n-van.info Au.pz-van_ak.info F.pbe-n-van.UPF Nb.pbe-nsp-van.UPF Si.pw91-n-van.UPF Au.pz-van_ak.UPF F.pw91-n-van.info N.bp-van_ak.info Si.pz-vbc.UPF Au.rel-pz-rrkjus.UPF F.pw91-n-van.UPF N.bp-van_ak.UPF Si.tpss-mt.UPF Ba.pbe-nsp-van.info Ga.pbe-nsp-van.info Nb.pw91-nsp-van.info Sn.pw91-n-van.info Ba.pbe-nsp-van.UPF Ga.pbe-nsp-van.UPF Nb.pw91-nsp-van.UPF Sn.pw91-n-van.UPF Ba.pw91-nsp-van.info Ga.pw91-nsp-van.info Nb.pz-sp-van.info Sn.pz-bhs.info Ba.pw91-nsp-van.UPF Ga.pw91-nsp-van.UPF Nb.pz-sp-van.UPF Sn.pz-bhs.UPF B.blyp-n-van_ak.info Ga.pz-bhs.info Ni.pbe-nd-rrkjus.UPF S.pbe-van_bm.info B.blyp-n-van_ak.UPF Ga.pz-bhs.UPF Ni.pz-nd-rrkjus.UPF S.pbe-van_bm.UPF B.bp-n-van_ak.info Ge.pw91-n-van.info N.pbe-rrkjus.UPF S.pw91-n-mt.info B.bp-n-van_ak.UPF Ge.pw91-n-van.UPF N.pbe-van_ak.info S.pw91-n-mt.UPF Be.pz-n-vbc.info Ge.pz-bhs.info N.pbe-van_ak.UPF S.pw91-van_ak.info Be.pz-n-vbc.UPF Ge.pz-bhs.UPF N.pbe-van_bm.info S.pw91-van_ak.UPF Be.star1s-pz-n-vbc.UPF Ge.tpss-n-mt.UPF N.pbe-van_bm.UPF S.pz-bhs.info Bi.pbe-d-mt.info H.blyp-van_ak.info N.pw91-van_ak.info S.pz-bhs.UPF Bi.pbe-d-mt.UPF H.blyp-van_ak.UPF N.pw91-van_ak.UPF S.pz-van_ak.info B.pbe-n-van_ak.info H.blyp-vbc.info N.pz-rrkjus.UPF S.pz-van_ak.UPF B.pbe-n-van_ak.UPF H.blyp-vbc.UPF N.pz-van_ak.info Sr.pbe-nsp-van.info B.pbe-n-van.info H.bp-van_ak.info N.pz-van_ak.UPF Sr.pbe-nsp-van.UPF B.pbe-n-van.UPF H.bp-van_ak.UPF N.pz-vbc.info Sr.pbe-sp-van.info B.pw91-n-van_ak.info He.pbe-mt_fhi.UPF N.pz-vbc.UPF Sr.pbe-sp-van.UPF B.pw91-n-van_ak.UPF He.pz-mt_fhi.UPF O.blyp-mt.info Sr.pw91-nsp-van.info B.pw91-n-van.info H.pbe-rrkjus.UPF O.blyp-mt.UPF Sr.pw91-nsp-van.UPF B.pw91-n-van.UPF H.pbe-van_ak.info O.blyp-van_ak.info Ta.pbe-nsp-van.info B.pz-bhs.UPF H.pbe-van_ak.UPF O.blyp-van_ak.UPF Ta.pbe-nsp-van.UPF B.pz-vbc.UPF H.pbe-van_bm.info O.bp-van_ak.info Ta.pw91-nsp-van.info Br.pbe-van_mit.info H.pbe-van_bm.UPF O.bp-van_ak.UPF Ta.pw91-nsp-van.UPF Br.pbe-van_mit.UPF H.pbe-vbc.UPF O.pbe-mt.UPF Te.pbe-rrkj.UPF Br.pw91-mt.info H.pw91-van_ak.info O.pbe-rrkjus.UPF Te.pz-bhs.info Br.pw91-mt.UPF H.pw91-van_ak.UPF O.pbe-van_ak.info Te.pz-bhs.UPF Br.pz-vbc.UPF H.pz-rrkjus.UPF O.pbe-van_ak.UPF Ti.blyp-sp-van_ak.info Ca.pbe-nsp-van.info H.pz-van_ak.info O.pbe-van_bm.info Ti.blyp-sp-van_ak.UPF Ca.pbe-nsp-van.UPF H.pz-van_ak.UPF O.pbe-van_bm.UPF Ti.bp-sp-van_ak.info Ca.pw91-nsp-van.info H.pz-vbc.UPF O.pw91-van_ak.info Ti.bp-sp-van_ak.UPF Ca.pw91-nsp-van.UPF H.tpss-mt.UPF O.pw91-van_ak.UPF Ti.pbe-sp-van_ak.info Ca.pz-n-vbc.UPF In.pbe-d-rrkjus.info O.pz-mt.info Ti.pbe-sp-van_ak.UPF C.blyp-mt.info In.pbe-d-rrkjus.UPF O.pz-mt.UPF Ti.pw91-nsp-van.info C.blyp-mt.UPF In.pz-bhs.info O.pz-rrkjus.UPF Ti.pw91-nsp-van.UPF C.blyp-van_ak.info In.pz-bhs.UPF O.pz-van_ak.info Ti.pw91-sp-van_ak.info C.blyp-van_ak.UPF In.pz-d-rrkjus.info O.pz-van_ak.UPF Ti.pw91-sp-van_ak.UPF C.bp-van_ak.info In.pz-d-rrkjus.UPF O.rel-pz-rrkjus.UPF Ti.pz-sp-van_ak.info C.bp-van_ak.UPF In.pz-n-bhs.info Os.pbe-n-van.info Ti.pz-sp-van_ak.UPF Cd.pbe-n-van.info In.pz-n-bhs.UPF Os.pbe-n-van.UPF Ti.pz-sp-van.info Cd.pbe-n-van.UPF I.pbe-mt_bw.info Os.pw91-n-van.info Ti.pz-sp-van.UPF Cd.pw91-n-van.info I.pbe-mt_bw.UPF Os.pw91-n-van.UPF Tl.pz-d-van.info Cd.pw91-n-van.UPF Ir.pbe-n-rrkjus.info O.tpss-mt.UPF Tl.pz-d-van.UPF Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF Ir.pbe-n-rrkjus.UPF P.blyp-mt.info V.pbe-n-van.UPF Cl.blyp-mt.info Ir.pbe-n-van.UPF P.blyp-mt.UPF V.pbe-sp-van.UPF Cl.blyp-mt.UPF Ir.pw91-n-van.UPF P.blyp-van_ak.info W.pbe-nsp-van.info Cl.pbe-n-van.info K.blyp-mt.info P.blyp-van_ak.UPF W.pbe-nsp-van.UPF Cl.pbe-n-van.UPF K.blyp-n-mt.UPF Pb.pbe-d-van.info W.pw91-nsp-van.info Cl.pw91-mt.info K.pz-n-vbc.info Pb.pbe-d-van.UPF W.pw91-nsp-van.UPF Cl.pw91-mt.UPF K.pz-n-vbc.UPF P.bp-van_ak.info W.pz-bhs.UPF Cl.pz-bhs.info K.pz-sp-van.info P.bp-van_ak.UPF Xe.pw91-n-van.info Cl.pz-bhs.UPF K.pz-sp-van.UPF Pb.pz-bhs.UPF Xe.pw91-n-van.UPF Co.pbe-nd-rrkjus.UPF Kr.pw91-n-van.info Pb.pz-d-van.info Y.pbe-nsp-van.info Co.pz-nd-rrkjus.UPF Kr.pw91-n-van.UPF Pb.pz-d-van.UPF Y.pbe-nsp-van.UPF Co.rel-pz-n-rrkjus.UPF La.pbe-nsp-van.info Pd.pbe-nd-rrkjus.UPF Y.pw91-nsp-van.info C.pbe-rrkjus.info La.pbe-nsp-van.UPF Pd.pbe-rrkjus.info Y.pw91-nsp-van.UPF C.pbe-rrkjus-test-diamond.pdf La.pw91-nsp-van.info Pd.pbe-rrkjus.UPF Zn.blyp-van_ak.info C.pbe-rrkjus-test-graphite.pdf La.pw91-nsp-van.UPF Pd.pz-nd-rrkjus.UPF Zn.blyp-van_ak.UPF C.pbe-rrkjus.UPF Li.blyp-s-mt.UPF Pd.pz-rrkjus.UPF Zn.bp-van_ak.info C.pbe-van_ak.info Li.blyp-s-van_ak.info P.pbe-n-van.info Zn.bp-van_ak.UPF C.pbe-van_ak.UPF Li.blyp-s-van_ak.UPF P.pbe-n-van.UPF Zn.pbe-van.info C.pbe-van_bm.info Li.bp-s-mt.UPF P.pbe-van_ak.info Zn.pbe-van.UPF C.pbe-van_bm.UPF Li.bp-s-van_ak.info P.pbe-van_ak.UPF Zn.pw91-n-van.info C.pw91-van_ak.info Li.bp-s-van_ak.UPF P.pw91-n-van.info Zn.pw91-n-van.UPF C.pw91-van_ak.UPF Li.pbe-n-van.info P.pw91-n-van.UPF Zn.pw91-van_ak.info C.pz-rrkjus.info Li.pbe-n-van.UPF P.pw91-van_ak.info Zn.pw91-van_ak.UPF C.pz-rrkjus.UPF Li.pbe-s-mt.UPF P.pw91-van_ak.UPF Zn.pz-van_ak.info C.pz-van_ak.info Li.pbe-s-van_ak.info P.pz-bhs.info Zn.pz-van_ak.UPF C.pz-van_ak.UPF Li.pbe-s-van_ak.UPF P.pz-bhs.UPF Zr.pbe-nsp-van.info C.pz-vbc.info Li.pw91-n-van.info P.pz-van_ak.info Zr.pbe-nsp-van.UPF C.pz-vbc.UPF Li.pw91-n-van.UPF P.pz-van_ak.UPF Zr.pw91-nsp-van.info C.rel-pz-rrkjus.UPF Li.pw91-s-mt.UPF Pt.pbe-nd-rrkjus.UPF Zr.pw91-nsp-van.UPF Cr.pbe-sp-van.info Li.pw91-s-van_ak.info Pt.pbe-n-van.info Zr.pw91-sp-rrkjus.info Cr.pbe-sp-van.UPF Li.pw91-s-van_ak.UPF Pt.pbe-n-van.UPF Zr.pw91-sp-rrkjus.UPF [devsharma at headnode pseudo]$ vi Y.pbe-nsp-van.UPF [devsharma at headnode pseudo]$ cd [devsharma at headnode ~]$ cd work/yvo/ [devsharma at headnode yvo]$ ls CRASH scf.out submit.sh temp yvo.inp [devsharma at headnode yvo]$ On Mon, Aug 24, 2009 at 2:24 PM, Paolo Giannozzi wrote: > dev sharma wrote: > > > Yes, /Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. > > if the code says it isn't there, it isn't there. Remember that > ALL processes must be able to access that file DURING PARALLEL > EXECUTION > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > 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/20090824/9d8306c8/attachment-0001.htm From decboy9 at gmail.com Mon Aug 24 11:13:09 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 24 Aug 2009 14:43:09 +0530 Subject: [Pw_forum] problem in parallel running In-Reply-To: <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> Message-ID: Sure Sir : ) My Input file is listed below &control calculation='scf', restart_mode='from_scratch', prefix='yvo', wf_collect=.true., pseudo_dir = '/home/devshama/pseudo/', outdir='/home/devsharma/work/yvo/temp' / &system ibrav =6, a=7.118300514, b= 7.118300514, c=6.289300454 , nat =24, ntyp= 3, ecutwfc = 40.0, occupations='fixed', / &electrons mixing_beta = 0.7 diagonalization = 'david' conv_thr = 1.0e-6 / &ions / ATOMIC_SPECIES Y 88.90585 Y.pbe-nsp-van.UPF V 50.9415 V.pbe-sp-van.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS {angstrom} / / K_POINTS {automatic} 4 4 4 0 0 0 1,1 Top On Mon, Aug 24, 2009 at 2:22 PM, xirainbow wrote: > Dear dev sharma: > > On 8/24/09, dev sharma wrote: >> >> Dear Sir, >> Yes, *Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. I >> had already checked it before pasting the problem.* > > > Can you give the input file? ?? > > > > ____________________________________ > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/d804caeb/attachment.htm From giannozz at democritos.it Mon Aug 24 11:18:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 24 Aug 2009 11:18:23 +0200 Subject: [Pw_forum] problem in parallel running In-Reply-To: References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> Message-ID: <4A925ADF.80301@democritos.it> dev sharma wrote: > pseudo_dir = '/home/devshama/pseudo/', > Yes, /Y.pbe-nsp-van.UPF is present there in > /home/devsharma/pseudo/. do you know the game "Find the differences", in which you have two apparently equal pictures differing just for a few details? Find the difference. There is one. -- Paolo Giannozzi, Democritos and University of Udine, Italy From decboy9 at gmail.com Mon Aug 24 11:24:28 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 24 Aug 2009 14:54:28 +0530 Subject: [Pw_forum] problem in parallel running In-Reply-To: <4A925ADF.80301@democritos.it> References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> <4A925ADF.80301@democritos.it> Message-ID: Thank you very much sir,I have found my mistake. And will take care in future also. With regards, Dev On Mon, Aug 24, 2009 at 2:48 PM, Paolo Giannozzi wrote: > dev sharma wrote: > > > pseudo_dir = '/home/devshama/pseudo/', > > > Yes, /Y.pbe-nsp-van.UPF is present there in > > /home/devsharma/pseudo/. > > do you know the game "Find the differences", in which you > have two apparently equal pictures differing just for a few > details? Find the difference. There is one. > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > 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/20090824/7fc0ddc5/attachment.htm From ttduyle at gmail.com Mon Aug 24 11:27:16 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 24 Aug 2009 05:27:16 -0400 Subject: [Pw_forum] problem in parallel running In-Reply-To: References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> Message-ID: <8974d3b20908240227k73a677cahe646a9eb6af13d7f@mail.gmail.com> Hi,Are you sure that your files are accessible by all the NODES? Please login to the nodes other than head node to make sure all the paths are correct. One of the way you may try is to use relative path. For instant, pseudo_dir = '../../pseudo' outdir = './temp' Good luck! On Mon, Aug 24, 2009 at 5:13 AM, dev sharma wrote: > Sure Sir : ) > My Input file is listed below > &control > calculation='scf', > restart_mode='from_scratch', > prefix='yvo', > wf_collect=.true., > pseudo_dir = '/home/devshama/pseudo/', > outdir='/home/devsharma/work/yvo/temp' > / > &system > ibrav =6, a=7.118300514, b= 7.118300514, c=6.289300454 > , nat =24, ntyp= 3, ecutwfc = 40.0, > occupations='fixed', > > > / > &electrons > mixing_beta = 0.7 > diagonalization = 'david' > conv_thr = 1.0e-6 > / > &ions > / > > ATOMIC_SPECIES > Y 88.90585 Y.pbe-nsp-van.UPF > V 50.9415 V.pbe-sp-van.UPF > O 15.9994 O.pbe-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > / > / > > K_POINTS {automatic} > 4 4 4 0 0 0 > > > 1,1 Top > > > > On Mon, Aug 24, 2009 at 2:22 PM, xirainbow wrote: > >> Dear dev sharma: >> >> On 8/24/09, dev sharma wrote: >>> >>> Dear Sir, >>> Yes, *Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. I >>> had already checked it before pasting the problem.* >> >> >> Can you give the input file? ?? >> >> >> >> ____________________________________ >> 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 mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/6879f3db/attachment.htm From oulihui666 at 126.com Mon Aug 24 10:58:14 2009 From: oulihui666 at 126.com (oulihui666) Date: Mon, 24 Aug 2009 16:58:14 +0800 (CST) Subject: [Pw_forum] Frequency and zero point energy In-Reply-To: References: Message-ID: <28773640.647331251104294956.JavaMail.coremail@bj126app29.126.com> Dear Gabriele Sclauzero, Thank you for your help. Best regards Lihui -- ====================================== Lihui Ou PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:oulihui666 at 126.com ====================================== >Date: Mon, 24 Aug 2009 08:45:32 +0200 >From: Gabriele Sclauzero >Subject: Re: [Pw_forum] Reply (was Frequency and zero point energy > calculations) >To: PWSCF Forum >Message-ID: <4A92370C.6040106 at sissa.it> >Content-Type: text/plain; charset=utf-8; format=flowed > > >Dear Lihui, > > I have an update to this answer: for phonon calculations based on data produced by >pw.x using gamma point tricks (i.e. K_POINTS GAMMA), you should use the code phcg.x in the >Gamma/ directory, not ph.x. > >regards, > >GS > >Gabriele Sclauzero wrote: >> Dear Lihui, >> >> oulihui666 wrote: >>> Dear Gabriele Sclauzero, >>> I am intend to calculate the frequency of CO2 molecule, so I should >>> perform scf calculation at first, when setting k points as gamma, it >>> will appear a error in the process of calculating frequency, as follows: >>> *********************************************************************** >>> from phq_readin. error #1 >>> cannot start from pw.x data file using Gamma-point tricks >>> *********************************************************************** >> >> From what I can understand, this does not mean that you cannot do the calculation for the >> Gamma point only, but rather that the calculation cannot be done using Gamma >> point-specific algorithms (which are much faster than the general ones). >> You should anyway be allowed to do the calculation using >> K_POINTS AUTOMATIC >> 1 1 1 0 0 0 >> which builds a k-point grid containing the Gamma point only, but does not use Gamma-point >> tricks. >> >> You can do the relaxations (and all other expensive pw calculations) using >> K_POINTS GAMMA >> and then, starting from the optimized atomic positions, do a nscf run using >> K_POINTS AUTOMATIC >> 1 1 1 0 0 0 >> before the phonon run. >> >> Cheers >> >> GS >> >> P.S: please avoid private mails and stick to the thread you started in the forum, so that >> anyone can help and know when your problem has been solved. Thanks! >> >> >> >>> So I do not set k point as gamma in scf calculation. >>> >>> Best regards >>> Lihui >>> >>> -- >>> ====================================== >>> Lihui Ou >>> PH.D Candidate in Electrochemistry >>> College of Chemistry and Molecular Science >>> Wuhan University,/430072/,Hubei Province,China >>> /E-mail:oulihui666 at 126.com / >>> ====================================== >>> >>> >>> ------------------------------------------------------------------------ >>> ???????????,www.yeah.net >> > >-- > > >o ------------------------------------------------ o >| Gabriele Sclauzero, PhD Student | >| c/o: SISSA & CNR-INFM Democritos, | >| via Beirut 2-4, 34014 Trieste (Italy) | >| email: sclauzer at sissa.it | >| phone: +39 040 3787 511 | >| skype: gurlonotturno | >o ------------------------------------------------ o > > >------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End of Pw_forum Digest, Vol 26, Issue 63 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/20d75891/attachment-0001.htm From hqzhou at nju.edu.cn Mon Aug 24 11:35:57 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 24 Aug 2009 17:35:57 +0800 Subject: [Pw_forum] problem in parallel running References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com><4A925554.1070406@democritos.it> Message-ID: <8135591B72A041DD9068092B1166C8CB@solarflare> Sharma, Let me try to put it clearer. Paolo means that the compute nodes involved in the computation must be able to "see" the folder /home/devsharma/pseudo, meaning the pseudo folder must be located on a NFS, which is shared by the head node, the one you submitted your job, and compute nodes, on which your job is executed. If your job was submitted to the head node itself, that will be very strange. You need to let us know your cluster environment. Huiqun Zhou @Nanjing University, China ----- Original Message ----- From: dev sharma To: PWSCF Forum Sent: Monday, August 24, 2009 5:10 PM Subject: Re: [Pw_forum] problem in parallel running Dear Sir, I am sending all the terminal commands to you. Please guide me., [devsharma at headnode ~]$ ls espresso-4.0.2 pseudo tmp work [devsharma at headnode ~]$ cd pseudo/ [devsharma at headnode pseudo]$ ls 0710.pdf Cr.pw91-sp-van.info Li.pz-n-vbc.UPF Pt.pw91-n-van.info Ag.pbe-d-rrkjus.info Cr.pw91-sp-van.UPF Li.pz-s-mt.UPF Pt.pw91-n-van.UPF Ag.pbe-d-rrkjus.UPF Cs.pbe-mt_bw.info Li.pz-s-van_ak.info Pt.pz-nd-rrkjus.UPF Ag.pz-d-rrkjus.UPF Cs.pbe-mt_bw.UPF Li.pz-s-van_ak.UPF Pt.pz-rrkjus.UPF Al.blyp-n-van_ak.info C.tpss-mt.UPF Mg.pw91-np-van.info Pt.rel-pz-n-rrkjus.UPF Al.blyp-n-van_ak.UPF Cu.blyp-n-van_ak.info Mg.pw91-np-van.UPF Re.pw91-n-van.info Al.bp-n-van_ak.info Cu.blyp-n-van_ak.UPF Mg.pz-bhs.UPF Re.pw91-n-van.UPF Al.bp-n-van_ak.UPF Cu.pbe-d-rrkjus.info Mg.pz-n-vbc.info Rh.pbe-nd-rrkjus.UPF Al.pbe-n-van.info Cu.pbe-d-rrkjus.UPF Mg.pz-n-vbc.UPF Rh.pbe-rrkjus.UPF Al.pbe-n-van.UPF Cu.pbe-n-van_ak.info Mn.pbe-sp-van.info Rh.pz-rrkjus.UPF Al.pbe-rrkj.UPF Cu.pbe-n-van_ak.UPF Mn.pbe-sp-van.UPF Ru.pbe-n-van.info Al.pw91-n-van.info Cu.pw91-n-van_ak.info Mo.pw91-n-van.info Ru.pbe-n-van.UPF Al.pw91-n-van.UPF Cu.pw91-n-van_ak.UPF Mo.pw91-n-van.UPF Ru.pw91-n-van.info Al.pz-vbc.UPF Cu.pz-d-rrkjus.UPF Na.blyp-sp-van_ak.info Ru.pw91-n-van.UPF Ar.pz-rrkj.info Cu.pz-n-van_ak.info Na.blyp-sp-van_ak.UPF S.blyp-mt.info Ar.pz-rrkj.UPF Cu.pz-n-van_ak.UPF Na.bp-sp-van_ak.info S.blyp-mt.UPF As.pbe-n-van.info Fe.blyp-sp-van_ak.info Na.bp-sp-van_ak.UPF S.blyp-van_ak.info As.pbe-n-van.UPF Fe.blyp-sp-van_ak.UPF Na.pbe-n-mt_bw.info S.blyp-van_ak.UPF As.pw91-n-van.info Fe.blyp-sp-van.info Na.pbe-n-mt_bw.UPF S.bp-van_ak.info As.pw91-n-van.UPF Fe.blyp-sp-van.UPF Na.pbe-n-van.UPF S.bp-van_ak.UPF As.pz-bhs.info Fe.bp-sp-van_ak.info Na.pbe-sp-van_ak.info Sb.pw91-n-van.info As.pz-bhs.UPF Fe.bp-sp-van_ak.UPF Na.pbe-sp-van_ak.UPF Sb.pw91-n-van.UPF Au.blyp-van_ak.info Fe.pbe-nd-rrkjus.UPF Na.pw91-n-mt.UPF Sb.pz-bhs.info Au.blyp-van_ak.UPF Fe.pbe-sp-van_ak.info Na.pw91-n-van.UPF Sb.pz-bhs.UPF Au.bp-van_ak.info Fe.pbe-sp-van_ak.UPF Na.pw91-sp-van_ak.info Sc.pbe-nsp-van.info Au.bp-van_ak.UPF Fe.pbe-sp-van.info Na.pw91-sp-van_ak.UPF Sc.pbe-nsp-van.UPF Au.pbe-nd-rrkjus.UPF Fe.pbe-sp-van_mit.info Na.pz-n-vbc.info Sc.pw91-nsp-van.info Au.pbe-nd-van.info Fe.pbe-sp-van_mit.UPF Na.pz-n-vbc.UPF Sc.pw91-nsp-van.UPF Au.pbe-nd-van.UPF Fe.pbe-sp-van.UPF Na.pz-sp-van_ak.info Se.pbe-van.info Au.pbe-van_ak.info Fe.pw91-sp-van_ak.info Na.pz-sp-van_ak.UPF Se.pbe-van.UPF Au.pbe-van_ak.UPF Fe.pw91-sp-van_ak.UPF Nb.elastic_constant_tests.pdf Se.pz-bhs.info Au.pw91-d-van.UPF Fe.pz-nd-rrkjus.UPF N.blyp-mt.info Se.pz-bhs.UPF Au.pw91-van_ak.info Fe.pz-sp-van_ak.info N.blyp-mt.UPF Si.pbe-n-van.info Au.pw91-van_ak.UPF Fe.pz-sp-van_ak.UPF N.blyp-van_ak.info Si.pbe-n-van.UPF Au.pz-d-rrkjus.UPF filename.upf N.blyp-van_ak.UPF Si.pbe-rrkj.UPF Au.pz-d-van.UPF F.pbe-n-van.info Nb.pbe-nsp-van.info Si.pw91-n-van.info Au.pz-van_ak.info F.pbe-n-van.UPF Nb.pbe-nsp-van.UPF Si.pw91-n-van.UPF Au.pz-van_ak.UPF F.pw91-n-van.info N.bp-van_ak.info Si.pz-vbc.UPF Au.rel-pz-rrkjus.UPF F.pw91-n-van.UPF N.bp-van_ak.UPF Si.tpss-mt.UPF Ba.pbe-nsp-van.info Ga.pbe-nsp-van.info Nb.pw91-nsp-van.info Sn.pw91-n-van.info Ba.pbe-nsp-van.UPF Ga.pbe-nsp-van.UPF Nb.pw91-nsp-van.UPF Sn.pw91-n-van.UPF Ba.pw91-nsp-van.info Ga.pw91-nsp-van.info Nb.pz-sp-van.info Sn.pz-bhs.info Ba.pw91-nsp-van.UPF Ga.pw91-nsp-van.UPF Nb.pz-sp-van.UPF Sn.pz-bhs.UPF B.blyp-n-van_ak.info Ga.pz-bhs.info Ni.pbe-nd-rrkjus.UPF S.pbe-van_bm.info B.blyp-n-van_ak.UPF Ga.pz-bhs.UPF Ni.pz-nd-rrkjus.UPF S.pbe-van_bm.UPF B.bp-n-van_ak.info Ge.pw91-n-van.info N.pbe-rrkjus.UPF S.pw91-n-mt.info B.bp-n-van_ak.UPF Ge.pw91-n-van.UPF N.pbe-van_ak.info S.pw91-n-mt.UPF Be.pz-n-vbc.info Ge.pz-bhs.info N.pbe-van_ak.UPF S.pw91-van_ak.info Be.pz-n-vbc.UPF Ge.pz-bhs.UPF N.pbe-van_bm.info S.pw91-van_ak.UPF Be.star1s-pz-n-vbc.UPF Ge.tpss-n-mt.UPF N.pbe-van_bm.UPF S.pz-bhs.info Bi.pbe-d-mt.info H.blyp-van_ak.info