From brad.malone at gmail.com Tue Dec 1 01:04:01 2009 From: brad.malone at gmail.com (Brad Malone) Date: Mon, 30 Nov 2009 16:04:01 -0800 Subject: [Pw_forum] Calculation of Raman tensor/intensity for material with indirect band overlap In-Reply-To: References: Message-ID: As a follow up on my previous post, I let the calculation run to completion on a less dense k-grid and saw the following output: ik 2 ibnd 17 linter: root not converged 0.748E+35 > kpoint 2 ibnd 17 pcgreen: root not converged 0.421E+23 > Non-scf u_k: avg # of iterations =137.0 > Non-scf Du_k: avg # of iterations =200.0 > > Dielectric constant from finite-differences > > ( NaN NaN NaN ) > ( NaN NaN NaN ) > ( NaN NaN NaN ) > > Computing Second order response > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > > > iter # 1 av.it.: 147.2 > thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > kpoint 2 ibnd 17 pcgreen: root not converged NaN > > > iter # 2 av.it.: 200.0 > thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > kpoint 1 ibnd 17 pcgreen: root not converged NaN > > > and so on. The code crashes at the end with the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 1 > factorization > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > but obviously the problem occurs well before this crash. Again, I am trying to calculate the Raman intensity for a material with a small indirect overlap. Should this not be possible? I know that DFPT is applicable (without modification) only for systems with a clear distinction between occupied and valence states (in order to clearly specify what the projectors over the occupied and unoccupied manifolds I guess?). For the indirect overlap case with fixed occupancies I would imagine that this would be possible. Anyway, just wanted to report on the results of my first post. If anyone knows what I can do to calculate the intensity or simply if it should or shouldn't work (and/or "why") I would greatly appreciate it. Best, Brad Malone UC Berkeley On Sun, Nov 22, 2009 at 11:36 AM, Brad Malone wrote: > Hi, I'm interested in calculating the Raman intensity for a material with a > small indirect band overlap within LDA (~0.3 eV). As has been mentioned many > times on this forum, Raman intensities cannot be calculated for a pure > metal. But should I expect to be able to calculate the intensity for a > material with a small, indirect band overlap? When I attempted to do so > (using lraman=.true. in the ph.x calculation) I received the following > messages: > > Computing Pc [DH,Drho] |psi> >> >> Derivative coefficient: 0.001000 Threshold: 1.00E-12 >> ik 1 ibnd 17 linter: root not converged 0.578E+08 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.763E+05 >> ik 1 ibnd 17 linter: root not converged 0.193E+11 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.119E+05 >> ik 1 ibnd 17 linter: root not converged 0.595E+09 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.182E+05 >> ik 1 ibnd 17 linter: root not converged 0.142E+31 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.224E+24 >> ik 1 ibnd 17 linter: root not converged 0.143E+30 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.170E+25 >> ik 1 ibnd 17 linter: root not converged 0.765E+28 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.151E+25 >> ik 1 ibnd 17 linter: root not converged 0.643E+09 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.460E+05 >> ik 1 ibnd 17 linter: root not converged 0.619E+10 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.547E+07 >> ik 1 ibnd 17 linter: root not converged 0.685E+09 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.810E+04 >> ik 1 ibnd 17 linter: root not converged 0.290E+34 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.848E+19 >> ik 1 ibnd 17 linter: root not converged 0.132E+33 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.333E+18 >> ik 1 ibnd 17 linter: root not converged 0.155E+34 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.133E+20 >> ik 1 ibnd 17 linter: root not converged 0.146E+06 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.442E+05 >> ik 1 ibnd 17 linter: root not converged 0.135E+07 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.169E+06 >> ik 1 ibnd 17 linter: root not converged 0.567E+08 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.493E+06 >> ik 1 ibnd 17 linter: root not converged 0.292E+27 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.518E+23 >> ik 1 ibnd 17 linter: root not converged 0.882E+28 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.215E+24 >> ik 1 ibnd 17 linter: root not converged 0.104E+29 >> kpoint 1 ibnd 17 pcgreen: root not converged 0.328E+23 >> ik 2 ibnd 17 linter: root not converged 0.585E+21 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.363E+23 >> ik 2 ibnd 17 linter: root not converged 0.505E+21 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.119E+22 >> ik 2 ibnd 17 linter: root not converged 0.117E+21 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.267E+22 >> ik 2 ibnd 17 linter: root not converged 0.159E+33 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.283E+27 >> ik 2 ibnd 17 linter: root not converged 0.367E+32 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.660E+27 >> ik 2 ibnd 17 linter: root not converged 0.876E+32 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.670E+28 >> ik 2 ibnd 17 linter: root not converged 0.249E+32 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.125E+28 >> ik 2 ibnd 17 linter: root not converged 0.348E+31 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.206E+26 >> ik 2 ibnd 17 linter: root not converged 0.141E+30 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.561E+25 >> ik 2 ibnd 17 linter: root not converged 0.520E+36 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.990E+24 >> ik 2 ibnd 17 linter: root not converged 0.140E+37 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.721E+24 >> ik 2 ibnd 17 linter: root not converged 0.836E+35 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.690E+25 >> ik 2 ibnd 17 linter: root not converged 0.246E+30 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.540E+24 >> ik 2 ibnd 17 linter: root not converged 0.517E+29 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.415E+25 >> ik 2 ibnd 17 linter: root not converged 0.133E+30 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.202E+26 >> ik 2 ibnd 17 linter: root not converged 0.570E+27 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.103E+21 >> ik 2 ibnd 17 linter: root not converged 0.270E+29 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.451E+22 >> ik 2 ibnd 17 linter: root not converged 0.381E+29 >> kpoint 2 ibnd 17 pcgreen: root not converged 0.346E+22 >> ik 3 ibnd 17 linter: root not converged 0.118E+34 >> > > and so on for each ik in the calculation. The code never crashed and I > stopped it prematurely due to concern about these messages (seeing values on > the order of 1E+34 is never calming). The code was also taking a very long > time to calculate each ik. From what I've read in the Lazzeri and Mauri > paper (PRL 90, 036401, 2003) some of the methods used to calculate the Raman > tensor can take a lot of linear response calculations and so maybe I > shouldn't expect it to go extremely fast. However, this root convergence > worries me. The 17th band, which is the only band that this problem occurs > for that I've seen, is the first conduction band of the system and is the > band that indirectly overlaps with the top of the valence band. Any help or > comments would be greatly appreciated! > > Thanks, > Brad Malone > UC Berkeley > > P.S. I used 'fixed' occupancies in the SCF run to avoid the 'elec. field' > error in the ph.x calculation. The fixed occupancy is what I would expect > for this material in experiment, as the GW bandstructure for this material > predicts it to be semiconducting. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/f59d0d5a/attachment-0001.htm From bipulrr at gmail.com Tue Dec 1 05:54:19 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 1 Dec 2009 10:24:19 +0530 Subject: [Pw_forum] NRAPP not giving phonon frequencies Message-ID: <3a749910911302054r787db777v5cad13d784e21060@mail.gmail.com> Dear Pwscf users, I am doing phonon calculation of LaMnO3 at gamma point, using the nrapp option. The input file is shown below. *phonons of LaMnO3-pero &inputph ! recover=.true., tr2_ph=1.0d-12, alpha_mix(1)= 0.6, prefix='lamno3', ! epsil=.true., ! ldisp=.true., ! nq1=2, nq2=2, nq3=2 ! iq1=6, iq2=6, iq3=6 lnscf= .true., nrapp=3, amass(1)= 138.9055, amass(2)=54.938049, amass(3)=15.9994, outdir = './OUT', fildyn='LaMnO3.dyn2', / 0.000000000 0.000000000 0.000000000 1 2 3* The calculation is finished with the following lines * End of self-consistent calculation Convergence has been achieved Stopping because representation 4 is not done* But in LaMnO3.dyn2 or in the output file, no where it is giving me frequencies. So can anybody tell me how to get the frequencies of only first three modes, rather than calculating all 60 modes? What I have to modify in my input file? Thanks -- Bipul Rakshit Research Fellow, 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/20091201/ca0556f1/attachment.htm From paulatto at sissa.it Tue Dec 1 08:44:27 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 1 Dec 2009 08:44:27 +0100 Subject: [Pw_forum] NRAPP not giving phonon frequencies In-Reply-To: <3a749910911302054r787db777v5cad13d784e21060@mail.gmail.com> References: <3a749910911302054r787db777v5cad13d784e21060@mail.gmail.com> Message-ID: <20091201084427.v62un9qolc044k0g@webmail.sissa.it> Quoting Bipul Rakshit : > The calculation is finished with the following lines > > * End of self-consistent calculation > Convergence has been achieved > Stopping because representation 4 is not done* > > But in LaMnO3.dyn2 or in the output file, no where it is giving me > frequencies. > So can anybody tell me how to get the frequencies of only first three modes, > rather than calculating all 60 modes? > What I have to modify in my input file? Dear Bipul, it is not possible to compute the frequency of a single mode; each mode gives you a line of the dynamical matrix; the matrix is then diagonalized and each eigenvalue correspond to a frequency. If you only compute the modes corresponding to the first atom you can still compute the frequency belonging to the first atom ***but*** under the approximation that all the other atoms have infinite masses; i.e. a mass much larger than the first one. This clearly is **not** your case, as Lanthanium is 2.5 times heavier than Manganese and almost 9 times heavier than Oxygen. Nevertheless, I'll give you the procedure as reference, but don't be tempted to use it in your case, unless you really know what you're doing. After computing the first 3 mode you have the first 3 lines of the dynamical matrix. You can take the 3x3 minor of the the matrix (first 3 rows and first 3 columns) and diagonalize it by hand (using octave, matlab or whatever software you prefer). The eigenvalues are the frequencies you are looking for in the said approximation. They are in Rydberg atomic units, you can get cm-1 multiplying by 109737. best regards. -- Lorenzo Paulatto (MS) SISSA & Democritos ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From bipulrr at gmail.com Tue Dec 1 08:57:34 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 1 Dec 2009 13:27:34 +0530 Subject: [Pw_forum] NRAPP not giving phonon frequencies In-Reply-To: <20091201084427.v62un9qolc044k0g@webmail.sissa.it> References: <3a749910911302054r787db777v5cad13d784e21060@mail.gmail.com> <20091201084427.v62un9qolc044k0g@webmail.sissa.it> Message-ID: <3a749910911302357w4c95eafat300b0daaa542879b@mail.gmail.com> Dear Lorenzo, Thanks for your reply. One more thing I want to ask is that, after computing first 3 modes using nrapp, where do i find the dynamical matrix? Because in LaMnO3.dyn2 file is empty, after the calculation is finished. Is the non-diagonalised matrix is printed elsewhere? regards On Tue, Dec 1, 2009 at 1:14 PM, Lorenzo Paulatto wrote: > Quoting Bipul Rakshit : > > The calculation is finished with the following lines > > > > * End of self-consistent calculation > > Convergence has been achieved > > Stopping because representation 4 is not done* > > > > But in LaMnO3.dyn2 or in the output file, no where it is giving me > > frequencies. > > So can anybody tell me how to get the frequencies of only first three > modes, > > rather than calculating all 60 modes? > > What I have to modify in my input file? > > > Dear Bipul, > it is not possible to compute the frequency of a single mode; each > mode gives you a line of the dynamical matrix; the matrix is then > diagonalized and each eigenvalue correspond to a frequency. If you > only compute the modes corresponding to the first atom you can still > compute the frequency belonging to the first atom ***but*** under the > approximation that all the other atoms have infinite masses; i.e. a > mass much larger than the first one. > > This clearly is **not** your case, as Lanthanium is 2.5 times heavier > than Manganese and almost 9 times heavier than Oxygen. Nevertheless, > I'll give you the procedure as reference, but don't be tempted to use > it in your case, unless you really know what you're doing. > > After computing the first 3 mode you have the first 3 lines of the > dynamical matrix. You can take the 3x3 minor of the the matrix (first > 3 rows and first 3 columns) and diagonalize it by hand (using octave, > matlab or whatever software you prefer). The eigenvalues are the > frequencies you are looking for in the said approximation. They are in > Rydberg atomic units, you can get cm-1 multiplying by 109737. > > best regards. > > > -- > Lorenzo Paulatto (MS) > SISSA & Democritos > > > > > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > 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/20091201/b2283e9d/attachment.htm From paulatto at sissa.it Tue Dec 1 09:42:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 1 Dec 2009 09:42:41 +0100 Subject: [Pw_forum] NRAPP not giving phonon frequencies In-Reply-To: <3a749910911302357w4c95eafat300b0daaa542879b@mail.gmail.com> References: <3a749910911302054r787db777v5cad13d784e21060@mail.gmail.com> <20091201084427.v62un9qolc044k0g@webmail.sissa.it> <3a749910911302357w4c95eafat300b0daaa542879b@mail.gmail.com> Message-ID: <20091201094241.4j5v4k0a04o4oscg@webmail.sissa.it> Quoting Bipul Rakshit : > One more thing I want to ask is that, after computing first 3 modes using > nrapp, where do i find the dynamical matrix? Because in LaMnO3.dyn2 file is > empty, after the calculation is finished. > > Is the non-diagonalised matrix is printed elsewhere? It is printed in output, or at least that's what I've got after doing some single-mode calculation: Dynamical matrix: 1 1 -0.276205 0.000000 1 2 -0.000065 0.000000 1 3 0.071921 0.000000 1 4 -0.102158 0.000000 [...] Which means M_{13} = 0.071921 + i 0.000000 Although, that happens when you use modenum=# in the input. Now that you made me recall it, I think that by using nrapp+list of representations you don't get the dynamical matrix line. You can just rerun the code with modeunm=1, 2 and 3 (three separate runs) and it will pop you the line in a few minutes (they are already computed, just not printed). You can also extract them by hand from file $otudir/_php$prefix.save/data-file.xml.1.$R where $R is the representation number. If your system has symmetry, this may not be correct. I think it is, but I am quite confused by the differences (if any) between nrapp, nat_todo, modenum and/or start_irr+last_irr. I would rather refrain from further comment than tell you something wrong. -- Lorenzo Paulatto SISSA & DEMOCRITOS ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From kazempoor2000 at yahoo.com Tue Dec 1 13:37:13 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 1 Dec 2009 04:37:13 -0800 (PST) Subject: [Pw_forum] short range potential Message-ID: <513093.70939.qm@web112518.mail.gq1.yahoo.com> Hi All If I have a charge in unit cell, Is it possible to separate the interaction contribution of this charge within unit cell (short range) and the interaction contribution with other cells(long range)? If yes, How? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091201/08998c62/attachment.htm From kazempoor2000 at yahoo.com Tue Dec 1 13:54:53 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 1 Dec 2009 04:54:53 -0800 (PST) Subject: [Pw_forum] Fw: short range potential Message-ID: <714256.80279.qm@web112518.mail.gq1.yahoo.com> Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ----- Forwarded Message ---- From: ali kazempour To: pw Sent: Tue, December 1, 2009 1:37:13 PM Subject: short range potential Hi All If I have a charge in unit cell, Is it possible to separate the interaction contribution of this charge within unit cell (short range) and the interaction contribution with other cells(long range)? If yes, How? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091201/901f7623/attachment.htm From paulatto at sissa.it Tue Dec 1 14:16:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 01 Dec 2009 14:16:11 +0100 Subject: [Pw_forum] short range potential In-Reply-To: <513093.70939.qm@web112518.mail.gq1.yahoo.com> References: <513093.70939.qm@web112518.mail.gq1.yahoo.com> Message-ID: Replying to message "[Pw_forum] short range potential" from ali kazempour (01/12/09): > If I have a charge in unit cell, Is it possible to separate the > interaction contribution of this charge within unit cell (short range) > and the interaction contribution with other cells(long range)? If yes, Dear Ali, I think it possible. Currently, I don't think anything like that is implemented.I have a vague idea on how it could be done. However, I don't think I have the time to make it clear to myself, and then explain it unless you are serious about implementing something in the code. The EE you were asking about a week ago should serve a similar purpose, have you given up with 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 vranjan at ncsu.edu Tue Dec 1 21:17:49 2009 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Tue, 1 Dec 2009 15:17:49 -0500 (EST) Subject: [Pw_forum] [Fwd: diagonalization failure (david, cg) for large numbers of bands] Message-ID: <56829.152.14.74.117.1259698669.squirrel@webmail.ncsu.edu> Hi, ## Summary: Running pw.x on 128-1024 processors, testing bulk 64-Si cell at gamma (gamma tricks not used because of incompatibility with subsequent calculations) with a "large" number of (extra) bands. No problems reported when nbnd is small. With 128-256 processors, when nbnd>1300, if using Davidson diag, program exits before completion of 1 scf step, with cholesky decomposition failure error; if using iterative diag (cg), fails at same stage with error "(ZHEGV*) failed". System is Cray XT4. ## Purpose: reproducing the beautiful results of PHYSICAL REVIEW B 79, 201104, 2009 for GWW education purposes. :) ## Background: I have found similar-looking problems reported here, and have tried several of the recommendations (switching to ndiag 1 at runtime to use serial diag instead of parallel; switching from david to cg). In addition, I have tried increasing the PW cutoff (to provide more PWs relative to requested bands for the sake of Davidson diag, but this does not really help). I also attempted to do a regular SCF calculation with no nbnd specification, followed by a NSCF calculation with extra bands specified. The same errors are obtained. ## Current status: I am now trying to rule out memory-related errors (via running on more nodes), and will update this thread accordingly if the problem is related to memory requirements. Running on 512 processors permitted nbnd=2500 (converged results should require ~3300 bands for this particular calculation, according to my understanding of the noted paper), and I have some 1024 processor runs queued up. It does not seem to me that such a system, even with so many states, should have such large memory demands, so am wondering if I am doing something stupendously wrong (or perhaps not exactly doing something wrong, but failing to do something glaringly obvious that would solve the problem). Below is my input file, followed by some brief technical specs in case such are helpful. ## Sample input file: &control calculation='scf' restart_mode='from_scratch', prefix='si' outdir='/scr/josepht/espresso/bsi64/Large_GAMMA/STEP_B/tmp' pseudo_dir='/scr/josepht/espresso/bsi64/pseudo' / &system ibrav= 8, celldm(1)= 20.52, celldm(2)= 1, celldm(3)=1, nat= 64, ntyp= 1, ecutwfc = 35.0, nosym=.true. nbnd = 3328, / &electrons diagonalization='david', conv_thr = 1.0d-8, mixing_beta = 0.5, / ATOMIC_SPECIES Si 1. Si.pbe-rrkj.UPF ATOMIC_POSITIONS (bohr) Si 0.00000000 0.00000000 0.00000000 Si 5.13000000 5.13000000 0.00000000 Si 0.00000000 5.13000000 5.13000000 Si 5.13000000 0.00000000 5.13000000 Si 2.56500000 2.56500000 2.56500000 Si 7.69500000 7.69500000 2.56500000 Si 7.69500000 2.56500000 7.69500000 Si 2.56500000 7.69500000 7.69500000 Si 10.26000000 0.00000000 0.00000000 Si 15.39000000 5.13000000 0.00000000 Si 10.26000000 5.13000000 5.13000000 Si 15.39000000 0.00000000 5.13000000 Si 12.82500000 2.56500000 2.56500000 Si 17.95500000 7.69500000 2.56500000 Si 17.95500000 2.56500000 7.69500000 Si 12.82500000 7.69500000 7.69500000 Si 0.00000000 10.26000000 0.00000000 Si 5.13000000 15.39000000 0.00000000 Si 0.00000000 15.39000000 5.13000000 Si 5.13000000 10.26000000 5.13000000 Si 2.56500000 12.82500000 2.56500000 Si 7.69500000 17.95500000 2.56500000 Si 7.69500000 12.82500000 7.69500000 Si 2.56500000 7.69500000 7.69500000 Si 10.26000000 0.00000000 0.00000000 Si 15.39000000 5.13000000 0.00000000 Si 10.26000000 5.13000000 5.13000000 Si 15.39000000 0.00000000 5.13000000 Si 12.82500000 2.56500000 2.56500000 Si 17.95500000 7.69500000 2.56500000 Si 17.95500000 2.56500000 7.69500000 Si 12.82500000 7.69500000 7.69500000 Si 0.00000000 10.26000000 0.00000000 Si 5.13000000 15.39000000 0.00000000 Si 0.00000000 15.39000000 5.13000000 Si 5.13000000 10.26000000 5.13000000 Si 2.56500000 12.82500000 2.56500000 Si 7.69500000 17.95500000 2.56500000 Si 7.69500000 12.82500000 7.69500000 Si 2.56500000 17.95500000 7.69500000 Si 0.00000000 0.00000000 10.26000000 Si 5.13000000 5.13000000 10.26000000 Si 0.00000000 5.13000000 15.39000000 Si 5.13000000 0.00000000 15.39000000 Si 2.56500000 2.56500000 12.82500000 Si 7.69500000 7.69500000 12.82500000 Si 7.69500000 2.56500000 17.95500000 Si 2.56500000 7.69500000 17.95500000 Si 10.26000000 10.26000000 0.00000000 Si 15.39000000 15.39000000 0.00000000 Si 10.26000000 15.39000000 5.13000000 Si 15.39000000 10.26000000 5.13000000 Si 12.82500000 12.82500000 2.56500000 Si 17.95500000 17.95500000 2.56500000 Si 17.95500000 12.82500000 7.69500000 Si 12.82500000 17.95500000 7.69500000 Si 10.26000000 0.00000000 10.26000000 Si 15.39000000 5.13000000 10.26000000 Si 10.26000000 5.13000000 15.39000000 Si 15.39000000 0.00000000 15.39000000 Si 12.82500000 2.56500000 12.82500000 Si 17.95500000 7.69500000 12.82500000 Si 17.95500000 2.56500000 17.95500000 Si 12.82500000 7.69500000 17.95500000 Si 0.00000000 10.26000000 10.26000000 Si 5.13000000 15.39000000 10.26000000 Si 0.00000000 15.39000000 15.39000000 Si 5.13000000 10.26000000 15.39000000 Si 2.56500000 12.82500000 12.82500000 Si 7.69500000 17.95500000 12.82500000 Si 7.69500000 12.82500000 17.95500000 Si 2.56500000 17.95500000 17.95500000 Si 10.26000000 10.26000000 10.26000000 Si 15.39000000 15.39000000 10.26000000 Si 10.26000000 15.39000000 15.39000000 Si 15.39000000 10.26000000 15.39000000 Si 12.82500000 12.82500000 12.82500000 Si 17.95500000 17.95500000 12.82500000 Si 17.95500000 12.82500000 17.95500000 Si 12.82500000 17.95500000 17.95500000 K_POINTS 1 0.0 0.0 0.0 1.0 ##END OF INPUT The above file runs when nbnd = 1280 , and (possibly) relevant output from the successful run includes: (Each subspace H/S matrix 400.00 Mb ( 5120,5120) ## Technical specs: Code was compiled on a Cray XT4 (unsure if compilation details would be helpful), and runs were performed on Cray XT4 nodes with two quad-core 2.3 GHz AMD Opteron processors with 16 GBytes of usable memory (requesting 4 cores per node). I've read here that the problem might be related to libraries/compilers (issues with PGI, ACML, etcetera)...if that is likely the case, I would be interested in insight regarding optimal compilation on Cray. Thanks in advance for any assistance, and I apologize if this question has essentially already been answered on the forum - I searched but did not come across an explicit solution to something matching this, though admit that the general theme is present in several independent threads. Joseph Turnbull Department of Physics NC State University From degironc at sissa.it Tue Dec 1 22:42:40 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 1 Dec 2009 22:42:40 +0100 Subject: [Pw_forum] [Fwd: diagonalization failure (david, cg) for large numbers of bands] In-Reply-To: <56829.152.14.74.117.1259698669.squirrel@webmail.ncsu.edu> References: <56829.152.14.74.117.1259698669.squirrel@webmail.ncsu.edu> Message-ID: <20091201224240.f0kzu07hxcsg4os8@webmail.sissa.it> Dear Vivek Ranjan... (or Joseph Turnbull ?), I do not know if this comment is relevant... I never tried to compute so large a fraction of the band structure. how many plane waves your basis set contains ? the default operation of davidson diagonalization is that the basis set is expanded up to diago_david_ndim times (default = 4 times) the number or required bands (nbnd) ... are you asking more that 1/4 of the total number of elements in your basis set ? it seams to me that NPW in your case should be something of the order of 8000, isn't it ? you could try using diago_david_ndim=2.. stefano Quoting Vivek Ranjan : > Hi, > > ## Summary: Running pw.x on 128-1024 processors, testing bulk 64-Si cell > at gamma > (gamma tricks not used because of incompatibility with subsequent > calculations) with > a "large" number of (extra) bands. No problems reported when nbnd is > small. With > 128-256 processors, when nbnd>1300, if using Davidson diag, program exits > before > completion of 1 scf step, with cholesky decomposition failure error; if using > iterative diag (cg), fails at same stage with error "(ZHEGV*) failed". > System is > Cray XT4. > > ## Purpose: reproducing the beautiful results of PHYSICAL REVIEW B 79, > 201104, 2009 > for GWW education purposes. :) > > ## Background: I have found similar-looking problems reported here, and > have tried > several of the recommendations (switching to ndiag 1 at runtime to use > serial diag > instead of parallel; switching from david to cg). > > In addition, I have tried increasing the PW cutoff (to provide more PWs > relative to > requested bands for the sake of Davidson diag, but this does not really > help). > > I also attempted to do a regular SCF calculation with no nbnd specification, > followed by a NSCF calculation with extra bands specified. The same > errors are > obtained. > > ## Current status: I am now trying to rule out memory-related errors (via > running > on more nodes), and will update this thread accordingly if the problem is > related to > memory requirements. Running on 512 processors permitted nbnd=2500 > (converged > results should require ~3300 bands for this particular calculation, > according to my > understanding of the noted paper), and I have some 1024 processor runs > queued up. > > It does not seem to me that such a system, even with so many states, > should have > such large memory demands, so am wondering if I am doing something > stupendously > wrong (or perhaps not exactly doing something wrong, but failing to do > something > glaringly obvious that would solve the problem). Below is my input file, > followed > by some brief technical specs in case such are helpful. > > ## Sample input file: > > &control > calculation='scf' > restart_mode='from_scratch', > prefix='si' > outdir='/scr/josepht/espresso/bsi64/Large_GAMMA/STEP_B/tmp' > pseudo_dir='/scr/josepht/espresso/bsi64/pseudo' > / > &system > ibrav= 8, > celldm(1)= 20.52, > celldm(2)= 1, > celldm(3)=1, > nat= 64, > ntyp= 1, > ecutwfc = 35.0, > nosym=.true. > nbnd = 3328, > / > &electrons > diagonalization='david', > conv_thr = 1.0d-8, > mixing_beta = 0.5, > / > ATOMIC_SPECIES > Si 1. Si.pbe-rrkj.UPF > ATOMIC_POSITIONS (bohr) > Si 0.00000000 0.00000000 0.00000000 > Si 5.13000000 5.13000000 0.00000000 > Si 0.00000000 5.13000000 5.13000000 > Si 5.13000000 0.00000000 5.13000000 > Si 2.56500000 2.56500000 2.56500000 > Si 7.69500000 7.69500000 2.56500000 > Si 7.69500000 2.56500000 7.69500000 > Si 2.56500000 7.69500000 7.69500000 > Si 10.26000000 0.00000000 0.00000000 > Si 15.39000000 5.13000000 0.00000000 > Si 10.26000000 5.13000000 5.13000000 > Si 15.39000000 0.00000000 5.13000000 > Si 12.82500000 2.56500000 2.56500000 > Si 17.95500000 7.69500000 2.56500000 > Si 17.95500000 2.56500000 7.69500000 > Si 12.82500000 7.69500000 7.69500000 > Si 0.00000000 10.26000000 0.00000000 > Si 5.13000000 15.39000000 0.00000000 > Si 0.00000000 15.39000000 5.13000000 > Si 5.13000000 10.26000000 5.13000000 > Si 2.56500000 12.82500000 2.56500000 > Si 7.69500000 17.95500000 2.56500000 > Si 7.69500000 12.82500000 7.69500000 > Si 2.56500000 7.69500000 7.69500000 > Si 10.26000000 0.00000000 0.00000000 > Si 15.39000000 5.13000000 0.00000000 > Si 10.26000000 5.13000000 5.13000000 > Si 15.39000000 0.00000000 5.13000000 > Si 12.82500000 2.56500000 2.56500000 > Si 17.95500000 7.69500000 2.56500000 > Si 17.95500000 2.56500000 7.69500000 > Si 12.82500000 7.69500000 7.69500000 > Si 0.00000000 10.26000000 0.00000000 > Si 5.13000000 15.39000000 0.00000000 > Si 0.00000000 15.39000000 5.13000000 > Si 5.13000000 10.26000000 5.13000000 > Si 2.56500000 12.82500000 2.56500000 > Si 7.69500000 17.95500000 2.56500000 > Si 7.69500000 12.82500000 7.69500000 > Si 2.56500000 17.95500000 7.69500000 > Si 0.00000000 0.00000000 10.26000000 > Si 5.13000000 5.13000000 10.26000000 > Si 0.00000000 5.13000000 15.39000000 > Si 5.13000000 0.00000000 15.39000000 > Si 2.56500000 2.56500000 12.82500000 > Si 7.69500000 7.69500000 12.82500000 > Si 7.69500000 2.56500000 17.95500000 > Si 2.56500000 7.69500000 17.95500000 > Si 10.26000000 10.26000000 0.00000000 > Si 15.39000000 15.39000000 0.00000000 > Si 10.26000000 15.39000000 5.13000000 > Si 15.39000000 10.26000000 5.13000000 > Si 12.82500000 12.82500000 2.56500000 > Si 17.95500000 17.95500000 2.56500000 > Si 17.95500000 12.82500000 7.69500000 > Si 12.82500000 17.95500000 7.69500000 > Si 10.26000000 0.00000000 10.26000000 > Si 15.39000000 5.13000000 10.26000000 > Si 10.26000000 5.13000000 15.39000000 > Si 15.39000000 0.00000000 15.39000000 > Si 12.82500000 2.56500000 12.82500000 > Si 17.95500000 7.69500000 12.82500000 > Si 17.95500000 2.56500000 17.95500000 > Si 12.82500000 7.69500000 17.95500000 > Si 0.00000000 10.26000000 10.26000000 > Si 5.13000000 15.39000000 10.26000000 > Si 0.00000000 15.39000000 15.39000000 > Si 5.13000000 10.26000000 15.39000000 > Si 2.56500000 12.82500000 12.82500000 > Si 7.69500000 17.95500000 12.82500000 > Si 7.69500000 12.82500000 17.95500000 > Si 2.56500000 17.95500000 17.95500000 > Si 10.26000000 10.26000000 10.26000000 > Si 15.39000000 15.39000000 10.26000000 > Si 10.26000000 15.39000000 15.39000000 > Si 15.39000000 10.26000000 15.39000000 > Si 12.82500000 12.82500000 12.82500000 > Si 17.95500000 17.95500000 12.82500000 > Si 17.95500000 12.82500000 17.95500000 > Si 12.82500000 17.95500000 17.95500000 > K_POINTS > 1 > 0.0 0.0 0.0 1.0 > > ##END OF INPUT > > The above file runs when nbnd = 1280 , and (possibly) relevant output from > the > successful run includes: > > (Each subspace H/S matrix 400.00 Mb ( 5120,5120) > > ## Technical specs: Code was compiled on a Cray XT4 (unsure if > compilation details > would be helpful), and runs were performed on Cray XT4 nodes with two > quad-core 2.3 > GHz AMD Opteron processors with 16 GBytes of usable memory (requesting 4 > cores per > node). > > I've read here that the problem might be related to libraries/compilers > (issues with > PGI, ACML, etcetera)...if that is likely the case, I would be interested > in insight > regarding optimal compilation on Cray. > > Thanks in advance for any assistance, and I apologize if this question has > essentially already been answered on the forum - I searched but did not > come across > an explicit solution to something matching this, though admit that the > general theme > is present in several independent threads. > > Joseph Turnbull > Department of Physics > NC State University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From brad.malone at gmail.com Tue Dec 1 22:58:46 2009 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 1 Dec 2009 13:58:46 -0800 Subject: [Pw_forum] [Fwd: diagonalization failure (david, cg) for large numbers of bands] Message-ID: Joseph, I've never tried computing quite that many bands (only gone up to about 1200 bands) or with that many atoms per cell. However, I've never not been able to get the bands to converge using both 'cg' diagonalization and also with increasing the cutoff. You mentioned that you have tried increasing the cutoff, but perhaps you haven't gone high enough? Here is a quote from Paolo that might be relevant in your situation: the algorithm used in PWscf is based on the assumption that > the number of Kohn-Sham states (aka bands) is much smaller > than the number of basis functions (i.e. plane waves). If this > assumption doesn't hold (and it doesn't if you calculate 500 > bands in fcc Si unless you use a very large cutoff) you may > run into trouble. Moreover iterative diagonalization becomes > slower and more memory-consuming than conventional > diagonalization. If you really need to do that, you need to > modify the code > > Best, Brad Malone UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091201/4a3b1540/attachment.htm From ynwuyang at gmail.com Wed Dec 2 00:45:37 2009 From: ynwuyang at gmail.com (yuning wu) Date: Tue, 01 Dec 2009 18:45:37 -0500 Subject: [Pw_forum] How to do virtual crystal approximation for paw pesudopotential? Message-ID: <4B15AAA1.6000302@gmail.com> Dear all, In virtual.f90, there is nothing about the PAW pesudopotential. I am curious why not add that part in. Is it hard in some way? Best, Yuning Wu From m.abbasnejad at gmail.com Wed Dec 2 09:41:35 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 2 Dec 2009 00:41:35 -0800 Subject: [Pw_forum] Born effective charge Message-ID: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> Hi, Trying to calculate the born effective charges of my case, I get NAN. The structure has been relaxed carefully. What may cause the problem? Thanks for any comment. Yours, M. Abbasnejad University of Tehran -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091202/f8978602/attachment.htm From paulatto at sissa.it Wed Dec 2 09:50:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 02 Dec 2009 09:50:11 +0100 Subject: [Pw_forum] How to do virtual crystal approximation for paw pesudopotential? In-Reply-To: <4B15AAA1.6000302@gmail.com> References: <4B15AAA1.6000302@gmail.com> Message-ID: Replying to message "[Pw_forum] How to do virtual crystal approximation for paw pesudopotential?" from yuning wu (02/12/09): > In virtual.f90, there is nothing about the PAW pesudopotential. I am > curious why not add that part in. Is it hard in some way? Dear Yuning Wu, virtual+paw is just not implemented. It shouldn't be too hard to implement, but you either have to do it yourself or wait for someone else to need it. If you are going to do it, feel free to ask me if you need some detail on the inner mechanisms of the code. 