N.pw91-van_ak.info S.pz-bhs.UPF Bi.pbe-d-mt.UPF H.blyp-van_ak.UPF N.pw91-van_ak.UPF S.pz-van_ak.info B.pbe-n-van_ak.info H.blyp-vbc.info N.pz-rrkjus.UPF S.pz-van_ak.UPF B.pbe-n-van_ak.UPF H.blyp-vbc.UPF N.pz-van_ak.info Sr.pbe-nsp-van.info B.pbe-n-van.info H.bp-van_ak.info N.pz-van_ak.UPF Sr.pbe-nsp-van.UPF B.pbe-n-van.UPF H.bp-van_ak.UPF N.pz-vbc.info Sr.pbe-sp-van.info B.pw91-n-van_ak.info He.pbe-mt_fhi.UPF N.pz-vbc.UPF Sr.pbe-sp-van.UPF B.pw91-n-van_ak.UPF He.pz-mt_fhi.UPF O.blyp-mt.info Sr.pw91-nsp-van.info B.pw91-n-van.info H.pbe-rrkjus.UPF O.blyp-mt.UPF Sr.pw91-nsp-van.UPF B.pw91-n-van.UPF H.pbe-van_ak.info O.blyp-van_ak.info Ta.pbe-nsp-van.info B.pz-bhs.UPF H.pbe-van_ak.UPF O.blyp-van_ak.UPF Ta.pbe-nsp-van.UPF B.pz-vbc.UPF H.pbe-van_bm.info O.bp-van_ak.info Ta.pw91-nsp-van.info Br.pbe-van_mit.info H.pbe-van_bm.UPF O.bp-van_ak.UPF Ta.pw91-nsp-van.UPF Br.pbe-van_mit.UPF H.pbe-vbc.UPF O.pbe-mt.UPF Te.pbe-rrkj.UPF Br.pw91-mt.info H.pw91-van_ak.info O.pbe-rrkjus.UPF Te.pz-bhs.info Br.pw91-mt.UPF H.pw91-van_ak.UPF O.pbe-van_ak.info Te.pz-bhs.UPF Br.pz-vbc.UPF H.pz-rrkjus.UPF O.pbe-van_ak.UPF Ti.blyp-sp-van_ak.info Ca.pbe-nsp-van.info H.pz-van_ak.info O.pbe-van_bm.info Ti.blyp-sp-van_ak.UPF Ca.pbe-nsp-van.UPF H.pz-van_ak.UPF O.pbe-van_bm.UPF Ti.bp-sp-van_ak.info Ca.pw91-nsp-van.info H.pz-vbc.UPF O.pw91-van_ak.info Ti.bp-sp-van_ak.UPF Ca.pw91-nsp-van.UPF H.tpss-mt.UPF O.pw91-van_ak.UPF Ti.pbe-sp-van_ak.info Ca.pz-n-vbc.UPF In.pbe-d-rrkjus.info O.pz-mt.info Ti.pbe-sp-van_ak.UPF C.blyp-mt.info In.pbe-d-rrkjus.UPF O.pz-mt.UPF Ti.pw91-nsp-van.info C.blyp-mt.UPF In.pz-bhs.info O.pz-rrkjus.UPF Ti.pw91-nsp-van.UPF C.blyp-van_ak.info In.pz-bhs.UPF O.pz-van_ak.info Ti.pw91-sp-van_ak.info C.blyp-van_ak.UPF In.pz-d-rrkjus.info O.pz-van_ak.UPF Ti.pw91-sp-van_ak.UPF C.bp-van_ak.info In.pz-d-rrkjus.UPF O.rel-pz-rrkjus.UPF Ti.pz-sp-van_ak.info C.bp-van_ak.UPF In.pz-n-bhs.info Os.pbe-n-van.info Ti.pz-sp-van_ak.UPF Cd.pbe-n-van.info In.pz-n-bhs.UPF Os.pbe-n-van.UPF Ti.pz-sp-van.info Cd.pbe-n-van.UPF I.pbe-mt_bw.info Os.pw91-n-van.info Ti.pz-sp-van.UPF Cd.pw91-n-van.info I.pbe-mt_bw.UPF Os.pw91-n-van.UPF Tl.pz-d-van.info Cd.pw91-n-van.UPF Ir.pbe-n-rrkjus.info O.tpss-mt.UPF Tl.pz-d-van.UPF Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF Ir.pbe-n-rrkjus.UPF P.blyp-mt.info V.pbe-n-van.UPF Cl.blyp-mt.info Ir.pbe-n-van.UPF P.blyp-mt.UPF V.pbe-sp-van.UPF Cl.blyp-mt.UPF Ir.pw91-n-van.UPF P.blyp-van_ak.info W.pbe-nsp-van.info Cl.pbe-n-van.info K.blyp-mt.info P.blyp-van_ak.UPF W.pbe-nsp-van.UPF Cl.pbe-n-van.UPF K.blyp-n-mt.UPF Pb.pbe-d-van.info W.pw91-nsp-van.info Cl.pw91-mt.info K.pz-n-vbc.info Pb.pbe-d-van.UPF W.pw91-nsp-van.UPF Cl.pw91-mt.UPF K.pz-n-vbc.UPF P.bp-van_ak.info W.pz-bhs.UPF Cl.pz-bhs.info K.pz-sp-van.info P.bp-van_ak.UPF Xe.pw91-n-van.info Cl.pz-bhs.UPF K.pz-sp-van.UPF Pb.pz-bhs.UPF Xe.pw91-n-van.UPF Co.pbe-nd-rrkjus.UPF Kr.pw91-n-van.info Pb.pz-d-van.info Y.pbe-nsp-van.info Co.pz-nd-rrkjus.UPF Kr.pw91-n-van.UPF Pb.pz-d-van.UPF Y.pbe-nsp-van.UPF Co.rel-pz-n-rrkjus.UPF La.pbe-nsp-van.info Pd.pbe-nd-rrkjus.UPF Y.pw91-nsp-van.info C.pbe-rrkjus.info La.pbe-nsp-van.UPF Pd.pbe-rrkjus.info Y.pw91-nsp-van.UPF C.pbe-rrkjus-test-diamond.pdf La.pw91-nsp-van.info Pd.pbe-rrkjus.UPF Zn.blyp-van_ak.info C.pbe-rrkjus-test-graphite.pdf La.pw91-nsp-van.UPF Pd.pz-nd-rrkjus.UPF Zn.blyp-van_ak.UPF C.pbe-rrkjus.UPF Li.blyp-s-mt.UPF Pd.pz-rrkjus.UPF Zn.bp-van_ak.info C.pbe-van_ak.info Li.blyp-s-van_ak.info P.pbe-n-van.info Zn.bp-van_ak.UPF C.pbe-van_ak.UPF Li.blyp-s-van_ak.UPF P.pbe-n-van.UPF Zn.pbe-van.info C.pbe-van_bm.info Li.bp-s-mt.UPF P.pbe-van_ak.info Zn.pbe-van.UPF C.pbe-van_bm.UPF Li.bp-s-van_ak.info P.pbe-van_ak.UPF Zn.pw91-n-van.info C.pw91-van_ak.info Li.bp-s-van_ak.UPF P.pw91-n-van.info Zn.pw91-n-van.UPF C.pw91-van_ak.UPF Li.pbe-n-van.info P.pw91-n-van.UPF Zn.pw91-van_ak.info C.pz-rrkjus.info Li.pbe-n-van.UPF P.pw91-van_ak.info Zn.pw91-van_ak.UPF C.pz-rrkjus.UPF Li.pbe-s-mt.UPF P.pw91-van_ak.UPF Zn.pz-van_ak.info C.pz-van_ak.info Li.pbe-s-van_ak.info P.pz-bhs.info Zn.pz-van_ak.UPF C.pz-van_ak.UPF Li.pbe-s-van_ak.UPF P.pz-bhs.UPF Zr.pbe-nsp-van.info C.pz-vbc.info Li.pw91-n-van.info P.pz-van_ak.info Zr.pbe-nsp-van.UPF C.pz-vbc.UPF Li.pw91-n-van.UPF P.pz-van_ak.UPF Zr.pw91-nsp-van.info C.rel-pz-rrkjus.UPF Li.pw91-s-mt.UPF Pt.pbe-nd-rrkjus.UPF Zr.pw91-nsp-van.UPF Cr.pbe-sp-van.info Li.pw91-s-van_ak.info Pt.pbe-n-van.info Zr.pw91-sp-rrkjus.info Cr.pbe-sp-van.UPF Li.pw91-s-van_ak.UPF Pt.pbe-n-van.UPF Zr.pw91-sp-rrkjus.UPF [devsharma at headnode pseudo]$ vi Y.pbe-nsp-van.UPF [devsharma at headnode pseudo]$ cd [devsharma at headnode ~]$ cd work/yvo/ [devsharma at headnode yvo]$ ls CRASH scf.out submit.sh temp yvo.inp [devsharma at headnode yvo]$ On Mon, Aug 24, 2009 at 2:24 PM, Paolo Giannozzi wrote: dev sharma wrote: > Yes, /Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. if the code says it isn't there, it isn't there. Remember that ALL processes must be able to access that file DURING PARALLEL EXECUTION P. -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ------------------------------------------------------------------------------ _______________________________________________ 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/20090824/e1a87ffa/attachment-0001.htm From ttduyle at gmail.com Mon Aug 24 11:32:05 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 24 Aug 2009 05:32:05 -0400 Subject: [Pw_forum] problem in parallel running In-Reply-To: <8974d3b20908240227k73a677cahe646a9eb6af13d7f@mail.gmail.com> References: <21fbc4790908240142t12b0d312nde3a5f46ade9c55b@mail.gmail.com> <21fbc4790908240152i1a550855jf8b17c9c3149dc86@mail.gmail.com> <8974d3b20908240227k73a677cahe646a9eb6af13d7f@mail.gmail.com> Message-ID: <8974d3b20908240232n6855f65cl389cd63a7bc61e97@mail.gmail.com> One more note: The error #29 should have appeared 4 times if the potential file is not there. From your output, I can say 3 (out of 4) nodes could not locate the absolute path. On Mon, Aug 24, 2009 at 5:27 AM, Duy Le wrote: > Hi,Are you sure that your files are accessible by all the NODES? Please > login to the nodes other than head node to make sure all the paths are > correct. > > One of the way you may try is to use relative path. For instant, > pseudo_dir = '../../pseudo' > outdir = './temp' > > Good luck! > > > On Mon, Aug 24, 2009 at 5:13 AM, dev sharma wrote: > >> Sure Sir : ) >> My Input file is listed below >> &control >> calculation='scf', >> restart_mode='from_scratch', >> prefix='yvo', >> wf_collect=.true., >> pseudo_dir = '/home/devshama/pseudo/', >> outdir='/home/devsharma/work/yvo/temp' >> / >> &system >> ibrav =6, a=7.118300514, b= 7.118300514, c=6.289300454 >> , nat =24, ntyp= 3, ecutwfc = 40.0, >> occupations='fixed', >> >> >> / >> &electrons >> mixing_beta = 0.7 >> diagonalization = 'david' >> conv_thr = 1.0e-6 >> / >> &ions >> / >> >> ATOMIC_SPECIES >> Y 88.90585 Y.pbe-nsp-van.UPF >> V 50.9415 V.pbe-sp-van.UPF >> O 15.9994 O.pbe-van_ak.UPF >> ATOMIC_POSITIONS {angstrom} >> / >> / >> >> K_POINTS {automatic} >> 4 4 4 0 0 0 >> >> >> 1,1 Top >> >> >> >> On Mon, Aug 24, 2009 at 2:22 PM, xirainbow wrote: >> >>> Dear dev sharma: >>> >>> On 8/24/09, dev sharma wrote: >>>> >>>> Dear Sir, >>>> Yes, *Y.pbe-nsp-van.UPF is present there in /home/devsharma/pseudo/. I >>>> had already checked it before pasting the problem.* >>> >>> >>> Can you give the input file? ?? >>> >>> >>> >>> ____________________________________ >>> 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 mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/bc4838df/attachment.htm From eyvaz_isaev at yahoo.com Mon Aug 24 13:56:37 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 24 Aug 2009 04:56:37 -0700 (PDT) Subject: [Pw_forum] Question about K-points In-Reply-To: <8974d3b20908231107i709ea652w59bcf0bd2db8254a@mail.gmail.com> Message-ID: <240184.26142.qm@web65716.mail.ac4.yahoo.com> Hi, --- On Sun, 8/23/09, Duy Le wrote: >How about the forces acting on the atoms in 2 cases? Are they too >different? There are no forces in CaF2 (antifluorite) type structure due to its high symmetry. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From paguado at gmail.com Mon Aug 24 14:03:44 2009 From: paguado at gmail.com (Pablo Aguado) Date: Mon, 24 Aug 2009 14:03:44 +0200 Subject: [Pw_forum] does cell_dofree work? Message-ID: Dear all, I'm playing around with the cell_dofree variable and I don't manage to make it work. Currently I'm trying to relax only the c lattice vector of a tetragonal cell together with the atomic coordinates, so I use the following: &control calculation = 'vc-relax' restart_mode = 'from_scratch' pseudo_dir = '***/pseudo/' outdir = '***/tmp' forc_conv_thr = 1d-3 / &system ibrav=6 celldm(1)=6.8 celldm(3)=1.1 nat=5 ntyp=3 nbnd=28 ecutwfc=30.0 occupations = 'fixed' / &electrons diagonalization = 'cg' conv_thr = 1d-8, mixing_beta=0.2, / &ions ion_dynamics = 'bfgs' bfgs_ndim = 5 ion_positions = 'from_input' / &cell cell_dynamics = 'bfgs' cell_dofree = 'z' / ATOMIC_SPECIES Pb 207.2 Pb.pz-d-van.UPF Ti 47.867 Ti.pz-sp-van_ak.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS crystal Pb 0.000 0.000 0.040 0 0 1 Ti 0.500 0.500 0.530 0 0 1 O 0.000 0.500 0.500 0 0 1 O 0.500 0.500 0.000 0 0 1 O 0.500 0.000 0.500 0 0 1 K_POINTS {automatic} 6 6 6 1 1 1 However, when I run PW, all the lattice vectors are relaxed. I've checked the mail list but it's not clear to me whether this variable is actually fully implemented or not. Am I doing something wrong? Thanks in advance, Pablo From yccheng.nju at gmail.com Mon Aug 24 15:24:27 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 24 Aug 2009 21:24:27 +0800 Subject: [Pw_forum] does cell_dofree work? In-Reply-To: References: Message-ID: As far as I know, cell-dofree does not work. 2009/8/24 Pablo Aguado > Dear all, > > I'm playing around with the cell_dofree variable and I don't manage to > make it work. Currently I'm trying to relax only the c lattice vector > of a tetragonal cell together with the atomic coordinates, so I use > the following: > > &control > calculation = 'vc-relax' > restart_mode = 'from_scratch' > pseudo_dir = '***/pseudo/' > outdir = '***/tmp' > forc_conv_thr = 1d-3 > / > &system > ibrav=6 > celldm(1)=6.8 > celldm(3)=1.1 > nat=5 > ntyp=3 > nbnd=28 > ecutwfc=30.0 > occupations = 'fixed' > / > &electrons > diagonalization = 'cg' > conv_thr = 1d-8, > mixing_beta=0.2, > / > &ions > ion_dynamics = 'bfgs' > bfgs_ndim = 5 > ion_positions = 'from_input' > / > &cell > cell_dynamics = 'bfgs' > cell_dofree = 'z' > / > ATOMIC_SPECIES > Pb 207.2 Pb.pz-d-van.UPF > Ti 47.867 Ti.pz-sp-van_ak.UPF > O 15.9994 O.pz-van_ak.UPF > ATOMIC_POSITIONS crystal > Pb 0.000 0.000 0.040 0 0 1 > Ti 0.500 0.500 0.530 0 0 1 > O 0.000 0.500 0.500 0 0 1 > O 0.500 0.500 0.000 0 0 1 > O 0.500 0.000 0.500 0 0 1 > K_POINTS {automatic} > 6 6 6 1 1 1 > > However, when I run PW, all the lattice vectors are relaxed. I've > checked the mail list but it's not clear to me whether this variable > is actually fully implemented or not. > > Am I doing something wrong? > > Thanks in advance, > > Pablo > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090824/563e2ae2/attachment.htm From paulatto at sissa.it Mon Aug 24 15:32:21 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 24 Aug 2009 15:32:21 +0200 Subject: [Pw_forum] does cell_dofree work? In-Reply-To: References: Message-ID: In data 24 agosto 2009 alle ore 14:03:44, Pablo Aguado ha scritto: > I'm playing around with the cell_dofree variable and I don't manage to > make it work. Currently I'm trying to relax only the c lattice vector > of a tetragonal cell together with the atomic coordinates, so I use > the following: As far as I know it works with damped dynamics, but not with bfgs. I've started to implement it some time ago, but than dropped for lack of time and interest. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From a_rastkar at azaruniv.edu Tue Aug 25 12:30:50 2009 From: a_rastkar at azaruniv.edu (Dr.rastegar) Date: Tue, 25 Aug 2009 15:00:50 +0430 Subject: [Pw_forum] pw_forum Message-ID: a_rastkar at azaruniv.edu arastghar at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090825/dddf93d5/attachment.htm From a_rastkar at azaruniv.edu Tue Aug 25 12:31:40 2009 From: a_rastkar at azaruniv.edu (Dr.rastegar) Date: Tue, 25 Aug 2009 15:01:40 +0430 Subject: [Pw_forum] (no subject) Message-ID: a_rastkar at azaruniv.edu arastghar at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090825/94249a84/attachment.htm From sylvian.cadars at cnrs-orleans.fr Tue Aug 25 15:17:32 2009 From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars) Date: Tue, 25 Aug 2009 15:17:32 +0200 Subject: [Pw_forum] Interferences between symmetry generation and "ecutrho" value Message-ID: <4A93E46C.20002@cnrs-orleans.fr> Hi, Playing with test files of the GIPAW_example, and more specifically the basic SCF "quartz.scf.in" calculation, I found the symmetry generation would fail for certain values of "ecutrho" (see list of the tests conducted below). Importantly, problems can occur even though one sticks to the default value (=4*ecutwfc). These errors seem to be independent of the ecutwfc value, at least this is what my tests suggest. Is this a known issue? Where does it come from? Is it predictable and avoidable? Thanks. All the best. Sylvian. --------------------------- ecutwfc ecutrho result --------------------------- 70 140 failed 70 210 OK 70 280 OK (=default) 70 300 OK 70 420 OK 70 600 failed 150 600 failed (=default) 150 - failed (ecutrho=600) 105 - OK (ecutrho=420) 200 800 OK 200 1200 OK -------------------------- The error messages that occur are the following: Max angular momentum in pseudopotentials (lmaxx) = 3 warning: symmetry operation # 7 not allowed. fractional translation: 0.0000000 0.0000000 -0.3333333 in crystal coordinates warning: symmetry operation # 8 not allowed. fractional translation: 0.0000000 0.0000000 0.3333333 in crystal coordinates warning: symmetry operation # 11 not allowed. fractional translation: 0.0000000 0.0000000 0.3333333 in crystal coordinates warning: symmetry operation # 12 not allowed. fractional translation: 0.0000000 0.0000000 -0.3333333 in crystal coordinates And 2 symmetry operations are found instead of 6 when everything works properly. 2 Sym.Ops. (no inversion) For convenience, here is a typical input file that fails: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/sc/espresso_tmp' , pseudo_dir = '/home/sc/PWscf/PseudoPotentials/PBE_090707/' , / &system ibrav = 0 celldm(1) = 1. nat = 9 ntyp = 2 ecutwfc = 150 ecutrho = 600 / &ELECTRONS electron_maxstep = 100 conv_thr = 5.0e-8 startingpot = 'atomic' startingwfc = 'atomic' mixing_mode = 'plain' mixing_beta = 0.7 diagonalization = 'david' diago_thr_init = 1.e-2 / ATOMIC_SPECIES Si 28.0855000 SiPBE_nc.UPF O 15.9994000 OPBE_nc.UPF ATOMIC_POSITIONS crystal Si 0.4701 0.0000 0.3333333333 Si 0.0000 0.4701 0.6666666667 Si -0.4701 -0.4701 0.0000000000 O 0.4139 0.2674 0.2144 O -0.2674 0.1465 0.5477333333 O -0.1465 -0.4139 0.8810666667 O 0.2674 0.4139 -0.2144 O 0.1465 -0.2674 0.4522666667 O -0.4139 -0.1465 0.1189333333 CELL_PARAMETERS hexagonal 4.642775480 -8.041523019 0.000000000 4.642775480 8.041523019 0.000000000 0.000000000 0.000000000 10.213406856 K_POINTS automatic 2 2 2 1 1 1 *Dr. Sylvian CADARS* CEMHTI-CNRS 1D, Av. de la Recherche Scientifique 45071 Orl?ans Cedex 2, France From sylvian.cadars at cnrs-orleans.fr Tue Aug 25 16:58:01 2009 From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars) Date: Tue, 25 Aug 2009 16:58:01 +0200 Subject: [Pw_forum] output redirection with gipaw.x Message-ID: <4A93FBF9.6040905@cnrs-orleans.fr> Hi, A few weeks ago, Paolo gave me a useful trick (see below) to redirect PW outputs when the "redirection doesn't work one's system". Specifically, the redirection using ">" does not work on my system, such that the output is written instead in the output file that is automatically generated by the submission system (OAR in this case). The trick was to go to PW/startup.f90 and change IF ( me_image /= root_image ) & OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' ) into IF ( me_image /= root_image ) THEN OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' ) ELSE OPEN( UNIT = stdout, FILE = 'some_file_name', STATUS = 'UNKNOWN' ) END IF I could not find the equivalent command lines in the GIPAW/ directory. How should I proceed to obtain a similar redirection to a default output file with GIPAW? Thanks. Best wishes. Sylvian Cadars CEMHTI-CNRS 1D, Av. de la Recherche Scientifique 45071 Orl?ans Cedex 2, France email: sylvian.cadars at cnrs-orleans.fr From ceresoli at MIT.EDU Tue Aug 25 17:07:54 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Tue, 25 Aug 2009 11:07:54 -0400 Subject: [Pw_forum] output redirection with gipaw.x In-Reply-To: <4A93FBF9.6040905@cnrs-orleans.fr> References: <4A93FBF9.6040905@cnrs-orleans.fr> Message-ID: <4A93FE4A.3030902@mit.edu> Sylvian Cadars wrote: > Hi, > A few weeks ago, Paolo gave me a useful trick (see below) to redirect PW > outputs when the "redirection doesn't work one's system". Specifically, > the redirection using ">" does not work on my system, such that the > output is written instead in the output file that is automatically > generated by the submission system (OAR in this case). > > The trick was to go to PW/startup.f90 and change > > IF ( me_image /= root_image ) & > OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' ) > > into Is this in PW/startup.f90? > > IF ( me_image /= root_image ) THEN > OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' ) > ELSE > OPEN( UNIT = stdout, FILE = 'some_file_name', STATUS = 'UNKNOWN' ) > END IF Then you don't need to care about GIPAW. GIPAW calls the same startup routine as PW does. From degironc at sissa.it Tue Aug 25 17:19:43 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 25 Aug 2009 17:19:43 +0200 Subject: [Pw_forum] Interferences between symmetry generation and "ecutrho" value In-Reply-To: <4A93E46C.20002@cnrs-orleans.fr> References: <4A93E46C.20002@cnrs-orleans.fr> Message-ID: <4A94010F.4070801@sissa.it> this issue has been discussed several times in this forum. please check the archive looking for "fractional translation" best regards, Stefano de Gironcoli - SISSA and DEMOCRITOS Sylvian Cadars wrote: > Hi, > > Playing with test files of the GIPAW_example, and more specifically the > basic SCF "quartz.scf.in" calculation, I found the symmetry generation > would fail for certain values of "ecutrho" (see list of the tests > conducted below). Importantly, problems can occur even though one sticks > to the default value (=4*ecutwfc). These errors seem to be independent > of the ecutwfc value, at least this is what my tests suggest. > Is this a known issue? Where does it come from? Is it predictable and > avoidable? > Thanks. > All the best. > > Sylvian. > > --------------------------- > ecutwfc ecutrho result > --------------------------- > 70 140 failed > 70 210 OK > 70 280 OK (=default) > 70 300 OK > 70 420 OK > 70 600 failed > 150 600 failed (=default) > 150 - failed (ecutrho=600) > 105 - OK (ecutrho=420) > 200 800 OK > 200 1200 OK > -------------------------- > > The error messages that occur are the following: > Max angular momentum in pseudopotentials (lmaxx) = 3 > warning: symmetry operation # 7 not allowed. fractional translation: > 0.0000000 0.0000000 -0.3333333 in crystal coordinates > warning: symmetry operation # 8 not allowed. fractional translation: > 0.0000000 0.0000000 0.3333333 in crystal coordinates > warning: symmetry operation # 11 not allowed. fractional translation: > 0.0000000 0.0000000 0.3333333 in crystal coordinates > warning: symmetry operation # 12 not allowed. fractional translation: > 0.0000000 0.0000000 -0.3333333 in crystal coordinates > > And 2 symmetry operations are found instead of 6 when everything works > properly. > 2 Sym.Ops. (no inversion) > > > For convenience, here is a typical input file that fails: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/sc/espresso_tmp' , > pseudo_dir = '/home/sc/PWscf/PseudoPotentials/PBE_090707/' , > / > &system > ibrav = 0 > celldm(1) = 1. > nat = 9 > ntyp = 2 > ecutwfc = 150 > ecutrho = 600 > / > &ELECTRONS > electron_maxstep = 100 > conv_thr = 5.0e-8 > startingpot = 'atomic' > startingwfc = 'atomic' > mixing_mode = 'plain' > mixing_beta = 0.7 > diagonalization = 'david' > diago_thr_init = 1.e-2 > / > ATOMIC_SPECIES > Si 28.0855000 SiPBE_nc.UPF > O 15.9994000 OPBE_nc.UPF > > ATOMIC_POSITIONS crystal > Si 0.4701 0.0000 0.3333333333 > Si 0.0000 0.4701 0.6666666667 > Si -0.4701 -0.4701 0.0000000000 > O 0.4139 0.2674 0.2144 > O -0.2674 0.1465 0.5477333333 > O -0.1465 -0.4139 0.8810666667 > O 0.2674 0.4139 -0.2144 > O 0.1465 -0.2674 0.4522666667 > O -0.4139 -0.1465 0.1189333333 > > CELL_PARAMETERS hexagonal > 4.642775480 -8.041523019 0.000000000 > 4.642775480 8.041523019 0.000000000 > 0.000000000 0.000000000 10.213406856 > > K_POINTS automatic > 2 2 2 1 1 1 > > > *Dr. Sylvian CADARS* > CEMHTI-CNRS > 1D, Av. de la Recherche Scientifique > 45071 Orl?ans Cedex 2, France > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Tue Aug 25 17:20:31 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 Aug 2009 17:20:31 +0200 Subject: [Pw_forum] Interferences between symmetry generation and "ecutrho" value In-Reply-To: <4A93E46C.20002@cnrs-orleans.fr> References: <4A93E46C.20002@cnrs-orleans.fr> Message-ID: On Aug 25, 2009, at 15:17 , Sylvian Cadars wrote: > I found the symmetry generation would fail for certain values of > "ecutrho" (...) Is this a known issue? Where does it come from? > Is it predictable and avoidable? http://www.quantum-espresso.org/user_guide/node54.html http://www.quantum-espresso.org/user_guide/node55.html P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sylvian.cadars at cnrs-orleans.fr Wed Aug 26 10:34:30 2009 From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars) Date: Wed, 26 Aug 2009 10:34:30 +0200 Subject: [Pw_forum] output redirection with gipaw.x In-Reply-To: References: Message-ID: <4A94F396.9060604@cnrs-orleans.fr> > ------------------------------------------------------------------------ > > Sujet: > Re: [Pw_forum] output redirection with gipaw.x > Exp?diteur: > Davide Ceresoli > Date: > Tue, 25 Aug 2009 11:07:54 -0400 > Destinataire: > PWSCF Forum > > Destinataire: > PWSCF Forum > > > Sylvian Cadars wrote: >> Hi, >> A few weeks ago, Paolo gave me a useful trick (see below) to redirect >> PW outputs when the "redirection doesn't work one's system". >> Specifically, the redirection using ">" does not work on my system, >> such that the output is written instead in the output file that is >> automatically generated by the submission system (OAR in this case). >> >> The trick was to go to PW/startup.f90 and change >> >> IF ( me_image /= root_image ) & >> OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' ) >> >> into > Is this in PW/startup.f90? >> >> IF ( me_image /= root_image ) THEN >> OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' ) >> ELSE >> OPEN( UNIT = stdout, FILE = 'some_file_name', STATUS = 'UNKNOWN' ) >> END IF > Then you don't need to care about GIPAW. GIPAW calls the same > startup routine as PW does. > Dear Davide, Thank you for your answer. If GIPAW calls the same startup routine as PW does, then something else does not work the same way between the pw and gipaw, since whereas pw.x now automatically writes the output into the default file ("some_file_name" in the example below) , gipaw.x does not, and keeps writing the files into the output of the submission system (OAR in my case). Is there something else I can try? Another problem I have with GIPAW is that is does not seem to use the environment variable "ESPRESSO_TMPDIR" when the "outdir" variable is not defined in the "&control" section, as PW does. This is particularly ennoying because I am trying to run both the 'scf' and 'nmr' calculations in a single job, in which the the temporary output (including "prefix.save") is a directory whose name includes the jobID (e.g., /work/login/espresso_tmp/jobID). This works very well for pw, but then the gipaw module does not locate the /work/login/espresso_tmp/jobID/prefix.save file, or so it seems to since I get the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from pp_check_file : error # 2 file ./scratch/test02.save not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Is this observation (namely that GIPAW does use the environment variable "ESPRESSO_TMPDIR" when "outdir" is not defined) correct? Is there another environment variable that plays the same role in the GIPAW module? Thanks. Sylvian. *Dr. Sylvian CADARS* CEMHTI-CNRS 1D, Av. de la Recherche Scientifique 45071 Orl?ans Cedex 2, France email: sylvian.cadars at cnrs-orleans.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090826/4fa7c025/attachment.htm From giannozz at democritos.it Wed Aug 26 11:18:06 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 Aug 2009 11:18:06 +0200 Subject: [Pw_forum] output redirection with gipaw.x In-Reply-To: <4A94F396.9060604@cnrs-orleans.fr> References: <4A94F396.9060604@cnrs-orleans.fr> Message-ID: <4A94FDCE.3050606@democritos.it> Sylvian Cadars wrote: > [...] pw.x now automatically writes the output into the default file > ("some_file_name" in the example below) , gipaw.x does not, and keeps > writing the files into the output of the submission system (...) > Is there something else I can try? you recompiled GIPAW, didn't you? and verified that gipaw.x is older than PW/startup.o, didn't you? > Another problem I have with GIPAW is that is does not seem to use the > environment variable "ESPRESSO_TMPDIR" that's true. Unfortunately GIPAW also uses a different input variable name ("tmp_dir" instead of "outdir"). The fix is however trivial: in GIPAW/gipaw_module.f90, replace line tmp_dir = './scratch/' with CALL get_env( 'ESPRESSO_TMPDIR', tmp_dir ) IF ( TRIM( tmp_dir ) == ' ' ) tmp_dir = './scratch/' P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From kazempoor2000 at yahoo.com Wed Aug 26 14:14:53 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 26 Aug 2009 05:14:53 -0700 (PDT) Subject: [Pw_forum] GWW Message-ID: <493794.69392.qm@web112520.mail.gq1.yahoo.com> Dear all ?In example02 of GWW part in cvs versions, at the end the file bands.dat will be generated. If we want to plot GW density of state How can I do that? Is it enough to run projecwfc.x or we have to again run scf and nscf?if yes, whether by gamma point or a path in nscf? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090826/e50280b0/attachment.htm From stenuit at sissa.it Wed Aug 26 19:24:30 2009 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Wed, 26 Aug 2009 19:24:30 +0200 Subject: [Pw_forum] GWW In-Reply-To: <493794.69392.qm@web112520.mail.gq1.yahoo.com> References: <493794.69392.qm@web112520.mail.gq1.yahoo.com> Message-ID: <20090826192430.m0m4pg74pw8ww88g@webmail.sissa.it> Dear Ali, To plot the DOS, you just have to do a SCF first. The nscf part can actually be avoid. What is important, is to have the wavefunctions (WFs) and the eigenvalues of all the states you want to compute the DOS. You can do this immediatly only in a SCF calculations. After this step, the code projwfc.x will check if a file bands.dat exists and (if yes) replaces the DFT eigenvalues by the GW eigenvalues (WFs are unchanged since we do a G0W0 calculation). Concerning the fact you want to do only the SCF part, to my understand, the accuracy of the empty states is less when you do only a SCF. A non-scf calculations will provide accurate filled and empty states (WFs and eigenvalues). Please also do not forget our GWW code computes only the states at the GAMMA POINT. Regards, Joe Quoting ali kazempour : > Dear all > ?In example02 of GWW part in cvs versions, at the end the file > bands.dat will be generated. > If we want to plot GW density of state How can I do that? Is it > enough to run projecwfc.x or we have to again run scf and nscf?if > yes, whether by gamma point or a path in nscf? > thanks a lot > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From siyouber at yahoo.fr Wed Aug 26 19:28:50 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Wed, 26 Aug 2009 10:28:50 -0700 (PDT) Subject: [Pw_forum] Pseudopotential for Li Message-ID: <586667.15628.qm@web26507.mail.ukl.yahoo.com> Dear PW users, I am using the PW code for the study of an ionic compound. As I know (Please tell me if I get wrong), one should know the chemical environment of the element in the compound and generate the pseudopotential according to it. But, if the generated pseudopotential is well transferable, there reference configuration is of lesser importance. I want to use a pseudopotential for Li+ ion and I am facing the following problems with the ld1.x code: 1) The Starting configuration 1s2 2s0 does'nt allow non linear core correction. Here is the section of the error message: Computing core charge for nlcc: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from set_rho_core : error # 1 error in bisection %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... why this problem? 2) Using the same starting configuration without nlcc, I get a positive pseudo-2s function, which is exactly the opposite of the expected result (when I plot the opposite, it seems to be correct). Can somebody explain this to me? 3) Considering nlcc is only possible if I start with the configuration 1s2 2s1.0 2p0.0, which is far from Li+. Despite this, I still get a positive pseudo-2s wawefunction. why? Please I am looking forward for your help ********************************* Bertrand SITAMTZE PhD student Department of physics University of Yaounde I-Cameroon ********************************* From sxu2 at ncsu.edu Wed Aug 26 21:53:53 2009 From: sxu2 at ncsu.edu (shu xu) Date: Wed, 26 Aug 2009 15:53:53 -0400 Subject: [Pw_forum] theory on Raman cross sections In-Reply-To: <36d476df0908261246w2d830f8fka32eee10164ddcd4@mail.gmail.com> References: <36d476df0908261246w2d830f8fka32eee10164ddcd4@mail.gmail.com> Message-ID: <36d476df0908261253y4042c013ie9226d200eb8145@mail.gmail.com> Dear users, > > I am studying the theory on Raman cross sections and do some calculations > about Raman. > Unfortunately the link of the pwscf tutorial is invalid now. I wonder if > someone had saved the content of this link and > can send me a copy of it? Thanks very much > > if you click the following > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html > > and then click "here " in the > "short reminder of the relevant theory can be found here > " > > you will find the link is invalid. What I need is the content in the link. > > Thanks ! > > Shu Xu > > Center of High Performance Simulation > Department of Physics > North Carolina State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090826/1b3de42f/attachment.htm From paulatto at sissa.it Wed Aug 26 21:56:44 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 26 Aug 2009 21:56:44 +0200 (CEST) Subject: [Pw_forum] Pseudopotential for Li In-Reply-To: <586667.15628.qm@web26507.mail.ukl.yahoo.com> References: <586667.15628.qm@web26507.mail.ukl.yahoo.com> Message-ID: <54147.78.12.159.112.1251316604.squirrel@webmail.sissa.it> Dear Bertrand, I'll try to give you some hint, but without knowing the details of your calculation there is no much one can say. On Wed, August 26, 2009 19:28, Bertrand SITAMTZE wrote: > I want to use a pseudopotential for Li+ ion and I am facing the following > problems with the ld1.x code: Why are you not using one of the 15 lithium pseudopotentials from the web site? On Wed, August 26, 2009 19:28, Bertrand SITAMTZE wrote: > why this problem? probably an unreasonable choice for the core charge cutoff radius. The default value is better than nothing, but does not work in all cases. > Can somebody explain this to me? Sign of wavefunctions is irrelevant. It is the square modulus that has a physical meaning. > 3) Considering nlcc is only possible if I start with the configuration > 1s2 2s1.0 2p0.0, which is far from Li+. Despite this, I still get a > positive pseudo-2s wawefunction. why? I don't understand this question. You can do a pseudopotential with 1s2 2s0, it won't have nay electron in valence, but should still work. BTW, all -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From denny.jackson at gmail.com Wed Aug 26 22:47:56 2009 From: denny.jackson at gmail.com (Denny Jackson) Date: Wed, 26 Aug 2009 13:47:56 -0700 Subject: [Pw_forum] matdyn file output Message-ID: Hello, I am having trouble understanding the output from ph.x in the matdyn file. I am looking at Barium Titanate in the cubic phase, but with broken symmetry and then relaxed. I'm trying to compare the linear response frequencies from ph.x to frozen phonon frequencies. From what I understand, the diagonalized dynamical matrix should give displacements of each atom. So in the output: omega( 4) = 3.763989 [THz] = 125.553988 [cm-1] ( 0.097362 0.000000 -0.116603 0.000000 -0.288197 0.000000 ) ( -0.066349 0.000000 0.077204 0.000000 0.200853 0.000000 ) ( -0.169282 0.000000 0.204883 0.000000 0.421687 0.000000 ) ( -0.159112 0.000000 0.218980 0.000000 0.474827 0.000000 ) ( -0.184271 0.000000 0.191581 0.000000 0.474679 0.000000 ) each column gives the real and imaginary components of the displacements in cartesian coordinates. I could not find what units these values have, first of all. I assume they are unitless and are a fraction of the lattice parameter. Also, each column should add up to zero to preserve symmetry, should it not? For higher frequencies in this calculation the columns do indeed add up to zero, but for lower frequencies (and negative frequencies) this is not the case. Does this indicate a problem with my pw calculation or something else? Is there a resource for good documentation on the matdyn file I have overlooked? Thanks for helping, Dennis Jackson Oregon State University denny.jackson at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090826/de025b05/attachment.htm From sclauzer at sissa.it Thu Aug 27 09:26:28 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 27 Aug 2009 09:26:28 +0200 Subject: [Pw_forum] theory on Raman cross sections In-Reply-To: <36d476df0908261253y4042c013ie9226d200eb8145@mail.gmail.com> References: <36d476df0908261246w2d830f8fka32eee10164ddcd4@mail.gmail.com> <36d476df0908261253y4042c013ie9226d200eb8145@mail.gmail.com> Message-ID: <4A963524.5010804@sissa.it> You are right, the link to the lecture notes seems to be broken (actually the linked file seems to be disappeared from the QE-Tutorial repository...). In the meantime you can have a look at Paolo Umari's lecture notes ("First-principles vibrational spectroscopies"), available on the Santa Barbara QE summer school webpage: http://www.quantum-espresso.org/wiki/index.php/QESB09 I believe it covers the same topics. Regards, Gabriele shu xu wrote: > > > Dear users, > > I am studying the theory on Raman cross sections and do some > calculations about Raman. > Unfortunately the link of the pwscf tutorial is invalid now. I > wonder if someone had saved the content of this link and > can send me a copy of it? Thanks very much > > if you click the following > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html > > > and then click "here " in the > "short reminder of the relevant theory can be found here > " > > you will find the link is invalid. What I need is the content in the > link. > > Thanks ! > > Shu Xu > > Center of High Performance Simulation > Department of Physics > North Carolina State University > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From siyouber at yahoo.fr Thu Aug 27 10:33:06 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Thu, 27 Aug 2009 01:33:06 -0700 (PDT) Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: Message-ID: <619839.69596.qm@web26501.mail.ukl.yahoo.com> > Message: 7 > Date: Wed, 26 Aug 2009 21:56:44 +0200 (CEST) > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Pseudopotential for Li > To: "PWSCF Forum" > Message-ID: <54147.78.12.159.112.1251316604.squirrel at webmail.sissa.it> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Lorenzo Thank very much for your answer, > I'll try to give you some hint, but without knowing the > details of your > calculation there is no much one can say. > > On Wed, August 26, 2009 19:28, Bertrand SITAMTZE wrote: > >? I want to use a pseudopotential for Li+ ion and > I am facing the following > >? problems with the ld1.x code: > > Why are you not using one of the 15 lithium > pseudopotentials from the web > site? I wanted to use the Li.pw91-s-van_ak.UPF. But, as we all know, this has to be tested.For this purpose I calculated the bulk properties of bcc lithium (lattice parameter and bulk modulus) and got good result. But I don't know how to regenerate the all electron and pseudo wavefunctions starting with the pseudopotential himself, in order to confirm the test. That is why I decided to generate a pseudopotential by myself. Do you know about this regeneration process? > On Wed, August 26, 2009 19:28, Bertrand SITAMTZE wrote: > >???why this problem? > > probably an unreasonable choice for the core charge cutoff > radius. The > default value is better than nothing, but does not work in > all cases. I used the default value > >? Can somebody explain this to me? > > Sign of wavefunctions is irrelevant. It is the square > modulus that has a > physical meaning. This remark is welcome. To my understand, I shouldn't care about the sign and for plotting, use the opposite for exact matching! > >? 3) Considering nlcc is only possible if I start > with the configuration > >? ? 