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 jhouska at kfy.zcu.cz Wed Dec 2 11:26:30 2009 From: jhouska at kfy.zcu.cz (Jiri Houska) Date: Wed, 02 Dec 2009 11:26:30 +0100 Subject: [Pw_forum] Partial temperatures Message-ID: <20091202112630.hjjn6k0mgow0cksk@webmail.zcu.cz> Hello, please let me have one more question on cp.x. I noticed that when running a MD run (starting with zero velocities and far-from-equilibrium amorphous structure) using cp.x and nose thermostats, there are VERY different partial temperatures for individual kinds of atoms. This happens even when using an individual thermostat for each atom kind (nhptyp = 1). Please is there a known reason for that? Total temperature as well as nose controlling of energy of electrons are OK. Thanks a lot! Jiri Houska Department of Physics University of West Bohemia From jwan at phy.cuhk.edu.hk Wed Dec 2 12:21:37 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Wed, 2 Dec 2009 19:21:37 +0800 Subject: [Pw_forum] dipole-dipole contribution in hyperfine calculation Message-ID: Dear GIPAW/PWSCF users, I'm testing the hyperfine calculation with gipaw via calculating the HF tensor of a bare C atom (occupation: 3 spin-up and 1 spin-down). I expect the dipole-diplole interaction should be non-zero (due to the 2 spin-up 2p-orbitals. However, I found that the dipole part is vanishing. Regards, Jones ******************************** HFI ******************************** C 1: g_n = 1.404823 MHz C 1 hfi_dipole 0.000000 0.000000 0.000000 C 1 hfi_dipole 0.000000 0.000000 0.000000 C 1 hfi_dipole 0.000000 0.000000 0.000000 C 1 hfi_dipole 0.000000 0.000000 0.000000 Fermi contact term: bare reconstruction total 0.000000 264.230322 264.230322 **** ZORA **** 0.000000 261.557210 261.557210 From cyrille.barreteau at cea.fr Wed Dec 2 14:19:44 2009 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Wed, 02 Dec 2009 14:19:44 +0100 Subject: [Pw_forum] question about constrained magnetization In-Reply-To: <1257860762.11470.15.camel@alex-laptop> References: <1257860762.11470.15.camel@alex-laptop> Message-ID: <4B166970.70407@cea.fr> Dear all, I want to perform a calculation using the penalization technique. In an unconstrained scf calculation the input_magnetization(i) (i=1,ntyp) variable contains the m/n initial value of atom of type i, and this quantity should obviously belong to [-1,1] interval. To perform a constrained magnetization of "atomic type" I have to set the variable constrained_magnetization='atomic' and the magnetization will be the one given by input_magnetization(i). Therefore now input_magnetization(i) is no longer m/n but m only. However it seems that the range of input_magnetization has not been modified and is still within [-1,1] interval. If ever I set input_magnetization(i)>1 then the code automatically replace it by 1 and I cannot explore values larger than 1. Is there a way to circumvent this problem? For clarity I have added below a simple example illustrating my problem. thanks in advance.. cyrille -- ================================================================== 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 ================================================================== ===============INPUT============= &control calculation = 'scf' restart_mode='from_scratch', prefix='chromium', tstress = .true. tprnfor = .true. pseudo_dir = '/home/phabibi/SOFTWARE/espresso-4.1.1/pseudo/', outdir='/home/phabibi/tmp/' / &system ibrav= 1, celldm(1) =5.44, nat= 2, ntyp= 2, nspin = 2, constrained_magnetization=atomic, lambda=5.0, starting_magnetization(1)=1.6,starting_magnetization(2)=-1.6, ecutwfc =40,ecutrho = 300, occupations='smearing',smearing='mp',degauss=0.005 / &electrons diagonalization='cg' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Cr1 51.9961 Cr-gpbe-n-campos.uspp.UPF Cr2 51.9961 Cr-gpbe-n-campos.uspp.UPF ATOMIC_POSITIONS Cr1 0.00 0.00 0.00 Cr2 0.50 0.50 0.50 K_POINTS automatic 10 10 10 0 0 0 ================================== ===============OUTPUT============= Program PWSCF v.4.1 starts ... Today is 2Dec2009 at 14:38:45 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... Generating pointlists ... new r_m : 0.3572 bravais-lattice index = 1 lattice parameter (a_0) = 5.4400 a.u. unit-cell volume = 160.9892 (a.u.)3 number of atoms/cell = 2 number of atomic types = 2 number of electrons = 12.00 number of Kohn-Sham states= 10 kinetic-energy cutoff = 40.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-08 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) celldm(1)= 5.440000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 1.000000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.000000 0.000000 ) b(2) = ( 0.000000 1.000000 0.000000 ) b(3) = ( 0.000000 0.000000 1.000000 ) PseudoPot. # 1 for Cr read from file Cr-gpbe-n-campos.uspp.UPF Pseudo is Ultrasoft + core correction, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 857 points, 3 beta functions with: l(1) = 0 l(2) = 1 l(3) = 2 Q(r) pseudized with 6 coefficients, rinner = 1.300 1.300 1.300 1.300 1.300 PseudoPot. # 2 for Cr read from file Cr-gpbe-n-campos.uspp.UPF Pseudo is Ultrasoft + core correction, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 857 points, 3 beta functions with: l(1) = 0 l(2) = 1 l(3) = 2 Q(r) pseudized with 6 coefficients, rinner = 1.300 1.300 1.300 1.300 1.300 atomic species valence mass pseudopotential Cr1 6.00 51.99610 Cr( 1.00) Cr2 6.00 51.99610 Cr( 1.00) Starting magnetic structure atomic species magnetization Cr1 1.000 Cr2 -1.000 ================================== From gregor.mali at ki.si Wed Dec 2 15:34:32 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Wed, 2 Dec 2009 15:34:32 +0100 Subject: [Pw_forum] NC PP without GIPAW reconstruction part In-Reply-To: <4B0AC7B2.7070501@mit.edu> References: <4B0AC7B2.7070501@mit.edu> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256016CC2A2@postar.ki.si> Dear PWscf/GIPAW users, I am trying to calculate hyperfine coupling on Li nuclei in La4LiMnO8 with GIPAW module (job='hyperfine'). For La I do not have a norm-conserving pseudopotential with GIPAW reconstruction part. This absence of the GIPAW related part in La....UPF file seems to cause GIPAW to abort calculation. I wonder if there is a way to circumvent the problem, i.e. to perform calculation of hyperfine coupling anyway (without calculating the coupling on La, of course). Thank you very much for your help. Gregor Mali Gregor Mali National Institute of Chemistry Ljubljana Slovenia From sclauzer at sissa.it Wed Dec 2 16:16:09 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 02 Dec 2009 16:16:09 +0100 Subject: [Pw_forum] question about constrained magnetization In-Reply-To: <4B166970.70407@cea.fr> References: <1257860762.11470.15.camel@alex-laptop> <4B166970.70407@cea.fr> Message-ID: <4B1684B9.4090502@sissa.it> Dear Cyrille, Cyrille Barreteau wrote: > Dear all, > > I want to perform a calculation using the penalization technique. > In an unconstrained scf calculation the input_magnetization(i) (i=1,ntyp) > variable contains the m/n initial value of atom of type i, and this > quantity should > obviously belong to [-1,1] interval. > To perform a constrained magnetization of "atomic type" I have to > set the variable constrained_magnetization='atomic' and the magnetization > will be the one given by input_magnetization(i). > Therefore now input_magnetization(i) is no longer m/n but m only. > However it seems that the range of input_magnetization has not been > modified and is still within [-1,1] interval. > If ever I set input_magnetization(i)>1 then the code automatically > replace it by 1 and I cannot explore values larger than 1. I see your problem, thanks for pointing it out. I think that as a quick fix you can try to substitute the following line in PW/add_bfield.f90 m2(1:npol,na) = m_loc(1:npol,na) - mcons(1:npol,nt) with m2(1:npol,na) = m_loc(1:npol,na) - mcons(1:npol,nt)*r_loc(na) and recompile. In the CVS version it should be line 67 of the file, just after IF (i_cons==1) THEN ! i_cons = 1 means that the npol components of the magnetization ! are constrained, they are given in the input-file Please let me know if it works. Regards, GS > > Is there a way to circumvent this problem? > For clarity I have added below a simple example illustrating my problem. > thanks in advance.. > > cyrille > -- 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 Wed Dec 2 19:48:00 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 2 Dec 2009 19:48:00 +0100 Subject: [Pw_forum] Born effective charge In-Reply-To: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> References: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> Message-ID: <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> How can we know if you do not provide any details on your input files? SB On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad wrote: > Hi, > > Trying to calculate the born effective charges of my case, I get NAN. The structure has been relaxed carefully. > What may cause the problem? > Thanks for any comment. > > Yours, > M. Abbasnejad > University of Tehran > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > 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/20091202/8cc97332/attachment-0001.htm From m.abbasnejad at gmail.com Wed Dec 2 20:23:32 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 2 Dec 2009 22:53:32 +0330 Subject: [Pw_forum] Born effective charge In-Reply-To: <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> References: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> Message-ID: <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> Dear Prof. Baroni, You are completely right. Here are the input files for Phonon calculation as an attachment. Yours, M. Abbasnejad On Wed, Dec 2, 2009 at 10:18 PM, Stefano Baroni wrote: > How can we know if you do not provide any details on your input files? SB > > On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad wrote: > > Hi, > > Trying to calculate the born effective charges of my case, I get NAN. The > structure has been relaxed carefully. > What may cause the problem? > Thanks for any comment. > > Yours, > M. Abbasnejad > University of Tehran > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > 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 > > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091202/d6cbb623/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: ph.in Type: application/octet-stream Size: 260 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091202/d6cbb623/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: test.in Type: application/octet-stream Size: 933 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091202/d6cbb623/attachment-0001.obj From masoud.aryanpour at gmail.com Thu Dec 3 00:03:04 2009 From: masoud.aryanpour at gmail.com (Masoud Aryanpour) Date: Wed, 2 Dec 2009 18:03:04 -0500 Subject: [Pw_forum] DFT+U: input for resp_mat.f90 Message-ID: Dear PW forum, I am following the presentations and exercises of Summer School in Santa Barbara for the calculation of parameter U. For the NiO example, all the calculations for the linear response of the system were finished normally. Next step: ./grepalfa_nio_r16 extracts and stores occupations versus the perturbations without any error. The final step, which is using program r.x to compute U fails: ./r.x < resp_mat.in leads to a crash. As the first guess the problem might be with the input file resp_mat.in(copied below). So I am wondering if there is any related document other than "Handson_ldau.pdf" , or link, or help file that explains the keywords used. Thanks in advance, Masoud Aryanpour Department of Geosciences Penn State University =============== resp_mat.in &input_mat ntyp = 2 na(1) = 8 na(2) = 8 nalfa = 5 magn = .true. filepos = 'pos_nio_r16' back = 'no' filednda = 'file.nio.r16' n1 = 5 n2 = 5 n3 = 5 &end -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091202/c2ed7af9/attachment.htm From quantumdft at gmail.com Thu Dec 3 02:11:37 2009 From: quantumdft at gmail.com (vega lew) Date: Thu, 3 Dec 2009 09:11:37 +0800 Subject: [Pw_forum] one more question about energy conservation Message-ID: <412f6c680912021711g67f51089wb0d1f4ce6dd5fcf5@mail.gmail.com> Dear all, It is said that the total energy and constant of motion should be conserved in the NVE process before temperature added. But during thousands of NVE steps, the total energy and Constant of motion is still changing in a small range. For example, from 2100 step to 5400 step, the Constant of motion is in range of -4369.53196 and -4369.53200; Meanwhile the total energy is changing in range of -4369.55203 and -4369.54708; Temperature is in range of 37 to 51. Show I think the NVE calculation is running very well and I could further add some temperature using nose thermostat? best vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091203/fac7a66d/attachment.htm From eyvaz_isaev at yahoo.com Thu Dec 3 03:54:14 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 2 Dec 2009 18:54:14 -0800 (PST) Subject: [Pw_forum] Born effective charge In-Reply-To: <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> Message-ID: <794789.57550.qm@web65703.mail.ac4.yahoo.com> Dear Mohaddeseh, Well, let us calculate total number of valence electrons for TiO2: 12+2*6=24, thus, total number of completely filled bands is 24/2=12, not 16, if CaF2-type TiO2 is semiconducting (as I can see from my 3-years old calculations, indeed, it is semiconducting). So, you included several conduction bands in your calculations that caused NAN (not NaN, pay attention). ecutwfc seems to be high, and ecutrho seems to be extremely large. Usually (for US-type PsP) ecutwfc 30-35 (Ry), rarely 40Ry, and ecutrho = (8 - 12) x ecutwfc. Though, you can perform some tests for yourself to find reliable ecutwfc and ecutrho. CaF2-type TiO2 is quite unstable phase (at least at T=0K) even up to quite high pressure range, if you like to know. 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 Wed, 12/2/09, mohaddeseh abbasnejad wrote: > From: mohaddeseh abbasnejad > Subject: Re: [Pw_forum] Born effective charge > To: "PWSCF Forum" > Date: Wednesday, December 2, 2009, 10:23 PM > Dear Prof. Baroni, > ? > You are completely right. > Here are the input files for Phonon calculation as an > attachment. > Yours, > M. Abbasnejad > ? > > > ? > On Wed, Dec 2, 2009 at 10:18 PM, > Stefano Baroni > wrote: > > > How can we know if you > do not provide any details on your input files? SB > > > > > > > On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad > wrote: > > > > > > Hi, > ? > Trying to calculate the born effective charges of my > case, I get NAN. The structure has been relaxed > carefully.. > What may cause the problem? > Thanks for any comment. > ? > Yours, > M. Abbasnejad > University of Tehran > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > > Tehran, P.O. Box: 14395-547- IRAN > Tel. No..: +98 21 6111 8634 ?& Fax No.: +98 21 8800 > 4781 > Cellphone: +989177317514 > E-Mail: ? ? m.abbasnejad at gmail.com > > Website: ?http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > > 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 > > > > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 ?& Fax No.: +98 21 8800 > 4781 > Cellphone: +989177317514 > E-Mail: ? ? m.abbasnejad at gmail.com > Website: ?http://physics.ut.ac.ir > > > --------------------------------------------------------- > > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mohnish.iitk at gmail.com Thu Dec 3 05:01:21 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 3 Dec 2009 09:31:21 +0530 Subject: [Pw_forum] surface energy convergence for thin films Message-ID: Dear users! I am calculating the energy of gallium nitride thin films of thickness of 1-10 layers. I am giving 'nstep' equal to 200 but the output file is not showing any message of convergence. The program is just completing the 200 iterations. I have played with all the parameters like 'mixing', 'smearing', etc. I am pasting the input file for 9 layer calculation. Can anybody please point out my mistake and get me out of it. Sincere Thanks in advance. &control calculation = 'vc-relax', restart_mode='restart', nstep=200, outdir='/home/rajpala/Desktop/wurtzite9', pseudo_dir='/home/rajpala/Desktop/wurtzite9' prefix='gan', tstress = .true., tprnfor = .true., / &system nosym =.TRUE.,ibrav= 4, a = 3.1427, c = 45,nat= 18, ntyp= 2, ecutwfc = 25,occupations='smearing',degauss=.02,smearing='m-v' / &electrons diagonalization='david' mixing_mode = 'local-TF' mixing_beta = 0.1 electron_maxstep=200 conv_thr = 1.0d-6 / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics='damp-w' / ATOMIC_SPECIES Ga 69.723 Ga.pbe-nsp-van.UPF N 14.0067 N.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Ga 0.33333333 0.66666666 0.0577 Ga 0.33333333 0.66666666 0.17327 Ga 0.00 0.00 0.1154 Ga 0.00 0.00 0.23105 Ga 0.33333333 0.66666666 0.288 Ga 0.00 0.00 0.3459 Ga 0.33333333 0.66666666 0.4045 Ga 0.00 0.00 0.4623 Ga 0.33333333 0.66666666 0.5206 N 0.0 0.0 0.0398 N 0.0 0.0 0.1553 N 0.33333333 0.66666666 0.0957 N 0.33333333 0.66666666 0.2130 N 0.0 0.0 0.2708 N 0.33333333 0.66666666 0.3279 N 0.0 0.0 0.3873 N 0.33333333 0.66666666 0.4443 N 0.0 0.0 0.5035 K_POINTS (automatic) 6 6 1 0 0 0 -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/f10cff5e/attachment-0001.htm From sclauzer at sissa.it Thu Dec 3 09:38:52 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 03 Dec 2009 09:38:52 +0100 Subject: [Pw_forum] surface energy convergence for thin films In-Reply-To: References: Message-ID: <4B17791C.3020707@sissa.it> mohnish pandey wrote: > Dear users! > I am calculating the energy of gallium nitride thin > films of thickness of 1-10 layers. I am giving 'nstep' equal to 200 but > the output file is not showing any message of convergence. The program > is just completing the 200 iterations. I have played with all the Iterations in the electronic self-consistent loop or iterations (displacements) in the ionic trajectory? Be careful that nstep refers to the latter, while electron_maxstep to the former. I suppose you are speaking of the electronic convergence. > parameters like 'mixing', 'smearing', etc. I am pasting the input file > for 9 layer calculation. Can anybody please point out my mistake and Have you tried to converge (in a scf run) the respective bulk phases before starting a complicated calculation in a complicated geometry? It' always better start with simple things and understand them before moving to more complicated (=interesting) cases. In you input file I see some problems: 1.Since you are using ultrasoft, you need to specify a meaningful value of ecutrho. Maybe you also need to increase ecutwfc. 2.Have you tried to visualize your structure (for instance with xcrysden) to see if all atoms are in the right place? 3.Why do you remove symmetry? It usually helps convergence GS > get me out of it. > Sincere Thanks in advance. > > > &control > calculation = 'vc-relax', > restart_mode='restart', > nstep=200, > outdir='/home/rajpala/Desktop/wurtzite9', > pseudo_dir='/home/rajpala/Desktop/wurtzite9' > prefix='gan', > tstress = .true., > tprnfor = .true., > / > &system > nosym =.TRUE.,ibrav= 4, a = 3.1427, c = 45,nat= 18, ntyp= 2, > ecutwfc = 25,occupations='smearing',degauss=.02,smearing='m-v' > / > &electrons > diagonalization='david' > mixing_mode = 'local-TF' > mixing_beta = 0.1 > electron_maxstep=200 > conv_thr = 1.0d-6 > / > &IONS > ion_dynamics='bfgs' > / > &CELL > cell_dynamics='damp-w' > / > ATOMIC_SPECIES > Ga 69.723 Ga.pbe-nsp-van.UPF > N 14.0067 N.pbe-rrkjus.UPF > ATOMIC_POSITIONS (crystal) > Ga 0.33333333 0.66666666 0.0577 > Ga 0.33333333 0.66666666 0.17327 > Ga 0.00 0.00 0.1154 > Ga 0.00 0.00 0.23105 > Ga 0.33333333 0.66666666 0.288 > Ga 0.00 0.00 0.3459 > Ga 0.33333333 0.66666666 0.4045 > Ga 0.00 0.00 0.4623 > Ga 0.33333333 0.66666666 0.5206 > N 0.0 0.0 0.0398 > N 0.0 0.0 0.1553 > N 0.33333333 0.66666666 0.0957 > N 0.33333333 0.66666666 0.2130 > N 0.0 0.0 0.2708 > N 0.33333333 0.66666666 0.3279 > N 0.0 0.0 0.3873 > N 0.33333333 0.66666666 0.4443 > N 0.0 0.0 0.5035 > K_POINTS (automatic) > 6 6 1 0 0 0 > > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Dec 3 09:43:48 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 03 Dec 2009 09:43:48 +0100 Subject: [Pw_forum] DFT+U: input for resp_mat.f90 In-Reply-To: References: Message-ID: <4B177A44.5000103@sissa.it> Masoud Aryanpour wrote: > Dear PW forum, > > I am following the presentations and exercises of Summer School in Santa > Barbara for the calculation of parameter U. > For the NiO example, all the calculations for the linear response of the > system were finished normally. > > Next step: ./grepalfa_nio_r16 extracts and stores occupations versus > the perturbations without any error. > > The final step, which is using program r.x to compute U fails: ./r.x < > resp_mat.in leads to a crash. Why does it crashes? Please try to recompile the code with some debugging options (for instance "-g -traceback -check all" with ifort) or some additional write statement to understand where the code crashes. > > As the first guess the problem might be with the input file resp_mat.in > (copied below). So I am wondering if there is any > related document other than "Handson_ldau.pdf" , or link, or help file > that explains the keywords used. Yes, the code itself... (resp_mat.f90) GS > > Thanks in advance, > Masoud Aryanpour > > Department of Geosciences > Penn State University > > > =============== resp_mat.in > &input_mat > ntyp = 2 > na(1) = 8 > na(2) = 8 > nalfa = 5 > magn = .true. > filepos = 'pos_nio_r16' > back = 'no' > filednda = 'file.nio.r16' > n1 = 5 > n2 = 5 > n3 = 5 > &end > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 dalcorso at sissa.it Thu Dec 3 10:16:30 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 03 Dec 2009 10:16:30 +0100 Subject: [Pw_forum] Born effective charge In-Reply-To: <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> References: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> Message-ID: <1259831790.3252.5.camel@dhcp-5-36.sissa.it> On Wed, 2009-12-02 at 22:53 +0330, mohaddeseh abbasnejad wrote: > Dear Prof. Baroni, > > You are completely right. > Here are the input files for Phonon calculation as an attachment. > Yours, > M. Abbasnejad > > Which version of QE are you using? I am not able to reproduce your problem on my PC. Andrea > > > On Wed, Dec 2, 2009 at 10:18 PM, Stefano Baroni > wrote: > How can we know if you do not provide any details on your > input files? SB > > > On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad wrote: > > > > > > Hi, > > > > Trying to calculate the born effective charges of my case, I > > get NAN. The structure has been relaxed carefully. > > What may cause the problem? > > Thanks for any comment. > > > > Yours, > > M. Abbasnejad > > University of Tehran > > > > -- > > --------------------------------------------------------- > > > > Mohaddeseh Abbasnejad, > > Room No. 323, Department of Physics, > > University of Tehran, North Karegar Ave., > > Tehran, P.O. Box: 14395-547- IRAN > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > > Cellphone: +989177317514 > > E-Mail: m.abbasnejad at gmail.com > > Website: http://physics.ut.ac.ir > > > > --------------------------------------------------------- > > > > > > _______________________________________________ > > 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 > > > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > 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 m.abbasnejad at gmail.com Thu Dec 3 10:25:26 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 3 Dec 2009 12:55:26 +0330 Subject: [Pw_forum] Born effective charge In-Reply-To: <1259831790.3252.5.camel@dhcp-5-36.sissa.it> References: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> <1259831790.3252.5.camel@dhcp-5-36.sissa.it> Message-ID: <7699a1950912030125t5b75363ena7e9387d4d6a10c1@mail.gmail.com> Dear Andrea, I am using version 4.1 of QE. Yours, M. Abbasnejad On Thu, Dec 3, 2009 at 12:46 PM, Dal Corso Andrea wrote: > On Wed, 2009-12-02 at 22:53 +0330, mohaddeseh abbasnejad wrote: > > Dear Prof. Baroni, > > > > You are completely right. > > Here are the input files for Phonon calculation as an attachment. > > Yours, > > M. Abbasnejad > > > > > Which version of QE are you using? I am not able to reproduce your > problem on my PC. > > > Andrea > > > > > > > > > On Wed, Dec 2, 2009 at 10:18 PM, Stefano Baroni > > wrote: > > How can we know if you do not provide any details on your > > input files? SB > > > > > > On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad wrote: > > > > > > > > > > Hi, > > > > > > Trying to calculate the born effective charges of my case, I > > > get NAN. The structure has been relaxed carefully. > > > What may cause the problem? > > > Thanks for any comment. > > > > > > Yours, > > > M. Abbasnejad > > > University of Tehran > > > > > > -- > > > --------------------------------------------------------- > > > > > > Mohaddeseh Abbasnejad, > > > Room No. 323, Department of Physics, > > > University of Tehran, North Karegar Ave., > > > Tehran, P.O. Box: 14395-547- IRAN > > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > > > Cellphone: +989177317514 > > > E-Mail: m.abbasnejad at gmail.com > > > Website: http://physics.ut.ac.ir > > > > > > --------------------------------------------------------- > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > -- > > --------------------------------------------------------- > > > > Mohaddeseh Abbasnejad, > > Room No. 323, Department of Physics, > > University of Tehran, North Karegar Ave., > > Tehran, P.O. Box: 14395-547- IRAN > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > > Cellphone: +989177317514 > > E-Mail: m.abbasnejad at gmail.com > > Website: http://physics.ut.ac.ir > > > > --------------------------------------------------------- > > > > _______________________________________________ > > 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 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/61bba69d/attachment.htm From gregor.mali at ki.si Thu Dec 3 10:51:24 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Thu, 3 Dec 2009 10:51:24 +0100 Subject: [Pw_forum] output of g_tensor in GIPAW In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256016CC2A2@postar.ki.si> References: <4B0AC7B2.7070501@mit.edu> <8C0B47760A05FB4AB504C9BCAD32D256016CC2A2@postar.ki.si> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256016CC34C@postar.ki.si> Dear PWscf/GIPAW users, does anybody know, what are the units and what is the actaul physical quantity, which is given as the output of the DFT/GIPAW calculation (job='g_tensor') and is named 'Delta g - total'? The tensor, that I've got as a result, has very large eigenvalues (on the order of 10^5). So either something is wrong with my calculations or the 'Delta g' tensor is not simply g-2.000, what I thought it would be. I also wonder in which coordinate system the tensor is expressed. Is this the same coordinate system as the one in which the dipolar-coupling tensor of 'hyperfine interaction calculation' is given? Thank you very much for your help. Gregor Mali Gregor Mali National Institute of Chemistry Ljubljana Slovenia From dalcorso at sissa.it Thu Dec 3 11:38:20 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 03 Dec 2009 11:38:20 +0100 Subject: [Pw_forum] Born effective charge In-Reply-To: <7699a1950912030125t5b75363ena7e9387d4d6a10c1@mail.gmail.com> References: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> <1259831790.3252.5.camel@dhcp-5-36.sissa.it> <7699a1950912030125t5b75363ena7e9387d4d6a10c1@mail.gmail.com> Message-ID: <1259836700.3252.11.camel@dhcp-5-36.sissa.it> On Thu, 2009-12-03 at 12:55 +0330, mohaddeseh abbasnejad wrote: > Dear Andrea, > > I am using version 4.1 of QE. 4.1 is working on my PC with one or two processors with one or two pools. It seems a problem of your system/ compiler / libraries. Did you check the examples? Do they work? Andrea > > Yours, > M. Abbasnejad > > > On Thu, Dec 3, 2009 at 12:46 PM, Dal Corso Andrea > wrote: > On Wed, 2009-12-02 at 22:53 +0330, mohaddeseh abbasnejad > wrote: > > Dear Prof. Baroni, > > > > You are completely right. > > Here are the input files for Phonon calculation as an > attachment. > > Yours, > > M. Abbasnejad > > > > > > Which version of QE are you using? I am not able to reproduce > your > problem on my PC. > > > Andrea > > > > > > > > > > On Wed, Dec 2, 2009 at 10:18 PM, Stefano Baroni > > > wrote: > > How can we know if you do not provide any details on > your > > input files? SB > > > > > > On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad > wrote: > > > > > > > > > > Hi, > > > > > > Trying to calculate the born effective charges of > my case, I > > > get NAN. The structure has been relaxed carefully. > > > What may cause the problem? > > > Thanks for any comment. > > > > > > Yours, > > > M. Abbasnejad > > > University of Tehran > > > > > > -- > > > > --------------------------------------------------------- > > > > > > Mohaddeseh Abbasnejad, > > > Room No. 323, Department of Physics, > > > University of Tehran, North Karegar Ave., > > > Tehran, P.O. Box: 14395-547- IRAN > > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 > 4781 > > > Cellphone: +989177317514 > > > E-Mail: m.abbasnejad at gmail.com > > > Website: http://physics.ut.ac.ir > > > > > > > --------------------------------------------------------- > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > -- > > --------------------------------------------------------- > > > > Mohaddeseh Abbasnejad, > > Room No. 323, Department of Physics, > > University of Tehran, North Karegar Ave., > > Tehran, P.O. Box: 14395-547- IRAN > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > > Cellphone: +989177317514 > > E-Mail: m.abbasnejad at gmail.com > > Website: http://physics.ut.ac.ir > > > > --------------------------------------------------------- > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > 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 Thu Dec 3 12:06:04 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 3 Dec 2009 03:06:04 -0800 (PST) Subject: [Pw_forum] short range coulomb interaction Message-ID: <872388.56282.qm@web112505.mail.gq1.yahoo.com> Hi Thanks for reply. But my problem is that I have 3D crystal( I can not use ee). I think that if I put my unit cell that is surrounded by vaccum in the middle of supercell, then I can separate the artifacts due to the interaction via periodic boundary conditions(remove the large range coloumb interaction). Then If the vaccum is big enough then I have a isolated cell that has a charge inside. my question is When I do charge calculation in isolated unit cell (separated by vaccumm), does the compensating charge distribut within whole cell or within isolated unit cell? Then, How can I identify the the interaction of charge and compensating backgroun(the short range part)? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/994af12e/attachment.htm From m.abbasnejad at gmail.com Thu Dec 3 12:08:01 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 3 Dec 2009 14:38:01 +0330 Subject: [Pw_forum] Born effective charge In-Reply-To: <1259836700.3252.11.camel@dhcp-5-36.sissa.it> References: <7699a1950912020041t6d1d87f3s49bcd9a18cfaf6b1@mail.gmail.com> <53599188-F2AB-460A-8BA1-39D6B9E89C12@sissa.it> <7699a1950912021123r1df7940fnac820612823dbdac@mail.gmail.com> <1259831790.3252.5.camel@dhcp-5-36.sissa.it> <7699a1950912030125t5b75363ena7e9387d4d6a10c1@mail.gmail.com> <1259836700.3252.11.camel@dhcp-5-36.sissa.it> Message-ID: <7699a1950912030308m5c65058x112e56f0050c271f@mail.gmail.com> Dear Andrea, I think you are right. Now I have checked it on another computer and it is working properly. and actually there is any problem with the input files. As you have mentioned, I think there might be some problems with the system. Thank you very much for your comment. Yours, M. Abbasnejad On Thu, Dec 3, 2009 at 2:08 PM, Dal Corso Andrea wrote: > On Thu, 2009-12-03 at 12:55 +0330, mohaddeseh abbasnejad wrote: > > Dear Andrea, > > > > I am using version 4.1 of QE. > > 4.1 is working on my PC with one or two processors with one or two > pools. It seems a problem of your system/ compiler / libraries. Did you > check the examples? Do they work? > > Andrea > > > > > > Yours, > > M. Abbasnejad > > > > > > On Thu, Dec 3, 2009 at 12:46 PM, Dal Corso Andrea > > wrote: > > On Wed, 2009-12-02 at 22:53 +0330, mohaddeseh abbasnejad > > wrote: > > > Dear Prof. Baroni, > > > > > > You are completely right. > > > Here are the input files for Phonon calculation as an > > attachment. > > > Yours, > > > M. Abbasnejad > > > > > > > > > > Which version of QE are you using? I am not able to reproduce > > your > > problem on my PC. > > > > > > Andrea > > > > > > > > > > > > > > > > > On Wed, Dec 2, 2009 at 10:18 PM, Stefano Baroni > > > > > wrote: > > > How can we know if you do not provide any details on > > your > > > input files? SB > > > > > > > > > On Dec 2, 2009, at 9:41 AM, mohaddeseh abbasnejad > > wrote: > > > > > > > > > > > > > > Hi, > > > > > > > > Trying to calculate the born effective charges of > > my case, I > > > > get NAN. The structure has been relaxed carefully. > > > > What may cause the problem? > > > > Thanks for any comment. > > > > > > > > Yours, > > > > M. Abbasnejad > > > > University of Tehran > > > > > > > > -- > > > > > > --------------------------------------------------------- > > > > > > > > Mohaddeseh Abbasnejad, > > > > Room No. 323, Department of Physics, > > > > University of Tehran, North Karegar Ave., > > > > Tehran, P.O. Box: 14395-547- IRAN > > > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 > > 4781 > > > > Cellphone: +989177317514 > > > > E-Mail: m.abbasnejad at gmail.com > > > > Website: http://physics.ut.ac.ir > > > > > > > > > > --------------------------------------------------------- > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > -- > > > --------------------------------------------------------- > > > > > > Mohaddeseh Abbasnejad, > > > Room No. 323, Department of Physics, > > > University of Tehran, North Karegar Ave., > > > Tehran, P.O. Box: 14395-547- IRAN > > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > > > Cellphone: +989177317514 > > > E-Mail: m.abbasnejad at gmail.com > > > Website: http://physics.ut.ac.ir > > > > > > --------------------------------------------------------- > > > > > > _______________________________________________ > > > 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 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > --------------------------------------------------------- > > > > Mohaddeseh Abbasnejad, > > Room No. 323, Department of Physics, > > University of Tehran, North Karegar Ave., > > Tehran, P.O. Box: 14395-547- IRAN > > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > > Cellphone: +989177317514 > > E-Mail: m.abbasnejad at gmail.com > > Website: http://physics.ut.ac.ir > > > > --------------------------------------------------------- > > > > _______________________________________________ > > 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 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/d2714d0c/attachment.htm From cyrille.barreteau at cea.fr Thu Dec 3 11:28:27 2009 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Thu, 03 Dec 2009 11:28:27 +0100 Subject: [Pw_forum] question about constrained magnetization In-Reply-To: <4B1684B9.4090502@sissa.it> References: <1257860762.11470.15.camel@alex-laptop> <4B166970.70407@cea.fr> <4B1684B9.4090502@sissa.it> Message-ID: <4B1792CB.1010709@cea.fr> Gabriele Sclauzero wrote: >Dear Cyrille, > >Cyrille Barreteau wrote: > > >>Dear all, >> >>I want to perform a calculation using the penalization technique. >>In an unconstrained scf calculation the input_magnetization(i) (i=1,ntyp) >>variable contains the m/n initial value of atom of type i, and this >>quantity should >>obviously belong to [-1,1] interval. >>To perform a constrained magnetization of "atomic type" I have to >>set the variable constrained_magnetization='atomic' and the magnetization >>will be the one given by input_magnetization(i). >>Therefore now input_magnetization(i) is no longer m/n but m only. >>However it seems that the range of input_magnetization has not been >>modified and is still within [-1,1] interval. >>If ever I set input_magnetization(i)>1 then the code automatically >>replace it by 1 and I cannot explore values larger than 1. >> >> > > > Dear Gabriele, With your quick fix now the input_magnetization is no longer the magnetization m but m/n as it is when there is no penalization. Therefore we avoid the problem due to the [-1,1] interval however this makes things a litlle "crooked" since the charge n is not precisely now (the charge inside the sphere does not integrate to the total charge per atom..). However with a little of mental gymnastic we can manage to obtain what we want:-) thanks cyrille -- ================================================================== 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 ================================================================== >I see your problem, thanks for pointing it out. I think that as a quick fix you can try to >substitute the following line in PW/add_bfield.f90 > > m2(1:npol,na) = m_loc(1:npol,na) - mcons(1:npol,nt) > >with > > m2(1:npol,na) = m_loc(1:npol,na) - mcons(1:npol,nt)*r_loc(na) > >and recompile. In the CVS version it should be line 67 of the file, just after > IF (i_cons==1) THEN > ! i_cons = 1 means that the npol components of the magnetization > ! are constrained, they are given in the input-file > >Please let me know if it works. > > >Regards, > >GS > > > > >>Is there a way to circumvent this problem? >>For clarity I have added below a simple example illustrating my problem. >>thanks in advance.. >> >> cyrille >> >> >> > > > From sclauzer at sissa.it Thu Dec 3 14:49:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 03 Dec 2009 14:49:47 +0100 Subject: [Pw_forum] question about constrained magnetization In-Reply-To: <4B1792CB.1010709@cea.fr> References: <1257860762.11470.15.camel@alex-laptop> <4B166970.70407@cea.fr> <4B1684B9.4090502@sissa.it> <4B1792CB.1010709@cea.fr> Message-ID: <4B17C1FB.3090105@sissa.it> Cyrille Barreteau wrote: > Gabriele Sclauzero wrote: > >> Dear Cyrille, >> >> Cyrille Barreteau wrote: >> >> >>> Dear all, >>> >>> I want to perform a calculation using the penalization technique. >>> In an unconstrained scf calculation the input_magnetization(i) (i=1,ntyp) >>> variable contains the m/n initial value of atom of type i, and this >>> quantity should >>> obviously belong to [-1,1] interval. >>> To perform a constrained magnetization of "atomic type" I have to >>> set the variable constrained_magnetization='atomic' and the magnetization >>> will be the one given by input_magnetization(i). >>> Therefore now input_magnetization(i) is no longer m/n but m only. >>> However it seems that the range of input_magnetization has not been >>> modified and is still within [-1,1] interval. >>> If ever I set input_magnetization(i)>1 then the code automatically >>> replace it by 1 and I cannot explore values larger than 1. >>> >>> >> >> > Dear Gabriele, > > With your quick fix now the input_magnetization is no longer the > magnetization m but m/n > as it is when there is no penalization. Therefore we avoid the problem > due to the [-1,1] interval > however this makes things a litlle "crooked" since the charge n is not > precisely now (the charge > inside the sphere does not integrate to the total charge per atom..). > However with a little of mental gymnastic we can manage to obtain what > we want:-) You are right, perhaps it is more practical to fix the magnetization (i.e. local magnetic moment) rather than the "atomic spin polarization". I think that the problem arises from the fact that the starting_magnetization keyword is used for two different things, which maybe should be called starting_spin_polarization for the unconstrained calculations and target_magnetization for constrained ones (of "atomic" type). Another quick fix that should meet your needs could be the following: let the PW/add_bfield.f90 subroutine as the original and in PW/input.f90 move the check on starting_magnetization DO nt = 1, ntyp ! IF ( starting_magnetization(nt) == sm_not_set ) THEN starting_magnetization(nt) = 0.0_dp ELSE IF ( starting_magnetization(nt) > 1.0_dp ) THEN starting_magnetization(nt) = 1.0_dp ELSE IF ( starting_magnetization(nt) <-1.0_dp ) THEN starting_magnetization(nt) =-1.0_dp END IF ! END DO AFTER the block of initialization of the magnetic contraints: SELECT CASE( TRIM( constrained_magnetization ) ) CASE( 'none' ) ! i_cons = 0 ! CASE( 'total' ) ! ... END SELECT Probably, the choice of the initial atomic spin polarization will not be the optimal one for a better convergence to the target magnetization. You can use this temporary solution until a more satisfactory implementation will be conceived and carried out. Thanks, Gabriele > > thanks > cyrille > -- 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 ceresoli at MIT.EDU Thu Dec 3 15:46:14 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Thu, 03 Dec 2009 09:46:14 -0500 Subject: [Pw_forum] output of g_tensor in GIPAW In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256016CC34C@postar.ki.si> References: <4B0AC7B2.7070501@mit.edu> <8C0B47760A05FB4AB504C9BCAD32D256016CC2A2@postar.ki.si> <8C0B47760A05FB4AB504C9BCAD32D256016CC34C@postar.ki.si> Message-ID: <4B17CF36.3000806@mit.edu> Gregor Mali wrote: > Dear PWscf/GIPAW users, > > does anybody know, what are the units and what is the actaul physical > quantity, which is given as the output of the DFT/GIPAW calculation > (job='g_tensor') and is named 'Delta g - total'? > > The tensor, that I've got as a result, has very large eigenvalues (on > the order of 10^5). So either something is wrong with my calculations or > the 'Delta g' tensor is not simply g-2.000, what I thought it would be. Hi Gregor, Delta_g_total is in ppm, that is: (g-2.0)*10^6. > I also wonder in which coordinate system the tensor is expressed. Is > this the same coordinate system as the one in which the dipolar-coupling > tensor of 'hyperfine interaction calculation' is given? It's all in Cartesian coordinates. > Thank you very much for your help. > > Gregor Mali Davide From mohnish.iitk at gmail.com Thu Dec 3 15:47:15 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 3 Dec 2009 20:17:15 +0530 Subject: [Pw_forum] confusion regarding parameter "press" and "press_conv_thr" in vc-relax calculation Message-ID: Dear users! I have subtle confusion between "press" and "press_conv_thr" . What does the Target pressure implies? And why we are using thee two parameters for pressure convergence. As in my case energy and force(=0.000) are converging but pressure is not converging so finally I am not achieving convergence with respect to ion dynamics. So pressure is creating a problem for me. Can anybody please help me out.? Thanks in advance. MOHNISH -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/dc10ed52/attachment.htm From degironc at sissa.it Thu Dec 3 15:57:27 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 03 Dec 2009 15:57:27 +0100 Subject: [Pw_forum] confusion regarding parameter "press" and "press_conv_thr" in vc-relax calculation In-Reply-To: References: Message-ID: <4B17D1D7.2030205@sissa.it> press is the external pressure you want to balance. press_conv_thr is the tolerance you accept to decide when to stop. (I think that the default is 0.5 kBar and should be ok) stefano mohnish pandey wrote: > Dear users! > I have subtle confusion between "press" and > "press_conv_thr" . What does the Target pressure implies? And why we > are using thee two parameters for pressure convergence. As in my case > energy and force(=0.000) are converging but pressure is not > converging so finally I am not achieving convergence with respect to > ion dynamics. So pressure is creating a problem for me. Can anybody > please help me out.? > > Thanks in advance. > MOHNISH > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From matteo at umn.edu Thu Dec 3 16:22:52 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 03 Dec 2009 09:22:52 -0600 Subject: [Pw_forum] DFT+U: input for resp_mat.f90 In-Reply-To: <4B177A44.5000103@sissa.it> References: <4B177A44.5000103@sissa.it> Message-ID: <4B17D7CC.5070003@umn.edu> dear Masoud, let me just add a brief explanation of the input below. > >> Thanks in advance, >> Masoud Aryanpour >> >> Department of Geosciences >> Penn State University >> >> >> =============== resp_mat.in >> &input_mat >> ntyp = 2 # of atomic types of which you are computing U >> na(1) = 8 # of atoms of type 1 etc >> na(2) = 8 >> nalfa = 5 >> magn = .true. # use this only if two atoms sit in crystallographically equivalent positions but have different magnetization: example the two kinds of Ni in NiO. in this case, in the pos_nio_r16 file you should specify (sign of) the magnetization after the crystalline coordinates of each atom: 1, -1 or 0 >> >> filepos = 'pos_nio_r16' # this file should contain the three unit cell vectors atomic crystal coordinates in the same order as decleared above (first type first, etc) >> back = 'no' # the response matrices are not constrained to have vanishing row or column sums >> filednda = 'file.nio.r16' # contains a list of file names containing n vs alpha for various atoms. of course the order of atoms must be compatible with the order of species as well >> n1 = 5 # size of the extrapolatin supercell >> n2 = 5 >> n3 = 5 >> &end >> please read PRB 71, 35105 regards, Matteo >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 xomiakk at gmail.com Thu Dec 3 17:03:54 2009 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Thu, 3 Dec 2009 22:03:54 +0600 Subject: [Pw_forum] PDOS Message-ID: Dear PWscf Users, I 've used projwfc.x post processing code to find the partial DOS. The second collunm of pdos_tot (dos(E)) agrees with the DOS obtained by dos.x PP , the third collumn (pdos(E)) is the sum of all ldos (from files like f.pdos_atm_4(C)_wfc_2(p)). I was confused to find discreapency of this values. What is the reason of such problem? I want to separate the contribution of pi and sigma from the DOS of my structure. What value of the total DOS should I use for comparison? Thank you, O.Sedelnikova -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/31b61a73/attachment.htm From sclauzer at sissa.it Thu Dec 3 17:21:54 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 03 Dec 2009 17:21:54 +0100 Subject: [Pw_forum] PDOS In-Reply-To: References: Message-ID: <4B17E5A2.7090404@sissa.it> Dear Olga, Olga Sedelnikova wrote: > Dear PWscf Users, > > I 've used projwfc.x post processing code to find the partial DOS. The > second collunm of pdos_tot (dos(E)) agrees with the DOS > obtained by dos.x PP , the third collumn (pdos(E)) is the sum of all > ldos (from files like f.pdos_atm_4(C)_wfc_2(p)). I was confused to find > discreapency of this values. Why do you expect that the sum of all PDOS should coincide with the DOS? They are not the same quantity. I expect them to be very different well above the Fermi energy. > What is the reason of such problem? It is not really a problem: it depends on the fact that PWs become a complete basis set in the solid as you increase the cutoff, while a set of plain atomic orbitals (as computed from an atomic calculation) aren't. > > I want to separate the contribution of pi and sigma from the DOS of my > structure. > What value of the total DOS should I use for comparison? I think you should use the summed PDOS, since you need the individual PDOSs to separate the pi and sigma contributions. As a drawback you will find that there will be some charge missing (try to sum the PDOS of the atoms in an isolated molecule for instance: the sum of all PDOSs may not give a integer number of electrons). Another method could be to separate KS eigenstates by symmetry (if this can distinguish pi from sigma: in an isolated molecule it could) and integrate the charges separately. This however requires some coding or simply some more hassle if you can manage to do it by using postprocessing subroutines (bands.x to identify symmetry, pp.x to plot charges densities and the sum up those with the same symmetry,...), and it seems feasible only for simple geometries. Regards GS > > Thank you, > O.Sedelnikova > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 uccaati at ucl.ac.uk Thu Dec 3 19:16:13 2009 From: uccaati at ucl.ac.uk (Antonio Tilocca) Date: Thu, 3 Dec 2009 18:16:13 +0000 (GMT) Subject: [Pw_forum] Partial temperatures Message-ID: Hi Jiri, I would not worry too much about having different partial temperatures in the initial stages of the CP run, especially if started from a non-optimized configuration, where some species might be farther away from equilibrium than others, and thus will move faster at the beginning. The partial temperatures will (should) eventually become closer to each other and to the target temperature in the equilibrated sample. Antonio Tilocca UCL > 3. Partial temperatures (Jiri Houska) >Hello, >please let me have one more question on cp.x. I noticed that when >running a MD run (starting with zero velocities and >far-from-equilibrium amorphous structure) using cp.x and nose >thermostats, there are VERY different partial temperatures for >individual kinds of atoms. This happens even when using an individual >thermostat for each atom kind (nhptyp = 1). Please is there a known >reason for that? Total temperature as well as nose controlling of >energy of electrons are OK. >Thanks a lot! >Jiri Houska >Department of Physics >University of West Bohemia From ismotochi at gmail.com Thu Dec 3 19:46:41 2009 From: ismotochi at gmail.com (isaac motochi) Date: Thu, 3 Dec 2009 21:46:41 +0300 Subject: [Pw_forum] PDOS In-Reply-To: <4B17E5A2.7090404@sissa.it> References: <4B17E5A2.7090404@sissa.it> Message-ID: <9d6ea92e0912031046r5ca884aaq96399b40e0ab94ff@mail.gmail.com> Dear Olga, Your ques on pdos on the forum can help me get to my starting point, Could you please sent me an input script for running the projwfc.x calculation. Are there preliminary calculations one needs to do before carrying out the projwfc.x as is the case with bands where one has to do scf, nscf, bands.x then finally plotband.x. If this preliminary calculations are done, what are they? I want to do a pdos on diamond surface. Please help Motochi Moi University-Kenya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091203/52bc0d42/attachment-0001.htm From samolyuk at gmail.com Thu Dec 3 19:47:26 2009 From: samolyuk at gmail.com (German Samolyuk) Date: Thu, 3 Dec 2009 13:47:26 -0500 Subject: [Pw_forum] how to specify initial ion velocities in pw.x Message-ID: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> As I understand from the discussion on the forum there is no regular way to specify initial velocity in md calculation trough pw.x. Can I specify initial velocity for some particular particle by hands in subroutine md_init(). I'm little bit confused by comment "notice that vel is not the real velocity" in the subroutine. If yes, should I use atomic units? Thank you in advance. German Samolyuk Oak Ridge National Laboratory From josepht at chips.ncsu.edu Thu Dec 3 23:04:45 2009 From: josepht at chips.ncsu.edu (josepht at chips.ncsu.edu) Date: Thu, 3 Dec 2009 17:04:45 -0500 (EST) Subject: [Pw_forum] [Fwd: diagonalization failure (david, cg) for large numbers of bands] In-Reply-To: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> Message-ID: <38832.152.14.74.107.1259877885.squirrel@chips.ncsu.edu> Hello all, Thanks Stefano and Brad for responding so quickly! It indeed runs with a truly massive cutoff (roughly 80 Ry), with regular Davidson diag (level 4); the 7 needed scf steps took 2:35:24s on 128 processors (Cray XT4). The issue is definitely related to needing more PWs, although I do not understand why such an enormous number is needed. Indeed, with a reasonable cutoff yielding several tens of thousands of PWs (more than twice 4*states), seeking to obtain ~3300 KS states did not seem - in my na?vet?- to be outrageous. With the large cutoff quoted above, 104415 PWs are used. I will check how much lower the cutoff can be if diagonalizing using Davidson level 2. Thanks again, Joseph Turnbull Department of Physics North Carolina State University From giannozz at democritos.it Fri Dec 4 10:26:24 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 04 Dec 2009 10:26:24 +0100 Subject: [Pw_forum] how to specify initial ion velocities in pw.x In-Reply-To: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> Message-ID: <4B18D5C0.1040101@democritos.it> German Samolyuk wrote: > I'm little bit confused by comment > "notice that vel is not the real velocity" in the subroutine. I think it is just a reminder that "vel" is not the velocity but the velocity times Delta T P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From mohnish.iitk at gmail.com Fri Dec 4 14:30:56 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 4 Dec 2009 19:00:56 +0530 Subject: [Pw_forum] from bfgs : error # Message-ID: Dear users , I am structural relaxation for zinc oxide wurtzite structure but after some scf cycle it is giving error. I am not able to debug it. I am pasting the error displayed in the output file. Can anybody please help me out. Thanks in advance. Mohnish number of scf cycles = 14 number of bfgs steps = 9 enthalpy old = -317.0354363374 Ry enthalpy new = -317.0354363339 Ry CASE: enthalpy_new > enthalpy_old new trust radius = 0.0000499998 bohr trust_radius < trust_radius_min resetting bfgs history %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from bfgs : error # 1 bfgs history already reset at previous step %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... p0_20790: p4_error: : 0 -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091204/4b4dd292/attachment.htm From giannozz at democritos.it Fri Dec 4 14:50:51 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 04 Dec 2009 14:50:51 +0100 Subject: [Pw_forum] from bfgs : error # In-Reply-To: References: Message-ID: <4B1913BB.6070808@democritos.it> mohnish pandey wrote: > enthalpy old = -317.0354363374 Ry > enthalpy new = -317.0354363339 Ry you are already at almost perfect convergence P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From samolyuk at gmail.com Fri Dec 4 19:42:14 2009 From: samolyuk at gmail.com (German Samolyuk) Date: Fri, 4 Dec 2009 13:42:14 -0500 Subject: [Pw_forum] how to specify initial ion velocities in pw.x In-Reply-To: <4B18D5C0.1040101@democritos.it> References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> <4B18D5C0.1040101@democritos.it> Message-ID: <5da157840912041042w3598170chdf33892d9b0770ff@mail.gmail.com> Thank you, does it mean that if I add after line number 466 of dynamics_module.f90 something like tau_old(1,100) = tau(1,100) - v_x*dt/alat tau_old(2,100) = tau(2,100) - v_y*dt/alat tau_old(3,100) = tau(3,100) - v_z*dt/alat it should be equivalent to set up initial velocity (v_x,v_y,v_z) to particle number 100? What units is used for dt? Is it atomic Hartree or atomic Rydberg? From mohnish.iitk at gmail.com Sat Dec 5 04:37:29 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 5 Dec 2009 09:07:29 +0530 Subject: [Pw_forum] Is there a large difference between vc-relax calculation using "damp", "damp-w" and "bfgs", "bfgs" algorithm Message-ID: Dear users ! I tried to calculate bulk energy and equilibrium lattice parameters of some system using vc-relax calculation. I done the calculation using both the algorithm naming (1)damped dynamics means 'ion_dynamics' as "damp" and 'cell_dynamics' as "damp-w" (2) BFGS means 'ion_dynamics' as "bfgs" and 'cell_dynamics' as"bfgs" . I have changed only these two things in these two alogorithm. But first case was taking very much time(~2hours) and wasnt convergence after 200 ionic steps whereas in the second case it took very less time (6-7 minutes) to get equilbrium bulk structure. Can anybody please explain me what is the thing which is making so much differnce? Sincere thanks in advance, Mohnish -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091205/8f08c437/attachment.htm From baroni at sissa.it Sat Dec 5 11:14:09 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 5 Dec 2009 11:14:09 +0100 Subject: [Pw_forum] Is there a large difference between vc-relax calculation using "damp", "damp-w" and "bfgs", "bfgs" algorithm In-Reply-To: References: Message-ID: <6F394F4E-BA69-468C-8BDB-0EF0593FFBE0@sissa.it> too short a time step? SB On Dec 5, 2009, at 4:37 AM, mohnish pandey wrote: > Dear users ! > I tried to calculate bulk energy and equilibrium lattice parameters of some system using vc-relax calculation. I done the calculation using both the algorithm naming (1)damped dynamics means 'ion_dynamics' as "damp" and 'cell_dynamics' as "damp-w" (2) BFGS means 'ion_dynamics' as "bfgs" and 'cell_dynamics' as"bfgs" . I have changed only these two things in these two alogorithm. But first case was taking very much time(~2hours) and wasnt convergence after 200 ionic steps whereas in the second case it took very less time (6-7 minutes) to get equilbrium bulk structure. Can anybody please explain me what is the thing which is making so much differnce? > Sincere thanks in advance, > Mohnish > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > _______________________________________________ > 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/20091205/b62d5e50/attachment.htm From wangqj1 at 126.com Sat Dec 5 13:16:44 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sat, 5 Dec 2009 20:16:44 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 29, Issue 69 In-Reply-To: References: Message-ID: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> Dear Lorenzo Paulatto: >???1.?Re:?about?relax?in?electric?field?(Lorenzo?Paulatto) >???2.?Re:?Pw_forum?Digest,?Vol?29,?Issue?68?(Johnson,?D.?Ray) >???3.?Calculation?of?projected?density?of?states?for individual >??????atoms?in?chain?(Dimpy?Sharma) >???4.?Re:?Calculation?of?projected?density?of?states?for?individual >??????atoms?in?chain?(Lorenzo?Paulatto) >???5.?cp.x?code?(Jiri?Houska) >???6.?Re:?cp.x?code?(Paolo?Giannozzi) >???7.?Trouble?with?parallel?running?ld1.x?(Pavel?A.?Akulov) > > >---------------------------------------------------------------------- > >Message:?1 >Date:?Tue,?24?Nov?2009?16:26:13?+0100 >From:?"Lorenzo?Paulatto"? >Subject:?Re:?