1s2 2s1.0 2p0.0, which is far from Li+. > Despite this, I still get a > >? ? positive? pseudo-2s wawefunction. > why? > > I don't understand this question. You can do a > pseudopotential with 1s2 > 2s0, it won't have nay electron in valence, but should > still work. BTW, > all > > > -- > Lorenzo Paulatto > SISSA? &? DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www:???http://people.sissa.it/~paulatto/ ********************************* Bertrand SITAMTZE PhD student Department of physics University of Yaounde I-Cameroon ********************************* From sylvian.cadars at cnrs-orleans.fr Thu Aug 27 10:49:34 2009 From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars) Date: Thu, 27 Aug 2009 10:49:34 +0200 Subject: [Pw_forum] output redirection and temporary directory with gipaw.x In-Reply-To: References: Message-ID: <4A96489E.3060207@cnrs-orleans.fr> Dear Paolo, >> [...] pw.x now automatically writes the output into the default file >> ("some_file_name" in the example below) , gipaw.x does not, and keeps >> writing the files into the output of the submission system (...) >> Is there something else I can try? > > you recompiled GIPAW, didn't you? and verified that gipaw.x is older > than PW/startup.o, didn't you? In fact I did not, and now it works fine, indeed. I should have thought about this... sorry! >> Another problem I have with GIPAW is that is does not seem to use the >> environment variable "ESPRESSO_TMPDIR" > > that's true. Unfortunately GIPAW also uses a different input variable > name ("tmp_dir" instead of "outdir"). The fix is however trivial: > in GIPAW/gipaw_module.f90, replace line > tmp_dir = './scratch/' > with > CALL get_env( 'ESPRESSO_TMPDIR', tmp_dir ) > IF ( TRIM( tmp_dir ) == ' ' ) tmp_dir = './scratch/' This works very well now, and I would even recommend that this should be implemented in the next distributed package should it not introduce problems, since I find it really useful for dealing with the temporary files. Thank you so much for such useful advice! Sylvian. -- ------------------------------------------------------------------------ *Dr. Sylvian CADARS* CEMHTI-CNRS 1D, Av. de la Recherche Scientifique 45071 Orl?ans Cedex 2, France email: sylvian.cadars at cnrs-orleans.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090827/139dd353/attachment.htm From paulatto at sissa.it Thu Aug 27 11:10:15 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 27 Aug 2009 11:10:15 +0200 Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: <619839.69596.qm@web26501.mail.ukl.yahoo.com> References: <619839.69596.qm@web26501.mail.ukl.yahoo.com> Message-ID: In data 27 agosto 2009 alle ore 10:33:06, Bertrand SITAMTZE ha scritto: > I wanted to use the Li.pw91-s-van_ak.UPF. But, as we all know, this has > to be tested. Normally pps from the quantum-espresso page have already been tested, and often used in some published work. Yet, doing some extra testing is always a good idea. > That is why I decided to generate a pseudopotential by myself. Do you > know about this regeneration process? A good point to start to generate a new pp is an old one. At the begging of the UPF file there is a short human-readable section where you can find most of the parameters used to generate the file. The reference energy for the second projector are actually missing, but you can usually find them easily. > I used the default value From the manual: If not specified, the matching radius is determined by the condition: rho_core(rcore) = 2*rho_valence(rcore) in you specific case it is probably too small. Furthermore, the pp you are trying to imitate includes the 1s electrons in valence: it is practically an all-electron pseudopotential. Hence, it has no core charge. Generating a pseudopotential for Lithium with only the 2s electron in valence, using core-charge correction, can be quite difficult; furthermore the result won't probably be very accurate. Nevertheless, it will also be much softer (it requires a much lower cutoff). best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kazempoor2000 at yahoo.com Thu Aug 27 12:16:18 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 27 Aug 2009 03:16:18 -0700 (PDT) Subject: [Pw_forum] GWW Message-ID: <552467.15244.qm@web112506.mail.gq1.yahoo.com> Dear Geoffrey thank you for reply. In our study about defect , one should be inportant is the accuracy of the band gap and also the right position of the induced level in it. then we also need to know about total energy. If for plotting dos, I do scf calculation ,should I define for K_POINTS? only Gamma point or we can use from a regular mesh? and the total energy after doing scf is total energy of the system with the G0W0 correction? Another question: how do you set the value of n_gauss=79? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090827/9606b10e/attachment.htm From siyouber at yahoo.fr Thu Aug 27 12:47:48 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Thu, 27 Aug 2009 03:47:48 -0700 (PDT) Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: Message-ID: <809077.35461.qm@web26503.mail.ukl.yahoo.com> Dear Lorenzo, Thank very much for the hints --- En date de?: Jeu 27.8.09, Lorenzo Paulatto a ?crit?: De: Lorenzo Paulatto Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li ?: "PWSCF Forum" Date: Jeudi 27 Ao?t 2009, 11h10 In data 27 agosto 2009 alle ore 10:33:06, Bertrand SITAMTZE? ha scritto: > I wanted to use the Li.pw91-s-van_ak.UPF. But, as we all know, this has? > to be tested. Normally pps from the quantum-espresso page have already been tested, and? often used in some published work. Yet, doing some extra testing is always? a good idea. > That is why I decided to generate a pseudopotential by myself. Do you? > know about this regeneration process? A good point to start to generate a new pp is an old one. At the begging? of the UPF file there is a short human-readable section where you can find? most of the parameters used to generate the file. The reference energy for? the second projector are actually missing, but you can usually find them? easily. > I used the default value From the manual: ???If not specified, the matching radius is determined ???by the condition:? rho_core(rcore) = 2*rho_valence(rcore) in you specific case it is probably too small. Furthermore, the pp you are trying to imitate includes the 1s electrons in? valence: it is practically an all-electron pseudopotential. Hence, it has? no core charge. Generating a pseudopotential for Lithium with only the 2s? electron in valence, using core-charge correction, can be quite difficult;? furthermore the result won't probably be very accurate. Nevertheless, it? will also be much softer (it requires a much lower cutoff). best regards -- Lorenzo Paulatto SISSA? &? DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www:???http://people.sissa.it/~paulatto/ ? ???*** save italian brains *** ? http://saveitalianbrains.wordpress.com/ _______________________________________________ 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/20090827/91429c24/attachment.htm From baroni at sissa.it Thu Aug 27 13:41:17 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 27 Aug 2009 13:41:17 +0200 Subject: [Pw_forum] matdyn file output In-Reply-To: References: Message-ID: <9D398E1A-E3BC-4C01-B5EA-225766F32B2D@sissa.it> On Aug 26, 2009, at 10:47 PM, Denny Jackson wrote: > Hello, Hi Denny: > > I am having trouble understanding the output from ph.x in the matdyn > file. I am looking at Barium Titanate in the cubic phase, but with > broken symmetry and then relaxed. > I'm trying to compare the linear response frequencies from ph.x to > frozen phonon frequencies. From what I understand, the diagonalized > dynamical matrix should give displacements of each atom. So in the > output: > > omega( 4) = 3.763989 [THz] = 125.553988 [cm-1] > ( 0.097362 0.000000 -0.116603 0.000000 -0.288197 0.000000 ) > ( -0.066349 0.000000 0.077204 0.000000 0.200853 0.000000 ) > ( -0.169282 0.000000 0.204883 0.000000 0.421687 0.000000 ) > ( -0.159112 0.000000 0.218980 0.000000 0.474827 0.000000 ) > ( -0.184271 0.000000 0.191581 0.000000 0.474679 0.000000 ) > > each column gives the real and imaginary components of the > displacements in cartesian coordinates. I could not find what units > these values have, first of all. I assume they are unitless and are > a fraction of the lattice parameter. the answer is, "does not matter". vibrational mode are identified by the direction and the relative magnitude of each atom's displacement. the absolute magnitude is a matter of convention. hope it is clear why it has to be so. if not, please revert to us and I'll try to explain. > Also, each column should add up to zero to preserve symmetry, should > it not? For higher frequencies in this calculation the columns do > indeed add up to zero, but for lower frequencies (and negative > frequencies) this is not the case. Does this indicate a problem > with my pw calculation or something else? not sure what you mean by "preserve the symmetry". what is sure is that zone-center acoustic modes correspond to a rigid translation of the whole crystal. for these modes, the atomic displacements certainly do not sum to zero. the other modes have to be orthogonal to acoustic ones, and that's why their displacements sum to zero. beware, though, that orthogonality holds with respect to the "vibrational metric" which is proportional to a diagonal matrix with the atomic masses on the diagonal ... > Is there a resource for good documentation on the matdyn file I have > overlooked? not that I know, but a good textbook on lattice dynamics (such as Born and Huang or Botteger) and/or molecular vibrations may help clarify some of the general concepts you need to master to understand what ph.x does ... Stefano B --- 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/20090827/ff1ad340/attachment-0001.htm From colonel.sreekar at gmail.com Thu Aug 27 14:40:31 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Thu, 27 Aug 2009 18:10:31 +0530 Subject: [Pw_forum] algaas scf calculation Message-ID: sir, i would like to make a self consistent calculation of algaas using espresso 4.0.5 and my input file for calculation is gaalas.scf.in ################## GaAlAs &control calculation = 'scf' restart_mode='from_scratch', prefix='gaalas', pseudo_dir = '/home/fubar/Desktop/programming/espresso-4.0.5/pseudo', outdir='/home/fubar/tmp' tprnfor = .true., tstress=.true. / &system ibrav= 2, celldm(1)=10.68, nat= 16, ntyp= 3, ecutwfc = 18.0, ecutrho = 50.0, / &electrons mixing_beta = 0.3 conv_thr = 1.0d-4 / ATOMIC_SPECIES Ga 1. Ga.pz-bhs.UPF As 74.92 As.gon.UPF Al 1. Al.pbe-rrkj.UPF ATOMIC_POSITIONS Ga 0.25 0.25 0.00 Ga 0.25 0.00 0.25 Ga 0.00 0.25 0.25 Ga 0.5 0.25 0.25 Ga 0.25 0.25 0.5 Ga 0.25 0.5 0.25 Ga 0.50 0.50 0.50 As 0.125 0.125 0.125 As 0.375 0.375 0.00 As 0.375 0.00 0.375 As 0.00 0.375 0.375 As 0.625 0.375 0.375 As 0.375 0.375 0.625 As 0.375 0.625 0.375 As 0.625 0.625 0.625 Al 0.00 0.00 0.00 K_POINTS {automatic} 2 2 2 0 0 0 ################# on terminal $./pw.x < gaalas.scf.in > gaalas.scf.out the output file is gaalas.scf.out ################# Program PWSCF v.4.0.5 starts ... Today is 27Aug2009 at 18: 5:35 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readpp : error # 3 inconsistent DFT read %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ################# i m not able to figure out the problem. i would be grateful for any help thanks in advance yours sincerely sreekar guddeti IIT BOMBAY physics undergrad India -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090827/c90022c0/attachment.htm From colonel.sreekar at gmail.com Thu Aug 27 14:53:00 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Thu, 27 Aug 2009 18:23:00 +0530 Subject: [Pw_forum] algaas scf calculation In-Reply-To: References: Message-ID: hello, sorry for posting something which has already been discussed in the forum. i figured out and it is something to do with matching the nature of pseudopotentials of all the entities involved. On Thu, Aug 27, 2009 at 6:10 PM, sreekar guddeti wrote: > > sir, > i would like to make a self consistent calculation of algaas using > espresso 4.0.5 and my input file for calculation is > > gaalas.scf.in > ################## > > GaAlAs > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='gaalas', > pseudo_dir = '/home/fubar/Desktop/programming/espresso-4.0.5/pseudo', > outdir='/home/fubar/tmp' > tprnfor = .true., tstress=.true. > / > &system > ibrav= 2, celldm(1)=10.68, nat= 16, ntyp= 3, > ecutwfc = 18.0, ecutrho = 50.0, > > / > &electrons > mixing_beta = 0.3 > conv_thr = 1.0d-4 > > / > ATOMIC_SPECIES > Ga 1. Ga.pz-bhs.UPF > As 74.92 As.gon.UPF > Al 1. Al.pbe-rrkj.UPF > ATOMIC_POSITIONS > Ga 0.25 0.25 0.00 > Ga 0.25 0.00 0.25 > Ga 0.00 0.25 0.25 > Ga 0.5 0.25 0.25 > Ga 0.25 0.25 0.5 > Ga 0.25 0.5 0.25 > Ga 0.50 0.50 0.50 > As 0.125 0.125 0.125 > As 0.375 0.375 0.00 > As 0.375 0.00 0.375 > As 0.00 0.375 0.375 > As 0.625 0.375 0.375 > As 0.375 0.375 0.625 > As 0.375 0.625 0.375 > As 0.625 0.625 0.625 > Al 0.00 0.00 0.00 > > K_POINTS {automatic} > 2 2 2 0 0 0 > > ################# > > on terminal $./pw.x < gaalas.scf.in > gaalas.scf.out > > the output file is > > gaalas.scf.out > ################# > Program PWSCF v.4.0.5 starts ... > Today is 27Aug2009 at 18: 5:35 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from readpp : error # 3 > inconsistent DFT read > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > ################# > > i m not able to figure out the problem. i would be grateful for any help > thanks in advance > > yours sincerely > sreekar guddeti > IIT BOMBAY > physics undergrad > India > -- > Sreekar Guddeti > > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090827/a322d0f4/attachment.htm From rana_nand at yahoo.com Thu Aug 27 21:37:16 2009 From: rana_nand at yahoo.com (nand) Date: Thu, 27 Aug 2009 12:37:16 -0700 (PDT) Subject: [Pw_forum] GaAs Band structure Message-ID: <382517.35584.qm@web112601.mail.gq1.yahoo.com> Sir, I am a research scholar at the Ranchi university, India. It will be a great help if you can help me with the band structure calculation for GaAs using Quantum Espresso. I do not get the correct band structure? even with the input file you? mentioned below. I am attaching the band structure pdf file which I produced using? input file given below. As you can see that the fermi level is wrongly located and the band gap is badly? underestimated. Please tell me about the possible fault(s) possible in my calculation. Thanking you in advance. Nand Rana, (Research Scholar) Ranchi, India.? ----------------------------------- input file for the scf calculation: &control calculation='scf', outdir='./tmp', prefix='gaas', pseudo_dir='/espresso-4.0.4/pseudo' / &system ibrav=2, celldm(1)=10.6827, nbnd=8, nat=2, ntyp=2, ecutwfc=40.0d0, occupations='fixed', nspin=1 / &electrons conv_thr=1d-6, mixing_beta=0.7, diagonalization='david' / ATOMIC_SPECIES Ga 69.723 Ga.pz-bhs.UPF As 74.92160 As.pz-bhs.UPF ATOMIC_POSITIONS alat Ga 0.0 0.0 0.0 As 0.25 0.25 0.25 K_POINTS automatic 10 10 10 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090827/4066d8f5/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: GaAs.pdf Type: application/pdf Size: 14069 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090827/4066d8f5/attachment-0001.pdf From ttduyle at gmail.com Thu Aug 27 23:25:10 2009 From: ttduyle at gmail.com (Duy Le) Date: Thu, 27 Aug 2009 17:25:10 -0400 Subject: [Pw_forum] GaAs Band structure In-Reply-To: <382517.35584.qm@web112601.mail.gq1.yahoo.com> References: <382517.35584.qm@web112601.mail.gq1.yahoo.com> Message-ID: <8974d3b20908271425icbafadao264a50a63d99d28@mail.gmail.com> Dear Nand, I don't see anything wrong with your calculated band structure. 1. There is a band gap so the Fermi level should be in the middle of the gap. If you want the dash line to locate in the middle of the gap, you could change the reference energy correspondingly when doing plotband.x 2. The gap must be underestimated. If this gap is too wrong to trust, check the lattice parameter. Best, On Thu, Aug 27, 2009 at 3:37 PM, nand wrote: > > > Sir, > I am a research scholar at the Ranchi university, India. It will be a great > help if you can help me with the band structure calculation for GaAs using > Quantum Espresso. > I do not get the correct band structure even with the input file you > mentioned below. I am attaching the band structure pdf file which I produced > using input file given below. As you can see that the fermi level is > wrongly located and the band gap is badly underestimated. Please tell me > about the possible fault(s) possible in my calculation. > Thanking you in advance. > Nand Rana, > (Research Scholar) > Ranchi, India. > > ----------------------------------- > input file for the scf calculation: > > &control > calculation='scf', > > outdir='./tmp', > prefix='gaas', > pseudo_dir='/espresso-4.0.4/pseudo' > / > > &system > ibrav=2, > celldm(1)=10.6827, > nbnd=8, > nat=2, > ntyp=2, > ecutwfc=40.0d0, > > occupations='fixed', > nspin=1 > / > > &electrons > conv_thr=1d-6, > mixing_beta=0.7, > diagonalization='david' > / > > ATOMIC_SPECIES > Ga 69.723 Ga.pz-bhs.UPF > As 74.92160 As.pz-bhs.UPF > > ATOMIC_POSITIONS alat > Ga 0.0 0.0 0.0 > As 0.25 0.25 0.25 > > K_POINTS automatic > 10 10 10 0 0 0 > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090827/9d4b003d/attachment.htm From colonel.sreekar at gmail.com Fri Aug 28 05:09:29 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Fri, 28 Aug 2009 08:39:29 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 26, Issue 73 In-Reply-To: References: Message-ID: actually u ve generated the correct band structure... just change the reference values in your xxxx.plotband.in( which acts as input file for ./plotband.x) 2nd line has 2 numbers which specify range of energies in ur plot 5th line is Fermi energy(can be inferred from bands.dat file) to mark as dashed line in plot 6th line has 2 values 1st value sets y axis numbering step.. 2nd value is set as reference zero level(generally the Fermi level itself) PS: other users correct me if m wrong sreekar guddeti IIT BOMBAY physics undergrad India On Fri, Aug 28, 2009 at 1:14 AM, wrote: > 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. algaas scf calculation (sreekar guddeti) > 2. Re: algaas scf calculation (sreekar guddeti) > 3. GaAs Band structure (nand) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Aug 2009 18:10:31 +0530 > From: sreekar guddeti > Subject: [Pw_forum] algaas scf calculation > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > sir, > i would like to make a self consistent calculation of algaas using espresso > 4.0.5 and my input file for calculation is > > gaalas.scf.in > ################## > > GaAlAs > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='gaalas', > pseudo_dir = '/home/fubar/Desktop/programming/espresso-4.0.5/pseudo', > outdir='/home/fubar/tmp' > tprnfor = .true., tstress=.true. > / > &system > ibrav= 2, celldm(1)=10.68, nat= 16, ntyp= 3, > ecutwfc = 18.0, ecutrho = 50.0, > > / > &electrons > mixing_beta = 0.3 > conv_thr = 1.0d-4 > > / > ATOMIC_SPECIES > Ga 1. Ga.pz-bhs.UPF > As 74.92 As.gon.UPF > Al 1. Al.pbe-rrkj.UPF > ATOMIC_POSITIONS > Ga 0.25 0.25 0.00 > Ga 0.25 0.00 0.25 > Ga 0.00 0.25 0.25 > Ga 0.5 0.25 0.25 > Ga 0.25 0.25 0.5 > Ga 0.25 0.5 0.25 > Ga 0.50 0.50 0.50 > As 0.125 0.125 0.125 > As 0.375 0.375 0.00 > As 0.375 0.00 0.375 > As 0.00 0.375 0.375 > As 0.625 0.375 0.375 > As 0.375 0.375 0.625 > As 0.375 0.625 0.375 > As 0.625 0.625 0.625 > Al 0.00 0.00 0.00 > > K_POINTS {automatic} > 2 2 2 0 0 0 > > ################# > > on terminal $./pw.x < gaalas.scf.in > gaalas.scf.out > > the output file is > > gaalas.scf.out > ################# > Program PWSCF v.4.0.5 starts ... > Today is 27Aug2009 at 18: 5:35 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from readpp : error # 3 > inconsistent DFT read > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > ################# > > i m not able to figure out the problem. i would be