[Pw_forum]?about?relax?in?electric?field >To:?"PWSCF?Forum"? >Message-ID:? >Content-Type:?text/plain;?charset=utf-8;?format=flowed;?delsp=yes > >Replying?to?message?"[Pw_forum]?about?relax?in?electric?field"?from?? >Q.J.Wang?(24/11/09): >>??PAY?ATTENTION:?EL?FIELD?AND?OCCUPATIONS > >Dear?Q.J.?Wang, >this?message?is?not?very?explicative,?but?it?means?that?Berry-phase?? >electric?field?is?not?really?well?defined?with?smearing?and?can?cause?? >problems.?In?particular,?it?is?not?defined?for?metals,?or?any?system?that?? >have?fractional?band?occupations. > >If?you?have?a?band?gap?and?your?smearing?is?much?smaller?than?that,?then?? >dipfield?may?work,?but?if?some?fractional?occupation?arises,?the?system?? >may?never?converge,?or?converge?to?some?meaningless?state. > >In?practice,?if?your?system?has?a?band?gap,?albeit?small,?you?should?try?? >to?use?fixed?occupations.?Otherwise,?you?cannot?use?dipfield. I only want to add a homogeneous finite electric field .In the instruction of the dipfield paremeter ,it said dipfield turn on only tefield is turn .So I don't know why you introduce the usage of parameter dipfield ? I have see the code of forces_bp_efield.f90 in version 4.1(my cluster installed) .It seems that :"PAY?ATTENTION:?EL?FIELD?AND?OCCUPATIONS" is not a error .My question is why when I turn on the lefield ,relax is so slower than without ? And one puzzled problem is ,at the start ,when the first iteration has not achieved the save file has turn up . My input file is as following ,please give me some advice ,the problem has puzzled some days ,but don't find effective solution until now . Best regards > >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:?6 >Date:?Tue,?24?Nov?2009?22:47:35?+0800?(CST) >From:?"Q.J.Wang"? >Subject:?[Pw_forum]?about?relax?in?electric?field >To:?pw_forum? >Message-ID: >????????<26724746.1247551259074055444.JavaMail.coremail at bj126app104.126.com> >Content-Type:?text/plain;?charset="gbk" > >Dear?all >???When?I?add?external?electric?field?to?optimize?the?structure?.It?runs?very?very?slower?than?not?add?the?electric?field?,?after?2?days?,the?output?file?is?still?as?following?: > >?iteration?#??1?????ecut=????30.00?Ry?????beta=0.20 >?????Davidson?diagonalization?with?overlap >?????ethr?=??1.00E-02,??avg?#?of?iterations?=??4.4 >?PAY?ATTENTION:?EL?FIELD?AND?OCCUPATIONS >?????Expectation?value?of?exp(iGx): >?(2.751012649613009E-016,-3.679346535033460E-017)??0.866025403784439 >?????Electronic?Dipole?per?cell?(a.u.)?-0.482785724081663 >?????Ionic?Dipole?per?cell?(a.u.)???3794.73195575151 >?PAY?ATTENTION:?EL?FIELD?AND?OCCUPATIONS >My?input?file?adhere?here: >&CONTROL >?????????????????calculation?=?'relax'?, >????????????????restart_mode?=?'from_scratch'?, >??????????????????pseudo_dir?=?'./'?, >??????????????????????prefix?=?'ZnO'?, >???????????????????????nstep?=?250?, >?????????????????????tprnfor?=?.true.?, >????????????????????lelfield?=?.true.?, >???????????????????nberrycyc?=?1?, >????????????????????????gdir?=?3?, >?/ >?&SYSTEM >???????????????????????ibrav?=?14, >???????????????????celldm(1)?=?18.6286, >???????????????????celldm(2)?=?0.6666667, >???????????????????celldm(3)?=?1.0733333, >???????????????????celldm(4)?=?0, >???????????????????celldm(5)?=?0, >???????????????????celldm(6)?=?-0.5, >?????????????????????????nat?=?48, >????????????????????????ntyp?=?3, >?????????????????????ecutwfc?=?30?, >?????????????????????ecutrho?=?300?, >???????????????????????nosym?=?.true.?, >?????????????????occupations?=?'smearing'?, >?????????????????????degauss?=?0.008?, >????????????????????smearing?=?'gaussian'?, >???????????????????????nspin?=?2?, >???starting_magnetization(1)?=?0.5, >???starting_magnetization(2)?=?0.5, >???starting_magnetization(3)?=?0.5, >?????????????????lda_plus_u?=?.false.?, >?/ >?&ELECTRONS >????????????????????conv_thr?=?1.D-7?, >?????????????????mixing_mode?=?'plain'?, >?????????????????mixing_beta?=?0.2?, >?????????????????startingwfc?=?'random'?, >??????????????????????efield?=?0?, >?/ >?&IONS >????????????????ion_dynamics?=?'bfgs'?, >?????????????????phase_space?=?'full'?, >?/ >ATOMIC_SPECIES >????O???15.00000??O.pbe-rrkjus.UPF >???Zn???65.00000??Zn.pbe-van.UPF >???Mn???54.94000??Mn.pbe-sp-van.UPF >ATOMIC_POSITIONS?angstrom >???Zn??????0.000000000????1.875966909????0.000000000????1??1??1 >????O??????0.000000000????1.875966909????1.991601344????1??1??1 >.................................................... >K_POINTS?automatic >??3?3?3???1?1?1 >I?don't?know?why?after?I?add?the?electric?field?,the?speed?of?relax?is?so?slow?? >Any?advice?will?be?appreciated?! > >-- > >Best?regards > >Q.J.Wang > >XiangTan?University >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20091124/c751ca32/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?29,?Issue?68 >**************************************** > > > >------------------------------ > >Message:?3 >Date:?Tue,?24?Nov?2009?17:39:39?-0000 >From:?"Dimpy?Sharma"? >Subject:?[Pw_forum]?Calculation?of?projected?density?of?states?for > individual?atoms?in?chain >To:? >Message-ID:? >Content-Type:?text/plain;?charset="iso-8859-1" > > >Hi?Quantum?espresso?users, > >I?have?calculated?projected?density?of?states?(PDOS)?for?my?system?which?contains?2?silicon?atoms?and?4?hydrogen?atoms.?Now?I?would?like?to?calculate?the?PDOS?for?my?individual?atoms?(i,e?for?Si1?,?Si2?)?.?I?would?like?to?know?for?calculating?the?PDOS?for?individual?atom,?which?atomic?coordinate?shall?I?need?to?give?in?my?input?file?,?as?I?cannot?give?atomic?coordinate?for?only?one?atom?of?Silicon?(?as?that?would?mean?PDOS?for?single?Silicon),?what?is?the?correct?way?of?approaching?? > >Thanks?a?million > >Dimpy > >UCC > >Ireland >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20091124/033345c5/attachment-0001.htm? > >------------------------------ > >Message:?4 >Date:?Tue,?24?Nov?2009?18:48:42?+0100 >From:?"Lorenzo?Paulatto"? >Subject:?Re:?[Pw_forum]?Calculation?of?projected?density?of?states?for > individual?atoms?in?chain >To:?"PWSCF?Forum"? >Message-ID:? >Content-Type:?text/plain;?charset=utf-8;?format=flowed;?delsp=yes > >Replying?to?message?"[Pw_forum]?Calculation?of?projected?density?of?states?? >for?individual?atoms?in?chain"?from?Dimpy?Sharma?(24/11/09): >>?I?would?like?to?know?for?calculating?the?PDOS?for?individual?atom > >Dear?Dimpy, >pdos?always?computes?the?projected?density?of?states?for?each?individual?? >atom. > >In?the?directory?where?you?have?executed?projwfc.x?you?will?have?a?bunch?? >of?file?with?names?like?this: >prefix.pdos_atm#4(Pd)_wfc#3(p) > >This?file?does?include?projection?on?the?3rd?wavefunction?(which?is?of?? >type?p)?belonging?to?the?4th?atom?(of?type?Pd).?Inside?the?file?itself?you?? >can?find?several?columns?that?belong?to?the?p_z,?p_x?and?p_y?orbitals?and?? >the?total.?It?is?all?explained?in?Doc/INPUT_PROJWFC.txt,?together?with?? >many?more?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/ > > >------------------------------ > >Message:?5 >Date:?Tue,?24?Nov?2009?20:04:28?+0100 >From:?Jiri?Houska? >Subject:?[Pw_forum]?cp.x?code >To:?pw_forum at pwscf.org >Message-ID:?<20091124200428.9ipx2zys00ws0wsc at webmail.zcu.cz> >Content-Type:?text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > >Hello, >please?I?am?quite?confused?about?the?cp.x?code?which?I?an?going?to?use: > >(I)?is?there?a?difference?between?(1)?scf?calculation?using?cp.x?and?? >(3)?scf?calculation?using?pw.x?? > >(II)?is?there?a?difference?between?(1)?scf?calculation?using?cp.x?and?? >(2)?cp?calculation?using?cp.x?with?electron_dynamics?=?(say)?'sd'?and?? >ion_dynamics?=?'none'?? > >(III)?how?critical?is?the?"ion_radius"?choice?...?e.g.?is?it?clever?to?? >make?it?equal?to?(known)?covalent?radius? > >Thanks?a?lot, >Jiri?Houska >University?of?West?Bohemia > > > > >------------------------------ > >Message:?6 >Date:?Tue,?24?Nov?2009?21:37:53?+0100 >From:?Paolo?Giannozzi? >Subject:?Re:?[Pw_forum]?cp.x?code >To:?PWSCF?Forum? >Message-ID:?<48987221-D34A-4B3C-95CB-D79ED30AC32A at democritos.it> >Content-Type:?text/plain;?charset=US-ASCII;?format=flowed > > >On?Nov?24,?2009,?at?20:04?,?Jiri?Houska?wrote: > >>?(I)?is?there?a?difference?between?(1)?scf?calculation?using?cp.x?and >>?(3)?scf?calculation?using?pw.x?? > >one?is?performed?with?damped?(fictitious)?dynamics?on?electrons, >another?with?traditional?self-consistency?on?the?charge?density > >>?(II)?is?there?a?difference?between?(1)?scf?calculation?using?cp.x?and >>?(2)?cp?calculation?using?cp.x?with?electron_dynamics?=?(say)?'sd'?and >>?ion_dynamics?=?'none'?? > >no,?but?steepest?descent?should?be?used?only?to?start?the?calculation: >it?is?very?inefficient > >>?(III)?how?critical?is?the?"ion_radius"?choice?...?e.g.?is?it?clever?to >>?make?it?equal?to?(known)?covalent?radius? > >the?defaults?should?be?ok.?The?so?called?ion?radius?is?used?to?broaden >the?point?charges?of?the?nuclei?into?a?gaussian?distribution?of?charges. >It?is?a?convenient?computational?trick. > >P. >--- >Paolo?Giannozzi,?Dept?of?Physics,?University?of?Udine >via?delle?Scienze?208,?33100?Udine,?Italy >Phone?+39-0432-558216,?fax?+39-0432-558222 > > > > > >------------------------------ > >Message:?7 >Date:?Wed,?25?Nov?2009?08:52:43?+0600 >From:?"Pavel?A.?Akulov"? >Subject:?[Pw_forum]?Trouble?with?parallel?running?ld1.x >To:?pw_forum at pwscf.org >Message-ID:?<20091125025207.M9749 at phys.tsu.ru> >Content-Type:?text/plain; charset=koi8-r > >Dear?PWSCF?users?and?developers! > >I've?faced?a?problem?of?parallel?running?ld1.x?program. >Stand-alone?version?works?well?(i've?tried?examples?in?atomic_doc), >but?parallel?version?gets?me?error: > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >from?ld1_readin?:?error?#?????????????????1 >reading?input?namelist >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >(even?in?examples). > >I?run?it?with?string(for?example?2?procs?h.in?in?/atomic_doc/all-electron) >"mpirun?-np?2?/path/ld1.x?-in?h.in?>?h.out" > >For?pw.x?this?works?well.?But?for?ld1.x?i?don't?know?what's?wrong. > >Help?me?please. > > >--? >Akulov?P. >Student,?Dept.?of?Physics >Tomsk?State?University > > > >------------------------------ > >_______________________________________________ >Pw_forum?mailing?list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End?of?Pw_forum?Digest,?Vol?29,?Issue?69 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091205/b3bb3299/attachment-0001.htm From baroni at sissa.it Sat Dec 5 15:58:13 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 5 Dec 2009 15:58:13 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 29, Issue 69 In-Reply-To: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> References: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> Message-ID: <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> answering this post would require some data mining ! Could you please post an intelligible message, indicating the topic in the "subject" header and your name and affiliation isomewhere in the text? Thanks - SB On Dec 5, 2009, at 1:16 PM, Q.J.Wang wrote: > Dear Lorenzo Paulatto: > > > 1. Re: about relax in electric field (Lorenzo Paulatto) > > 2. Re: Pw_forum Digest, Vol 29, Issue 68 (Johnson, D. Ray) > > 3. Calculation of projected density of states for individual > > atoms in chain (Dimpy Sharma) > > 4. Re: Calculation of projected density of states for individual > > atoms in chain (Lorenzo Paulatto) > > 5. cp.x code (Jiri Houska) > > 6. Re: cp.x code (Paolo Giannozzi) > > 7. Trouble with parallel running ld1.x (Pavel A. Akulov) > > + tons of garbage ... --- 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/20091205/1c672c8c/attachment.htm From giannozz at democritos.it Sat Dec 5 21:35:45 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 05 Dec 2009 20:35:45 -0000 Subject: [Pw_forum] Is there a large difference between vc-relax calculation using "damp", "damp-w" and "bfgs", "bfgs" algorithm In-Reply-To: References: Message-ID: <199911300441.28220.giannozz@democritos.it> On Saturday 05 December 2009 04:37, mohnish pandey wrote: > \Can anybody please explain me what is the thing which is > making so much differnce? damped dynamics is very robust but its performance relies upon a good choice of the time step and of the damping (if available). anyway, if bfgs works well, why bother? P. -- Paolo Giannozzi, Democritos and Udine University From wangqj1 at 126.com Sun Dec 6 10:39:54 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sun, 6 Dec 2009 17:39:54 +0800 (CST) Subject: [Pw_forum] about relax in electric field In-Reply-To: References: Message-ID: <2992647.493721260092394095.JavaMail.coremail@bj126app29.126.com> Dear Lorenzo Paulatto I am very sorry for my last letter .I don't know why it become some garbage, now I send it again . I only want to add a homogeneous finite electric field .In the instruction of the dipfield paremeter ,it said dipfield turn on only tefield is turn .So I don't know why you introduce the usage of parameter dipfield ? I have see the code of forces_bp_efield.f90 in version 4.1(my cluster installed) .It seems that :"PAY ATTENTION:EL FIELD AND OCCUPATIONS" is not a error .My question is why when I turn on the lefield ,relax is so slower than without adding efield ? And one puzzled problem is ,at the start ,when the first iteration has not achieved the save file has turn up . Best regards Q.J.Wang XiangTan University ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091206/a521f9aa/attachment.htm From wangqj1 at 126.com Sun Dec 6 13:30:07 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sun, 6 Dec 2009 20:30:07 +0800 (CST) Subject: [Pw_forum] forces_bp_efield.f90 Message-ID: <7574101.532631260102607967.JavaMail.coremail@bj126app104.126.com> Dear all In the forces_bp_efield.f90,one part of code is as following: ! --- Check that we are working with an insulator with no empty bands --- IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) & WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS' So I want to know the forces_bp_efield.f90 only fit to insulator ? If my system is half metallic ,can I use this code to relax ? If my system have odd electrons ,how to set it ? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091206/59991a94/attachment.htm From wangqj1 at 126.com Sun Dec 6 13:32:14 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sun, 6 Dec 2009 20:32:14 +0800 (CST) Subject: [Pw_forum] forces_bp_efield.f90 Message-ID: <21250355.533451260102734868.JavaMail.coremail@bj126app104.126.com> Dear all In the forces_bp_efield.f90,one part of code is as following: ! --- Check that we are working with an insulator with no empty bands --- IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) & WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS' So I want to know the forces_bp_efield.f90 only fit to insulator ? If my system is half metallic ,can I use this code to relax ? If my system have odd electrons ,how to set it ? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091206/eb8561de/attachment.htm From wangqj1 at 126.com Sun Dec 6 13:38:23 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sun, 6 Dec 2009 20:38:23 +0800 (CST) Subject: [Pw_forum] forces_bp_efield.f90 Message-ID: <21997305.535591260103103136.JavaMail.coremail@bj126app104.126.com> Dear all In the forces_bp_efield.f90,one part of code is as following: ! --- Check that we are working with an insulator with no empty bands --- IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) & WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS' So I want to know the forces_bp_efield.f90 only fit to insulator ? If my system is half metallic ,can I use this code to relax ? If my system have odd electrons ,how to set it ? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091206/eb9b3272/attachment.htm From damien.connetable at ensiacet.fr Mon Dec 7 00:01:13 2009 From: damien.connetable at ensiacet.fr (damien) Date: Mon, 07 Dec 2009 00:01:13 +0100 Subject: [Pw_forum] US or PAW pseudopotentials and Raman spectra Message-ID: <4B1C37B9.4070809@ensiacet.fr> Dear all, I wanted to know if, in a near future, it will be envisaged to have an implementation of Raman spectra with Ultra Soft or/and PAW pseudopotentials? your sincerely damien conn?table -------------- next part -------------- A non-text attachment was scrubbed... Name: damien_connetable.vcf Type: text/x-vcard Size: 396 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091207/bf361e8f/attachment.vcf From wangqj1 at 126.com Mon Dec 7 01:46:04 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Mon, 7 Dec 2009 08:46:04 +0800 (CST) Subject: [Pw_forum] forces_bp_efield.f90 Message-ID: <3178762.27501260146764559.JavaMail.coremail@bj126app103.126.com> Dear all In the forces_bp_efield.f90,one part of code is as following: ! --- Check that we are working with an insulator with no empty bands --- IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) & WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS' So I want to know the forces_bp_efield.f90 only fit to insulator ? If my system is half metallic ,can I use this code to relax ? If my system have odd electrons ,how to set it ? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091207/58c79016/attachment.htm From wangqj1 at 126.com Mon Dec 7 02:28:11 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Mon, 7 Dec 2009 09:28:11 +0800 (CST) Subject: [Pw_forum] forces_bp_efield.f90 In-Reply-To: References: Message-ID: <2376991.56711260149291238.JavaMail.coremail@bj126app103.126.com> Dear all In the forces_bp_efield.f90,one part of code is as following: ! --- Check that we are working with an insulator with no empty bands --- IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) & WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS' So I want to know the forces_bp_efield.f90 only fit to insulator ? If my system is half metallic ,can I use this code to relax ? If my system have odd electrons ,how to set it ? -- Best regards Q.J.Wang XiangTan University ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091207/47838a54/attachment.htm From pbsorokin at gmail.com Mon Dec 7 07:47:59 2009 From: pbsorokin at gmail.com (Pavel B Sorokin) Date: Mon, 7 Dec 2009 13:47:59 +0700 Subject: [Pw_forum] Fixing position of the atoms during the relaxation of the cell Message-ID: <1398846173.20091207134759@gmail.com> Dear PWSCF community! I need to freeze the position of some atoms during vc-relax mode. In the manual I found that I should type something like that ATOMIC_POSITIONS angstrom X1 x1 y1 z1 0 0 0 X2 x2 y2 z2 1 1 1 ... if I want to fix atom 1. This option works in the relax calculation but unfortunately doesn't work in vc-relax mode. May you give me any tips how I can solve this problem? Thanks!! -- Sincerely yours, Pavel Sorokin From baroni at sissa.it Mon Dec 7 08:13:54 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 7 Dec 2009 08:13:54 +0100 Subject: [Pw_forum] forces_bp_efield.f90 In-Reply-To: <2376991.56711260149291238.JavaMail.coremail@bj126app103.126.com> References: <2376991.56711260149291238.JavaMail.coremail@bj126app103.126.com> Message-ID: <38146C8F-82BD-4A15-9405-B292E77E9F67@sissa.it> Dear Q.J. Wang, please, consider that the probability of getting a polite and informative answer to your posts is fairly independent of the number of times you send your post. It is my past experience that the probability of receiving a rude and uninformative answer, instead, increases exponentially with the number of posts. The larger the number, the higher the chance, the ruder and less informative the answer. This being said, here is the answer. Hope it is polite enough, even though it may be not too informative. I do not know what "forces_bp_efield" does. If, as it seems, it deals with an applied electric field, it seems natural to me that it only works (it should only be used) for insulators. In a metal an applied electric field is completely screened by conduction electrons. Stefano On Dec 7, 2009, at 2:28 AM, Q.J.Wang wrote: > Dear all > In the forces_bp_efield.f90,one part of code is as following: > ! --- Check that we are working with an insulator with no empty bands --- > IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) & > WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS' > So I want to know the forces_bp_efield.f90 only fit to insulator ? If my system is half metallic ,can I use this code to relax ? If my system have odd electrons ,how to set it ? > > > > -- > Best regards > > Q.J.Wang > > XiangTan University > > _______________________________________________ > 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/20091207/2c2e139c/attachment.htm From sclauzer at sissa.it Mon Dec 7 09:32:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 7 Dec 2009 09:32:25 +0100 Subject: [Pw_forum] Fixing position of the atoms during the relaxation of the cell In-Reply-To: <1398846173.20091207134759@gmail.com> References: <1398846173.20091207134759@gmail.com> Message-ID: <20091207093225.cpph98qn8k0wcggw@webmail.sissa.it> Dear Pavel, I don't know much of vc-relax, but I think that when the cell size is modified during the relaxation, atomic positions are rescaled accordingly (I suspect I've read it in a recent post on the forum, but it seems quite plausible to me. Don't you think so?) Maybe there are some other tricks to fix some atoms (why don't you put that atom in the origin, for instance?), but I'm not aware of any. I hope someone more expert will help you better than I could, in the meanwhile please try to dig a bit in the forum archives. Gabriele Sclauzero SISSA & Democritos Quoting Pavel B Sorokin : > Dear PWSCF community! > > I need to freeze the position of some atoms during vc-relax mode. > In the manual I found that I should type something like that > > ATOMIC_POSITIONS angstrom > X1 x1 y1 z1 0 0 0 > X2 x2 y2 z2 1 1 1 > ... > > if I want to fix atom 1. > > This option works in the relax calculation but unfortunately doesn't > work in vc-relax mode. May you give me any tips how I can solve this > problem? > > Thanks!! > > -- > Sincerely yours, > Pavel Sorokin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From wangqj1 at 126.com Mon Dec 7 10:43:10 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Mon, 7 Dec 2009 17:43:10 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 30, Issue 15 In-Reply-To: References: Message-ID: <17632377.486781260178990585.JavaMail.coremail@bj126app26.126.com> Dear all I am very sorry that my post turn up error as to the same email send many times. -- Best regards Q.J.Wang XiangTan University ?2009-12-07?15:56:58?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:?forces_bp_efield.f90?(Stefano?Baroni) > > >---------------------------------------------------------------------- > >Message:?1 >Date:?Mon,?7?Dec?2009?08:13:54?+0100 >From:?Stefano?Baroni? >Subject:?Re:?[Pw_forum]?forces_bp_efield.f90 >To:?PWSCF?Forum? >Message-ID:?<38146C8F-82BD-4A15-9405-B292E77E9F67 at sissa.it> >Content-Type:?text/plain;?charset="iso-8859-1" > >Dear?Q.J.?Wang, > >please,?consider?that?the?probability?of?getting?a?polite?and?informative?answer?to?your?posts?is?fairly?independent?of?the?number?of?times?you?send?your?post.?It?is?my?past?experience?that?the?probability?of?receiving?a?rude?and?uninformative?answer,?instead,?increases?exponentially?with?the?number?of?posts.?The?larger?the?number,?the?higher?the?chance,?the?ruder?and?less?informative?the?answer. > >This?being?said,?here?is?the?answer.?Hope?it?is?polite?enough,?even?though?it?may?be?not?too?informative. > >I?do?not?know?what?"forces_bp_efield"?does.?If,?as?it?seems,?it?deals?with?an?applied?electric?field,?it?seems?natural?to?me?that?it?only?works?(it?should?only?be?used)?for?insulators.?In?a?metal?an?applied?electric?field?is?completely?screened?by?conduction?electrons. > >Stefano > >On?Dec?7,?2009,?at?2:28?AM,?Q.J.Wang?wrote: > >>?Dear?all >>??????In?the?forces_bp_efield.f90,one?part?of?code?is?as?following: >>??????!??---?Check?that?we?are?working?with?an?insulator?with?no?empty?bands?--- >>????IF?((degauss?>?0.01d0)?.OR.?(nbnd?/=?nelec/2))?& >>?????????WRITE?(stdout,*)?'PAY?ATTENTION:?EL?FIELD?AND?OCCUPATIONS' >>?So?I?want?to?know?the?forces_bp_efield.f90?only?fit?to?insulator???If?my?system?is?half?metallic?,can?I?use?this?code?to?relax???If?my?system?have?odd?electrons?,how?to?set?it?? >>? >>? >>? >>?-- >>?Best?regards >>?? >>?Q.J.Wang >>?? >>?XiangTan?University >>?? >>?_______________________________________________ >>?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/20091207/2c2e139c/attachment.html? > >------------------------------ > >_______________________________________________ >Pw_forum?mailing?list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End?of?Pw_forum?Digest,?Vol?30,?Issue?15 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091207/5986c267/attachment.htm From paulatto at sissa.it Mon Dec 7 11:09:23 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 7 Dec 2009 11:09:23 +0100 Subject: [Pw_forum] forces_bp_efield.f90 In-Reply-To: <38146C8F-82BD-4A15-9405-B292E77E9F67@sissa.it> References: <2376991.56711260149291238.JavaMail.coremail@bj126app103.126.com> <38146C8F-82BD-4A15-9405-B292E77E9F67@sissa.it> Message-ID: <20091207110923.1a5hjymg0ggk4owc@webmail.sissa.it> Dear Q.J. Wang, what Stefano Baroni says is correct: applying an electric field via Berry phase (lefield=.true.) does not work for metals. The code does no issue an error because you may still know what you are doing, e.g. using the smearing in an insulator. Or having an odd number of electrons in an isolated molecule. In a metal a constant external field only have an effect on the surface, usually limited to 2-3 layers of atoms. 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 Horde http://www.horde.org/ From pbsorokin at gmail.com Mon Dec 7 14:35:24 2009 From: pbsorokin at gmail.com (Pavel B Sorokin) Date: Mon, 7 Dec 2009 20:35:24 +0700 Subject: [Pw_forum] Fixing position of the atoms during the relaxation of the cell In-Reply-To: <20091207093225.cpph98qn8k0wcggw@webmail.sissa.it> References: <1398846173.20091207134759@gmail.com> <20091207093225.cpph98qn8k0wcggw@webmail.sissa.it> Message-ID: <1138907472.20091207203524@gmail.com> Dear Gabriele. Thank you for your answer. I've digged in the forum and don't find the answer. Yes, it seems that atomic positions are rescaling during the cell relaxation... About the putting of my atom in the origin.. I need to fix more than one atom. Anyway, thanks! > Dear Pavel, > I don't know much of vc-relax, but I think that when the cell size > is modified during the relaxation, atomic positions are rescaled > accordingly (I suspect I've read it in a recent post on the forum, but > it seems quite plausible to me. Don't you think so?) > Maybe there are some other tricks to fix some atoms (why don't you put > that atom in the origin, for instance?), but I'm not aware of any. > I hope someone more expert will help you better than I could, in the > meanwhile please try to dig a bit in the forum archives. > Gabriele Sclauzero > SISSA & Democritos > Quoting Pavel B Sorokin : >> Dear PWSCF community! >> >> I need to freeze the position of some atoms during vc-relax mode. >> In the manual I found that I should type something like that >> >> ATOMIC_POSITIONS angstrom >> X1 x1 y1 z1 0 0 0 >> X2 x2 y2 z2 1 1 1 >> ... >> >> if I want to fix atom 1. >> >> This option works in the relax calculation but unfortunately doesn't >> work in vc-relax mode. May you give me any tips how I can solve this >> problem? >> >> Thanks!! >> -- Sincerely yours, Pavel Sorokin From ceresoli at MIT.EDU Mon Dec 7 15:53:06 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Mon, 07 Dec 2009 09:53:06 -0500 Subject: [Pw_forum] Fixing position of the atoms during the relaxation of the cell In-Reply-To: <1398846173.20091207134759@gmail.com> References: <1398846173.20091207134759@gmail.com> Message-ID: <4B1D16D2.1010705@mit.edu> Pavel B Sorokin wrote: > Dear PWSCF community! > > I need to freeze the position of some atoms during vc-relax mode. > In the manual I found that I should type something like that > > ATOMIC_POSITIONS angstrom > X1 x1 y1 z1 0 0 0 > X2 x2 y2 z2 1 1 1 > ... > > if I want to fix atom 1. > > This option works in the relax calculation but unfortunately doesn't > work in vc-relax mode. May you give me any tips how I can solve this > problem? > > Thanks!! > Dear Pavel, this old post could be relevant. I don't know how much the vc-relax subroutine have been modified since last year. http://www.democritos.it/pipermail/pw_forum/2007-October/007374.html Davide From pbsorokin at gmail.com Mon Dec 7 17:28:01 2009 From: pbsorokin at gmail.com (Pavel B Sorokin) Date: Mon, 7 Dec 2009 23:28:01 +0700 Subject: [Pw_forum] Fixing position of the atoms during the relaxation of the cell In-Reply-To: <4B1D16D2.1010705@mit.edu> References: <1398846173.20091207134759@gmail.com> <4B1D16D2.1010705@mit.edu> Message-ID: <13210105136.20091207232801@gmail.com> Dear Davide. I moved coordinates of fixed atoms to the first lines but the situation didn't changed. Anyway, thank you. > Pavel B Sorokin wrote: >> Dear PWSCF community! >> >> I need to freeze the position of some atoms during vc-relax mode. >> In the manual I found that I should type something like that >> >> ATOMIC_POSITIONS angstrom >> X1 x1 y1 z1 0 0 0 >> X2 x2 y2 z2 1 1 1 >> ... >> >> if I want to fix atom 1. >> >> This option works in the relax calculation but unfortunately doesn't >> work in vc-relax mode. May you give me any tips how I can solve this >> problem? >> >> Thanks!! >> > Dear Pavel, > this old post could be relevant. I don't know how much > the vc-relax subroutine have been modified since last year. > http://www.democritos.it/pipermail/pw_forum/2007-October/007374.html Sincerely yours, Pavel Sorokin From stewart at cnf.cornell.edu Mon Dec 7 19:42:50 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Mon, 07 Dec 2009 13:42:50 -0500 Subject: [Pw_forum] sorting phonon bands based on symmetry/eigenvectors In-Reply-To: <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> References: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> Message-ID: <4B1D4CAA.70003@cnf.cornell.edu> Hi everyone, I was wondering if anyone has written a script or program to sort the phonon frequencies based on their band index or branch. This would be very helpful for both plotting and post-analysis. Currently when you use matdyn for a given set of q-vectors, it prints out the phonon frequencies in order from lowest to highest. However, this does not take into account the possibility of band crossings which can lead to changes in the order of the bands. Matdyn also prints out the eigenvectors for the phonons so it should be possible to analyze this and then sort them. If someone has already addressed this issue, I would be very interested in any tools that can handle this. Thanks, Derek ################################ Derek Stewart, Ph. D. Senior Research Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 Stefano Baroni wrote: > answering this post would require some data mining ! > Could you please post an intelligible message, indicating the topic in > the "subject" header and your name and affiliation isomewhere in the text? > Thanks - SB > > On Dec 5, 2009, at 1:16 PM, Q.J.Wang wrote: > >> Dear Lorenzo Paulatto: >> >> > 1. Re: about relax in electric field (Lorenzo Paulatto) >> > 2. Re: Pw_forum Digest, Vol 29, Issue 68 (Johnson, D. Ray) >> > 3. Calculation of projected density of states for individual >> > atoms in chain (Dimpy Sharma) >> > 4. Re: Calculation of projected density of states for individual >> > atoms in chain (Lorenzo Paulatto) >> > 5. cp.x code (Jiri Houska) >> > 6. Re: cp.x code (Paolo Giannozzi) >> > 7. Trouble with parallel running ld1.x (Pavel A. Akulov) >> > >> > > + tons of garbage ... > > > > > --- > 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 > From miguel.martinez at ehu.es Mon Dec 7 19:51:45 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Mon, 7 Dec 2009 19:51:45 +0100 Subject: [Pw_forum] sorting phonon bands based on symmetry/eigenvectors In-Reply-To: <4B1D4CAA.70003@cnf.cornell.edu> References: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> <4B1D4CAA.70003@cnf.cornell.edu> Message-ID: <20091207195145.0abf4981@lcpybm> Dear Derek, I recently discovered that plotband.x is also able to plot phonon bands as well as band structures. Just set all the references to 0. In any case, if you have the IFC you shouldn't have issues distinguishing crossing from anticrossing. Adding more points to the dispersion bands is almost free, after all. At least it is in the smallish systems I've done phonon calculations for. Regards, Miguel On Mon, 07 Dec 2009 13:42:50 -0500 Derek Stewart wrote: > Hi everyone, > > I was wondering if anyone has written a script or program to sort the > phonon frequencies based on their band index or branch. This would > be very helpful for both plotting and post-analysis. Currently when > you use matdyn for a given set of q-vectors, it prints out the phonon > frequencies in order from lowest to highest. However, this does not > take into account the possibility of band crossings which can lead to > changes in the order of the bands. Matdyn also prints out the > eigenvectors for the phonons so it should be possible to analyze this > and then sort them. If someone has already addressed this issue, I > would be very interested in any tools that can handle this. > > Thanks, > > Derek > > ################################ > Derek Stewart, Ph. D. > Senior Research Associate > ** New Webpage ** > http://sites.google.com/site/dft4nano/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > > > > > Stefano Baroni wrote: > > answering this post would require some data mining ! > > Could you please post an intelligible message, indicating the topic > > in the "subject" header and your name and affiliation isomewhere in > > the text? Thanks - SB > > > > On Dec 5, 2009, at 1:16 PM, Q.J.Wang wrote: > > > >> Dear Lorenzo Paulatto: > >> > >> > 1. Re: about relax in electric field (Lorenzo Paulatto) > >> > 2. Re: Pw_forum Digest, Vol 29, Issue 68 (Johnson, D. Ray) > >> > 3. Calculation of projected density of states for > >> > individual atoms in chain (Dimpy Sharma) > >> > 4. Re: Calculation of projected density of states for > >> > individual atoms in chain (Lorenzo Paulatto) > >> > 5. cp.x code (Jiri Houska) > >> > 6. Re: cp.x code (Paolo Giannozzi) > >> > 7. Trouble with parallel running ld1.x (Pavel A. Akulov) > >> > > >> > > > > + tons of garbage ... > > > > > > > > > > --- > > 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 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---------------------------------------- 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 wangqj1 at 126.com Tue Dec 8 07:52:57 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Tue, 8 Dec 2009 14:52:57 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 30, Issue 16 In-Reply-To: References: Message-ID: <12534634.484631260255177806.JavaMail.coremail@bj126app52.126.com> Dear Stefano Baroni and Lorenzo Paulatto, >Message: 3 >Date: Mon, 7 Dec 2009 11:09:23 +0100 >From: Lorenzo Paulatto >Subject: Re: [Pw_forum] forces_bp_efield.f90 >To: pw_forum at pwscf.org >Message-ID: <20091207110923.1a5hjymg0ggk4owc at webmail.sissa.it> >Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > >Dear Q.J. Wang, >what Stefano Baroni says is correct: applying an electric field via >Berry phase (lefield=.true.) does not work for metals. The code does >no issue an error because you may still know what you are doing, e.g. >using the smearing in an insulator. Or having an odd number of >electrons in an isolated molecule. > >In a metal a constant external field only have an effect on the >surface, usually limited to 2-3 layers of atoms. The system I study is not insulator ,it is semiconductor(doped ZnO)and the system has odd electrons .This can not apply an electic field via Berry phase ? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091208/c6018b4b/attachment.htm From cyrille.barreteau at cea.fr Tue Dec 8 09:24:53 2009 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Tue, 08 Dec 2009 09:24:53 +0100 Subject: [Pw_forum] question about constrained magnetization In-Reply-To: <4B17C1FB.3090105@sissa.it> References: <1257860762.11470.15.camel@alex-laptop> <4B166970.70407@cea.fr> <4B1684B9.4090502@sissa.it> <4B1792CB.1010709@cea.fr> <4B17C1FB.3090105@sissa.it> Message-ID: <4B1E0D55.7000502@cea.fr> Dear Gabriele The last solution that you provided seems to be the most adapted to my problem. The choice of the initial moment is maybe not the most adapted but this not a very big problem.. thanks for this very quick fix:-) cyrille -- ================================================================== 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 ================================================================== Gabriele Sclauzero wrote: >Cyrille Barreteau wrote: > > >>Gabriele Sclauzero wrote: >> >> >> >>>Dear Cyrille, >>> >>>Cyrille Barreteau wrote: >>> >>> >>> >>> >>>>Dear all, >>>> >>>>I want to perform a calculation using the penalization technique. >>>>In an unconstrained scf calculation the input_magnetization(i) (i=1,ntyp) >>>>variable contains the m/n initial value of atom of type i, and this >>>>quantity should >>>>obviously belong to [-1,1] interval. >>>>To perform a constrained magnetization of "atomic type" I have to >>>>set the variable constrained_magnetization='atomic' and the magnetization >>>>will be the one given by input_magnetization(i). >>>>Therefore now input_magnetization(i) is no longer m/n but m only. >>>>However it seems that the range of input_magnetization has not been >>>>modified and is still within [-1,1] interval. >>>>If ever I set input_magnetization(i)>1 then the code automatically >>>>replace it by 1 and I cannot explore values larger than 1. >>>> >>>> >>>> >>>> >>> >>> >>> >>> >>Dear Gabriele, >> >>With your quick fix now the input_magnetization is no longer the >>magnetization m but m/n >>as it is when there is no penalization. Therefore we avoid the problem >>due to the [-1,1] interval >>however this makes things a litlle "crooked" since the charge n is not >>precisely now (the charge >>inside the sphere does not integrate to the total charge per atom..). >>However with a little of mental gymnastic we can manage to obtain what >>we want:-) >> >> > >You are right, perhaps it is more practical to fix the magnetization (i.e. local magnetic >moment) rather than the "atomic spin polarization". >I think that the problem arises from the fact that the starting_magnetization keyword is >used for two different things, which maybe should be called starting_spin_polarization for >the unconstrained calculations and target_magnetization for constrained ones (of "atomic" >type). >Another quick fix that should meet your needs could be the following: let the >PW/add_bfield.f90 subroutine as the original and in PW/input.f90 move the check on >starting_magnetization > DO nt = 1, ntyp > ! > IF ( starting_magnetization(nt) == sm_not_set ) THEN > starting_magnetization(nt) = 0.0_dp > ELSE IF ( starting_magnetization(nt) > 1.0_dp ) THEN > starting_magnetization(nt) = 1.0_dp > ELSE IF ( starting_magnetization(nt) <-1.0_dp ) THEN > starting_magnetization(nt) =-1.0_dp > END IF > ! > END DO > >AFTER the block of initialization of the magnetic contraints: > > SELECT CASE( TRIM( constrained_magnetization ) ) > CASE( 'none' ) > ! > i_cons = 0 > ! > CASE( 'total' ) > ! > ... > END SELECT > >Probably, the choice of the initial atomic spin polarization will not be the optimal one >for a better convergence to the target magnetization. >You can use this temporary solution until a more satisfactory implementation will be >conceived and carried out. > > >Thanks, > > >Gabriele > > > > > >>thanks >> cyrille >> >> >> > > > From paulatto at sissa.it Tue Dec 8 10:08:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 08 Dec 2009 10:08:34 +0100 Subject: [Pw_forum] Fixing position of the atoms during the relaxation of the cell In-Reply-To: <1138907472.20091207203524@gmail.com> References: <1398846173.20091207134759@gmail.com> <20091207093225.cpph98qn8k0wcggw@webmail.sissa.it> <1138907472.20091207203524@gmail.com> Message-ID: Replying to message "Re: [Pw_forum] Fixing position of the atoms during the relaxation of the cell" from Pavel B Sorokin (07/12/09): > Thank you for your answer. I've digged in the forum and don't find > the answer. Yes, it seems that atomic positions are rescaling during > the cell relaxation... Dear Pavel, which algorithm are you using for vc-relax? The bfgs one uses a totally different code base than the dynamics-based ones. I *suspect* the behaviour you are seeing may depend on the algorithm, but I don't remember the details, I could check once I know what are you are actually doing. 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 Tue Dec 8 10:19:45 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 08 Dec 2009 10:19:45 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 30, Issue 16 In-Reply-To: <12534634.484631260255177806.JavaMail.coremail@bj126app52.126.com> References: <12534634.484631260255177806.JavaMail.coremail@bj126app52.126.com> Message-ID: Replying to message "Re: [Pw_forum] Pw_forum Digest, Vol 30, Issue 16" from Q.J.Wang (08/12/09): > The system I study is not insulator ,it is semiconductor(doped ZnO)and > the system has odd electrons .This can not apply an electic field via > Berry phase ? Dear QJ, a semiconductor *is* (at zero temperature) an insulator, and it has an even number of electrons per cell. ZnO is a semi-conductor, doped ZnO is a conductor, maybe with a low density of carriers, but still a conductor. What matters for the Berry phase method is if you have partially occupied bands, you do. Anyway, you are free to try, but it is your responsibility to study the theory and see if it makes sense. There are actually not many people that can give you a meaningful advice on this subject (without even knowing your system). 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 Dec 8 12:56:22 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 8 Dec 2009 17:26:22 +0530 Subject: [Pw_forum] problem while running parallel version of espresso-4.1.1 Message-ID: <3a749910912080356j3427160flbf0d6ccfe9172a51@mail.gmail.com> Dear PWSCF users, I am using a Linux clusters, with ifort and mkl libraries. I am running a calculation of LaMnO3 with 20 atoms. Following the the part of the output which i am getting on running scf calculations. The strange thing is, although it shows approximately 26 secs for each iterations, but almost after 4 hrs it able to complete only 4 scf only. * total cpu time spent up to now is 8.15 secs per-process dynamical memory: 20.0 Mb Self-consistent Calculation iteration # 1 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 2.0 total cpu time spent up to now is 26.64 secs total energy = -1612.92488505 Ry Harris-Foulkes estimate = -1599.80692247 Ry estimated scf accuracy < 15.29925563 Ry total magnetization = 0.00 Bohr mag/cell absolute magnetization = 19.65 Bohr mag/cell iteration # 2 ecut= 25.00 Ry beta=0.50 * I compiled the espresso in parallel without any error. I am running this calculations on 16 processors, and in 4 hrs it completes only 4 scf cycles. with the mail i am sending you the make.sys file and the input file. Can anybody tell me why the calculations taking so much time? Is there any other flags i have to use in make.sys file to speed up the calculations*? *Kindly tell me if you need any other information about the machines * *Bipul Rakshit Research Fellow 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/20091208/847c7f2f/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: LaMnO3.zip Type: application/zip Size: 6624 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091208/847c7f2f/attachment.zip From paulatto at sissa.it Tue Dec 8 13:09:54 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 08 Dec 2009 13:09:54 +0100 Subject: [Pw_forum] problem while running parallel version of espresso-4.1.1 In-Reply-To: <3a749910912080356j3427160flbf0d6ccfe9172a51@mail.gmail.com> References: <3a749910912080356j3427160flbf0d6ccfe9172a51@mail.gmail.com> Message-ID: Replying to message "[Pw_forum] problem while running parallel version of espresso-4.1.1" from Bipul Rakshit (08/12/09): > I am running this > calculations on 16 processors, and in 4 hrs it completes only 4 scf Dear Bipul, you output file says that you are running on *32* processors, this would cause some massive slow-down if you only have 16 of them available. You could also use more pools, especially if the processors are in different PCs that are connected via not-so-fast network. 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 daijiayu at nudt.edu.cn Tue Dec 8 14:26:57 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Tue, 08 Dec 2009 21:26:57 +0800 Subject: [Pw_forum] nondegenerate electrons in DFT. Message-ID: <460278817.06271@nudt.edu.cn> Dear Users, Recently, i was dealing with systems with nondegenerate electrons, that is, when T/T_F > 1 (T_F is the fermi temperature). I read some papers, and somebody said that the calculation for these system is prohibitive in DFT. I did not know why they said so. As my understanding, there is no limit in DFT to do with these system. Although electrons are fermi particles, but the fermi distribution promise the right states of electrons in the calculations. And i did not find any explanation about this in the textbook of DFT in my hand. As an example, when the temperature is high enough, so that T/T_F is greater than 1, we can increase the bands window to deal with these cases, i think. Is it correct for my understanding? Thanks a lot. Jiayu ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From stewart at cnf.cornell.edu Tue Dec 8 16:07:54 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Tue, 08 Dec 2009 10:07:54 -0500 Subject: [Pw_forum] sorting phonon bands based on symmetry/eigenvectors In-Reply-To: <20091207195145.0abf4981@lcpybm> References: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> <4B1D4CAA.70003@cnf.cornell.edu> <20091207195145.0abf4981@lcpybm> Message-ID: <4B1E6BCA.50806@cnf.cornell.edu> Hi Miguel, Thank you for your quick response and advice. I agree that with the cheap cost of calculating phonon points once you have the IFC, a visual inspection of the plot is usually enough to order the phonon dispersion along a given symmetry line in the Brillouin Zone. However, I would like to be able to sort the phonon frequencies for a large number of q-vectors in the Brillouin zone (not just restricted to a single symmetry line) and for this it would be very helpful if I can automate the process. I know that for electronic bands, it is possible to determine the symmetry character of a given electronic band using sym_band.f90. Would it be possible to use the same subroutines to determine the symmetry character of the phonon bands? I could then sort based on this output. If anyone has some thoughts on this, I would be very interested. Thanks, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 Miguel Mart?nez wrote: > Dear Derek, > > I recently discovered that plotband.x is also able to plot phonon bands > as well as band structures. Just set all the references to 0. In any > case, if you have the IFC you shouldn't have issues distinguishing > crossing from anticrossing. Adding more points to the dispersion bands > is almost free, after all. At least it is in the smallish systems I've > done phonon calculations for. > > Regards, > > Miguel > > On Mon, 07 Dec 2009 13:42:50 -0500 Derek Stewart > wrote: > >> Hi everyone, >> >> I was wondering if anyone has written a script or program to sort the >> phonon frequencies based on their band index or branch. This would >> be very helpful for both plotting and post-analysis. Currently when >> you use matdyn for a given set of q-vectors, it prints out the phonon >> frequencies in order from lowest to highest. However, this does not >> take into account the possibility of band crossings which can lead to >> changes in the order of the bands. Matdyn also prints out the >> eigenvectors for the phonons so it should be possible to analyze this >> and then sort them. If someone has already addressed this issue, I >> would be very interested in any tools that can handle this. >> >> Thanks, >> >> Derek >> >> ################################ >> Derek Stewart, Ph. D. >> Senior Research Associate >> ** New Webpage ** >> http://sites.google.com/site/dft4nano/ >> 250 Duffield Hall >> Cornell Nanoscale Facility (CNF) >> Ithaca, NY 14853 >> stewart (at) cnf.cornell.edu >> (607) 255-2856 >> >> >> >> >> >> From marzari at MIT.EDU Tue Dec 8 16:19:07 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 08 Dec 2009 10:19:07 -0500 Subject: [Pw_forum] nondegenerate electrons in DFT. In-Reply-To: <460278817.06271@nudt.edu.cn> References: <460278817.06271@nudt.edu.cn> Message-ID: <4B1E6E6B.1010707@mit.edu> Jiayu Dai wrote: > Dear Users, > > Recently, i was dealing with systems with nondegenerate electrons, that is, when > T/T_F > 1 (T_F is the fermi temperature). I read some papers, and somebody said > that the calculation for these system is prohibitive in DFT. I did not know why > they said so. As my understanding, there is no limit in DFT to do with these > system. Although electrons are fermi particles, but the fermi distribution promise > the right states of electrons in the calculations. And i did not find any > explanation about this in the textbook of DFT in my hand. > > As an example, when the temperature is high enough, so that T/T_F is greater than > 1, we can increase the bands window to deal with these cases, i think. Is it > correct for my understanding? > > Thanks a lot. > > Jiayu > Correct - you would use Fermi-Dirac for the electronic occupations, and include enough bands to make sure the the highest bands are almost empty. This is the canonical extension to DFT according to Mermin (look at his Phys Rev papers from the late 60s) - note that the true xc functional would be temperature-dependent, but you would use a 0 temperature one. There might be early work (Singwi ?) on the matter. 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 jwan at phy.cuhk.edu.hk Tue Dec 8 19:37:32 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Wed, 9 Dec 2009 02:37:32 +0800 Subject: [Pw_forum] hyperfine calculation Message-ID: Dear pwscf users Does anyone here have experience on HF calculation using gipaw? I made extensive test on hyperfine tensor calculation using the gipaw code, and I couldn't get reasonable result except free hydrogen atom. For H atom, the Fermi contact term (A_s) obtained (~1480) is within 10% of published work [e.g. Van de Walle and Blochl, PRB 47, 4244 (1993)]. However, the results for Si is unreasonable. The Fermi contact is only ~ 1% of the published data, and the dipole term (A_p) is zero, which is impossible. Jones Wan Published result: A_s ~ 1400 for H, A_s ~ -4200 and A_p ~ -100 [Van de Walle, PRB 47, 4244 (1993)]. My calculation results: HF of H: H 1: g_n = 5.585693 MHz H 1 hfi_dipole 0.000000 0.000000 0.000000 H 1 hfi_dipole 0.000000 0.000000 0.000000 H 1 hfi_dipole 0.000000 0.000000 0.000000 H 1 hfi_dipole 0.000000 0.000000 0.000000 Fermi contact term: bare reconstruction total 0.000000 1484.328021 1484.328021 **** ZORA **** 0.000000 1485.026008 1485.026008 HF of Si: Si 1: g_n = -1.110574 MHz Si 1 hfi_dipole 0.000000 0.000000 0.000000 Si 1 hfi_dipole 0.000000 0.000000 0.000000 Si 1 hfi_dipole 0.000000 0.000000 0.000000 Si 1 hfi_dipole 0.000000 0.000000 0.000000 Fermi contact term: bare reconstruction total 0.000000 45.266354 45.266354 **** ZORA **** 0.000000 42.470825 42.470825 From ceresoli at MIT.EDU Tue Dec 8 20:01:00 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Tue, 08 Dec 2009 14:01:00 -0500 Subject: [Pw_forum] hyperfine calculation In-Reply-To: References: Message-ID: <4B1EA26C.4060802@mit.edu> Jones Tsz-Kai Wan wrote: > Dear pwscf users > > Does anyone here have experience on HF calculation using gipaw? > > I made extensive test on hyperfine tensor calculation using the gipaw > code, and I couldn't get reasonable result except free hydrogen atom. > For H atom, the Fermi contact term (A_s) obtained (~1480) is within > 10% of published work [e.g. Van de Walle and Blochl, PRB 47, 4244 > (1993)]. However, the results for Si is unreasonable. The Fermi > contact is only ~ 1% of the published data, and the dipole term (A_p) > is zero, which is impossible. > > Jones Wan > > Published result: > A_s ~ 1400 for H, A_s ~ -4200 and A_p ~ -100 [Van de Walle, PRB 47, > 4244 (1993)]. Dear Jones Wan, because in Si the spin-density comes from p orbitals. The exchange potential generated by the p orbitals, polarizes slightly the 3s orbital, strongly the 2s electrons, which are not included in the pseudopotential. One has to perform the core-relaxation. For further details, see the following post: http://www.democritos.it/pipermail/pw_forum/2009-September/014475.html Davide From jwan at phy.cuhk.edu.hk Wed Dec 9 03:32:12 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Wed, 9 Dec 2009 10:32:12 +0800 Subject: [Pw_forum] hyperfine calculation In-Reply-To: <4B1EA26C.4060802@mit.edu> References: <4B1EA26C.4060802@mit.edu> Message-ID: Dear Davide, I read the post before. I guess we actually have two problems: the Fermi-contact term and dipole-dipole term. Regarding the Fermi contact term, can you send me the code you mentioned so that I give it a try? Also, I don't think that the core-relaxation would completely cancel the dipole-dipole term. Regards, Jones On Wed, Dec 9, 2009 at 3:01 AM, Davide Ceresoli wrote: > Jones Tsz-Kai Wan wrote: >> Dear pwscf users >> >> Does anyone here have experience on HF calculation using gipaw? >> >> I made extensive test on hyperfine tensor calculation using the gipaw >> code, and I couldn't get reasonable result except free hydrogen atom. >> For H atom, the Fermi contact term (A_s) obtained (~1480) is within >> 10% of published work [e.g. Van de Walle and Blochl, PRB 47, 4244 >> (1993)]. However, the results for Si is unreasonable. The Fermi >> contact is only ~ 1% of the published data, and the dipole term (A_p) >> is zero, which is impossible. >> >> Jones Wan >> >> Published result: >> A_s ~ 1400 for H, A_s ~ -4200 and A_p ~ -100 [Van de Walle, PRB 47, >> 4244 (1993)]. > Dear Jones Wan, > ? ? because in Si the spin-density comes from p orbitals. The exchange > potential generated by the p orbitals, polarizes slightly the 3s orbital, > strongly the 2s electrons, which are not included in the pseudopotential. > One has to perform the core-relaxation. For further details, see the > following post: > http://www.democritos.it/pipermail/pw_forum/2009-September/014475.html > > Davide > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From gregor.mali at ki.si Wed Dec 9 08:02:04 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Wed, 9 Dec 2009 08:02:04 +0100 Subject: [Pw_forum] hyperfine calculation In-Reply-To: References: Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> Dear Jones Wan > > HF of Si: > > Si 1: g_n = -1.110574 MHz > Si 1 hfi_dipole 0.000000 0.000000 0.000000 > Si 1 hfi_dipole 0.000000 0.000000 0.000000 > Si 1 hfi_dipole 0.000000 0.000000 0.000000 > > Si 1 hfi_dipole 0.000000 0.000000 0.000000 > > Fermi contact term: bare reconstruction total > 0.000000 45.266354 45.266354 > **** ZORA **** > 0.000000 42.470825 42.470825 So far I've never obtained dipole coupling equal to zero! Are you sure that there are no mistakes in your spin-polarized scf calculation? (For example, the materials that I study are paramagnetic at room temperature, and antiferromagnetic at low temperature. However, if I want to obtain information on hyperfine coupling related to the paramagnetic state, I start with ferromagnetic arrangement of spins. This arrangement more accurately resembles the state of my material at room temperature and strong external magnetic field. I mention this because one reason for zero dipole term might be antiferromagnetic arrangement of spins. In such an arrangement contributions of neighbouring spins to dipole tensor could cancel one another.) Best regards. Gregor Gregor Mali National Institute of Chemistry Ljubljana, Slovenia From gregor.mali at ki.si Wed Dec 9 09:01:35 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Wed, 9 Dec 2009 09:01:35 +0100 Subject: [Pw_forum] GIPAW and spin-density maps In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> Dear PWscf/GIPAW users, GIPAW module of QE employs (GI)PAW approach to reconstruct wavefunctuions in the core region and then calculates different physical observables that depend a lot on the electronic wavefuction at or close to the nucleus (e.g. chemical shift, hyperfine coupling, ...). Are these reconstructed wavefunctions saved and can they be used by postprocessing routines to generate spin-density maps? If yes, is the procedure then simply: 1. scf calculation, 2. gipaw calculation, 3. postprocessing, where 'prefix' is kept the same in all input files? Thank you. Gregor Mali Gregor Mali National Institute of Chemistry Ljubljana From jwan at phy.cuhk.edu.hk Wed Dec 9 09:02:52 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Wed, 9 Dec 2009 16:02:52 +0800 Subject: [Pw_forum] hyperfine calculation In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> Message-ID: Dear Gregor, I'm just calculating HF tensor of an isolated Si atom, so I don't think magnetic response matters. Below is summary of calculation. QE version 4.1.1 Spin-polarization: 3 up and 1 down Simulation cell: 10-angstrom cubic simulation cell Ewfccut: 30 Ry PP of Si:obtained at http://www-int.impmc.upmc.fr/~software/gipaw/pseudopotentials.html Besides Si atom, I also got zero dipole term for C, N, and O. Regards, Jones On Wed, Dec 9, 2009 at 3:02 PM, Gregor Mali wrote: > Dear Jones Wan > >> >> HF of Si: >> >> ?Si ? 1: g_n = -1.110574 ? ? ? ? ? ? ? ? ?MHz >> ?Si ? 1 ?hfi_dipole ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 >> ?Si ? 1 ?hfi_dipole ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 >> ?Si ? 1 ?hfi_dipole ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 >> >> ?Si ? 1 ?hfi_dipole ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 >> >> Fermi contact term: ? ? ? ?bare ? ? reconstruction ? ? ?total >> ? ? ? ? ? ? ? ? ? ? ? ? ?0.000000 ? ? ?45.266354 ? ? ?45.266354 >> ?