grateful for any help > thanks in advance > > yours sincerely > sreekar guddeti > IIT BOMBAY > physics undergrad > India > -- > Sreekar Guddeti > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090827/c90022c0/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Thu, 27 Aug 2009 18:23:00 +0530 > From: sreekar guddeti > Subject: Re: [Pw_forum] algaas scf calculation > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > hello, > sorry for posting something which has already been discussed in the forum. > i > figured out and it is something to do with matching the nature of > pseudopotentials of all the entities involved. > > > > On Thu, Aug 27, 2009 at 6:10 PM, sreekar guddeti > wrote: > > > > > sir, > > i would like to make a self consistent calculation of algaas using > > espresso 4.0.5 and my input file for calculation is > > > > gaalas.scf.in > > ################## > > > > GaAlAs > > &control > > calculation = 'scf' > > restart_mode='from_scratch', > > prefix='gaalas', > > pseudo_dir = '/home/fubar/Desktop/programming/espresso-4.0.5/pseudo', > > outdir='/home/fubar/tmp' > > tprnfor = .true., tstress=.true. > > / > > &system > > ibrav= 2, celldm(1)=10.68, nat= 16, ntyp= 3, > > ecutwfc = 18.0, ecutrho = 50.0, > > > > / > > &electrons > > mixing_beta = 0.3 > > conv_thr = 1.0d-4 > > > > / > > ATOMIC_SPECIES > > Ga 1. Ga.pz-bhs.UPF > > As 74.92 As.gon.UPF > > Al 1. Al.pbe-rrkj.UPF > > ATOMIC_POSITIONS > > Ga 0.25 0.25 0.00 > > Ga 0.25 0.00 0.25 > > Ga 0.00 0.25 0.25 > > Ga 0.5 0.25 0.25 > > Ga 0.25 0.25 0.5 > > Ga 0.25 0.5 0.25 > > Ga 0.50 0.50 0.50 > > As 0.125 0.125 0.125 > > As 0.375 0.375 0.00 > > As 0.375 0.00 0.375 > > As 0.00 0.375 0.375 > > As 0.625 0.375 0.375 > > As 0.375 0.375 0.625 > > As 0.375 0.625 0.375 > > As 0.625 0.625 0.625 > > Al 0.00 0.00 0.00 > > > > K_POINTS {automatic} > > 2 2 2 0 0 0 > > > > ################# > > > > on terminal $./pw.x < gaalas.scf.in > gaalas.scf.out > > > > the output file is > > > > gaalas.scf.out > > ################# > > Program PWSCF v.4.0.5 starts ... > > Today is 27Aug2009 at 18: 5:35 > > > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > PAW > > > > Current dimensions of program pwscf are: > > Max number of different atomic species (ntypx) = 10 > > Max number of k-points (npk) = 40000 > > Max angular momentum in pseudopotentials (lmaxx) = 3 > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from readpp : error # 3 > > inconsistent DFT read > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > ################# > > > > i m not able to figure out the problem. i would be grateful for any help > > thanks in advance > > > > yours sincerely > > sreekar guddeti > > IIT BOMBAY > > physics undergrad > > India > > -- > > Sreekar Guddeti > > > > > > > -- > Sreekar Guddeti > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090827/a322d0f4/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Thu, 27 Aug 2009 12:37:16 -0700 (PDT) > From: nand > Subject: [Pw_forum] GaAs Band structure > To: pw_forum at pwscf.org > Message-ID: <382517.35584.qm at web112601.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > > Sir, > I am a research scholar at the Ranchi university, India. It will be a > great help if you can help me with the band structure calculation for > GaAs using Quantum Espresso. > > I do not get the correct band structure? even with the input file you? > mentioned below. I am attaching the band structure pdf file which I > produced using? input file given below. As you can see that the fermi level > is > wrongly located and the band gap is badly? underestimated. Please tell > me about the possible fault(s) possible in my calculation. > > Thanking you in advance. > Nand Rana, > (Research Scholar) > Ranchi, India.? > ----------------------------------- > input file for the scf calculation: > > &control > calculation='scf', > outdir='./tmp', > prefix='gaas', > pseudo_dir='/espresso-4.0.4/pseudo' > / > > &system > ibrav=2, > celldm(1)=10.6827, > nbnd=8, > nat=2, > ntyp=2, > ecutwfc=40.0d0, > occupations='fixed', > nspin=1 > / > > &electrons > conv_thr=1d-6, > mixing_beta=0.7, > diagonalization='david' > / > > ATOMIC_SPECIES > Ga 69.723 Ga.pz-bhs.UPF > As 74.92160 As.pz-bhs.UPF > > ATOMIC_POSITIONS alat > Ga 0.0 0.0 0.0 > As 0.25 0.25 0.25 > > K_POINTS automatic > 10 10 10 0 0 0 > > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090827/4066d8f5/attachment.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: GaAs.pdf > Type: application/pdf > Size: 14069 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20090827/4066d8f5/attachment.pdf > > ------------------------------ > > _______________________________________________ > 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 73 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090828/93abce00/attachment-0001.htm From liuyongduo at hotmail.com Fri Aug 28 06:44:37 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Fri, 28 Aug 2009 12:44:37 +0800 Subject: [Pw_forum] ph.x can only address LDA potentials? Message-ID: Dear Pw user: I am trying to calculate Raman spectrum of some stuff. But it seems that the ph.x complains whenever I use potentials other than LDA. It gives error messages like: The phonon code with ### and raman, elop or elph is not yet available. So, is the lda-potentail our only choice? But the calculated Raman mode is very bad comparative to the experimental results. For instance, SiH4, it gives: # mode [cm-1] [THz] IR Raman depol 1 0.00 0.0000 0.0000 0.0791 0.7500 2 0.00 0.0000 0.0000 0.1194 0.7500 3 0.00 0.0000 0.0000 0.0679 0.7500 4 0.00 0.0000 0.0000 0.0970 0.7500 5 0.00 0.0000 0.0000 0.0051 0.7500 6 0.00 0.0000 0.0000 0.0235 0.7500 7 634.67 19.0268 1.0902 1.1145 0.7500 8 634.67 19.0268 1.0902 1.1145 0.7500 9 634.67 19.0268 1.0902 1.1145 0.7500 10 819.69 24.5735 0.0000 8.4725 0.7500 11 819.69 24.5735 0.0000 8.4725 0.7500 12 2524.31 75.6765 0.0000 267.0683 0.0000 ? this one? 13 2546.65 76.3462 3.3789 81.6301 0.7500 14 2546.65 76.3462 3.3789 81.6301 0.7500 15 2546.65 76.3462 3.3789 81.6301 0.7500 but the experimental value is 2187 cm-1 best Yongduo _________________________________________________________________ ????? Windows Live ????????????? http://www.microsoft.com/china/windows/windowslive/products/photo-gallery-edit.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090828/a8f39ae7/attachment.htm From lanhaiping at gmail.com Fri Aug 28 07:07:00 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 28 Aug 2009 13:07:00 +0800 Subject: [Pw_forum] GaAs Band structure In-Reply-To: <382517.35584.qm@web112601.mail.gq1.yahoo.com> References: <382517.35584.qm@web112601.mail.gq1.yahoo.com> Message-ID: Hi, Several comments: 1, it seems you use NCPP pseudopotentials . Therefore , 40 Ry for enenrgy cutoff is not enough to get convergent results. 2, You can do alignment of so-called fermi level, which is meaningless since you deal with a semiconductor. 3, Underestimation of energy gap is well accepted in LDA calculations. Hope helps Regards On Fri, Aug 28, 2009 at 3:37 AM, nand wrote: > > > Sir, > I am a research scholar at the Ranchi university, India. It will be a great > help if you can help me with the band structure calculation for GaAs using > Quantum Espresso. > I do not get the correct band structure even with the input file you > mentioned below. I am attaching the band structure pdf file which I produced > using input file given below. As you can see that the fermi level is > wrongly located and the band gap is badly underestimated. Please tell me > about the possible fault(s) possible in my calculation. > Thanking you in advance. > Nand Rana, > (Research Scholar) > Ranchi, India. > > ----------------------------------- > input file for the scf calculation: > > &control > calculation='scf', > outdir='./tmp', > prefix='gaas', > pseudo_dir='/espresso-4.0.4/pseudo' > / > > &system > ibrav=2, > celldm(1)=10.6827, > nbnd=8, > nat=2, > ntyp=2, > ecutwfc=40.0d0, > occupations='fixed', > nspin=1 > / > > &electrons > conv_thr=1d-6, > mixing_beta=0.7, > diagonalization='david' > / > > ATOMIC_SPECIES > Ga 69.723 Ga.pz-bhs.UPF > As 74.92160 As.pz-bhs.UPF > > ATOMIC_POSITIONS alat > Ga 0.0 0.0 0.0 > As 0.25 0.25 0.25 > > K_POINTS automatic > 10 10 10 0 0 0 > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090828/d3318080/attachment.htm From sclauzer at sissa.it Fri Aug 28 08:56:57 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 28 Aug 2009 08:56:57 +0200 Subject: [Pw_forum] ph.x can only address LDA potentials? In-Reply-To: References: Message-ID: <4A977FB9.7070002@sissa.it> Dear pw user, ??? wrote: > Dear Pw user: > > > I am trying to calculate Raman spectrum of some stuff. But it seems > that the ph.x complains whenever I use potentials other than LDA. It > gives error messages like: > > * The phonon code with ### and raman, elop or elph is not yet > available.* What are you hiding under ###? The only error message that I could find in the ph.x sources and can match yours is: [sclauzer at brenta:/scratch/sclauzer-exec/espresso-4.1/PH]$ grep available *.f90 ... phq_readin.f90: 'The phonon code with paw and raman, elop or elph is not yet available',1) ... This message does not mean that you cannot use any DFT functional other than LDA, but that you cannot use PAW together with Raman or El-Ph coupling calculations for instance. You can always use ultrasoft pseudopotentials (US-PPs) instead of projector augmented waves, and I think that with US PPs there are no such limitations. For PAW, well you may have to wait some time, or think about implementing it yourself and then contributing it to the community. > > So, is the lda-potentail our only choice? But the calculated > Raman mode is very bad comparative to the experimental results. For > instance, SiH4, it gives: > > # mode [cm-1] [THz] IR Raman depol > 1 0.00 0.0000 0.0000 0.0791 0.7500 > 2 0.00 0.0000 0.0000 0.1194 0.7500 > 3 0.00 0.0000 0.0000 0.0679 0.7500 > 4 0.00 0.0000 0.0000 0.0970 0.7500 > 5 0.00 0.0000 0.0000 0.0051 0.7500 > 6 0.00 0.0000 0.0000 0.0235 0.7500 > 7 634.67 19.0268 1.0902 1.1145 0.7500 > 8 634.67 19.0268 1.0902 1.1145 0.7500 > 9 634.67 19.0268 1.0902 1.1145 0.7500 > 10 819.69 24.5735 0.0000 8.4725 0.7500 > 11 819.69 24.5735 0.0000 8.4725 0.7500 > * 12 2524.31 75.6765 0.0000 267.0683 0.0000* ? this > one? > 13 2546.65 76.3462 3.3789 81.6301 0.7500 > 14 2546.65 76.3462 3.3789 81.6301 0.7500 > 15 2546.65 76.3462 3.3789 81.6301 0.7500 > > > but the experimental value is 2187 cm-1 It may be that LDA overestimates a frequency. Anyway, are you sure you converged with respect to all relevant parameters, cut-offs,...? What is the lattice parameter you used? ...? regards, Gabriele > > > best > > > Yongduo > > ------------------------------------------------------------------------ > ????? Windows Live ?????? ??????? > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From i_camps at yahoo.com.br Fri Aug 28 16:42:01 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Fri, 28 Aug 2009 11:42:01 -0300 Subject: [Pw_forum] << running QE in parallel >> Message-ID: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> Hello all, I have a question about running QE in parallel. I installed LAM/MPI and then compiled QE with the parallel default options. Then I started running the examples. In the output of example 03, I get the following: *************************** ?Program PWSCF???? v.4.1??? starts ... ???? Today is 28Aug2009 at 11:30:28 ???? Parallel version (MPI) ???? Number of processors in use:?????? 1 ???? For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW ???? Current dimensions of program pwscf are: ???? Max number of different atomic species (ntypx) = 10 ???? Max number of k-points (npk) =? 40000 ???? Max angular momentum in pseudopotentials (lmaxx) =? 3 ???? Waiting for input... ???? file O.pz-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file C.pz-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? gamma-point specific algorithms are used ???? Subspace diagonalization in iterative solution of the eigenvalue problem: ???? Too few procs for parallel algorithm ?????? we need at least 4 procs per pool ???? a serial algorithm will be used .................. *************************** So as you can see, pw.x is running in serial mode. How do I solve this issue? My system: Processor:?AMD Phenom(tm) II X4 940 @ 3GHz (Deneb) Memory: 8GB RAM Lam version (from laminfo): 7.1.4 OS: Ubuntu 9.04 64bits (up-to-date) Environment variables: export TOPDIR='/software/espresso-4.1' export BIN_DIR=$TOPDIR/bin export PSEUDO_DIR=$TOPDIR/pseudo export TMP_DIR=/scratch export PARA_PREFIX="mpiexec -n 4" export PARA_POSTFIX="-npool 1" PWgui="/software/PWgui-4.1" Regards, Camps From paulatto at sissa.it Fri Aug 28 16:57:09 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 28 Aug 2009 16:57:09 +0200 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> Message-ID: Dear Camps, let's have a look at all the output, not just the last line: In data 28 agosto 2009 alle ore 16:42:01, I. Camps ha scritto: > ... > Parallel version (MPI) This mean you have actually compiled the parallel version, good! > Number of processors in use: 1 But you are running it with only one processor. > Subspace diagonalization in iterative solution of the eigenvalue > problem: > Too few procs for parallel algorithm > we need at least 4 procs per pool > a serial algorithm will be used Having only one processor, you also have less than 4 processors per pool, hence matrix diagonalization is done serially. There must be an error in one of these lines, or in the way you combine them together. I cannot say which, because I don't use lam and I don't have access to the script you've used. > export PARA_PREFIX="mpiexec -n 4" > export PARA_POSTFIX="-npool 1" > PWgui="/software/PWgui-4.1" Double-check the script, maybe you only have to replace -n with -np. best regards. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From i_camps at yahoo.com.br Fri Aug 28 17:11:59 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Fri, 28 Aug 2009 12:11:59 -0300 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> Message-ID: <612c95fa0908280811s44042d4cyf5025879c80dbc2f@mail.gmail.com> Thanks Lorenzo, > But you are running it with only one processor. > Having only one processor, you also have less than 4 processors per pool, > hence matrix diagonalization is done serially. ok, it is single processor with 4 cores. In other softwares, each core is understood as a single processor, so at the end, I am able to run job paralle in 4 "single" processors. How do QE understand the number of processors? > There must be an error in one of these lines, or in the way you combine > them together. I cannot say which, because I don't use lam and I don't > have access to the script you've used. I am using the script that come inside the example tar downloaded from QE site. > Double-check the script, maybe you only have to replace -n with -np. Changed, same result. Thanks in advance. Camps ___ On Fri, Aug 28, 2009 at 11:57 AM, Lorenzo Paulatto wrote: > Dear Camps, > let's have a look at all the output, not just the last line: > > > In data 28 agosto 2009 alle ore 16:42:01, I. Camps > ha scritto: >> ... >> ? ? ?Parallel version (MPI) > > This mean you have actually compiled the parallel version, good! > >> ? ? ?Number of processors in use: ? ? ? 1 > > But you are running it with only one processor. > >> ? ? ?Subspace diagonalization in iterative solution of the eigenvalue >> problem: >> ? ? ?Too few procs for parallel algorithm >> ? ? ? ?we need at least 4 procs per pool >> ? ? ?a serial algorithm will be used > > Having only one processor, you also have less than 4 processors per pool, > hence matrix diagonalization is done serially. > > There must be an error in one of these lines, or in the way you combine > them together. I cannot say which, because I don't use lam and I don't > have access to the script you've used. > >> export PARA_PREFIX="mpiexec -n 4" >> export PARA_POSTFIX="-npool 1" >> PWgui="/software/PWgui-4.1" > > Double-check the script, maybe you only have to replace -n with -np. > > best regards. > > > -- > Lorenzo Paulatto > SISSA ?& ?DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: ? http://people.sissa.it/~paulatto/ > > ? ? *** save italian brains *** > ?http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From paulatto at sissa.it Fri Aug 28 17:26:36 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 28 Aug 2009 17:26:36 +0200 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: <612c95fa0908280811s44042d4cyf5025879c80dbc2f@mail.gmail.com> References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> <612c95fa0908280811s44042d4cyf5025879c80dbc2f@mail.gmail.com> Message-ID: In data 28 agosto 2009 alle ore 17:11:59, I. Camps ha scritto: > ok, it is single processor with 4 cores. In other softwares, each > core is understood as a single processor, so at the end, I am able to > run job paralle in 4 "single" processors. How do QE understand the > number of processors? Each core is actually a processor, and that's the way QE reports it. You are actually running on only one core. > I am using the script that come inside the example tar downloaded from > QE site. There are many scripts in the examples tarball. Please refer to the mpiexec documentation. If you are referreing to environment_variables, maybe you haven't noticed that the PARA_PREFIX variable is defined twice, one after each other, if you have changed the first, than your modification is overwritten immediately afterwards (yes, it is a error of the script). regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From i_camps at yahoo.com.br Fri Aug 28 17:38:40 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Fri, 28 Aug 2009 12:38:40 -0300 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> Message-ID: <612c95fa0908280838r1b42a293n68e1b1bc8bd5b913@mail.gmail.com> SOLVED! The problem is the script run_example. If I run the input file directly from the prompt using $PARA_PREFIX pw.x $PARA_POSTFIX < al001.rx.in > al001.rx.out I get the following output: *************************** Program PWSCF v.4.1 starts ... Today is 28Aug2009 at 12:34:42 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Subspace diagonalization in iterative solution of the eigenvalue problem: a parallel distributed memory algorithm will be used, eigenstates matrixes will be distributed block like on ortho sub-group = 2* 2 procs ........ *************************** []s, Camps On Fri, Aug 28, 2009 at 11:42 AM, I. Camps wrote: > Hello all, > > I have a question about running QE in parallel. > > I installed LAM/MPI and then compiled QE with the parallel default options. > > Then I started running the examples. In the output of example 03, I > get the following: > > *************************** > ?Program PWSCF???? v.4.1??? starts ... > ???? Today is 28Aug2009 at 11:30:28 > > ???? Parallel version (MPI) > > ???? Number of processors in use:?????? 1 > > ???? For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > ???? Current dimensions of program pwscf are: > ???? Max number of different atomic species (ntypx) = 10 > ???? Max number of k-points (npk) =? 40000 > ???? Max angular momentum in pseudopotentials (lmaxx) =? 