**** ZORA **** >> ? ? ? ? ? ? ? ? ? ? ? ? ?0.000000 ? ? ?42.470825 ? ? ?42.470825 > > So far I've never obtained dipole coupling equal to zero! Are you sure > that there are no mistakes in your spin-polarized scf calculation? > > (For example, the materials that I study are paramagnetic at room > temperature, and antiferromagnetic at low temperature. However, if I > want to obtain information on hyperfine coupling related to the > paramagnetic state, I start with ferromagnetic arrangement of spins. > This arrangement more accurately resembles the state of my material at > room temperature and strong external magnetic field. > I mention this because one reason for zero dipole term might be > antiferromagnetic arrangement of spins. In such an arrangement > contributions of neighbouring spins to dipole tensor could cancel one > another.) > > Best regards. > > Gregor > > Gregor Mali > National Institute of Chemistry > Ljubljana, Slovenia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From baroni at sissa.it Wed Dec 9 09:08:22 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 9 Dec 2009 09:08:22 +0100 Subject: [Pw_forum] sorting phonon bands based on symmetry/eigenvectors In-Reply-To: <4B1E6BCA.50806@cnf.cornell.edu> References: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> <4B1D4CAA.70003@cnf.cornell.edu> <20091207195145.0abf4981@lcpybm> <4B1E6BCA.50806@cnf.cornell.edu> Message-ID: Derek: I do not think/know that/if anything is implemented already, but you problem was elegantly addressed some time ago by Karin Rabe who introduced the concept of "vibrational Wannier function" (or something like that). You may want to browse the literature and report to us if you find anything meaningful/interesting. I maintain, though, that the process you want to automate can be automated using IFC as well. Cheers - Stefano On Dec 8, 2009, at 4:07 PM, Derek Stewart wrote: > Hi Miguel, > > Thank you for your quick response and advice. I agree that with the > cheap cost of calculating phonon points once you have the IFC, a visual > inspection of the plot is usually enough to order the phonon dispersion > along a given symmetry line in the Brillouin Zone. > > However, I would like to be able to sort the phonon frequencies for a > large number of q-vectors in the Brillouin zone (not just restricted to > a single symmetry line) and for this it would be very helpful if I can > automate the process. > > I know that for electronic bands, it is possible to determine the > symmetry character of a given electronic band using sym_band.f90. Would > it be possible to use the same subroutines to determine the symmetry > character of the phonon bands? I could then sort based on this output. > If anyone has some thoughts on this, I would be very interested. > > Thanks, > > Derek > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > ** New Webpage ** > http://sites.google.com/site/dft4nano/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > > > > > Miguel Mart?nez wrote: >> Dear Derek, >> >> I recently discovered that plotband.x is also able to plot phonon bands >> as well as band structures. Just set all the references to 0. In any >> case, if you have the IFC you shouldn't have issues distinguishing >> crossing from anticrossing. Adding more points to the dispersion bands >> is almost free, after all. At least it is in the smallish systems I've >> done phonon calculations for. >> >> Regards, >> >> Miguel >> >> On Mon, 07 Dec 2009 13:42:50 -0500 Derek Stewart >> wrote: >> >>> Hi everyone, >>> >>> I was wondering if anyone has written a script or program to sort the >>> phonon frequencies based on their band index or branch. This would >>> be very helpful for both plotting and post-analysis. Currently when >>> you use matdyn for a given set of q-vectors, it prints out the phonon >>> frequencies in order from lowest to highest. However, this does not >>> take into account the possibility of band crossings which can lead to >>> changes in the order of the bands. Matdyn also prints out the >>> eigenvectors for the phonons so it should be possible to analyze this >>> and then sort them. If someone has already addressed this issue, I >>> would be very interested in any tools that can handle this. >>> >>> Thanks, >>> >>> Derek >>> >>> ################################ >>> Derek Stewart, Ph. D. >>> Senior Research Associate >>> ** New Webpage ** >>> http://sites.google.com/site/dft4nano/ >>> 250 Duffield Hall >>> Cornell Nanoscale Facility (CNF) >>> Ithaca, NY 14853 >>> stewart (at) cnf.cornell.edu >>> (607) 255-2856 >>> >>> >>> >>> >>> >>> > > > _______________________________________________ > 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/20091209/54a4ba03/attachment.htm From daijiayu at nudt.edu.cn Wed Dec 9 13:26:49 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Wed, 09 Dec 2009 20:26:49 +0800 Subject: [Pw_forum] nondegenerate electrons in DFT. Message-ID: <460361609.23504@nudt.edu.cn> > > Correct - you would use Fermi-Dirac for the electronic occupations, and > include > enough bands to make sure the the highest bands are almost empty. > Thanks a lot. Therefore, we can deal with the nondegenerate electrons using this way. However, i think the convergence and the computational speed should be a problem in this case. > This is the canonical extension to DFT according to Mermin (look at his > Phys Rev papers > from the late 60s) - note that the true xc functional would be > temperature-dependent, but > you would use a 0 temperature one. There might be early work (Singwi ?) > on the matter. > About the effect of xc functional in MD, there is a work recently talking about it(High Energy Density Physics,5,2009,74). And the found small influence. Therefore, i think we can use a zero temperature xc functional here. Thanks. Jiayu ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From stewart at cnf.cornell.edu Wed Dec 9 17:04:09 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 09 Dec 2009 11:04:09 -0500 Subject: [Pw_forum] sorting phonon bands based on symmetry/eigenvectors In-Reply-To: References: <12251594.273541260015404415.JavaMail.coremail@bj126app104.126.com> <9EE66876-C70D-4C0A-9155-01B3D263DDBE@sissa.it> <4B1D4CAA.70003@cnf.cornell.edu> <20091207195145.0abf4981@lcpybm> <4B1E6BCA.50806@cnf.cornell.edu> Message-ID: <4B1FCA79.5070204@cnf.cornell.edu> Dear Stefano, Thank you very much for the suggestion. I'll see what I can find regarding the vibrational Wannier functions and I will be glad to report back if I come across some interesting options. Regards, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 Stefano Baroni wrote: > Derek: I do not think/know that/if anything is implemented already, > but you problem was elegantly addressed some time ago by Karin Rabe > who introduced the concept of "vibrational Wannier function" (or > something like that). You may want to browse the literature and report > to us if you find anything meaningful/interesting. I maintain, though, > that the process you want to automate can be automated using IFC as > well. Cheers - Stefano > > On Dec 8, 2009, at 4:07 PM, Derek Stewart wrote: > >> Hi Miguel, >> >> Thank you for your quick response and advice. I agree that with the >> cheap cost of calculating phonon points once you have the IFC, a visual >> inspection of the plot is usually enough to order the phonon dispersion >> along a given symmetry line in the Brillouin Zone. >> >> However, I would like to be able to sort the phonon frequencies for a >> large number of q-vectors in the Brillouin zone (not just restricted to >> a single symmetry line) and for this it would be very helpful if I can >> automate the process. >> >> I know that for electronic bands, it is possible to determine the >> symmetry character of a given electronic band using sym_band.f90. Would >> it be possible to use the same subroutines to determine the symmetry >> character of the phonon bands? I could then sort based on this output. >> If anyone has some thoughts on this, I would be very interested. >> >> Thanks, >> >> Derek >> >> ################################ >> Derek Stewart, Ph. D. >> Scientific Computation Associate >> ** New Webpage ** >> http://sites.google.com/site/dft4nano/ >> 250 Duffield Hall >> Cornell Nanoscale Facility (CNF) >> Ithaca, NY 14853 >> stewart (at) cnf.cornell.edu >> (607) 255-2856 >> >> >> >> >> Miguel Mart?nez wrote: >>> Dear Derek, >>> >>> I recently discovered that plotband.x is also able to plot phonon bands >>> as well as band structures. Just set all the references to 0. In any >>> case, if you have the IFC you shouldn't have issues distinguishing >>> crossing from anticrossing. Adding more points to the dispersion bands >>> is almost free, after all. At least it is in the smallish systems I've >>> done phonon calculations for. >>> >>> Regards, >>> >>> Miguel >>> >>> On Mon, 07 Dec 2009 13:42:50 -0500 Derek Stewart >>> wrote: >>> >>>> Hi everyone, >>>> >>>> I was wondering if anyone has written a script or program to sort the >>>> phonon frequencies based on their band index or branch. This would >>>> be very helpful for both plotting and post-analysis. Currently when >>>> you use matdyn for a given set of q-vectors, it prints out the phonon >>>> frequencies in order from lowest to highest. However, this does not >>>> take into account the possibility of band crossings which can lead to >>>> changes in the order of the bands. Matdyn also prints out the >>>> eigenvectors for the phonons so it should be possible to analyze this >>>> and then sort them. If someone has already addressed this issue, I >>>> would be very interested in any tools that can handle this. >>>> >>>> Thanks, >>>> >>>> Derek >>>> >>>> ################################ >>>> Derek Stewart, Ph. D. >>>> Senior Research Associate >>>> ** New Webpage ** >>>> http://sites.google.com/site/dft4nano/ >>>> 250 Duffield Hall >>>> Cornell Nanoscale Facility (CNF) >>>> Ithaca, NY 14853 >>>> stewart (at) cnf.cornell.edu >>>> (607) 255-2856 >>>> >>>> >>>> >>>> >>>> >>>> >> >> >> _______________________________________________ >> 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 > From shanetaylor at u.boisestate.edu Wed Dec 9 20:58:20 2009 From: shanetaylor at u.boisestate.edu (Shane Taylor) Date: Wed, 9 Dec 2009 12:58:20 -0700 Subject: [Pw_forum] compilation error Message-ID: <958e0dde0912091158x4793d78ax98eac38c108b75e3@mail.gmail.com> Dear all, I am using fedora linux, when I try to compile I get the following message: configure: success [shane at Newton espresso-4.1.1]$ make all test -d bin || mkdir bin if test -d iotk ; then \ ( cd iotk ; if test "make" = "" ; then make TLDEPS= lib+util ; \ else make TLDEPS= lib+util ; fi ) ; fi make[1]: Entering directory `/home/shane/Download/espresso-4.1.1/iotk' cd src ; make lib+util make[2]: Entering directory `/home/shane/Download/espresso-4.1.1/iotk/src' ( cd ../../bin ; ln -sf ../iotk/src/iotk_print_kinds.x . ) ( cd ../../bin ; ln -sf ../iotk/src/iotk.x . ) ( cd ../../bin ; ln -sf ../iotk/tools/iotk . ) make[2]: Leaving directory `/home/shane/Download/espresso-4.1.1/iotk/src' make[1]: Leaving directory `/home/shane/Download/espresso-4.1.1/iotk' ( cd Modules ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/home/shane/Download/espresso-4.1.1/Modules' gfortran -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../EE -I../GIPAW -c fft_scalar.f90 gfortran -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../EE -I../GIPAW -c fft_parallel.f90 gfortran -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../EE -I../GIPAW -c griddim.f90 make[1]: Leaving directory `/home/shane/Download/espresso-4.1.1/Modules' ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/home/shane/Download/espresso-4.1.1/clib' cc -O3 -D__GFORTRAN -D__FFTW -I../include -c memstat.c In file included from /usr/include/stdio.h:910, from /usr/include/malloc.h:27, from memstat.c:25: /usr/include/bits/stdio.h: In function ?memstat_?: /usr/include/bits/stdio.h:38: error: nested function ?vprintf? declared ?extern? /usr/include/bits/stdio.h:37: error: static declaration of ?vprintf? follows non-static declaration /usr/include/bits/stdio.h:46: error: nested function ?getchar? declared ?extern? /usr/include/bits/stdio.h:45: error: static declaration of ?getchar? follows non-static declaration /usr/include/stdio.h:522: note: previous declaration of ?getchar? was here /usr/include/bits/stdio.h:55: error: nested function ?fgetc_unlocked? declared ?extern? /usr/include/bits/stdio.h:54: error: static declaration of ?fgetc_unlocked? follows non-static declaration /usr/include/stdio.h:545: note: previous declaration of ?fgetc_unlocked? was here In file included from /usr/include/stdio.h:910, from /usr/include/malloc.h:27, from memstat.c:25: /usr/include/bits/stdio.h:65: error: nested function ?getc_unlocked? declared ?extern? /usr/include/bits/stdio.h:64: error: static declaration of ?getc_unlocked? follows non-static declaration /usr/include/stdio.h:534: note: previous declaration of ?getc_unlocked? was here /usr/include/bits/stdio.h:72: error: nested function ?getchar_unlocked? declared ?extern? /usr/include/bits/stdio.h:71: error: static declaration of ?getchar_unlocked? follows non-static declaration /usr/include/stdio.h:535: note: previous declaration of ?getchar_unlocked? was here /usr/include/bits/stdio.h:81: error: nested function ?putchar? declared ?extern? /usr/include/bits/stdio.h:80: error: static declaration of ?putchar? follows non-static declaration /usr/include/bits/stdio.h:90: error: nested function ?fputc_unlocked? declared ?extern? /usr/include/bits/stdio.h:89: error: static declaration of ?fputc_unlocked? follows non-static declaration /usr/include/bits/stdio.h:100: error: nested function ?putc_unlocked? declared ?extern? /usr/include/bits/stdio.h:99: error: static declaration of ?putc_unlocked? follows non-static declaration /usr/include/bits/stdio.h:107: error: nested function ?putchar_unlocked? declared ?extern? /usr/include/bits/stdio.h:106: error: static declaration of ?putchar_unlocked? follows non-static declaration In file included from /usr/include/stdio.h:910, from /usr/include/malloc.h:27, from memstat.c:25: /usr/include/bits/stdio.h:127: error: nested function ?feof_unlocked? declared ?extern? /usr/include/bits/stdio.h:126: error: static declaration of ?feof_unlocked? follows non-static declaration /usr/include/stdio.h:811: note: previous declaration of ?feof_unlocked? was here /usr/include/bits/stdio.h:134: error: nested function ?ferror_unlocked? declared ?extern? /usr/include/bits/stdio.h:133: error: static declaration of ?ferror_unlocked? follows non-static declaration /usr/include/stdio.h:812: note: previous declaration of ?ferror_unlocked? was here make[1]: *** [memstat.o] Error 1 make[1]: Leaving directory `/home/shane/Download/espresso-4.1.1/clib' make: *** [libs] Error 2 Can someone explain exactly why this doesn't work and how I might go about fixing it? Shane Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091209/d3b67bfb/attachment.htm From jjr19 at zips.uakron.edu Wed Dec 9 21:17:25 2009 From: jjr19 at zips.uakron.edu (James J Ramsey) Date: Wed, 9 Dec 2009 15:17:25 -0500 Subject: [Pw_forum] compilation error In-Reply-To: <958e0dde0912091158x4793d78ax98eac38c108b75e3@mail.gmail.com> References: <958e0dde0912091158x4793d78ax98eac38c108b75e3@mail.gmail.com> Message-ID: <46e014700912091217y226d724dn56a4cc2c78034472@mail.gmail.com> On Wed, Dec 9, 2009 at 2:58 PM, Shane Taylor wrote: > Dear all, > > I am using fedora linux, when I try to compile I get the following message: > cc -O3 -D__GFORTRAN -D__FFTW -I../include? -c memstat.c > In file included from /usr/include/stdio.h:910, > ???????????????? from /usr/include/malloc.h:27, > ???????????????? from memstat.c:25: > /usr/include/bits/stdio.h: In function ?memstat_?: > /usr/include/bits/stdio.h:38: error: nested function ?vprintf? declared > ?extern? > /usr/include/bits/stdio.h:37: error: static declaration of ?vprintf? follows > non-static declaration > /usr/include/bits/stdio.h:46: -- snip -- > Can someone explain exactly why this doesn't work and how I might go about > fixing it? See this e-mail in the archives: http://www.democritos.it/pipermail/pw_forum/2009-October/014531.html Basically, an #include statement is used *inside* a C function, which is both bad style and contrary to the ISO C99 spec. The compiler on your version Fedora is enforcing the spec. From giannozz at democritos.it Wed Dec 9 21:15:04 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 9 Dec 2009 21:15:04 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <958e0dde0912091158x4793d78ax98eac38c108b75e3@mail.gmail.com> References: <958e0dde0912091158x4793d78ax98eac38c108b75e3@mail.gmail.com> Message-ID: On Dec 9, 2009, at 20:58 , Shane Taylor wrote: > > In file included from /usr/include/stdio.h:910, > from /usr/include/malloc.h:27, > from memstat.c:25: > /usr/include/bits/stdio.h: In function ?memstat_?: > /usr/include/bits/stdio.h:38: error: nested function ?vprintf? > declared ?extern? [...] this should be the same problem as here: http://www.democritos.it/pipermail/pw_forum/2009-October/014531.html Modified clib/memstat.c file attached. Will be fixed in all subsequent releases. P. -------------- next part -------------- A non-text attachment was scrubbed... Name: memstat.c Type: application/octet-stream Size: 848 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091209/c89504c7/attachment.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Thu Dec 10 09:02:57 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 10 Dec 2009 09:02:57 +0100 Subject: [Pw_forum] question about constrained magnetization In-Reply-To: <4B1E0D55.7000502@cea.fr> References: <1257860762.11470.15.camel@alex-laptop> <4B166970.70407@cea.fr> <4B1684B9.4090502@sissa.it> <4B1792CB.1010709@cea.fr> <4B17C1FB.3090105@sissa.it> <4B1E0D55.7000502@cea.fr> Message-ID: <4B20AB31.1080403@sissa.it> Cyrille Barreteau wrote: > Dear Gabriele > > The last solution that you provided seems to be the most adapted to my > problem. > The choice of the initial moment is maybe not the most adapted but this I think there is a possibility to fix this as well, but I don't know if this solution may have any bad side effects. You should move the check on starting magnetization after reading the pseudopotential, i.e. right after CALL readpp () AND convert from "starting magnetization" to "starting spin polarization" before checking: ! ! ... read pseudopotentials ! CALL readpp() ! DO nt = 1, ntyp ! IF ( starting_magnetization(nt) == sm_not_set ) THEN starting_magnetization(nt) = 0.0_dp ELSE starting_magnetization(nt) = starting_magnetization(nt)/zv(nt) IF ( starting_magnetization(nt) > 1.0_dp ) THEN starting_magnetization(nt) = 1.0_dp ELSE IF ( starting_magnetization(nt) <-1.0_dp ) THEN starting_magnetization(nt) =-1.0_dp END IF END IF ! END DO starting_magnetization_ = starting_magnetization You will also need to include zv from the ions_base module, by substituting USE ions_base, ONLY : if_pos, ityp, tau, extfor, & with: USE ions_base, ONLY : if_pos, ityp, tau, extfor, zv,& at the beginning of the subroutine iosys. Regards, Gabriele > not a > very big problem.. thanks for this very quick fix:-) > > cyrille > -- 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 Thu Dec 10 14:34:39 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Thu, 10 Dec 2009 19:04:39 +0530 (IST) Subject: [Pw_forum] simulated STM image Message-ID: <43003.172.16.1.1.1260452079.squirrel@172.16.1.1> Dear all, I have been trying to find the simulated STM images for some surfaces. I have some doubts about the procedure: 1) The option of 'stm_wfc_matching' is not working. According to some forum posts, it has been disabled for some latest versions. The working of that option itself was not very clear to me from documentation, but why was that disabled? And if necessary, can I use the wave-functions and charge density files from the latest version for the older version post-processing tools, to get this option working? 2) I am interested to know that because from calculations what we get is ILDOS and we plot it some fixed plane. This will correspond to "constant-height" mode of the STM experiments. However, more common mode in experiments is "constant-current"; and that wave-function matching option has some z and dz parameters which probably were used to get the image corresponding to the latter mode. Is that correct guess? 3) I have seen some papers which give simulated STM images calculated at "constant-current" mode using QE (e.g. - Valentin, JCP 2007). So does there exist some post-processing tool to calculate that? If yes, where can I find it? Thanks and regards, Madhura. -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From padmaja_patnaik at yahoo.co.uk Fri Dec 11 21:17:00 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 11 Dec 2009 20:17:00 +0000 (GMT) Subject: [Pw_forum] Preference of impurity Message-ID: <884255.16332.qm@web26105.mail.ukl.yahoo.com> Dear all My query is not related to Quantum-espresso code, as it is supposed to be in this forum. I want to know which impurities are preferred for a semiconductor for practical use, those creating a shallow level or those creating a deep level ? I would also like to know any material which can give me details of this information. Thanks in advance. Regards 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/20091211/990e438f/attachment.htm From giannozz at democritos.it Sat Dec 12 10:19:54 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Dec 2009 10:19:54 +0100 Subject: [Pw_forum] simulated STM image In-Reply-To: <43003.172.16.1.1.1260452079.squirrel@172.16.1.1> References: <43003.172.16.1.1.1260452079.squirrel@172.16.1.1> Message-ID: On Dec 10, 2009, at 14:34 , Madhura Marathe wrote: > 1) The option of 'stm_wfc_matching' is not working [...] why > was that disabled? because it wasn't working any longer > And if necessary, can I use the wave-functions and charge density > files > from the latest version for the older version post-processing > tools, to > get this option working? no. As far as I know, it has never been working in any public version of QE. It may have worked in some old version lost (forever) in cyberspace. > 2) [...] wave-function matching option has some z and dz parameters > which probably were used to get the image corresponding to the > latter mode. > Is that correct guess? I don't think so. The idea of wavefunction matching is to fit the exponential tail of the wavefunction to an analytical function, thus reducing the noise > 3) I have seen some papers which give simulated STM images > calculated at > "constant-current" mode using QE (e.g. - Valentin, JCP 2007). So does > there exist some post-processing tool to calculate that? not that I know 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 Dec 12 11:28:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Dec 2009 11:28:08 +0100 Subject: [Pw_forum] US or PAW pseudopotentials and Raman spectra In-Reply-To: <4B1C37B9.4070809@ensiacet.fr> References: <4B1C37B9.4070809@ensiacet.fr> Message-ID: On Dec 7, 2009, at 24:01 , damien wrote: > I wanted to know if, in a near future, it will be envisaged to have > an implementation > of Raman spectra with Ultra Soft or/and PAW pseudopotentials? You need to perform a 2nd-order response calculation to an electric field with USPP or PAW. It is not a trivial extension. 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 mtt_turion at hotmail.com Sat Dec 12 12:33:15 2009 From: mtt_turion at hotmail.com (mtt physics) Date: Sat, 12 Dec 2009 18:33:15 +0700 Subject: [Pw_forum] How to calculate a, c/a of BaTiO3 in perrovskite structure In-Reply-To: References: Message-ID: Dear all I have a problem I set alat=7.40 7.41 7.42 7.43 7.44 7.45 7.46 7.47 7.48 7.49 7.50 and I vary clat=1.005 1.010 1.015 1.020 1.025 1.030 1.035 1.040 1.045 1.050 1.055 1.060 1.065 when alat increase clat decrease to neary perfect cubic How I must be going the problem Abdulmutta I am alone > From: pw_forum-request at pwscf.org > Subject: Pw_forum Digest, Vol 30, Issue 23 > To: pw_forum at pwscf.org > Date: Sat, 12 Dec 2009 09:00:38 +0100 > > 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. Preference of impurity (Padmaja Patnaik) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Dec 2009 20:17:00 +0000 (GMT) > From: Padmaja Patnaik > Subject: [Pw_forum] Preference of impurity > To: pw_forum at pwscf.org > Message-ID: <884255.16332.qm at web26105.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > My query is not related to Quantum-espresso code, as it is supposed to be in this forum. I want to know which impurities are preferred for a semiconductor for practical use, those creating a shallow level or those creating a deep level ? I would also like to know any material which can give me details of this information. > Thanks in advance. > > Regards > 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/20091211/990e438f/attachment.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 30, Issue 23 > **************************************** _________________________________________________________________ Windows Live Hotmail: ?????????????????????????????? Facebook ????????????????? Hotmail? http://www.microsoft.com/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:th-th:SI_SB_4:092009 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091212/27bed8e3/attachment.htm From paulatto at sissa.it Sat Dec 12 13:30:53 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 12 Dec 2009 13:30:53 +0100 Subject: [Pw_forum] How to calculate a, c/a of BaTiO3 in perrovskite structure In-Reply-To: References: Message-ID: <20091212133053.yn9y0jyudcc48kwc@webmail.sissa.it> Quoting mtt physics : > when alat increase clat decrease to neary perfect cubic > How I must be going the problem Dear Abdulmutta, that sound all right to me; think of an extreme case: what would cause the anisotropy when the cell parameter is so large that atoms cannot interact with each other any more? Best regards. P.S. try to put some more effort in asking a question, i.e. provide a sample input and output, explanation in detail why do you think there is something wrong, reread what you've written (I'm bad at this). As a rule of thumb, you cannot expect people to spend more time answering that you spent asking. -- 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 Horde http://www.horde.org/ From giannozz at democritos.it Sat Dec 12 15:00:19 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Dec 2009 15:00:19 +0100 Subject: [Pw_forum] GIPAW and spin-density maps In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> <8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> Message-ID: On Dec 9, 2009, at 9:01 , Gregor Mali wrote: > Are these reconstructed wavefunctions saved and can they be used by > postprocessing routines to generate spin-density maps? reconstructed wavefunctions are not saved, and not even calculated, AFAIK, because they consist of two pieces: a "smooth" part, expanded into plane waves, and an "augmentation part", defined on radial grids, centered around the nuclear positions. The info needed to reconstruct all-electron orbitals is available, though. Currently it is possible to plot reconstructed charge densities using PAW (courtesy of Lorenzo) (PAW, not GIPAW), but you need a very dense FFT grid to get decent plots. 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 Sat Dec 12 15:03:24 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Dec 2009 15:03:24 +0100 Subject: [Pw_forum] how to specify initial ion velocities in pw.x In-Reply-To: <5da157840912041042w3598170chdf33892d9b0770ff@mail.gmail.com> References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> <4B18D5C0.1040101@democritos.it> <5da157840912041042w3598170chdf33892d9b0770ff@mail.gmail.com> Message-ID: <48151239-97C5-467C-B9B1-FC03B901AE05@democritos.it> On Dec 4, 2009, at 19:42 , German Samolyuk wrote: > does it mean that if I add after line number 466 of > dynamics_module.f90 > something like > > tau_old(1,100) = tau(1,100) - v_x*dt/alat > tau_old(2,100) = tau(2,100) - v_y*dt/alat > tau_old(3,100) = tau(3,100) - v_z*dt/alat > > it should be equivalent to set up initial velocity (v_x,v_y,v_z) to > particle number 100? quite likely. Unfortunately the way dynamics_mofdule is written makes the seting of initial velocities not straoghtforward > What units is used for dt? Is it atomic Hartree or atomic Rydberg? atomic Rydberg (in PWscf; in CP, atomic Hartree...) 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 madhura at jncasr.ac.in Sun Dec 13 18:00:19 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Sun, 13 Dec 2009 22:30:19 +0530 (IST) Subject: [Pw_forum] simulated STM image In-Reply-To: References: <43003.172.16.1.1.1260452079.squirrel@172.16.1.1> Message-ID: <43373.172.16.1.1.1260723619.squirrel@172.16.1.1> Dear Paolo, Thanks for the reply, but what I really wanted to know is whether there was some bug because of which that option was discontinued or just because it became incompatible with modifications in other part of the code? In the second case, one can just modify its format. However, because it is not for the 'constant-density' mode I guess I won't modify it. Now to get 'constant-density' mode - finding the constant-height STM images at various heights (range relevant for the system under study) and then using 'grep' or something to get required quantity - should work. Is that reasonable process? Or there are some problems with that which I can not see? Thanks once again. Madhura. > > On Dec 10, 2009, at 14:34 , Madhura Marathe wrote: > >> 1) The option of 'stm_wfc_matching' is not working [...] why >> was that disabled? > > because it wasn't working any longer > >> And if necessary, can I use the wave-functions and charge density >> files >> from the latest version for the older version post-processing >> tools, to >> get this option working? > > no. As far as I know, it has never been working in any public version > of QE. > It may have worked in some old version lost (forever) in cyberspace. > >> 2) [...] wave-function matching option has some z and dz parameters >> which probably were used to get the image corresponding to the >> latter mode. >> Is that correct guess? > > I don't think so. The idea of wavefunction matching is to fit the > exponential > tail of the wavefunction to an analytical function, thus reducing the > noise > >> 3) I have seen some papers which give simulated STM images >> calculated at >> "constant-current" mode using QE (e.g. - Valentin, JCP 2007). So does >> there exist some post-processing tool to calculate that? > > not that I know > > 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 > -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From gregor.mali at ki.si Mon Dec 14 09:00:23 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Mon, 14 Dec 2009 09:00:23 +0100 Subject: [Pw_forum] GIPAW and spin-density maps In-Reply-To: References: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si><8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256017CDDA8@postar.ki.si> Dear Paolo, Thank you for the explanation and the suggestion. Gregor > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi > Sent: 12. december 2009 15:00 > To: PWSCF Forum > Subject: Re: [Pw_forum] GIPAW and spin-density maps > > > On Dec 9, 2009, at 9:01 , Gregor Mali wrote: > > > Are these reconstructed wavefunctions saved and can they be used by > > postprocessing routines to generate spin-density maps? > > reconstructed wavefunctions are not saved, and not even > calculated, AFAIK, because they consist of two pieces: a > "smooth" part, expanded into plane waves, and an > "augmentation part", defined on radial grids, centered around > the nuclear positions. The info needed to reconstruct > all-electron orbitals is available, though. > > Currently it is possible to plot reconstructed charge > densities using PAW (courtesy of Lorenzo) (PAW, not GIPAW), > but you need a very dense FFT grid to get decent plots. > > 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 > From fedainanir at yahoo.com Mon Dec 14 20:54:15 2009 From: fedainanir at yahoo.com (fedai inanir) Date: Mon, 14 Dec 2009 11:54:15 -0800 (PST) Subject: [Pw_forum] Problems computing Cholesky decomposition Message-ID: <213123.75882.qm@web114008.mail.gq1.yahoo.com> Dear all, I am trying to run nanotribology computations for a 24-atom graphene-like cluster on monolayer graphene of a 7x7 supercell. However, execution of the code leads to an error message: "Problems computing Cholesky decomposition". I looked up for this in the forum. I tried the recommendations I found out but none of them worked. I also tried diagonalization='david-serial' in the ELECTRONS namespace. I would be delighted if someone has any suggestions to solve this problem. The input file is below: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/fedai/tmp/' , pseudo_dir = '/home/fedai/espresso-4.1/pseudo/' , prefix = 'graphene' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 4, celldm(1) = 32.5350, celldm(3) = 0.2, nat = 152, ntyp = 1, ecutwfc = 32.0 , / &ELECTRONS conv_thr = 1.0d-6 , mixing_beta = 0.3 , diagonalization='cg-serial' / ATOMIC_SPECIES C 12.01000 C.pz-rrkjus.UPF ATOMIC_POSITIONS bohr C 0.000000000 0.000000000 0.000000000 1 1 1 C 2.323902961 -1.341706000 0.000000000 1 1 1 C -2.323902961 4.025118000 0.000000000 1 1 1 C 0.000000000 2.683412000 0.000000000 1 1 1 C -4.647805922 8.050236000 0.000000000 1 1 1 C -2.323902961 6.708530000 0.000000000 1 1 1 C -6.971708882 12.075354000 0.000000000 1 1 1 C -4.647805922 10.733648000 0.000000000 1 1 1 C -9.295611843 16.100472000 0.000000000 1 1 1 C -6.971708882 14.758766000 0.000000000 1 1 1 C -11.619514804 20.125590000 0.000000000 1 1 1 C -9.295611843 18.783884000 0.000000000 1 1 1 C -13.943417765 24.150708000 0.000000000 1 1 1 C -11.619514804 22.809002000 0.000000000 1 1 1 C -16.267320726 28.175826000 0.000000000 1 1 1 C -13.943417765 26.834120000 0.000000000 1 1 1 C 4.647805922 0.000000000 0.000000000 1 1 1 C 6.971708882 -1.341706000 0.000000000 1 1 1 C 2.323902961 4.025118000 0.000000000 1 1 1 C 4.647805922 2.683412000 0.000000000 1 1 1 C 0.000000000 8.050236000 0.000000000 1 1 1 C 2.323902961 6.708530000 0.000000000 1 1 1 C -2.323902961 12.075354000 0.000000000 1 1 1 C 0.000000000 10.733648000 0.000000000 1 1 1 C -4.647805922 16.100472000 0.000000000 1 1 1 C -2.323902961 14.758766000 0.000000000 1 1 1 C -6.971708882 20.125590000 0.000000000 1 1 1 C -4.647805922 18.783884000 0.000000000 1 1 1 C -9.295611843 24.150708000 0.000000000 1 1 1 C -6.971708882 22.809002000 0.000000000 1 1 1 C -11.619514804 28.175826000 0.000000000 1 1 1 C -9.295611843 26.834120000 0.000000000 1 1 1 C 9.295611843 0.000000000 0.000000000 1 1 1 C 11.619514804 -1.341706000 0.000000000 1 1 1 C 6.971708882 4.025118000 0.000000000 1 1 1 C 9.295611843 2.683412000 0.000000000 1 1 1 C 4.647805922 8.050236000 0.000000000 1 1 1 C 6.971708882 6.708530000 0.000000000 1 1 1 C 2.323902961 12.075354000 0.000000000 1 1 1 C 4.647805922 10.733648000 0.000000000 1 1 1 C 0.000000000 16.100472000 0.000000000 1 1 1 C 2.323902961 14.758766000 0.000000000 1 1 1 C -2.323902961 20.125590000 0.000000000 1 1 1 C 0.000000000 18.783884000 0.000000000 1 1 1 C -4.647805922 24.150708000 0.000000000 1 1 1 C -2.323902961 22.809002000 0.000000000 1 1 1 C -6.971708882 28.175826000 0.000000000 1 1 1 C -4.647805922 26.834120000 0.000000000 1 1 1 C 13.943417765 0.000000000 0.000000000 1 1 1 C 16.267320726 -1.341706000 0.000000000 1 1 1 C 11.619514804 4.025118000 0.000000000 1 1 1 C 13.943417765 2.683412000 0.000000000 1 1 1 C 9.295611843 8.050236000 0.000000000 1 1 1 C 11.619514804 6.708530000 0.000000000 1 1 1 C 6.971708882 12.075354000 0.000000000 1 1 1 