3 > ???? Waiting for input... > ???? file O.pz-rrkjus.UPF: wavefunction(s)? 2S renormalized > ???? file C.pz-rrkjus.UPF: wavefunction(s)? 2S renormalized > > ???? gamma-point specific algorithms are used > > > ???? Subspace diagonalization in iterative solution of the eigenvalue problem: > ???? Too few procs for parallel algorithm > ?????? we need at least 4 procs per pool > ???? a serial algorithm will be used > > .................. > *************************** > > So as you can see, pw.x is running in serial mode. > > How do I solve this issue? > > My system: > Processor:?AMD Phenom(tm) II X4 940 @ 3GHz (Deneb) > Memory: 8GB RAM > Lam version (from laminfo): 7.1.4 > OS: Ubuntu 9.04 64bits (up-to-date) > Environment variables: > > export TOPDIR='/software/espresso-4.1' > export BIN_DIR=$TOPDIR/bin > export PSEUDO_DIR=$TOPDIR/pseudo > export TMP_DIR=/scratch > export PARA_PREFIX="mpiexec -n 4" > export PARA_POSTFIX="-npool 1" > PWgui="/software/PWgui-4.1" > > > Regards, > > Camps > From ttduyle at gmail.com Fri Aug 28 17:40:15 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 28 Aug 2009 11:40:15 -0400 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> <612c95fa0908280811s44042d4cyf5025879c80dbc2f@mail.gmail.com> Message-ID: <8974d3b20908280840n1f84ab05x638c6d06abc6defd@mail.gmail.com> could you pls type directly: mpirun (or mpiexec) -np 4 pw.x < input.in > output.out Best, On Fri, Aug 28, 2009 at 11:26 AM, Lorenzo Paulatto wrote: > In data 28 agosto 2009 alle ore 17:11:59, I. Camps > ha scritto: > > ok, it is single processor with 4 cores. In other softwares, each > > core is understood as a single processor, so at the end, I am able to > > run job paralle in 4 "single" processors. How do QE understand the > > number of processors? > > Each core is actually a processor, and that's the way QE reports it. You > are actually running on only one core. > > > > I am using the script that come inside the example tar downloaded from > > QE site. > > There are many scripts in the examples tarball. Please refer to the > mpiexec documentation. If you are referreing to environment_variables, > maybe you haven't noticed that the PARA_PREFIX variable is defined twice, > one after each other, if you have changed the first, than your > modification is overwritten immediately afterwards (yes, it is a error of > the script). > > regards > > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090828/0743fc2f/attachment.htm From andreas.linscheid at fu-berlin.de Fri Aug 28 18:34:08 2009 From: andreas.linscheid at fu-berlin.de (Andreas Linscheid) Date: Fri, 28 Aug 2009 18:34:08 +0200 Subject: [Pw_forum] Correlated wave-function in real space Message-ID: <4A980700.8050002@fu-berlin.de> Dear PWSCF users, I am currently writing an extension to the post processing part, combining information by an other program, to compute the superconducting order parameter in real space. In order to do this I need to calculate a correlated wave-function in real space, like CONJG(psi_nk(R - Constvect)) * psi_nk(R + Constvect), where R and Constvect are 3D real space vectors and Constvect is held fixed. I didn't succeed up to now, so I ask for help. My final goal is to find the corresponding FFT index, ir <=> R so that I can add (or subtract) S: R -> R+(-)S <=> ir_plus(minus) I figured out that the error in my program is where I touch the index ir, so it seems I misunderstood something of the correspondence between 1D consequtively ordered grid index ir and 3D real space vector R. My underlying question is therefore: How can I evaluate a given wavefunction psi(ir,ibnd) in real space at a given 3D vector R? What I tried up to now: 1. To get a better understanding of the wavefunction in real space, I tried to reproduce the sum of wavefunction (absolute value squared), Result(ir) = sum(irreducible grid k,bands) coeff_nk*|wavefunc_at_k(ir)|^2 using the normal ouput (chdens.f90), by avoiding the fourier-interpolation in chdens.f90 and plotting it directly. (This means:) I compute the wavefunction like in local_dos.f90. call gk_sort (xk(1,ik), ngm, g, ecutwfc / tpiba2, npw, igk, g2kin) !load the PW coefficients of the hit irreducible k point call davcio (evc, nwordwfc, iunwfc, kfull_to_irred(ik), - 1) do ig = 1, npw do ibnd = 1, nbnd wavefunc_at_k ( nls(igk(ig)),ibnd) = evc (ig, ibnd) enddo enddo call cft3s (wavefunc_at_k(:,ibnd), nr1s, nr2s, nr3s, nrx1s, nrx2s, nrx3s, 2) I get the right result, i.e. I can reproduce the charge density when setting all coefficients above the fermi level to zero, only when I don't touch the index ir. 2. According to the FAQ I assumed that after the FFT, wavefunc_at_k ( ir,ibnd) is the wavefunction of band iband at the cartesian coordinate R(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + DBLE(k-1)/DBLE(nrx3s)*at(:,3) when ir = k + (j-1)*nrx3s +(i-1)*nrx3s*nrx2s Therefore I though that I should be able to reproduce the Result above (maybe in a different numerical resolution) when simply writing directly a file. k = nrx3s/2 !look at the boron plane do i = 1, nrx1s do j = 1, nrx2s Rvect(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + DBLE(k-1)/DBLE(nrx3s)*at(:,3) ir = 1 + (j-1)*nrx3s + (i-1)*nrx3s*nrx2s + (k-1) write(13,'(2f10.5,f15.8)') Rvect(1),Rvect(2),Result(ir) write(13,*) enddo enddo Well I get something different which does not even have the symmetry group of the lattice. I also tried this in lattice coords: R(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + DBLE(k-1)/DBLE(nrx3s)*at(:,3) call cryst_to_cart(1,R,bg,-1) Neither did this work (of cause the same problem). If anyone can confirm, that my thoughts are (in principle) right, I at least know that the bug must be somewhere else. I very much appreciate your help!! Andreas Linscheid (Fu-Berlin, AG-Gross) From liuyongduo at hotmail.com Fri Aug 28 20:26:30 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Sat, 29 Aug 2009 02:26:30 +0800 Subject: [Pw_forum] ph.x can only address LDA potentials? (Gabriele Sclauzero) In-Reply-To: References: Message-ID: Thank you very much! but I've already tried Ultra soft or some other forms of GGA, and it seems that the third derivative of energy is not yet implemented for USpps or GGA.(I forgot the exact error messages) For SiH4, the energy w.r.t any possible parameter converge very well. The cutoff I am using is 70ry which is more than enough actually for that potential (Si.pz-vbc.UPS) Since the SiH4 is in gas phase, so I used a big box to put the SiH4. So no worry about the lattice parameters. But the result is very bad-20% higher than the experimental one.. Any body who have done Raman spectra can give me some help? (badly needed) best Yongduo Liu University of California, Los Angeles Materials Science and Engineering 310-467-8389 > > Message: 1 > Date: Fri, 28 Aug 2009 08:56:57 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] ph.x can only address LDA potentials? > To: PWSCF Forum > Message-ID: <4A977FB9.7070002 at sissa.it> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear pw user, > > ??? wrote: > > Dear Pw user: > > > > > > I am trying to calculate Raman spectrum of some stuff. But it seems > > that the ph.x complains whenever I use potentials other than LDA. It > > gives error messages like: > > > > * The phonon code with ### and raman, elop or elph is not yet > > available.* > > What are you hiding under ###? The only error message that I could find in the ph.x > sources and can match yours is: > > [sclauzer at brenta:/scratch/sclauzer-exec/espresso-4.1/PH]$ grep available *.f90 > ... > phq_readin.f90: 'The phonon code with paw and raman, elop or elph is not yet available',1) > ... > > This message does not mean that you cannot use any DFT functional other than LDA, but that > you cannot use PAW together with Raman or El-Ph coupling calculations for instance. You > can always use ultrasoft pseudopotentials (US-PPs) instead of projector augmented waves, > and I think that with US PPs there are no such limitations. For PAW, well you may have to > wait some time, or think about implementing it yourself and then contributing it to the > community. > > > > > > So, is the lda-potentail our only choice? But the calculated > > Raman mode is very bad comparative to the experimental results. For > > instance, SiH4, it gives: > > > > # mode [cm-1] [THz] IR Raman depol > > 1 0.00 0.0000 0.0000 0.0791 0.7500 > > 2 0.00 0.0000 0.0000 0.1194 0.7500 > > 3 0.00 0.0000 0.0000 0.0679 0.7500 > > 4 0.00 0.0000 0.0000 0.0970 0.7500 > > 5 0.00 0.0000 0.0000 0.0051 0.7500 > > 6 0.00 0.0000 0.0000 0.0235 0.7500 > > 7 634.67 19.0268 1.0902 1.1145 0.7500 > > 8 634.67 19.0268 1.0902 1.1145 0.7500 > > 9 634.67 19.0268 1.0902 1.1145 0.7500 > > 10 819.69 24.5735 0.0000 8.4725 0.7500 > > 11 819.69 24.5735 0.0000 8.4725 0.7500 > > * 12 2524.31 75.6765 0.0000 267.0683 0.0000* ? this > > one? > > 13 2546.65 76.3462 3.3789 81.6301 0.7500 > > 14 2546.65 76.3462 3.3789 81.6301 0.7500 > > 15 2546.65 76.3462 3.3789 81.6301 0.7500 > > > > > > but the experimental value is 2187 cm-1 > > It may be that LDA overestimates a frequency. Anyway, are you sure you converged with > respect to all relevant parameters, cut-offs,...? What is the lattice parameter you used? > ...? > > regards, > > Gabriele > > > > > > > > best > > > > > > Yongduo > > _________________________________________________________________ ?Windows Live ??????????Messenger? http://www.windowslive.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090829/94b18eee/attachment.htm From denny.jackson at gmail.com Fri Aug 28 21:30:56 2009 From: denny.jackson at gmail.com (Denny Jackson) Date: Fri, 28 Aug 2009 12:30:56 -0700 Subject: [Pw_forum] Polarization testing warning Message-ID: Hello, When calculating the polarization with Berry Phase I get the "!!! NOT THOROUGHLY TESTED !!!" warning. I was wondering how reliable the results will be. Thank you, Denny Jackson Oregon State University denny.jackson at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090828/861f0862/attachment.htm From matteo at umn.edu Fri Aug 28 21:45:48 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Fri, 28 Aug 2009 14:45:48 -0500 Subject: [Pw_forum] Correlated wave-function in real space In-Reply-To: <4A980700.8050002@fu-berlin.de> References: <4A980700.8050002@fu-berlin.de> Message-ID: <4A9833EC.2050107@umn.edu> Dear Andreas I'm not sure I understood correctly what you want to do. I have a couple of questions/comments: 1) are you trying to reconstruct localized wavefunctions from the Kohn-Sham states? This is what Wannier functions are all about. 2) If you want a translated wfc from the fourier transform of the original one, you just have to multiply each Fourier transform at a given k by e^ik*S where S is the the amount of translation you want to apply. However when you bring it back in real space I guess you will obtain only the part of the translated wavefunction that is inside the first unit cell. Hope this helps. Matteo Andreas Linscheid wrote: > Dear PWSCF users, > > I am currently writing an extension to the post processing part, > combining information by an other program, to compute the > superconducting order parameter in real space. In order to do this I > need to calculate a correlated wave-function in real space, like > > CONJG(psi_nk(R - Constvect)) * psi_nk(R + Constvect), > > where R and Constvect are 3D real space vectors and Constvect is held > fixed. I didn't succeed up to now, so I ask for help. > My final goal is to find the corresponding FFT index, ir <=> R so that I > can add (or subtract) S: R -> R+(-)S <=> ir_plus(minus) > I figured out that the error in my program is where I touch the index > ir, so it seems I misunderstood something of the correspondence between > 1D consequtively ordered grid index ir and 3D real space vector R. My > underlying question is therefore: > > How can I evaluate a given wavefunction psi(ir,ibnd) in real space at a > given 3D vector R? > > What I tried up to now: > 1. To get a better understanding of the wavefunction in real space, I > tried to reproduce the sum of wavefunction (absolute value squared), > > Result(ir) = sum(irreducible grid k,bands) coeff_nk*|wavefunc_at_k(ir)|^2 > > using the normal ouput (chdens.f90), by avoiding the > fourier-interpolation in chdens.f90 and plotting it directly. (This means:) > I compute the wavefunction like in local_dos.f90. > > call gk_sort (xk(1,ik), ngm, g, ecutwfc / tpiba2, npw, igk, g2kin) > !load the PW coefficients of the hit irreducible k point > call davcio (evc, nwordwfc, iunwfc, kfull_to_irred(ik), - 1) > > do ig = 1, npw > do ibnd = 1, nbnd > wavefunc_at_k ( nls(igk(ig)),ibnd) = evc (ig, ibnd) > enddo > enddo > > call cft3s (wavefunc_at_k(:,ibnd), nr1s, nr2s, nr3s, nrx1s, nrx2s, nrx3s, 2) > > I get the right result, i.e. I can reproduce the charge density when > setting all coefficients above the fermi level to zero, only when I > don't touch the index ir. > > 2. According to the FAQ I assumed that after the FFT, wavefunc_at_k ( > ir,ibnd) is the wavefunction of band iband at the cartesian coordinate > > R(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + > DBLE(k-1)/DBLE(nrx3s)*at(:,3) > when > ir = k + (j-1)*nrx3s +(i-1)*nrx3s*nrx2s > > Therefore I though that I should be able to reproduce the Result above > (maybe in a different numerical resolution) when simply writing directly > a file. > > k = nrx3s/2 !look at the boron plane > do i = 1, nrx1s > do j = 1, nrx2s > Rvect(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + > DBLE(j-1)/DBLE(nrx2s)*at(:,2) + DBLE(k-1)/DBLE(nrx3s)*at(:,3) > ir = 1 + (j-1)*nrx3s + (i-1)*nrx3s*nrx2s + (k-1) > write(13,'(2f10.5,f15.8)') Rvect(1),Rvect(2),Result(ir) > write(13,*) > enddo > enddo > > Well I get something different which does not even have the symmetry > group of the lattice. I also tried this in lattice coords: > > R(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + > DBLE(k-1)/DBLE(nrx3s)*at(:,3) > call cryst_to_cart(1,R,bg,-1) > > Neither did this work (of cause the same problem). If anyone can > confirm, that my thoughts are (in principle) right, I at least know that > the bug must be somewhere else. > > I very much appreciate your help!! > > Andreas Linscheid > (Fu-Berlin, AG-Gross) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From eyvaz_isaev at yahoo.com Fri Aug 28 21:53:25 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 28 Aug 2009 12:53:25 -0700 (PDT) Subject: [Pw_forum] ph.x can only address LDA potentials? (Gabriele Sclauzero) In-Reply-To: Message-ID: <511683.74883.qm@web65701.mail.ac4.yahoo.com> Hi, --- On Fri, 8/28/09, ??? wrote: > But the result is very bad-20% higher than the experimental > one.. Which one is higher? Sometime 20% error looks acceptable, > Any body who have done Raman spectra can give me some help? The message from phq_setup.f90 is: 'third order derivatives not implemented with GGA' Well, you try to calculate the Raman activity in SiH4, most likely via QE 4.1. The message (and immediate stop) appeared in this version, but it is absent in previous versions up to 4.0.5. But not sure the result will be correct (with versions <=4.0.5). The restriction might be due to complex integrals within GGA. Did you try US+LDA? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > but I've already tried Ultra soft or some other forms > of GGA, and it seems that the third derivative of energy is > not yet implemented for USpps or GGA.(I forgot the exact > error messages) > > For SiH4, the energy w.r.t any possible parameter converge > very well. The cutoff I am using is 70ry which is more than > enough actually for that potential (Si.pz-vbc.UPS) > Since the SiH4 is in gas phase, so I used a big box to put > the SiH4. So no worry about the lattice parameters. > > But the result is very bad-20% higher than the experimental > one.. > > Any body who have done Raman spectra can give me some help? > (badly needed) > > > best > > > Yongduo Liu > > University of California, Los Angeles > Materials Science and Engineering > > 310-467-8389 > > > > > > Message: 1 > > Date: Fri, 28 Aug 2009 08:56:57 +0200 > > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] ph.x can only address LDA > potentials? > > To: PWSCF Forum > > Message-ID: <4A977FB9.7070002 at sissa.it> > > Content-Type: text/plain; charset=UTF-8; > format=flowed > > > > Dear pw user, > > > > ??? wrote: > > > Dear Pw user: > > > > > > > > > I am trying to calculate Raman spectrum of > some stuff. But it seems > > > that the ph.x complains whenever I use potentials > other than LDA. It > > > gives error messages like: > > > > > > * The phonon code with ### and raman, elop or > elph is not yet > > > available.* > > > > What are you hiding under ###? The only error message > that I could find in the ph.x > > sources and can match yours is: > > > > > [sclauzer at brenta:/scratch/sclauzer-exec/espresso-4.1/PH]$ > grep available *.f90 > > ... > > phq_readin.f90: 'The phonon code with paw and > raman, elop or elph is not yet available',1) > > ... > > > > This message does not mean that you cannot use any DFT > functional other than LDA, but that > > you cannot use PAW together with Raman or El-Ph > coupling calculations for instance. You > > can always use ultrasoft pseudopotentials (US-PPs) > instead of projector augmented waves, > > and I think that with US PPs there are no such > limitations. For PAW, well you may have to > > wait some time, or think about implementing it > yourself and then contributing it to the > > community. > > > > > > > > > > So, is the lda-potentail our only choice? > But the calculated > > > Raman mode is very bad comparative to the > experimental results. For > > > instance, SiH4, it gives: > > > > > > # mode [cm-1] [THz] IR > Raman depol > > > 1 0.00 0.0000 0.0000 > 0.0791 0.7500 > > > 2 0.00 0.0000 0.0000 > 0.1194 0.7500 > > > 3 0.00 0.0000 0.0000 > 0.0679 0.7500 > > > 4 0.00 0.0000 0.0000 > 0.0970 0.7500 > > > 5 0.00 0.0000 0.0000 > 0.0051 0.7500 > > > 6 0.00 0.0000 0.0000 > 0.0235 0.7500 > > > 7 634.67 19.0268 1.0902 > 1.1145 0.7500 > > > 8 634.67 19.0268 1.0902 > 1.1145 0.7500 > > > 9 634.67 19.0268 1.0902 > 1.1145 0.7500 > > > 10 819.69 24.5735 0.0000 > 8.4725 0.7500 > > > 11 819.69 24.5735 0.0000 > 8.4725 0.7500 > > > * 12 2524.31 75.6765 0.0000 > 267.0683 0.0000* ? this > > > one? > > > 13 2546.65 76.3462 3.3789 > 81.6301 0.7500 > > > 14 2546.65 76.3462 3.3789 > 81.6301 0.7500 > > > 15 2546.65 76.3462 3.3789 > 81.6301 0.7500 > > > > > > > > > but the experimental value is 2187 cm-1 > > > > It may be that LDA overestimates a frequency. Anyway, > are you sure you converged with > > respect to all relevant parameters, cut-offs,...? What > is the lattice parameter you used? > > ...? > > > > regards, > > > > Gabriele > > > > > > > > > > > > > best > > > > > > > > > Yongduo > > > > > > ????????????? > ????????????????! ????? > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From liuyongduo at hotmail.com Fri Aug 28 22:09:41 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Sat, 29 Aug 2009 04:09:41 +0800 Subject: [Pw_forum] ph.x can only address LDA potentials? (Gabriele Sclauzero) In-Reply-To: References: Message-ID: Ok i know where was my problem. Thank Gabriele! I was not using the equilibrium configuration under that potential.. best Yongduo UCLA MSE department > From: pw_forum-request at pwscf.org > Subject: Pw_forum Digest, Vol 26, Issue 76 > To: pw_forum at pwscf.org > Date: Fri, 28 Aug 2009 18:58:23 +0200 > > 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: ph.x can only address LDA potentials? (Gabriele Sclauzero) > 2. << running QE in parallel >> (I. Camps) > 3. Re: << running QE in parallel >> (Lorenzo Paulatto) > 4. Re: << running QE in parallel >> (I. Camps) > 5. Re: << running QE in parallel >> (Lorenzo Paulatto) > 6. Re: << running QE in parallel >> (I. Camps) > 7. Re: << running QE in parallel >> (Duy Le) > 8. Correlated wave-function in real space (Andreas Linscheid) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 Aug 2009 08:56:57 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] ph.x can only address LDA potentials? > To: PWSCF Forum > Message-ID: <4A977FB9.7070002 at sissa.it> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear pw user, > > ??? wrote: > > Dear Pw user: > > > > > > I am trying to calculate Raman spectrum of some stuff. But it seems > > that the ph.x complains whenever I use potentials other than LDA. It > > gives error messages like: > > > > * The phonon code with ### and raman, elop or elph is not yet > > available.* > > What are you hiding under ###? The only error message that I could find in the ph.x > sources and can match yours is: > > [sclauzer at brenta:/scratch/sclauzer-exec/espresso-4.1/PH]$ grep available *.f90 > ... > phq_readin.f90: 'The phonon code with paw and raman, elop or elph is not yet available',1) > ... > > This message does not mean that you cannot use any DFT functional other than LDA, but that > you cannot use PAW together with Raman or El-Ph coupling calculations for instance. You > can always use ultrasoft pseudopotentials (US-PPs) instead of projector augmented waves, > and I think that with US PPs there are no such limitations. For PAW, well you may have to > wait some time, or think about implementing it yourself and then contributing it to the > community. > > > > > > So, is the lda-potentail our only choice? But the calculated > > Raman mode is very bad comparative to the experimental results. For > > instance, SiH4, it gives: > > > > # mode [cm-1] [THz] IR Raman depol > > 1 0.00 0.0000 0.0000 0.0791 0.7500 > > 2 0.00 0.0000 0.0000 0.1194 0.7500 > > 3 0.00 0.0000 0.0000 0.0679 0.7500 > > 4 0.00 0.0000 0.0000 0.0970 0.7500 > > 5 0.00 0.0000 0.0000 0.0051 0.7500 > > 6 0.00 0.0000 0.0000 0.0235 0.7500 > > 7 634.67 19.0268 1.0902 1.1145 0.7500 > > 8 634.67 19.0268 1.0902 1.1145 0.7500 > > 9 634.67 19.0268 1.0902 1.1145 0.7500 > > 10 819.69 24.5735 0.0000 8.4725 0.7500 > > 11 819.69 24.5735 0.0000 8.4725 0.7500 > > * 12 2524.31 75.6765 0.0000 267.0683 0.0000* ? this > > one? > > 13 2546.65 76.3462 3.3789 81.6301 0.7500 > > 14 2546.65 76.3462 3.3789 81.6301 0.7500 > > 15 2546.65 76.3462 3.3789 81.6301 0.7500 > > > > > > but the experimental value is 2187 cm-1 > > It may be that LDA overestimates a frequency. Anyway, are you sure you converged with > respect to all relevant parameters, cut-offs,...? What is the lattice parameter you used? > ...? > > regards, > > Gabriele > > > > > > > > best > > > > > > Yongduo > > > > ------------------------------------------------------------------------ > > ????? Windows Live ?????? ??????? > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > _________________________________________________________________ ?Windows Live ??????????Messenger? http://www.windowslive.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090829/8daee272/attachment-0001.htm From bipulrr at gmail.com Sat Aug 29 06:02:00 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sat, 29 Aug 2009 09:32:00 +0530 Subject: [Pw_forum] LDA and U and OP Message-ID: <3a749910908282102j75c5cb1csb0dd06c69a5c1f99@mail.gmail.com> Dear Pwscf users, In the paper ? Inorg. Chem. year 2008, Vol 47, 6608 the author used GGA+U and GGA+OP (OP=orbital polarisation) So just want to ask, whether GGA+OP is implemented in espresso or what one can do to implement it? Give me some reference if possible. regards -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090829/185f5cb1/attachment.htm From liuyongduo at hotmail.com Sat Aug 29 20:11:48 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Sun, 30 Aug 2009 02:11:48 +0800 Subject: [Pw_forum] error message : from calbec : error # 3 size mismatch Message-ID: Dear PW users I am doing some test calculations about Raman spectra, but I came across a strange error when testing H2 Here is my h2.scf.in,: &control calculation='scf' pseudo_dir = '/home/yongduo/QuantumEspresso/espresso-4.1/pseudo', outdir='/home/yongduo/tmp/' title='Test H2 gamma only' prefix='h2' tprnfor=.true. / &system ibrav=0, nat=2, ntyp= 1, ecutwfc =60.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / CELL_PARAMETERS cubic 20 0.0 0.0 0.0 20 0.0 0.0 0.0 20 ATOMIC_SPECIES H 1.008 H.pz-vbc.UPF ATOMIC_POSITIONS (alat) H 0.002235005 0.000000000 0.000000000 H 0.074814995 0.000000000 0.000000000 K_POINTS 1 0 0 0 1 This step was successful, but error came out when ph.x began to do the Electric Fields Calculation. My input: Normal modes for H2 &inputph tr2_ph=1.0d-14, prefix='h2', amass(1)=1.008, outdir='/home/yongduo/tmp', epsil=.true., trans=.true., asr=.true. lraman = .true. fildyn='h2.dyn' / 0.0 0.0 0.0 Output .......... Electric Fields Calculation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from calbec : error # 3 size mismatch %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Anybody knows what does that mean? Any help will be highly appreciated! best Yongduo Liu UCLA MSE _________________________________________________________________ Messenger??????????????????Messenger??? http://im.live.cn/safe/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090830/0cfb3039/attachment.htm From sclauzer at sissa.it Mon Aug 31 09:16:02 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 31 Aug 2009 09:16:02 +0200 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: <612c95fa0908280838r1b42a293n68e1b1bc8bd5b913@mail.gmail.com> References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> <612c95fa0908280838r1b42a293n68e1b1bc8bd5b913@mail.gmail.com> Message-ID: <4A9B78B2.5020000@sissa.it> I. Camps wrote: > SOLVED! And so, where is the problem exactly? I've often used the example scripts in parallel by setting the environment variables in environment_variables file and I could always run without any problem. > > The problem is the script run_example. Please, try to idenfity where the problem is (if any)? I think that the scripts usually work fine. It is not clear to me the procedure you followed to run the script the first time (when you could not run with more processes). Regards, Gabriele > If I run the input file directly from the prompt using > > $PARA_PREFIX pw.x $PARA_POSTFIX < al001.rx.in > al001.rx.out > > I get the following output: > > *************************** > Program PWSCF v.4.1 starts ... > Today is 28Aug2009 at 12:34:42 > > Parallel version (MPI) > > Number of processors in use: 4 > R & G space division: proc/pool = 4 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From cyrille.barreteau at cea.fr Mon Aug 31 08:17:20 2009 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Mon, 31 Aug 2009 08:17:20 +0200 Subject: [Pw_forum] LDA and U and OP In-Reply-To: <3a749910908282102j75c5cb1csb0dd06c69a5c1f99@mail.gmail.com> References: <3a749910908282102j75c5cb1csb0dd06c69a5c1f99@mail.gmail.com> Message-ID: <4A9B6AF0.1070608@cea.fr> Dear Bipul Rakshit, Your question is somewhat related to a recent one (who did not receive an answer I think) about LDA+U for non collinear systems. I do not think this "option" has been implemented yet but it might be on the way (correct me if I am wrong).. The paper you are refering to is based on Wien2K calculation where LDA+U and OP are implemented. OP is a kind of ansatz introduced by Brooks and Eriksson 20 years ago. Solovyev showed 10 years ago that OP can in fact be derived in some special cases from the full version of LDA+U (including the three Racah parameters and SOC). However there is no clear justification of OP in general. regards cyrille ps: see a recent paper from our group: PRB76 024412 (2007). -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/IRAMIS/SPCSI | email cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://iramis.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html ================================================================== Bipul Rakshit wrote: > Dear Pwscf users, > In the paper ? Inorg. Chem. year 2008, Vol 47, 6608 > the author used GGA+U and GGA+OP (OP=orbital polarisation) > So just want to ask, whether GGA+OP is implemented in espresso or what > one can do to implement it? > Give me some reference if possible. > regards > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From andreas.linscheid at fu-berlin.de Mon Aug 31 10:48:42 2009 From: andreas.linscheid at fu-berlin.de (Andreas Linscheid) Date: Mon, 31 Aug 2009 10:48:42 +0200 Subject: [Pw_forum] Correlated wave-function in real space In-Reply-To: <4A9833EC.2050107@umn.edu> References: <4A980700.8050002@fu-berlin.de> <4A9833EC.2050107@umn.edu> Message-ID: <4A9B8E6A.5090103@fu-berlin.de> Dear Matteo, Thank you for your quick respond! My question is quite unusual, and I hope that I can clarify what I want. We expand the superconducting order parameter chi = in a Kohn-Sham orbital basis and solve the Kohn-Sham-Bogoliobov-deGennes equations for the expansion coefficients. What I doing now, is to multiply the basis with this expansion coefficients to recover the original quantity, chi. Therefore I am fine with the Kohn Sham states in their real space representation. We want to have this quantity in a center of mass coordinate system R= r+r', S=r-r'. Since this is a 6 dim. quantity we fix S to a certain vector and then have something like the charge to plot. I am writing a new module (routine) which computes this quantity chi for fixed S. This uses the module chdens.f90 to plot the desired quantity, like every other PW routine (I know). Because of the not-working part of my program does essentially take the 1D index of the wavefunction and knows what 3D vector this (should) correspond to, ir => (i,j,k) => R then adds the 3D vector, R => R +S, to obtain a new 1D index corresponding to R+S R+S => ir' (This is the crucial point), I was doing some experiments, as described below, that failed. Ok, the question is: Is it correct that 1. The 3D real space vector R in lattice coordinates, that corresponds to ir, where ir = k + (j-1)*nrx3s +(i-1)*nrx3s*nrx2s is R(1) = DBLE(i)/DBLE(nrx1s) R(2) = DBLE(j)/DBLE(nrx2s) R(3) = DBLE(k)/DBLE(nrx3s) ? (I am using nrx1s instead of nr1s on purpose!) 2. Is it correct, that the 3D vector to the same index ir in karthesian coordinates is R(:) = DBLE(i)/DBLE(nrx1s)*at(:,1) + DBLE(j)/DBLE(nrx2s)*at(:,2) + DBLE(k)/DBLE(nrx3s)*at(:,3) ? (I think in FAQ, this is described with nr3s,) 3. Can I take this vector (for example in lattice coords) and add R(:) = R(:) + S(:) map back to first unit cell R(:) = R(:)-nint(R(:)) and map it back onto the real space FFT grid point (i_n,j_n,k_n): i_n =nint(nrx1s*R(1)) + 1 j_n =nint(nrx2s*R(2)) + 1 k_n =nint(nrx3s*R(3)) + 1 What then has the the 1D index: ir_n = k_n + (j_n-1)*nrx3s +(i_n-1)*nrx3s*nrx2s Because if all this is correct I have the error somewhere else. I hope I have clarified my problem?! Thank you very much, Andreas Matteo Cococcioni wrote: > Dear Andreas > > I'm not sure I understood correctly what you want to do. I have a couple > of questions/comments: > > 1) are you trying to reconstruct localized wavefunctions from the > Kohn-Sham states? This is what Wannier functions are all about. > > 2) If you want a translated wfc from the fourier transform of the > original one, you just have to multiply > each Fourier transform at a given k by e^ik*S where S is the the amount > of translation you want to apply. > However when you bring it back in real space I guess you will obtain > only the part of the translated wavefunction > that is inside the first unit cell. > > Hope this helps. > > Matteo > > > Andreas Linscheid wrote: > >> Dear PWSCF users, >> >> I am currently writing an extension to the post processing part, >> combining information by an other program, to compute the >> superconducting order parameter in real space. In order to do this I >> need to calculate a correlated wave-function in real space, like >> >> CONJG(psi_nk(R - Constvect)) * psi_nk(R + Constvect), >> >> where R and Constvect are 3D real space vectors and Constvect is held >> fixed. I didn't succeed up to now, so I ask for help. >> My final goal is to find the corresponding FFT index, ir <=> R so that I >> can add (or subtract) S: R -> R+(-)S <=> ir_plus(minus) >> I figured out that the error in my program is where I touch the index >> ir, so it seems I misunderstood something of the correspondence between >> 1D consequtively ordered grid index ir and 3D real space vector R. My >> underlying question is therefore: >> >> How can I evaluate a given wavefunction psi(ir,ibnd) in real space at a >> given 3D vector R? >> >> What I tried up to now: >> 1. To get a better understanding of the wavefunction in real space, I >> tried to reproduce the sum of wavefunction (absolute value squared), >> >> Result(ir) = sum(irreducible grid k,bands) coeff_nk*|wavefunc_at_k(ir)|^2 >> >> using the normal ouput (chdens.f90), by avoiding the >> fourier-interpolation in chdens.f90 and plotting it directly. (This means:) >> I compute the wavefunction like in local_dos.f90. >> >> call gk_sort (xk(1,ik), ngm, g, ecutwfc / tpiba2, npw, igk, g2kin) >> !load the PW coefficients of the hit irreducible k point >> call davcio (evc, nwordwfc, iunwfc, kfull_to_irred(ik), - 1) >> >> do ig = 1, npw >> do ibnd = 1, nbnd >> wavefunc_at_k ( nls(igk(ig)),ibnd) = evc (ig, ibnd) >> enddo >> enddo >> >> call cft3s (wavefunc_at_k(:,ibnd), nr1s, nr2s, nr3s, nrx1s, nrx2s, nrx3s, 2) >> >> I get the right result, i.e. I can reproduce the charge density when >> setting all coefficients above the fermi level to zero, only when I >> don't touch the index ir. >> >> 2. According to the FAQ I assumed that after the FFT, wavefunc_at_k ( >> ir,ibnd) is the wavefunction of band iband at the cartesian coordinate >> >> R(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + >> DBLE(k-1)/DBLE(nrx3s)*at(:,3) >> when >> ir = k + (j-1)*nrx3s +(i-1)*nrx3s*nrx2s >> >> Therefore I though that I should be able to reproduce the Result above >> (maybe in a different numerical resolution) when simply writing directly >> a file. >> >> k = nrx3s/2 !look at the boron plane >> do i = 1, nrx1s >> do j = 1, nrx2s >> Rvect(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + >> DBLE(j-1)/DBLE(nrx2s)*at(:,2) + DBLE(k-1)/DBLE(nrx3s)*at(:,3) >> ir = 1 + (j-1)*nrx3s + (i-1)*nrx3s*nrx2s + (k-1) >> write(13,'(2f10.5,f15.8)') Rvect(1),Rvect(2),Result(ir) >> write(13,*) >> enddo >> enddo >> >> Well I get something different which does not even have the symmetry >> group of the lattice. I also tried this in lattice coords: >> >> R(:) = DBLE(i-1)/DBLE(nrx1s)*at(:,1) + DBLE(j-1)/DBLE(nrx2s)*at(:,2) + >> DBLE(k-1)/DBLE(nrx3s)*at(:,3) >> call cryst_to_cart(1,R,bg,-1) >> >> Neither did this work (of cause the same problem). If anyone can >> confirm, that my thoughts are (in principle) right, I at least know that >> the bug must be somewhere else. >> >> I very much appreciate your help!! >> >> Andreas Linscheid >> (Fu-Berlin, AG-Gross) >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > From sh.shapt at gmail.com Mon Aug 31 11:49:23 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Mon, 31 Aug 2009 10:49:23 +0100 Subject: [Pw_forum] Default values used in Quantum espresso manuals Message-ID: Hi There, I am a new user in quantum espresso , thus I would like to ask one question how do the default values in the quantum espresso manuals have been choosed? I mean to say that in quantum espresso manuals we find forc_conv_thr =1.0D-3 conv_thr =1.0D-6 etot_conv_thr=1.0D-4 How did the values calculated? Thanks Shaptarishi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/23296440/attachment.htm From dalcorso at sissa.it Mon Aug 31 11:56:38 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Mon, 31 Aug 2009 11:56:38 +0200 Subject: [Pw_forum] error message : from calbec : error # 3 size mismatch In-Reply-To: References: Message-ID: <1251712598.3526.15.camel@dhpc-5-36.sissa.it> Dear Yongduo Liu There was a bug in the routine PH/dvpsi_e.f90 for the case in which all atoms are described by a local potential. This is now fixed in the cvs version. HTH, Andrea On Sun, 2009-08-30 at 02:11 +0800, ??? wrote: > Dear PW users > > > I am doing some test calculations about Raman spectra, but I came > across a strange error when testing H2 > > Here is my h2.scf.in,: > > &control > calculation='scf' > pseudo_dir = '/home/yongduo/QuantumEspresso/espresso-4.1/pseudo', > outdir='/home/yongduo/tmp/' > title='Test H2 gamma only' > prefix='h2' > tprnfor=.true. > / > &system > ibrav=0, nat=2, ntyp= 1, > ecutwfc =60.0 > / > &electrons > mixing_mode='plain' > mixing_beta = 0.7, > conv_thr = 1.0d-8 > / > CELL_PARAMETERS cubic > 20 0.0 0.0 > 0.0 20 0.0 > 0.0 0.0 20 > ATOMIC_SPECIES > H 1.008 H.pz-vbc.UPF > ATOMIC_POSITIONS (alat) > H 0.002235005 0.000000000 0.000000000 > H 0.074814995 0.000000000 0.000000000 > K_POINTS > 1 > 0 0 0 1 > > This step was successful, but error came out when ph.x began to do the > Electric Fields Calculation. > > My input: > > Normal modes for H2 > &inputph > tr2_ph=1.0d-14, > prefix='h2', > amass(1)=1.008, > outdir='/home/yongduo/tmp', > epsil=.true., > trans=.true., > asr=.true. > lraman = .true. > fildyn='h2.dyn' > / > 0.0 0.0 0.0 > > > Output > > .......... > Electric Fields Calculation > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > from calbec : error # 3 > size mismatch > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > stopping ... > > > > Anybody knows what does that mean? Any help will be highly > appreciated! > > best > > Yongduo Liu > > > UCLA > MSE > > > > > > > > > > > > > > > > > ______________________________________________________________________ > ????? Windows Live Messenger ???????? ????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34151 Trieste (Italy) e-mail: dalcorso at sissa.it From kazempoor2000 at yahoo.com Mon Aug 31 13:01:25 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 31 Aug 2009 04:01:25 -0700 (PDT) Subject: [Pw_forum] error-GWW Message-ID: <440425.59917.qm@web112503.mail.gq1.yahoo.com> Hi I examine the example 2 of GWW example for TiO2 like Si. But after finishing phonon calculation one error happen: ?task #???????? 6 ???? from? pzpotrf? : error #?????? 224 ????? problems computing cholesky decomposition and then another error : ?task #???????? 1 ???? from pp_check_file : error #???????? 