C 9.295611843 10.733648000 0.000000000 1 1 1 C 4.647805922 16.100472000 0.000000000 1 1 1 C 6.971708882 14.758766000 0.000000000 1 1 1 C 2.323902961 20.125590000 0.000000000 1 1 1 C 4.647805922 18.783884000 0.000000000 1 1 1 C 0.000000000 24.150708000 0.000000000 1 1 1 C 2.323902961 22.809002000 0.000000000 1 1 1 C -2.323902961 28.175826000 0.000000000 1 1 1 C 0.000000000 26.834120000 0.000000000 1 1 1 C 18.591223687 0.000000000 0.000000000 1 1 1 C 20.915126647 -1.341706000 0.000000000 1 1 1 C 16.267320726 4.025118000 0.000000000 1 1 1 C 18.591223687 2.683412000 0.000000000 1 1 1 C 13.943417765 8.050236000 0.000000000 1 1 1 C 16.267320726 6.708530000 0.000000000 1 1 1 C 11.619514804 12.075354000 0.000000000 1 1 1 C 13.943417765 10.733648000 0.000000000 1 1 1 C 9.295611843 16.100472000 0.000000000 1 1 1 C 11.619514804 14.758766000 0.000000000 1 1 1 C 6.971708882 20.125590000 0.000000000 1 1 1 C 9.295611843 18.783884000 0.000000000 1 1 1 C 4.647805922 24.150708000 0.000000000 1 1 1 C 6.971708882 22.809002000 0.000000000 1 1 1 C 2.323902961 28.175826000 0.000000000 1 1 1 C 4.647805922 26.834120000 0.000000000 1 1 1 C 23.239029608 0.000000000 0.000000000 1 1 1 C 25.562932569 -1.341706000 0.000000000 1 1 1 C 20.915126647 4.025118000 0.000000000 1 1 1 C 23.239029608 2.683412000 0.000000000 1 1 1 C 18.591223687 8.050236000 0.000000000 1 1 1 C 20.915126647 6.708530000 0.000000000 1 1 1 C 16.267320726 12.075354000 0.000000000 1 1 1 C 18.591223687 10.733648000 0.000000000 1 1 1 C 13.943417765 16.100472000 0.000000000 1 1 1 C 16.267320726 14.758766000 0.000000000 1 1 1 C 11.619514804 20.125590000 0.000000000 1 1 1 C 13.943417765 18.783884000 0.000000000 1 1 1 C 9.295611843 24.150708000 0.000000000 1 1 1 C 11.619514804 22.809002000 0.000000000 1 1 1 C 6.971708882 28.175826000 0.000000000 1 1 1 C 9.295611843 26.834120000 0.000000000 1 1 1 C 27.886835530 0.000000000 0.000000000 1 1 1 C 30.210738491 -1.341706000 0.000000000 1 1 1 C 25.562932569 4.025118000 0.000000000 1 1 1 C 27.886835530 2.683412000 0.000000000 1 1 1 C 23.239029608 8.050236000 0.000000000 1 1 1 C 25.562932569 6.708530000 0.000000000 1 1 1 C 20.915126647 12.075354000 0.000000000 1 1 1 C 23.239029608 10.733648000 0.000000000 1 1 1 C 18.591223687 16.100472000 0.000000000 1 1 1 C 20.915126647 14.758766000 0.000000000 1 1 1 C 16.267320726 20.125590000 0.000000000 1 1 1 C 18.591223687 18.783884000 0.000000000 1 1 1 C 13.943417765 24.150708000 0.000000000 1 1 1 C 16.267320726 22.809002000 0.000000000 1 1 1 C 11.619514804 28.175826000 0.000000000 1 1 1 C 13.943417765 26.834120000 0.000000000 1 1 1 C 32.534641451 0.000000000 0.000000000 1 1 1 C 34.858544412 -1.341706000 0.000000000 1 1 1 C 30.210738491 4.025118000 0.000000000 1 1 1 C 32.534641451 2.683412000 0.000000000 1 1 1 C 27.886835530 8.050236000 0.000000000 1 1 1 C 30.210738491 6.708530000 0.000000000 1 1 1 C 25.562932569 12.075354000 0.000000000 1 1 1 C 27.886835530 10.733648000 0.000000000 1 1 1 C 23.239029608 16.100472000 0.000000000 1 1 1 C 25.562932569 14.758766000 0.000000000 1 1 1 C 20.915126647 20.125590000 0.000000000 1 1 1 C 23.239029608 18.783884000 0.000000000 1 1 1 C 18.591223687 24.150708000 0.000000000 1 1 1 C 20.915126647 22.809002000 0.000000000 1 1 1 C 16.267320726 28.175826000 0.000000000 1 1 1 C 18.591223687 26.834120000 0.000000000 1 1 1 C 2.323902961 12.075354000 6.670736000 1 1 1 C 2.323902961 14.758766000 6.670736000 1 1 1 C 4.647805922 8.050236000 6.670736000 1 1 1 C 4.647805922 10.733648000 6.670736000 1 1 1 C 4.647805922 16.100472000 6.670736000 1 1 1 C 4.647805922 18.783884000 6.670736000 1 1 1 C 6.971708882 12.075354000 6.670736000 1 1 1 C 6.971708882 14.758766000 6.670736000 1 1 1 C 6.971708882 6.708530000 6.670736000 1 1 1 C 6.971708882 20.125590000 6.670736000 1 1 1 C 9.295611843 8.050236000 6.670736000 1 1 1 C 9.295611843 10.733648000 6.670736000 1 1 1 C 9.295611843 16.100472000 6.670736000 1 1 1 C 9.295611843 18.783884000 6.670736000 1 1 1 C 11.619514804 6.708530000 6.670736000 1 1 1 C 11.619514804 12.075354000 6.670736000 1 1 1 C 11.619514804 14.758766000 6.670736000 1 1 1 C 11.619514804 20.125590000 6.670736000 1 1 1 C 13.943417765 8.050236000 6.670736000 1 1 1 C 13.943417765 10.733648000 6.670736000 1 1 1 C 13.943417765 16.100472000 6.670736000 1 1 1 C 13.943417765 18.783884000 6.670736000 1 1 1 C 16.267320726 12.075354000 6.670736000 1 1 1 C 16.267320726 14.758766000 6.670736000 1 1 1 K_POINTS automatic 7 7 1 0 0 0 Dr. Fedai Inanir Rize University Deparment of Physics Rize Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091214/619cb4fa/attachment.htm From afloris at physik.fu-berlin.de Mon Dec 14 23:01:36 2009 From: afloris at physik.fu-berlin.de (Andrea Floris) Date: Mon, 14 Dec 2009 23:01:36 +0100 (CET) Subject: [Pw_forum] electron-phonon and nspin=2 Message-ID: Dear users, I have a question about el-ph calculation in magnetic systems (nspin). In PH/phq_readin.f90, there is the line IF (elph.AND.lsda) CALL errore ('phq_readin', 'El-ph and spin not & implemented', 1) that stops a el-ph calculation when nspin=2.. But having a look at the file PH/elphon.f90 (containing the routines elphon, elphel and elphsum) I think that the current implementation allows for such a calculation (unless really minor modifications are needed). In fact in the wavefunctions the spin is attached to the k point, and the scf perturbed potential dvscfin (i.e. dV_Hxc(is)) is always spin resolved. So the elph matrix-elements will be spin dependent through the k point, coupling always k and (k+q) states with the same spin. Of course one can always comment out the line, but my question is: Is there a particular reason for this call in PH/phq_readin.f90? Or is it just because k-summed quantities like total \lambda or the linewiths will not be printed in a spin resolved way? Thank for your answer, Andrea --------------- Dr. Andrea Floris Institut fuer Theoretische Physik Freie Universitaet Berlin Arnimallee 14 D-14195 Berlin Germany e-mail: andrea.floris at fu-berlin.de From sclauzer at sissa.it Tue Dec 15 08:42:48 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 15 Dec 2009 08:42:48 +0100 Subject: [Pw_forum] Problems computing Cholesky decomposition In-Reply-To: <213123.75882.qm@web114008.mail.gq1.yahoo.com> References: <213123.75882.qm@web114008.mail.gq1.yahoo.com> Message-ID: <4B273DF8.4090207@sissa.it> Dear Fedai, fedai inanir wrote: > Dear all, > > I am trying to run nanotribology computations for a 24-atom > graphene-like cluster on monolayer graphene of a 7x7 supercell. However, > execution of the code leads to an error message: "Problems computing > Cholesky decomposition". I looked up for this in the forum. I tried the > recommendations I found out but none of them worked. I also tried > diagonalization='david-serial' in the ELECTRONS namespace. I would be > delighted if someone has any suggestions to solve this problem. > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 32.5350, > > celldm(3) = 0.2, > > nat = 152, > > ntyp = 1, > > ecutwfc = 32.0 , > > ATOMIC_SPECIES > > C 12.01000 C.pz-rrkjus.UPF > You are using an ultrasoft pseudopotential, hence you need to specify a cutoff for the charge density as well, ecutrho > 4*ecutwfc. People choose ecutrho ~ 8*ecutwfc, but it is usually good habit to check convergence when you start using a pseudopotential file. Anyway the problem is in your input atomic coordinates, I think. The atoms at z=6.670736000 are too close to those at x=0. Remember that the code uses PBCs in all three directions! Probably you need to change celldm(3) to a more suitable value. Try to visualize your system with xcrysden before repeating the calculation. Also I would suggest to start with simpler examples and get used to the code input/output before moving to systems with hundreds of atoms. Regards, Gabriele > > > Dr. Fedai Inanir > Rize University > Deparment of Physics > Rize > Turkey > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 giannozz at democritos.it Tue Dec 15 09:24:51 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Dec 2009 09:24:51 +0100 Subject: [Pw_forum] electron-phonon and nspin=2 In-Reply-To: References: Message-ID: <4B2747D3.20003@democritos.it> Andrea Floris wrote: > IF (elph.AND.lsda) CALL errore ('phq_readin', 'El-ph and spin not & > implemented', 1) I think spin-polarized electron-phonon calculations are implemented, but untested. Since nobody has ever reported if it works, the check is still there. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From yukihiro_okuno at fujifilm.co.jp Wed Dec 16 04:23:53 2009 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Wed, 16 Dec 2009 12:23:53 +0900 Subject: [Pw_forum] How to Download GWW Message-ID: Dear PWSCF users. I'm interested in the GWW of PWSCF. http://gww.qe-forge.org/index.php?page=intro , and want to use it. But the anonymous cvs need the password and further the server https://qe-forge.org/projects/q-e cannot be connected. How to download the GWW ? Or, GWW is not opened for anonymous users ? Sincerely. Yukihiro Okuno. From sclauzer at sissa.it Wed Dec 16 08:35:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 16 Dec 2009 08:35:45 +0100 Subject: [Pw_forum] How to Download GWW In-Reply-To: References: Message-ID: <4B288DD1.1090606@sissa.it> Dear Yukihiro, yukihiro_okuno at fujifilm.co.jp wrote: > Dear PWSCF users. > > I'm interested in the GWW of PWSCF. > > http://gww.qe-forge.org/index.php?page=intro > > , and want to use it. > > But the anonymous cvs need the password and further the server > > https://qe-forge.org/projects/q-e the above address is wrong, you should use http://qe-forge.org/projects/q-e instead. Please follow the instructions for anonymous CVS download, available at http://qe-forge.org/scm/?group_id=10 or download the latest nightly snapshot from http://qe-forge.org/snapshots.php?group_id=10 HTH GS > > cannot be connected. > > How to download the GWW ? > > Or, GWW is not opened for anonymous users ? > > > Sincerely. > > Yukihiro Okuno. > > _______________________________________________ > 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 zxf888 at 163.com Wed Dec 16 15:57:06 2009 From: zxf888 at 163.com (Xiang-Feng Zhou) Date: Wed, 16 Dec 2009 22:57:06 +0800 (CST) Subject: [Pw_forum] problem of q2r.in In-Reply-To: References: Message-ID: <4418248.295951260975426906.JavaMail.coremail@bj163app134.163.com> Dear Members, I felt sorry to ask the problem again because it seems there is a hint in the archive of the forum. I am testing electron phonon interaction (EPI) by using espresso-4.1 now. I succeeded in reproducing the results of example 07. However, I am failed in applying it to other systems due to the errors message coming from ?q2r.x.? forrtl: severe (59): list-directed I/O syntax error, unit 51, file /home/zxf/work-pwscf/restart-bc5/a2Fq2r.51 Image PC Routine Line Source q2r.x 00000000009BB67E Unknown Unknown Unknown q2r.x 00000000009BA87E Unknown Unknown Unknown q2r.x 000000000097FBFE Unknown Unknown Unknown q2r.x 000000000092A15D Unknown Unknown Unknown q2r.x 0000000000929A4A Unknown Unknown Unknown q2r.x 0000000000950B01 Unknown Unknown Unknown q2r.x 000000000094F7CD Unknown Unknown Unknown q2r.x 000000000040E6CF Unknown Unknown Unknown q2r.x 0000000000409C0D Unknown Unknown Unknown q2r.x 00000000004075C2 Unknown Unknown Unknown libc.so.6 000000324CA1D974 Unknown Unknown Unknown q2r.x 00000000004074E9 Unknown Unknown Unknown Considering the success of example07 in comparison to the failure of my test, I guess whether the failure come from the format of my input or other reasons? The corresponding files are as follows (bc.scf.fit.in, bc.scf.in, and bc.elph.in run smoothly, q2r.in failed): Any suggestions are greatly appreciated. Thanks in advance. Best regards, Xiang-Feng Zhou School of Physics, NankaiUniversity Tianjin, China bc.scf.fit.in &control calculation='scf' restart_mode='from_scratch', prefix='bc', pseudo_dir = '/home/zxf/pseudo_pwscf/', outdir='/home/zxf/temp/' / &system ibrav = 4, A = 2.50224, B = 2.50224, C = 6.27537, cosAB = 0.0, cosAC = 0.0, cosBC = -0.5, nat = 6, ntyp = 2, ecutwfc = 65.0 , occupations='smearing', smearing='methfessel-paxton', degauss=0.05, la2F = .true., / &electrons conv_thr = 1.0d-12 mixing_beta = 0.7 / ATOMIC_SPECIES B 10.81100 B.pz-vbc.UPF C 12.01099 C.pz-vbc.UPF ATOMIC_POSITIONS {crystal} B 0.000000000 0.000000000 0.007174590 C 0.000000000 0.000000000 0.259639975 C 0.333333333 0.666666667 0.338266995 C 0.333333333 0.666666667 0.581696984 C 0.666666667 0.333333333 0.664374798 C 0.666666667 0.333333333 0.899914618 K_POINTS {automatic} 16 16 16 0 0 0 bc.scf.in &control calculation='scf' restart_mode='from_scratch', prefix='bc', pseudo_dir = '/home/zxf/pseudo_pwscf/', outdir='/home/zxf/temp/' / &system ibrav = 4, A = 2.50224, B = 2.50224, C = 6.27537, cosAB = 0.0, cosAC = 0.0, cosBC = -0.5, nat = 6, ntyp = 2, ecutwfc = 65.0 , occupations='smearing', smearing='methfessel-paxton', degauss=0.05 / &electrons conv_thr = 1.0d-12 mixing_beta = 0.7 / ATOMIC_SPECIES B 10.81100 B.pz-vbc.UPF C 12.01099 C.pz-vbc.UPF ATOMIC_POSITIONS {crystal} B 0.000000000 0.000000000 0.007174590 C 0.000000000 0.000000000 0.259639975 C 0.333333333 0.666666667 0.338266995 C 0.333333333 0.666666667 0.581696984 C 0.666666667 0.333333333 0.664374798 C 0.666666667 0.333333333 0.899914618 K_POINTS {automatic} 8 8 8 0 0 0 bc.elph.in Electron-phonon coefficients for Al &inputph tr2_ph=1.0d-10, prefix='bc', fildvscf='bcdv', amass(1)=10.81100, amass(2)=12.01099, outdir='/home/zxf/temp/', fildyn='bc.dyn', elph=.true., trans=.true., ldisp=.true. nq1=4, nq2=4, nq3=4 / q2r.in &input zasr='simple', fildyn='bc.dyn', flfrc='bc444.fc', la2F=.true. / matdyn.in.freq &input asr='simple', amass(1)=10.81100, amass(2)=12.01099, flfrc='bc5444.fc', flfrq='bc5444.freq', la2F=.true., dos=.false. / 76 0.000000 0.000000 0.000000 0 0.000000 0.000000 0.100000 0 0.000000 0.000000 0.200000 0 0.000000 0.000000 0.300000 0 0.000000 0.000000 0.400000 0 0.000000 0.000000 0.500000 0 -0.018519 0.037037 0.500000 0 -0.037037 0.074074 0.500000 0 -0.055556 0.111111 0.500000 0 -0.074074 0.148148 0.500000 0 -0.092593 0.185185 0.500000 0 -0.111111 0.222222 0.500000 0 -0.129630 0.259259 0.500000 0 -0.148148 0.296296 0.500000 0 -0.166667 0.333333 0.500000 0 -0.185185 0.370370 0.500000 0 -0.203704 0.407407 0.500000 0 -0.222222 0.444444 0.500000 0 -0.240741 0.481481 0.500000 0 -0.259259 0.518519 0.500000 0 -0.277778 0.555556 0.500000 0 -0.296296 0.592593 0.500000 0 -0.314815 0.629630 0.500000 0 -0.333333 0.666667 0.500000 0 -0.333333 0.666667 0.400000 0 -0.333333 0.666667 0.300000 0 -0.333333 0.666667 0.200000 0 -0.333333 0.666667 0.100000 0 -0.333333 0.666667 0.000000 0 -0.314815 0.629630 0.000000 0 -0.296296 0.592593 0.000000 0 -0.277778 0.555556 0.000000 0 -0.259259 0.518519 0.000000 0 -0.240741 0.481481 0.000000 0 -0.222222 0.444444 0.000000 0 -0.203704 0.407407 0.000000 0 -0.185185 0.370370 0.000000 0 -0.166667 0.333333 0.000000 0 -0.148148 0.296296 0.000000 0 -0.129630 0.259259 0.000000 0 -0.111111 0.222222 0.000000 0 -0.092593 0.185185 0.000000 0 -0.074074 0.148148 0.000000 0 -0.055556 0.111111 0.000000 0 -0.037037 0.074074 0.000000 0 -0.018519 0.037037 0.000000 0 0.000000 0.000000 0.000000 0 0.000000 0.033333 0.000000 0 0.000000 0.066667 0.000000 0 0.000000 0.100000 0.000000 0 0.000000 0.133333 0.000000 0 0.000000 0.166667 0.000000 0 0.000000 0.200000 0.000000 0 0.000000 0.233333 0.000000 0 0.000000 0.266667 0.000000 0 0.000000 0.300000 0.000000 0 0.000000 0.333333 0.000000 0 0.000000 0.366667 0.000000 0 0.000000 0.400000 0.000000 0 0.000000 0.433333 0.000000 0 0.000000 0.466667 0.000000 0 0.000000 0.500000 0.000000 0 0.000000 0.500000 0.100000 0 0.000000 0.500000 0.200000 0 0.000000 0.500000 0.300000 0 0.000000 0.500000 0.400000 0 0.000000 0.500000 0.500000 0 -0.037037 0.518519 0.500000 0 -0.074074 0.537037 0.500000 0 -0.111111 0.555556 0.500000 0 -0.148148 0.574074 0.500000 0 -0.185185 0.592593 0.500000 0 -0.222222 0.611111 0.500000 0 -0.259259 0.629630 0.500000 0 -0.296296 0.648148 0.500000 0 -0.333333 0.666667 0.500000 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091216/a43f9214/attachment-0001.htm From samolyuk at gmail.com Wed Dec 16 16:46:37 2009 From: samolyuk at gmail.com (German Samolyuk) Date: Wed, 16 Dec 2009 10:46:37 -0500 Subject: [Pw_forum] how to specify initial ion velocities in pw.x In-Reply-To: <48151239-97C5-467C-B9B1-FC03B901AE05@democritos.it> References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> <4B18D5C0.1040101@democritos.it> <5da157840912041042w3598170chdf33892d9b0770ff@mail.gmail.com> <48151239-97C5-467C-B9B1-FC03B901AE05@democritos.it> Message-ID: <5da157840912160746k253c5af9ld620c33be3cf5a3a@mail.gmail.com> Thank you! It works. German. German Samolyuk, Oak Ridge National Laboratory, USA On Sat, Dec 12, 2009 at 9:03 AM, Paolo Giannozzi wrote: > > On Dec 4, 2009, at 19:42 , German Samolyuk wrote: > >> does it mean that if I add after line number 466 of >> dynamics_module.f90 >> something like >> >> tau_old(1,100) = tau(1,100) - v_x*dt/alat >> tau_old(2,100) = tau(2,100) - v_y*dt/alat >> tau_old(3,100) = tau(3,100) - v_z*dt/alat >> >> it should be equivalent to set up initial velocity (v_x,v_y,v_z) to >> particle number 100? > > quite likely. Unfortunately the way dynamics_mofdule is written makes > the seting of initial velocities not straoghtforward > >> What units is used for dt? Is it atomic Hartree or atomic Rydberg? > > atomic Rydberg (in PWscf; in CP, atomic Hartree...) > > 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 > From majdoub at gmail.com Wed Dec 16 18:02:41 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 11:02:41 -0600 Subject: [Pw_forum] graphene on BN calculation Message-ID: Dear all, I am a new user of pwscf. I am trying to run a calculation of graphene (1 layer) on BN (2 layers) in a supercell with vacuum. After that I need to run the same system in the presence of a saw tooth potential and get the potential file as output. I am not sure that I am doing it the right way. I am using 40 processors and I the calculations look very slow to me. I really appreciate your help and suggestions for this calculation. Thank you in advance for your help. Sab Maj Department of Mechanical Engineering University of Houston Here is my input file: &control title = 'GphBN' calculation = 'relax' outdir = '/pwscf/pwscftemp/relaxGphBN' prefix = 'GphBN' pseudo_dir = '/pwscf/input/Gph-BN/pseudopot-C-B-N' verbosity = 'high' tprnfor = .t. tstress = .t. restart_mode = 'from_scratch' / &system ibrav = 0, celldm(1) = 1.0 nat = 72, ntyp = 3, ecutwfc = 25.0 ecutrho = 250.0 occupations = 'smearing' smearing = 'gaussian' degauss = 0.003675 / &electrons mixing_beta = 0.05 diagonalization = 'cg' / &ions trust_radius_ini = 0.10 / &cell ATOMIC_SPECIES B 10.81100 B.pz-vbc.UPF C 12.01070 C.pz-vbc.UPF N 14.00674 N.pz-vbc.UPF ATOMIC_POSITIONS angstrom B 0.710000 8.607000 11.306000 B 0.710000 11.066000 11.306000 B 2.840000 7.377000 11.306000 B 0.710000 6.148000 11.306000 B 6.390000 6.148000 8.000000 B 6.390000 8.607000 8.000000 B 6.390000 11.066000 8.000000 B 2.840000 9.836000 11.306000 B 7.100000 7.377000 11.306000 B 7.100000 9.836000 11.306000 B 7.100000 12.295000 11.306000 B 4.970000 11.066000 11.306000 B 2.840000 12.295000 11.306000 B 4.970000 6.148000 11.306000 B 4.970000 8.607000 11.306000 B 4.260000 7.377000 8.000000 B 2.130000 11.066000 8.000000 B 2.130000 8.607000 8.000000 B 2.130000 6.148000 8.000000 B 4.260000 9.836000 8.000000 B 0.000000 7.377000 8.000000 B 0.000000 9.836000 8.000000 B 4.260000 12.295000 8.000000 B 0.000000 12.295000 8.000000 C 2.130000 6.148000 14.612000 C 2.130000 8.607000 14.612000 C 2.130000 11.066000 14.612000 C 0.000000 12.295000 14.612000 C 0.000000 9.836000 14.612000 C 0.000000 7.377000 14.612000 C 0.710000 11.066000 14.612000 C 0.710000 8.607000 14.612000 C 0.710000 6.148000 14.612000 C 6.390000 8.607000 14.612000 C 6.390000 6.148000 14.612000 C 4.970000 11.066000 14.612000 C 6.390000 11.066000 14.612000 C 7.100000 12.295000 14.612000 C 7.100000 9.836000 14.612000 C 7.100000 7.377000 14.612000 C 4.970000 8.607000 14.612000 C 2.840000 12.295000 14.612000 C 2.840000 9.836000 14.612000 C 2.840000 7.377000 14.612000 C 4.260000 7.377000 14.612000 C 4.970000 6.148000 14.612000 C 4.260000 12.295000 14.612000 C 4.260000 9.836000 14.612000 N 0.000000 12.295000 11.306000 N 0.000000 9.836000 11.306000 N 0.000000 7.377000 11.306000 N 2.840000 7.377000 8.000000 N 2.840000 9.836000 8.000000 N 2.840000 12.295000 8.000000 N 4.970000 11.066000 8.000000 N 4.970000 8.607000 8.000000 N 4.970000 6.148000 8.000000 N 7.100000 12.295000 8.000000 N 7.100000 9.836000 8.000000 N 7.100000 7.377000 8.000000 N 0.710000 6.148000 8.000000 N 0.710000 8.607000 8.000000 N 0.710000 11.066000 8.000000 N 6.390000 11.066000 11.306000 N 6.390000 8.607000 11.306000 N 6.390000 6.148000 11.306000 N 2.130000 11.066000 11.306000 N 2.130000 8.607000 11.306000 N 2.130000 6.148000 11.306000 N 4.260000 12.295000 11.306000 N 4.260000 9.836000 11.306000 N 4.260000 7.377000 11.306000 K_POINTS automatic 30 30 1 1 1 0 CELL_PARAMETERS 8.51980 0.00000 0.00000 0.00000 7.37600 0.00000 0.00000 0.00000 22.6120 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091216/69dd3ecb/attachment.htm From paulatto at sissa.it Wed Dec 16 18:22:28 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 16 Dec 2009 18:22:28 +0100 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] graphene on BN calculation" from mohamed sabri majdoub (16/12/09): > I am not sure that I am doing it the right way. I am using 40 processors > and I the calculations look very slow to me. Well, it's a big system. You can speed it up by using tqr=.true. (real-space augmentation charge). There is also an experimental real-space algorithm, but I don't know how reliable it is at the moment (you can contact baris _at_ sissa.it for additional info). > tstress = .t. there is no need to print the stress, and it takes time to compute (not much) > diagonalization = 'cg' For better performance you should use the default (david). If you have some problem with it, you should ask for help on the forum before falling back to cg, which is non much more robust and quite a bit slower. Also, diagonalization errors are most of the time input errors/bad atomic positions. > K_POINTS automatic > 30 30 1 1 1 0 this is a huge number of k-points for such a cell, are you sure you need all of them? Remember that every time you increase the cell size by N you can reduce the number of k-points by the same factor. (e.g. a 2x2x2 super-cell only need on eighth of the k-points of the original cell). Computation time scales linearly with the number of points, e.g. "10 10 1 1 1 0" will be about 9 times faster. 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 ceresoli at MIT.EDU Wed Dec 16 20:37:02 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Wed, 16 Dec 2009 14:37:02 -0500 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: References: Message-ID: <4B2936DE.5020008@mit.edu> mohamed sabri majdoub wrote: > Dear all, > > I am a new user of pwscf. > I am trying to run a calculation of graphene (1 layer) on BN (2 layers) > in a supercell with vacuum. > After that I need to run the same system in the presence of a saw tooth > potential and get the potential file as output. > I am not sure that I am doing it the right way. I am using 40 processors > and I the calculations look very slow to me. > I really appreciate your help and suggestions for this calculation. > Thank you in advance for your help. > > Sab Maj Dear Sab Maj, have a look at your structure with XCrysden. There is something wrong with the lattice spacing. Atoms are sitting on top of each other. Remember that celldm(1) is in bohrradius, not in angstrom. This can save you a lot of time! Davide -- +----------------------------------------------------------+ Davide Ceresoli DMSE 13-4084 Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge, MA 02139-4307 Phone: (617) 253-6026 Mobile:(857) 756-0455, +39-347-1001570(it) Skype: dceresoli +----------------------------------------------------------+ From majdoub at gmail.com Wed Dec 16 21:06:33 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 14:06:33 -0600 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: References: Message-ID: Thank you a lot Mr Lorenzo for your suggestions. I will try them and thank you again for your help. Regards, On Wed, Dec 16, 2009 at 11:22 AM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] graphene on BN calculation" from mohamed > sabri majdoub (16/12/09): > > > I am not sure that I am doing it the right way. I am using 40 processors > > and I the calculations look very slow to me. > > Well, it's a big system. You can speed it up by using tqr=.true. > (real-space augmentation charge). There is also an experimental real-space > algorithm, but I don't know how reliable it is at the moment (you can > contact baris _at_ sissa.it for additional info). > > > tstress = .t. > > there is no need to print the stress, and it takes time to compute (not > much) > > > diagonalization = 'cg' > > For better performance you should use the default (david). If you have > some problem with it, you should ask for help on the forum before falling > back to cg, which is non much more robust and quite a bit slower. Also, > diagonalization errors are most of the time input errors/bad atomic > positions. > > > > K_POINTS automatic > > 30 30 1 1 1 0 > > this is a huge number of k-points for such a cell, are you sure you need > all of them? Remember that every time you increase the cell size by N you > can reduce the number of k-points by the same factor. (e.g. a 2x2x2 > super-cell only need on eighth of the k-points of the original cell). > Computation time scales linearly with the number of points, e.g. "10 10 1 > 1 1 0" will be about 9 times faster. > > 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/20091216/d709db9e/attachment-0001.htm From majdoub at gmail.com Wed Dec 16 21:13:15 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 14:13:15 -0600 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: <4B2936DE.5020008@mit.edu> References: <4B2936DE.5020008@mit.edu> Message-ID: Dear Davide, Thank you very much for your help. I build the structure my self and I extensionally put the atoms of graphene and BN layers on the top of each other. I have to try also 2 other configurations where BN layers are not centred on the carbon atoms in graphene. Do you think there is a problem with this configuration? (I am using VMD to visualize the structure). What is wrong in the lattice spacing? What do you mean? Thank you for pointing out that celldim(1) is in bohrradius. I will correct it. Thanks a lot! On Wed, Dec 16, 2009 at 1:37 PM, Davide Ceresoli wrote: > mohamed sabri majdoub wrote: > > Dear all, > > > > I am a new user of pwscf. > > I am trying to run a calculation of graphene (1 layer) on BN (2 layers) > > in a supercell with vacuum. > > After that I need to run the same system in the presence of a saw tooth > > potential and get the potential file as output. > > I am not sure that I am doing it the right way. I am using 40 processors > > and I the calculations look very slow to me. > > I really appreciate your help and suggestions for this calculation. > > Thank you in advance for your help. > > > > Sab Maj > Dear Sab Maj, > have a look at your structure with XCrysden. There is something > wrong with the lattice spacing. Atoms are sitting on top of each > other. Remember that celldm(1) is in bohrradius, not in angstrom. > This can save you a lot of time! > > Davide > > > -- > +----------------------------------------------------------+ > Davide Ceresoli > DMSE 13-4084 > Massachusetts Institute of Technology > 77 Massachusetts Avenue > Cambridge, MA 02139-4307 > Phone: (617) 253-6026 > Mobile:(857) 756-0455, +39-347-1001570(it) > Skype: dceresoli > +----------------------------------------------------------+ > _______________________________________________ > 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/20091216/8c881dc1/attachment.htm From ceresoli at MIT.EDU Wed Dec 16 21:45:28 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Wed, 16 Dec 2009 15:45:28 -0500 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: References: <4B2936DE.5020008@mit.edu> Message-ID: <4B2946E8.4020509@mit.edu> mohamed sabri majdoub wrote: > Dear Davide, > > Thank you very much for your help. > I build the structure my self and I extensionally put the atoms of > graphene and BN layers on the top of each other. > I have to try also 2 other configurations where BN layers are not > centred on the carbon atoms in graphene. > Do you think there is a problem with this configuration? (I am using VMD > to visualize the structure). > What is wrong in the lattice spacing? What do you mean? > Thank you for pointing out that celldim(1) is in bohrradius. I think you should enter: celldm(1) = 1.8897261 (1.8897261 = 1/0.052917721). Davide From ceresoli at MIT.EDU Wed Dec 16 21:51:06 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Wed, 16 Dec 2009 15:51:06 -0500 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: <4B2946E8.4020509@mit.edu> References: <4B2936DE.5020008@mit.edu> <4B2946E8.4020509@mit.edu> Message-ID: <4B29483A.2080407@mit.edu> Davide Ceresoli wrote: > (1.8897261 = 1/0.052917721). I meant: (1.8897261 = 1/0.52917721). From majdoub at gmail.com Wed Dec 16 22:00:33 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 15:00:33 -0600 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: <4B29483A.2080407@mit.edu> References: <4B2936DE.5020008@mit.edu> <4B2946E8.4020509@mit.edu> <4B29483A.2080407@mit.edu> Message-ID: I got it Davide. You mean conversion from angstrom to Bohr radius close to 0.53 Angstrom. So, there is no other problem except this that you noticed. Thank you very much again. On Wed, Dec 16, 2009 at 2:51 PM, Davide Ceresoli wrote: > Davide Ceresoli wrote: > > (1.8897261 = 1/0.052917721). > I meant: (1.8897261 = 1/0.52917721). > > _______________________________________________ > 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/20091216/2ef7a9a2/attachment.htm From majdoub at gmail.com Wed Dec 16 23:24:16 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 16:24:16 -0600 Subject: [Pw_forum] Saw tooth potential details Message-ID: Dear users, I was reading the documentation for the saw tooth like potential in pwscf. However, I still did not understood it in full. Can anybody gives me more details about how the potential is implemented. I need to apply an electric field to a supercell of graphene and BN layers with both ends in vacuum. eamp = 0.002. Amplitude of the electric field (in a.u. = 51.44 10^10 V/m ) The sawlike potential increases with slope "eamp" in the region from (emaxpos+eopreg-1) to (emaxpos), then decreases to 0 until (emaxpos+eopreg), in units of the crystal vector "edir". Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result. Used only if tefield is .TRUE. The following keywords that need to be used are still not clear. In particular the position of the slope change.Does it need to be in vacuum? emaxpos=0.5 (Position of the maximum of the sawlike potential along crystal axis "edir"); eopreg=0.5 (Zone in the unit cell where the sawlike potential decreases.)