2 ???? file /p5/batch/kazempou/tio2.save not found waht is the reason? thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/dd7f9a0e/attachment.htm From i_camps at yahoo.com.br Mon Aug 31 13:59:30 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Mon, 31 Aug 2009 08:59:30 -0300 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: <4A9B78B2.5020000@sissa.it> References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> <612c95fa0908280838r1b42a293n68e1b1bc8bd5b913@mail.gmail.com> <4A9B78B2.5020000@sissa.it> Message-ID: <612c95fa0908310459p2221b904j5b55148c0c7ea724@mail.gmail.com> Dear Gabriele, I just follow the steps in the README: 1-) Went to the example folder 2-) ./run_example Doing this, the example script run but in serial mode. When I run the input files directly from the prompt using the same command in the script (i.e. using the environment_variables), I went to parallel mode. So, I am afraid that the problem is how my bash interpreter "understand" the commands in the script. I am running Ubuntu 9.04 64bits up-dated. Regards, Camps ___ Jonathan Swift - "May you live every day of your life." On Mon, Aug 31, 2009 at 4:16 AM, Gabriele Sclauzero wrote: > > I. Camps wrote: > > SOLVED! > > And so, where is the problem exactly? I've often used the example scripts > in parallel by > setting the environment variables in environment_variables file and I could > always run > without any problem. > > > > > The problem is the script run_example. > > Please, try to idenfity where the problem is (if any)? I think that the > scripts usually > work fine. It is not clear to me the procedure you followed to run the > script the first > time (when you could not run with more processes). > > > Regards, > > Gabriele > > > If I run the input file directly from the prompt using > > > > $PARA_PREFIX pw.x $PARA_POSTFIX < al001.rx.in > al001.rx.out > > > > I get the following output: > > > > *************************** > > Program PWSCF v.4.1 starts ... > > Today is 28Aug2009 at 12:34:42 > > > > Parallel version (MPI) > > > > Number of processors in use: 4 > > R & G space division: proc/pool = 4 > > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/00df3568/attachment-0001.htm From sclauzer at sissa.it Mon Aug 31 14:10:07 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 31 Aug 2009 14:10:07 +0200 Subject: [Pw_forum] << running QE in parallel >> In-Reply-To: <612c95fa0908310459p2221b904j5b55148c0c7ea724@mail.gmail.com> References: <612c95fa0908280742q49c3f111r44e055cb0b3bc3c7@mail.gmail.com> <612c95fa0908280838r1b42a293n68e1b1bc8bd5b913@mail.gmail.com> <4A9B78B2.5020000@sissa.it> <612c95fa0908310459p2221b904j5b55148c0c7ea724@mail.gmail.com> Message-ID: <4A9BBD9F.7040004@sissa.it> I. Camps wrote: > Dear Gabriele, > > I just follow the steps in the README: > 1-) Went to the example folder > 2-) ./run_example You may need to modify the environment_variables file in the examples/ directory before step 2. This file is sourced (i.e. read and interpreted) at the beginning of all example??/run_example scripts and this sets some environment variables. To understand if the variables have been set correctly just place something like echo "$PARA_PREFIX pw.x $PARA_POSTFIX" at the beginning of run_example (after environment_variables file has been sourced) and you will see. HTH GS > > Doing this, the example script run but in serial mode. > > When I run the input files directly from the prompt using the same > command in the script (i.e. using the environment_variables), I went to > parallel mode. > > So, I am afraid that the problem is how my bash interpreter "understand" > the commands in the script. I am running Ubuntu 9.04 64bits up-dated. > > Regards, > > Camps > ___ > Jonathan Swift > - > "May you live every day of your life." > > On Mon, Aug 31, 2009 at 4:16 AM, Gabriele Sclauzero > wrote: > > > I. Camps wrote: > > SOLVED! > > And so, where is the problem exactly? I've often used the example > scripts in parallel by > setting the environment variables in environment_variables file and > I could always run > without any problem. > > > > > The problem is the script run_example. > > Please, try to idenfity where the problem is (if any)? I think that > the scripts usually > work fine. It is not clear to me the procedure you followed to run > the script the first > time (when you could not run with more processes). > > > Regards, > > Gabriele > > > If I run the input file directly from the prompt using > > > > $PARA_PREFIX pw.x $PARA_POSTFIX < al001.rx.in > > al001.rx.out > > > > I get the following output: > > > > *************************** > > Program PWSCF v.4.1 starts ... > > Today is 28Aug2009 at 12:34:42 > > > > Parallel version (MPI) > > > > Number of processors in use: 4 > > R & G space division: proc/pool = 4 > > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ttduyle at gmail.com Mon Aug 31 16:31:28 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 31 Aug 2009 10:31:28 -0400 Subject: [Pw_forum] Default values used in Quantum espresso manuals In-Reply-To: References: Message-ID: <8974d3b20908310731m6e915698m21e43a0bd27a0dc5@mail.gmail.com> Hi, conv = convergence thr = threshold forc = on the force etot = on the total energy So, the keywords say everything. They are the convergence threshold or convergence condition. They are arbitrarily defined as users' needs. The default values are the conventional values, I guess. Best, On Mon, Aug 31, 2009 at 5:49 AM, Shaptrishi Sharma wrote: > Hi There, > I am a new user in quantum espresso , thus I would like to ask one question > how do the default values in the quantum espresso manuals have been choosed? > I mean to say that in quantum espresso manuals we find > forc_conv_thr =1.0D-3 > conv_thr =1.0D-6 > etot_conv_thr=1.0D-4 > > How did the values calculated? > > Thanks > Shaptarishi > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/7351c1d4/attachment.htm From liuyongduo at hotmail.com Mon Aug 31 20:06:40 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Tue, 1 Sep 2009 02:06:40 +0800 Subject: [Pw_forum] Vol 26, Issue 80Re: error message : from calbec : error # 3 size mismatch In-Reply-To: References: Message-ID: Dear Andrea Thank you very much! But my version is the latest version 4.1. What is cvs version by the way? best Yongduo University of California, Los Angeles Materials Sciences > Message: 5 > Date: Mon, 31 Aug 2009 11:56:38 +0200 > From: Dal Corso Andrea > Subject: Re: [Pw_forum] error message : from calbec : error # 3 size > mismatch > To: PWSCF Forum > Message-ID: <1251712598.3526.15.camel at dhpc-5-36.sissa.it> > Content-Type: text/plain; charset=utf-8 > > Dear Yongduo Liu > > There was a bug in the routine PH/dvpsi_e.f90 for the case in which all > atoms are described by a local potential. This is now fixed in the cvs > version. > > HTH, > > Andrea > > On Sun, 2009-08-30 at 02:11 +0800, ??? wrote: > > Dear PW users > > > > > > I am doing some test calculations about Raman spectra, but I came > > across a strange error when testing H2 > > > > Here is my h2.scf.in,: > > > > &control > > calculation='scf' > > pseudo_dir = '/home/yongduo/QuantumEspresso/espresso-4.1/pseudo', > > outdir='/home/yongduo/tmp/' > > title='Test H2 gamma only' > > prefix='h2' > > tprnfor=.true. > > / > > &system > > ibrav=0, nat=2, ntyp= 1, > > ecutwfc =60.0 > > / > > &electrons > > mixing_mode='plain' > > mixing_beta = 0.7, > > conv_thr = 1.0d-8 > > / > > CELL_PARAMETERS cubic > > 20 0.0 0.0 > > 0.0 20 0.0 > > 0.0 0.0 20 > > ATOMIC_SPECIES > > H 1.008 H.pz-vbc.UPF > > ATOMIC_POSITIONS (alat) > > H 0.002235005 0.000000000 0.000000000 > > H 0.074814995 0.000000000 0.000000000 > > K_POINTS > > 1 > > 0 0 0 1 > > > > This step was successful, but error came out when ph.x began to do the > > Electric Fields Calculation. > > > > My input: > > > > Normal modes for H2 > > &inputph > > tr2_ph=1.0d-14, > > prefix='h2', > > amass(1)=1.008, > > outdir='/home/yongduo/tmp', > > epsil=.true., > > trans=.true., > > asr=.true. > > lraman = .true. > > fildyn='h2.dyn' > > / > > 0.0 0.0 0.0 > > > > > > Output > > > > .......... > > Electric Fields Calculation > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%%%% > > from calbec : error # 3 > > size mismatch > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%%%% > > > > stopping ... > > > > > > > > Anybody knows what does that mean? Any help will be highly > > appreciated! > > > > best > > > > Yongduo Liu > > > > > > UCLA > > MSE > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _________________________________________________________________ ????????????360??????? http://club.msn.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/d8d98efd/attachment.htm From giannozz at democritos.it Mon Aug 31 20:23:51 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 31 Aug 2009 20:23:51 +0200 Subject: [Pw_forum] Default values used in Quantum espresso manuals In-Reply-To: References: Message-ID: <6358454B-0EB5-44D9-A64E-98667E04E998@democritos.it> On Aug 31, 2009, at 11:49 , Shaptrishi Sharma wrote: > forc_conv_thr =1.0D-3 > conv_thr =1.0D-6 > etot_conv_thr=1.0D-4 > How did the values calculated? they were not "calculated" but estimated so that for a typical system they yield sufficiently small errors for most purposes, without forcing excessive computation. No warranty they fit your specific case. This is why you can change them. They are provided to give at least a rough guide and an order of magnitude. conv_thr has a precise meaning: the error on the energy due to incomplete self-consistency is smaller than conv_thr, in Ry. The two other criteria, for structural optimization, do not have a direct relation with the error on atomic positions due to incomplete structural optimization, but unless you have a pathologic system (with floppy modes, saddle points, almost flat energy surface) you will get accurate positions. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From udayagiri3 at gmail.com Mon Aug 31 20:18:55 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Mon, 31 Aug 2009 23:48:55 +0530 Subject: [Pw_forum] cohesive energy Message-ID: Hi all i am claculating cohesive energy of V using pwscf but i got -8.15 ev/atom against an experimental value of 5.3 ev/atom which is almost 50% off can anybody say what is going wrong with the calculation. the method i used is calculate the total energy of a bcc crystal with 1 atom and deduct the energy of isolated atom from it. the following input files are for finding the total energy for isolated atom and the atom in the crystal. Please tell me if my methodology is wrong. *cohesive energy=E per atom (in the crystal)-E per atom (isolated)* *input file for finding the total energy of an isolated atom* &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='vanadium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=1 celldm(1)=30, nat=1, ntyp=1 ecutwfc=25, ecutrho=100, occupations='smearing', smearing='mv', degauss=0.010000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.3 / ATOMIC_SPECIES V 50.9415 V.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) V 0.00000000 0.00000000 0.00000000 K_POINTS {automatic} 1 1 1 0 0 0 *input file for finding the total energy of the atom in the crystal* &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='vanadium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=3 celldm(1)=5.654, nat=1, ntyp=1 ecutwfc=25, ecutrho=100, occupations='smearing', smearing='mv', degauss=0.010000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.3 / ATOMIC_SPECIES V 50.9415 V.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) V 0.00000000 0.00000000 0.00000000 K_POINTS {automatic} 8 8 8 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/4222ed0f/attachment.htm From giannozz at democritos.it Mon Aug 31 20:32:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 31 Aug 2009 20:32:38 +0200 Subject: [Pw_forum] Vol 26, Issue 80Re: error message : from calbec : error # 3 size mismatch In-Reply-To: References: Message-ID: On Aug 31, 2009, at 20:06 , ??? wrote: > Thank you very much! But my version is the latest version 4.1. less latest than you think. There will be a bug fix version soon. No warranty it will contain that specific fix > What is cvs version by the way? http://www.quantum-espresso.org/developer_man/ developer_man.html#SECTION00090000000000000000 P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From udayagiri3 at gmail.com Mon Aug 31 20:37:02 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Tue, 1 Sep 2009 00:07:02 +0530 Subject: [Pw_forum] calculating cohesive energy Message-ID: Hi all i am claculating cohesive energy of V using pwscf but i got -8.15 ev/atom against an experimental value of 5.3 ev/atom which is almost 50% off can anybody say what is going wrong with the calculation. the method i used is calculate the total energy of a bcc crystal with 1 atom and deduct the energy of isolated atom from it. the following input files are for finding the total energy for isolated atom and the atom in the crystal. Please tell me if my methodology is wrong. *cohesive energy=E per atom (in the crystal)-E per atom (isolated)* *input file for finding the total energy of an isolated atom* &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='vanadium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=1 celldm(1)=30, nat=1, ntyp=1 ecutwfc=25, ecutrho=100, occupations='smearing', smearing='mv', degauss=0.010000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.3 / ATOMIC_SPECIES V 50.9415 V.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) V 0.00000000 0.00000000 0.00000000 K_POINTS {automatic} 1 1 1 0 0 0 *input file for finding the total energy of the atom in the crystal* &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='vanadium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=3 celldm(1)=5.654, nat=1, ntyp=1 ecutwfc=25, ecutrho=100, occupations='smearing', smearing='mv', degauss=0.010000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.3 / ATOMIC_SPECIES V 50.9415 V.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) V 0.00000000 0.00000000 0.00000000 K_POINTS {automatic} 8 8 8 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/05923e2d/attachment-0001.htm From baroni at sissa.it Mon Aug 31 20:54:04 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 31 Aug 2009 20:54:04 +0200 Subject: [Pw_forum] calculating cohesive energy In-Reply-To: References: Message-ID: No need to post twice the same message ... Don't now about your specific system, but it is not unusual that DFT overestimate binding energies (less so for PBE than LDA) Please, do not forget to sign your posts, including your affiliation SB On Aug 31, 2009, at 8:37 PM, udayagiri sai babu wrote: > Hi all > i am claculating cohesive energy of V using pwscf but i got -8.15 ev/ > atom against an experimental value of 5.3 ev/atom which is almost > 50% off can anybody say what is going wrong with the calculation. > the method i used is calculate the total energy of a bcc crystal > with 1 atom and deduct the energy of isolated atom from it. the > following input files are for finding the total energy for isolated > atom and the atom in the crystal. Please tell me if my methodology > is wrong. > > cohesive energy=E per atom (in the crystal)-E per atom (isolated) > > input file for finding the total energy of an isolated atom > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/ > softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=30, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 1 1 1 0 0 0 > > input file for finding the total energy of the atom in the crystal > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.654, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 8 8 8 0 0 0 > _______________________________________________ > 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/20090831/bb70b467/attachment.htm From lanhaiping at gmail.com Mon Aug 31 20:55:58 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 1 Sep 2009 02:55:58 +0800 Subject: [Pw_forum] cohesive energy In-Reply-To: References: Message-ID: Hi, A comment: Spin polarization calculation should be applied for the isolated atom. Hope it helps, and please supply your affiliation regards On Tue, Sep 1, 2009 at 2:18 AM, udayagiri sai babu wrote: > Hi all > i am claculating cohesive energy of V using pwscf but i got -8.15 ev/atom > against an experimental value of 5.3 ev/atom which is almost 50% off can > anybody say what is going wrong with the calculation. the method i used is > calculate the total energy of a bcc crystal with 1 atom and deduct the > energy of isolated atom from it. the following input files are for finding > the total energy for isolated atom and the atom in the crystal. Please tell > me if my methodology is wrong. > > *cohesive energy=E per atom (in the crystal)-E per atom (isolated)* > > *input file for finding the total energy of an isolated atom* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=30, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 1 1 1 0 0 0 > > *input file for finding the total energy of the atom in the crystal* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.654, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 8 8 8 0 0 0 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/a995238d/attachment.htm From ttduyle at gmail.com Mon Aug 31 21:25:45 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 31 Aug 2009 15:25:45 -0400 Subject: [Pw_forum] calculating cohesive energy In-Reply-To: References: Message-ID: <8974d3b20908311225g2acfef47lf1980c66906979d5@mail.gmail.com> Hi, I think you may need to increase the k-point mesh for bulk calculation and do the spin-polarized for isolated atom. Another point: the calculated cohesive energy in general depends very much not only on the functional but also the pseudized potential (cutoff radius, configuration...). So one may consider to calculate it with many different available potentials. Best, On Mon, Aug 31, 2009 at 2:54 PM, Stefano Baroni wrote: > No need to post twice the same message ...Don't now about your specific > system, but it is not unusual that DFT overestimate binding energies (less > so for PBE than LDA) > Please, do not forget to sign your posts, including your affiliation > SB > > On Aug 31, 2009, at 8:37 PM, udayagiri sai babu wrote: > > Hi all > i am claculating cohesive energy of V using pwscf but i got -8.15 ev/atom > against an experimental value of 5.3 ev/atom which is almost 50% off can > anybody say what is going wrong with the calculation. the method i used is > calculate the total energy of a bcc crystal with 1 atom and deduct the > energy of isolated atom from it. the following input files are for finding > the total energy for isolated atom and the atom in the crystal. Please tell > me if my methodology is wrong. > > *cohesive energy=E per atom (in the crystal)-E per atom (isolated)* > > *input file for finding the total energy of an isolated atom* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=30, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 1 1 1 0 0 0 > > *input file for finding the total energy of the atom in the crystal* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.654, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 8 8 8 0 0 0 > _______________________________________________ > 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 > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/c2a9415e/attachment-0001.htm