? How the sawlike potential is modeled. Thank you in advance for your help and comment. Here is the system I want to apply electric field to it: &control title = 'GphBN' calculation = 'relax' outdir = '/pwscf/pwscftemp/relaxGphBN' prefix = 'GphBN' pseudo_dir = /pwscf/input/Gph-BN/pseudopot-C-B-N' verbosity = 'high' tprnfor = .t. restart_mode = 'from_scratch' / &system ibrav = 0, celldm(1) = 1.8897261 nat = 72, ntyp = 3, ecutwfc = 25.0 ecutrho = 250.0 occupations = 'smearing' smearing = 'gaussian' degauss = 0.003675 / &electrons mixing_beta = 0.05 diagonalization = 'david' / &ions trust_radius_ini = 0.10 / &cell ATOMIC_SPECIES B 10.81100 B.pz-vbc.UPF C 12.01070 C.pz-vbc.UPF N 14.00674 N.pz-vbc.UPF ATOMIC_POSITIONS angstrom B 0.710000 8.607000 11.306000 B 0.710000 11.066000 11.306000 B 2.840000 7.377000 11.306000 B 0.710000 6.148000 11.306000 B 6.390000 6.148000 8.000000 B 6.390000 8.607000 8.000000 B 6.390000 11.066000 8.000000 B 2.840000 9.836000 11.306000 B 7.100000 7.377000 11.306000 B 7.100000 9.836000 11.306000 B 7.100000 12.295000 11.306000 B 4.970000 11.066000 11.306000 B 2.840000 12.295000 11.306000 B 4.970000 6.148000 11.306000 B 4.970000 8.607000 11.306000 B 4.260000 7.377000 8.000000 B 2.130000 11.066000 8.000000 B 2.130000 8.607000 8.000000 B 2.130000 6.148000 8.000000 B 4.260000 9.836000 8.000000 B 0.000000 7.377000 8.000000 B 0.000000 9.836000 8.000000 B 4.260000 12.295000 8.000000 B 0.000000 12.295000 8.000000 C 2.130000 6.148000 14.612000 C 2.130000 8.607000 14.612000 C 2.130000 11.066000 14.612000 C 0.000000 12.295000 14.612000 C 0.000000 9.836000 14.612000 C 0.000000 7.377000 14.612000 C 0.710000 11.066000 14.612000 C 0.710000 8.607000 14.612000 C 0.710000 6.148000 14.612000 C 6.390000 8.607000 14.612000 C 6.390000 6.148000 14.612000 C 4.970000 11.066000 14.612000 C 6.390000 11.066000 14.612000 C 7.100000 12.295000 14.612000 C 7.100000 9.836000 14.612000 C 7.100000 7.377000 14.612000 C 4.970000 8.607000 14.612000 C 2.840000 12.295000 14.612000 C 2.840000 9.836000 14.612000 C 2.840000 7.377000 14.612000 C 4.260000 7.377000 14.612000 C 4.970000 6.148000 14.612000 C 4.260000 12.295000 14.612000 C 4.260000 9.836000 14.612000 N 0.000000 12.295000 11.306000 N 0.000000 9.836000 11.306000 N 0.000000 7.377000 11.306000 N 2.840000 7.377000 8.000000 N 2.840000 9.836000 8.000000 N 2.840000 12.295000 8.000000 N 4.970000 11.066000 8.000000 N 4.970000 8.607000 8.000000 N 4.970000 6.148000 8.000000 N 7.100000 12.295000 8.000000 N 7.100000 9.836000 8.000000 N 7.100000 7.377000 8.000000 N 0.710000 6.148000 8.000000 N 0.710000 8.607000 8.000000 N 0.710000 11.066000 8.000000 N 6.390000 11.066000 11.306000 N 6.390000 8.607000 11.306000 N 6.390000 6.148000 11.306000 N 2.130000 11.066000 11.306000 N 2.130000 8.607000 11.306000 N 2.130000 6.148000 11.306000 N 4.260000 12.295000 11.306000 N 4.260000 9.836000 11.306000 N 4.260000 7.377000 11.306000 K_POINTS automatic 10 10 1 1 1 0 CELL_PARAMETERS 8.51980 0.00000 0.00000 0.00000 7.37600 0.00000 0.00000 0.00000 22.6120 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091216/d4a99f8b/attachment-0001.htm From majdoub at gmail.com Wed Dec 16 23:34:22 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 16:34:22 -0600 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: <4B29483A.2080407@mit.edu> References: <4B2936DE.5020008@mit.edu> <4B2946E8.4020509@mit.edu> <4B29483A.2080407@mit.edu> Message-ID: Dear Davide, If I change celldim(1)=1.8897261 (in Bohr radius unit), this means that the crystal lattice vectors are in Bohr too (same unit as alat). Crystal lattice vectors: v1(1) v1(2) v1(3) ... 1st lattice vector v2(1) v2(2) v2(3) ... 2nd lattice vector v3(1) v3(2) v3(3) ... 3rd lattice vector In alat units if celldm(1) was specified or in a.u. otherwise. Am I right? If yes then I need to change the following to Bohr units : CELL_PARAMETERS 8.51980 0.00000 0.00000 0.00000 7.37600 0.00000 0.00000 0.00000 22.6120 Thanks! On Wed, Dec 16, 2009 at 2:51 PM, Davide Ceresoli wrote: > Davide Ceresoli wrote: > > (1.8897261 = 1/0.052917721). > I meant: (1.8897261 = 1/0.52917721). > > _______________________________________________ > 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/20091216/ec2137d6/attachment.htm From ptanhphys at gmail.com Thu Dec 17 00:59:01 2009 From: ptanhphys at gmail.com (TuanAnh Pham) Date: Wed, 16 Dec 2009 15:59:01 -0800 Subject: [Pw_forum] Saw tooth potential details In-Reply-To: References: Message-ID: Dear Mohamed, This is one example: - In &control: You should add tefield = .true. dipfield = .true. The second is dipole correction - In &system, you should add edir = 3 ! This is the direction of applied field eamp = 0.002 ! Amplitude of e-field-should be small emaxpos = 0.9 eopreg = 0.2 In this way, the potential increase from (emaxpos+eopreg-1)=0.1 to (emaxpos) = 0.9 then decrease to 0 until (emaxpos+eopreg)=1.1 (in the units of the crystal vector edir). You can draw this to see why it is called sawtooth potential. It is better to have your system in the middle of the super-cell, and the vacuum region should be large enough so that you can *make sure* that your system lies between (emaxpos+eopreg-1) and (emaxpos+eopreg). The change of slope *must* be in the vacuum region. You can find some more information here: R. Resta and K. Kunc, Phys. Rev. B 34, 7146 (1986) Good luck, On Wed, Dec 16, 2009 at 2:24 PM, mohamed sabri majdoub wrote: > Dear users, > > I was reading the documentation for the saw tooth like potential in pwscf. > However, I still did not understood it in full. Can anybody gives me more > details about how the potential is implemented. > I need to apply an electric field to a supercell of graphene and BN layers > with both ends in vacuum. eamp = 0.002. > > > Amplitude of the electric field (in a.u. = 51.44 10^10 V/m ) > The sawlike potential increases with slope "eamp" in the > > region from (emaxpos+eopreg-1) to (emaxpos), then decreases > to 0 until (emaxpos+eopreg), in units of the crystal > vector "edir". Important: the change of slope of this > potential must be located in the empty region, or else > unphysical forces will result. Used only if tefield is .TRUE. > > The following keywords that need to be used are still not clear. In > particular the position of the slope change.Does it need to be in vacuum? > emaxpos=0.5 (Position of the maximum of the sawlike potential along crystal > axis "edir"); eopreg=0.5 (Zone in the unit cell where the sawlike > potential decreases.)? > How the sawlike potential is modeled. > Thank you in advance for your help and comment. > > Here is the system I want to apply electric field to it: > > &control > title = 'GphBN' > calculation = 'relax' > outdir = '/pwscf/pwscftemp/relaxGphBN' > prefix = 'GphBN' > pseudo_dir = /pwscf/input/Gph-BN/pseudopot-C-B-N' > verbosity = 'high' > tprnfor = .t. > restart_mode = 'from_scratch' > > / > &system > ibrav = 0, > celldm(1) = 1.8897261 > nat = 72, > ntyp = 3, > ecutwfc = 25.0 > ecutrho = 250.0 > occupations = 'smearing' > smearing = 'gaussian' > degauss = 0.003675 > > / > &electrons > mixing_beta = 0.05 > diagonalization = 'david' > > / > &ions > trust_radius_ini = 0.10 > > / > &cell > > ATOMIC_SPECIES > B 10.81100 B.pz-vbc.UPF > C 12.01070 C.pz-vbc.UPF > N 14.00674 N.pz-vbc.UPF > ATOMIC_POSITIONS angstrom > B 0.710000 8.607000 11.306000 > B 0.710000 11.066000 11.306000 > B 2.840000 7.377000 11.306000 > B 0.710000 6.148000 11.306000 > B 6.390000 6.148000 8.000000 > B 6.390000 8.607000 8.000000 > B 6.390000 11.066000 8.000000 > B 2.840000 9.836000 11.306000 > B 7.100000 7.377000 11.306000 > B 7.100000 9.836000 11.306000 > B 7.100000 12.295000 11.306000 > B 4.970000 11.066000 11.306000 > B 2.840000 12.295000 11.306000 > B 4.970000 6.148000 11.306000 > B 4.970000 8.607000 11.306000 > B 4.260000 7.377000 8.000000 > B 2.130000 11.066000 8.000000 > B 2.130000 8.607000 8.000000 > B 2.130000 6.148000 8.000000 > B 4.260000 9.836000 8.000000 > B 0.000000 7.377000 8.000000 > B 0.000000 9.836000 8.000000 > B 4.260000 12.295000 8.000000 > B 0.000000 12.295000 8.000000 > C 2.130000 6.148000 14.612000 > C 2.130000 8.607000 14.612000 > C 2.130000 11.066000 14.612000 > C 0.000000 12.295000 14.612000 > C 0.000000 9.836000 14.612000 > C 0.000000 7.377000 14.612000 > C 0.710000 11.066000 14.612000 > C 0.710000 8.607000 14.612000 > C 0.710000 6.148000 14.612000 > C 6.390000 8.607000 14.612000 > C 6.390000 6.148000 14.612000 > C 4.970000 11.066000 14.612000 > C 6.390000 11.066000 14.612000 > C 7.100000 12.295000 14.612000 > C 7.100000 9.836000 14.612000 > C 7.100000 7.377000 14.612000 > C 4.970000 8.607000 14.612000 > C 2.840000 12.295000 14.612000 > C 2.840000 9.836000 14.612000 > C 2.840000 7.377000 14.612000 > C 4.260000 7.377000 14.612000 > C 4.970000 6.148000 14.612000 > C 4.260000 12.295000 14.612000 > C 4.260000 9.836000 14.612000 > N 0.000000 12.295000 11.306000 > N 0.000000 9.836000 11.306000 > N 0.000000 7.377000 11.306000 > N 2.840000 7.377000 8.000000 > N 2.840000 9.836000 8.000000 > N 2.840000 12.295000 8.000000 > N 4.970000 11.066000 8.000000 > N 4.970000 8.607000 8.000000 > N 4.970000 6.148000 8.000000 > N 7.100000 12.295000 8.000000 > N 7.100000 9.836000 8.000000 > N 7.100000 7.377000 8.000000 > N 0.710000 6.148000 8.000000 > N 0.710000 8.607000 8.000000 > N 0.710000 11.066000 8.000000 > N 6.390000 11.066000 11.306000 > N 6.390000 8.607000 11.306000 > N 6.390000 6.148000 11.306000 > N 2.130000 11.066000 11.306000 > N 2.130000 8.607000 11.306000 > N 2.130000 6.148000 11.306000 > N 4.260000 12.295000 11.306000 > N 4.260000 9.836000 11.306000 > N 4.260000 7.377000 11.306000 > K_POINTS automatic > 10 10 1 1 1 0 > CELL_PARAMETERS > 8.51980 0.00000 0.00000 > 0.00000 7.37600 0.00000 > 0.00000 0.00000 22.6120 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Tuan Anh Pham Department of Chemistry University of California, Davis Phone: 530-752-0957 Homepage: http://angstrom.ucdavis.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091216/3a4ec154/attachment.htm From ceresoli at MIT.EDU Thu Dec 17 01:30:18 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Wed, 16 Dec 2009 19:30:18 -0500 (EST) Subject: [Pw_forum] graphene on BN calculation In-Reply-To: References: <4B2936DE.5020008@mit.edu> <4B2946E8.4020509@mit.edu> <4B29483A.2080407@mit.edu> Message-ID: On Wed, 16 Dec 2009, mohamed sabri majdoub wrote: > Dear Davide, > > If I change celldim(1)=1.8897261 (in Bohr radius unit), this means that the crystal lattice > vectors are in Bohr too (same unit as alat). Yes, the lattice vectors must be bohrradius unit. > Crystal lattice vectors: > v1(1) v1(2) v1(3) ... 1st lattice vector > > v2(1) v2(2) v2(3) ... 2nd lattice vector > v3(1) v3(2) v3(3) ... 3rd lattice vector > In alat units if celldm(1) was specified or in a.u. otherwise. > Am I right? If yes then I need to change the following to Bohr units : > > CELL_PARAMETERS > 8.51980 0.00000 0.00000 > 0.00000 7.37600 0.00000 > 0.00000 0.00000 22.6120 You can change them to bohr units and set celldm(1)=1.0, or you leave them unchanged but set celldm(1)=1.8897261. In any case, the product CELL_PARAMETERS*celldm(1) must always match your wanted lattice spacings in bohr units, not in angstrom. This is in contrast with ATOMIC_POSITIONS, where one can choose to enter them in angstrom/bohr/alat/crystal units. HTH. Davide From majdoub at gmail.com Thu Dec 17 02:05:10 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Wed, 16 Dec 2009 19:05:10 -0600 Subject: [Pw_forum] graphene on BN calculation In-Reply-To: References: <4B2936DE.5020008@mit.edu> <4B2946E8.4020509@mit.edu> <4B29483A.2080407@mit.edu> Message-ID: Thank you Davide for the clarification. On Wed, Dec 16, 2009 at 6:30 PM, Davide Ceresoli wrote: > On Wed, 16 Dec 2009, mohamed sabri majdoub wrote: > > > Dear Davide, > > > > If I change celldim(1)=1.8897261 (in Bohr radius unit), this means that > the crystal lattice > > vectors are in Bohr too (same unit as alat). > Yes, the lattice vectors must be bohrradius unit. > > > Crystal lattice vectors: > > v1(1) v1(2) v1(3) ... 1st lattice vector > > > > v2(1) v2(2) v2(3) ... 2nd lattice vector > > v3(1) v3(2) v3(3) ... 3rd lattice vector > > In alat units if celldm(1) was specified or in a.u. otherwise. > > Am I right? If yes then I need to change the following to Bohr units : > > > > CELL_PARAMETERS > > 8.51980 0.00000 0.00000 > > 0.00000 7.37600 0.00000 > > 0.00000 0.00000 22.6120 > You can change them to bohr units and set celldm(1)=1.0, or > you leave them unchanged but set celldm(1)=1.8897261. > > In any case, the product CELL_PARAMETERS*celldm(1) must always > match your wanted lattice spacings in bohr units, not in angstrom. > > This is in contrast with ATOMIC_POSITIONS, where one can choose > to enter them in angstrom/bohr/alat/crystal units. > > HTH. > > Davide > > > _______________________________________________ > 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/20091216/9140c1b9/attachment-0001.htm From eyvaz_isaev at yahoo.com Thu Dec 17 11:20:26 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 17 Dec 2009 02:20:26 -0800 (PST) Subject: [Pw_forum] problem of q2r.in In-Reply-To: <4418248.295951260975426906.JavaMail.coremail@bj163app134.163.com> Message-ID: <685366.26358.qm@web65707.mail.ac4.yahoo.com> Hi, --- On Wed, 12/16/09, Xiang-Feng Zhou wrote: > > forrtl: severe > (59): list-directed I/O syntax error, unit 51, file > /home/zxf/work-pwscf/restart-bc5/a2Fq2r.51 > Have you tried to see what is inside of a2Fq2r.51 file? There might be something like NaN or **************. Otherwise, it might be corrupted. 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 kazempoor2000 at yahoo.com Thu Dec 17 12:39:09 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 17 Dec 2009 03:39:09 -0800 (PST) Subject: [Pw_forum] zn normconserving with 3s and 3p Message-ID: <319953.63805.qm@web112519.mail.gq1.yahoo.com> Dear all Has anyone the normconserving pseudopotential for Zn that include 3s and 3p as valence electrons. thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091217/5cf26a22/attachment.htm From kondor.jess at gmail.com Thu Dec 17 16:50:21 2009 From: kondor.jess at gmail.com (Jess Kondor) Date: Thu, 17 Dec 2009 10:50:21 -0500 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> Message-ID: <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> Dear all, ?I have some trouble in understanding why equivalent (if I am not wrong) representation of the crystal structure leads to different symmetry (as shown in the output from pw.x). All input/output files are attached. I work with rhombohedral unit cell, alat = 5.46 Ang, gamma =60.36. First, I let PWscf to build lattice vectors using the following settings: ? ? ? ? ? ? ? ? ? ? ? ibrav = 5 , ? ? ? ? ? ? ? ? ? celldm(1) = 10.317903898 ? ? ? ? ? ? ? ? ? celldm(4) = 0.494548768 ...... The code generates lattice vectors: ? ? celldm(1)= ?10.317904 ?celldm(2)= ? 0.000000 ?celldm(3)= ? 0.000000 ? ? celldm(4)= ? 0.494549 ?celldm(5)= ? 0.000000 ?celldm(6)= ? 0.000000 ? ? crystal axes: (cart. coord. in units of a_0) ? ? ? ? ? ? ? a(1) = ( ?0.502718 -0.290245 ?0.814268 ) ? ? ? ? ? ? ? a(2) = ( ?0.000000 ?0.580489 ?0.814268 ) ? ? ? ? ? ? ? a(3) = ( -0.502718 -0.290245 ?0.814268 ) ? ? reciprocal axes: (cart. coord. in units 2 pi/a_0) ? ? ? ? ? ? ? b(1) = ( ?0.994593 -0.574229 ?0.409366 ) ? ? ? ? ? ? ? b(2) = ( ?0.000000 ?1.148457 ?0.409366 ) ? ? ? ? ? ? ? b(3) = ( -0.994593 -0.574229 ?0.409366 ) and shows that ? ?6 Sym.Ops. (no inversion) ? ? point group C_3v (3m) ? ? there are ?3 classes ? ? the character table: ? ? ? E ? ? 2C3 ? 3s_v A_1 ? ?1.00 ?1.00 ?1.00 A_2 ? ?1.00 ?1.00 -1.00 E ? ? ?2.00 -1.00 ?0.00 ? ? the symmetry operations in each class: ? ? E ? ? ? ?1 ? ? 2C3 ? ? ?2 ? ?3 ? ? 3s_v ? ? 4 ? ?5 ? ?6 However, I prefer to work with lattice vectors directly and then changed my settings from : ? ? ? ? ? ? ? ? ? ? ? ibrav = 5 , ? ? ? ? ? ? ? ? ? celldm(1) = 10.317903898 ? ? ? ? ? ? ? ? ? celldm(4) = 0.494548768 to: ? ? ? ? ? ? ? ? ? ? ? ibrav = 0 , ? ? ? ? ? ? ? ? ? celldm(1) = 10.317903898 ? ? ? ? ? ? ? ? ? ?....... ? ?CELL_PARAMETERS ? ? ? ? ? ? ? ?0.502718 -0.290245 ?0.814268 ? ? ? ? ? ? ? ?0.000000 ?0.580489 ?0.814268 ? ? ? ? ? ? ? -0.502718 -0.290245 ?0.814268 CELL_PARAMETERS were taken from the output when I use first settings (see above, crystal axes: (cart. coord. in units of a_0)). ?However, now the code shows different symmetry: 2 Sym.Ops. (no inversion) ? ? point group C_s (m) ? ? there are ?2 classes ? ? the character table: ? ? ? E ? ? s A' ? ? 1.00 ?1.00 A'' ? ?1.00 -1.00 Frankly speaking, I cannot identify what I did wrong. I think, there is a simple explanation, but I failed to find one. Any ideas? Best wishes, -- ===================================== Jess Kondor NSTI ===================================== -------------- next part -------------- A non-text attachment was scrubbed... Name: files2.tar.gz Type: application/x-gzip Size: 5002 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091217/1642c970/attachment.bin From paulatto at sissa.it Thu Dec 17 17:04:54 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 17 Dec 2009 17:04:54 +0100 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> Message-ID: Replying to message "[Pw_forum] Fwd: different symmetry when using equivalent representation" from Jess Kondor (17/12/09): > I have some trouble in understanding why equivalent (if I am not > wrong) representation of the crystal structure leads to different > symmetry (as shown in the output from pw.x). All input/output > files are attached. Dear Jess, the code threshold for checking the symmetry is too strict for the number of significant digits you have specified for the basis vectors (I see you have copied them from the output of test1.inp, but apparently it is not enough). You recover all 6 symmetry operations if you specify the cell parameters with more digits, e.g. 0.502718227240668 -0.290244503823931 0.814268083618657 0.000000000000000 0.580489007647862 0.814268083618657 -0.502718227240668 -0.290244503823931 0.814268083618657 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 kondor.jess at gmail.com Thu Dec 17 17:22:37 2009 From: kondor.jess at gmail.com (Jess Kondor) Date: Thu, 17 Dec 2009 11:22:37 -0500 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> Message-ID: <1d9d5d9d0912170822o167db726qa21e857ab2ed5ead@mail.gmail.com> On Thu, Dec 17, 2009 at 11:04 AM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] Fwd: different symmetry when using > equivalent representation" from Jess Kondor (17/12/09): >> ?I have some trouble in understanding why equivalent (if I am not >> wrong) representation of the crystal structure leads to different >> symmetry (as shown in the output from pw.x). All input/output >> files are attached. > > Dear Jess, > the code threshold for checking the symmetry is too strict for the number > of significant digits you have specified for the basis vectors (I see you > have copied them from the output of test1.inp, but apparently it is not > enough). > > You recover all 6 symmetry operations if you specify the cell parameters > with more digits, e.g. > ? ?0.502718227240668 ?-0.290244503823931 ? 0.814268083618657 > ? ?0.000000000000000 ? 0.580489007647862 ? 0.814268083618657 > ? -0.502718227240668 ?-0.290244503823931 ? 0.814268083618657 > > 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 > Dear Lorenzo, Thanks a lot for the solution. How many digits do I need? I agree, that output basis vectors are printed with 6 significant digits and this is not enough. However, if I change 'scf' to 'vc-relax', the code prints CELL_PARAMETERS with much more digits (9), and this is still not enough to find all 6 symmetries. 0.502718227 -0.290244504 0.814268084 0.000000000 0.580489008 0.814268084 -0.502718227 -0.290244504 0.814268084 Probably, it is better to change a source code to print more digits in order to allow simple cut/and/paste from output/to input without using extra tools? Thanks a lot! -- ===================================== Jess Kondor NSTI ===================================== From giannozz at democritos.it Thu Dec 17 17:53:41 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Dec 2009 17:53:41 +0100 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: <1d9d5d9d0912170822o167db726qa21e857ab2ed5ead@mail.gmail.com> References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> <1d9d5d9d0912170822o167db726qa21e857ab2ed5ead@mail.gmail.com> Message-ID: <4B2A6215.1040103@democritos.it> Jess Kondor wrote: > Thanks a lot for the solution. How many digits do I need? http://www.quantum-espresso.org/user_guide/node56.html P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From kondor.jess at gmail.com Thu Dec 17 18:08:17 2009 From: kondor.jess at gmail.com (Jess Kondor) Date: Thu, 17 Dec 2009 12:08:17 -0500 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: <4B2A6215.1040103@democritos.it> References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> <1d9d5d9d0912170822o167db726qa21e857ab2ed5ead@mail.gmail.com> <4B2A6215.1040103@democritos.it> Message-ID: <1d9d5d9d0912170908r758d22abp3784bf6cc0b84760@mail.gmail.com> On Thu, Dec 17, 2009 at 11:53 AM, Paolo Giannozzi wrote: > Jess Kondor wrote: > >> ?Thanks a lot for the solution. How many digits do I need? > > http://www.quantum-espresso.org/user_guide/node56.html > > 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 > Thanks, Paolo, I read that before posting. The reason I indeed asked this question is why code cannot find all symmetries if lattice vectors are given with nine (9) significant digits, while 'accep=1.d-5', 5 digits? probably, it does sound stupid, but ... -- ===================================== Jess Kondor NSTI ===================================== From giannozz at democritos.it Thu Dec 17 18:12:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Dec 2009 18:12:40 +0100 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: <1d9d5d9d0912170908r758d22abp3784bf6cc0b84760@mail.gmail.com> References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> <1d9d5d9d0912170822o167db726qa21e857ab2ed5ead@mail.gmail.com> <4B2A6215.1040103@democritos.it> <1d9d5d9d0912170908r758d22abp3784bf6cc0b84760@mail.gmail.com> Message-ID: <4B2A6688.8010209@democritos.it> Jess Kondor wrote: > Thanks, Paolo, I read that before posting. The reason I indeed asked > this question is why code cannot find all symmetries if lattice > vectors are given with nine (9) significant digits maybe they aren't as "significant" as you think they are. In any event, what the code does overrides what we think it should do. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Dec 18 08:33:24 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 Dec 2009 08:33:24 +0100 Subject: [Pw_forum] Fwd: different symmetry when using equivalent representation In-Reply-To: <1d9d5d9d0912170908r758d22abp3784bf6cc0b84760@mail.gmail.com> References: <1d9d5d9d0912170737h68cda8d9qd65a9463c9edfefa@mail.gmail.com> <1d9d5d9d0912170750q6c5c04r120af6329416514e@mail.gmail.com> <1d9d5d9d0912170822o167db726qa21e857ab2ed5ead@mail.gmail.com> <4B2A6215.1040103@democritos.it> <1d9d5d9d0912170908r758d22abp3784bf6cc0b84760@mail.gmail.com> Message-ID: <5F59CD4B-208E-40FF-A780-44284D5ED288@democritos.it> On Dec 17, 2009, at 18:08 , Jess Kondor wrote: > The reason I indeed asked this question is why code > cannot find all symmetries if lattice vectors are given > with nine (9) significant digits for lattice vectors (not atomic positions) actually there is a different check. This is performed in either PW/hexsym.f90 or PW/cubicsym.f90 (depending on the kind of symmetry) and is much stricter (maybe too much). See lines: if ( abs(DBLE(nint(value))-value) > 1.0d-8) then ! ! if a noninteger is obtained, this implies that this operation ! is not a symmetry operation for the given lattice ! go to 10 end if 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 sh.shapt at gmail.com Fri Dec 18 14:07:25 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Fri, 18 Dec 2009 13:07:25 +0000 Subject: [Pw_forum] Calculating number of bands Message-ID: Hi there, I would like to calculate the number of bands for my system with 300 atoms. What I used to do earlier was I multiplied the total number of atoms with the valency and then divide the total number of bands by two in order to get the valence band numbers, but now when I following this method, it is showing me that 'too few bands'. is there any other method also? can anyone please give give any suggestions Thanks and regards SS Msc (Physics) Pune university Pune -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091218/aacdfc8f/attachment.htm From paulatto at sissa.it Fri Dec 18 14:11:13 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 18 Dec 2009 14:11:13 +0100 Subject: [Pw_forum] Calculating number of bands In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] Calculating number of bands" from Shaptrishi Sharma (18/12/09): > I would like to calculate the number of bands for my system with 300 > atoms. > What I used to do earlier was I multiplied the total number of atoms with > the valency and then divide the total number of bands by two in order to > get the valence band numbers, but now when I following this method, it is > showing me that 'too few bands'. > > is there any other method also? Dear Shaptrishi, your method is correct, i.e. you take half the number of electrons, rounded up if necessary. Maybe you've just missed some electrons (do you have any pseudopotential with semi-core orbitals in valence?) If you use a smearing you need more bands, the default is 20% more and at least 4 more. By the way, why don't you stick to the default value? It usually works, and even if it causes any problem you can always change it by hand when necessary. 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 irida at ims.demokritos.gr Fri Dec 18 14:45:30 2009 From: irida at ims.demokritos.gr (Iris Theofilou) Date: Fri, 18 Dec 2009 15:45:30 +0200 Subject: [Pw_forum] exit status=139 Message-ID: <200912181345.nBIDjUNc017667@mail.ims.demokritos.gr> Hello, I have just installed quantum espresso-4.1.1 in my computer which has linux ubuntu 9.10 operating system. I tried to run the examples and while the examples 1,3,5 had no problem running, when I tried to run examples 2,4,6,7 I got the following message : running the phonon calculation at X...Segmentation fault Error condition encountered during test: exit status = 139 Aborting Does anyone have any ideas what to do? Thanks in advance, Iris From irida at ims.demokritos.gr Fri Dec 18 14:43:37 2009 From: irida at ims.demokritos.gr (Iris Theofilou) Date: Fri, 18 Dec 2009 15:43:37 +0200 Subject: [Pw_forum] exit status=139 Message-ID: <200912181343.nBIDhbYR017585@mail.ims.demokritos.gr> Hello, I have just installed quantum espresso-4.1.1 in my computer which has linux ubuntu 9.10 operating system. I tried to run the examples and while the examples 1,3,5 had no problem running, when I tried to run examples 2,4,6,7 I got the following message : running the phonon calculation at X...Segmentation fault Error condition encountered during test: exit status = 139 Aborting Does anyone have any ideas what to do? Thanks in advance, Iris From paulatto at sissa.it Fri Dec 18 15:09:51 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 18 Dec 2009 15:09:51 +0100 Subject: [Pw_forum] exit status=139 In-Reply-To: <200912181345.nBIDjUNc017667@mail.ims.demokritos.gr> References: <200912181345.nBIDjUNc017667@mail.ims.demokritos.gr> Message-ID: Replying to message "[Pw_forum] exit status=139" from Iris Theofilou (18/12/09): > running the phonon calculation at X...Segmentation fault > Error condition encountered during test: exit status = 139 > Aborting Dear Iris, you didn't provide enough information for an accurate reply: which compile did you use to compile QE and the full output of the problematic calculation (you can find it in the "result" subdirectory of the example). If you are using the default compilers from ubuntu (gcc and gfortran) be aware that the phonon code is often miscompiled by gfortran, giving strange and random errors. Please have a look at the user guide , especially the second chapter; it is boring but it usually pays off on the long run. 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 irida at ims.demokritos.gr Fri Dec 18 17:26:25 2009 From: irida at ims.demokritos.gr (Iris Theofilou) Date: Fri, 18 Dec 2009 18:26:25 +0200 Subject: [Pw_forum] exit status=139 Message-ID: <200912181626.nBIGQPuV024947@mail.ims.demokritos.gr> Dear Lorenzo, I'm not sure which one it was used, but it must be one (or more) of the ubuntu compilers. Their versions are: gcc (Ubuntu 4.4.1-4ubuntu8) 4.4.1 Copyright (C) 2009 Free Software Foundation, Inc. GNU Fortran (Ubuntu 4.4.1-4ubuntu8) 4.4.1 Copyright (C) 2009 Free Software Foundation, Inc. cpp (Ubuntu 4.4.1-4ubuntu8) 4.4.1 Copyright (C) 2009 Free Software Foundation, Inc. The whole error message of the run_example(02) is: running the scf calculation... done running the phonon calculation at Gamma...Segmentation fault done running the phonon calculation at X...Segmentation fault Error condition encountered during test: exit status = 139 Aborting I'm also including the 2 results files for phonon calculations (see attachments) If it is only a gfortran problem which compiler should I use? perhaps ifort v.9?? Thanks in advance, Iris > Replying to message "[Pw_forum] exit status=139" from Iris Theofilou > (18/12/09): > > running the phonon calculation at X...Segmentation fault > > Error condition encountered during test: exit status = 139 > > Aborting > > > Dear Iris, > you didn't provide enough information for an accurate reply: which compile > did you use to compile QE and the full output of the problematic > calculation (you can find it in the "result" subdirectory of the example). > > If you are using the default compilers from ubuntu (gcc and gfortran) be > aware that the phonon code is often miscompiled by gfortran, giving > strange and random errors. Please have a look at the user guide > , especially > the second chapter; it is boring but it usually pays off on the long run. > > 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 -------------- A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 3220 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091218/e815068d/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 15652 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091218/e815068d/attachment-0003.obj From giannozz at democritos.it Fri Dec 18 17:49:21 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 Dec 2009 17:49:21 +0100 Subject: [Pw_forum] exit status=139 In-Reply-To: <200912181626.nBIGQPuV024947@mail.ims.demokritos.gr> References: <200912181626.nBIGQPuV024947@mail.ims.demokritos.gr> Message-ID: <9D8E2656-B0F8-4928-9313-904507DC4514@democritos.it> On Dec 18, 2009, at 17:26 , Iris Theofilou wrote: > I'm not sure which one it was used the one that appears in "make.sys" at line MPIF90=... or F90=... Presumably, gfortran... > running the phonon calculation at Gamma...Segmentation fault ...which in fact doesn't produce a correct executable for the phonon code. Given the type of error, it is very hard to locate what is going wrong. > which compiler should I use? perhaps ifort v.9?? you didn't follow Lorenzo's advice ("read the user guide"), did you? Use a compiler that is less buggy than the code you want to compile. G95 works nicely, but the executable it produces is not very fast. The intel compiler produces faster executables, especially together with the mkl library, but don't trust too much the first releases of each major new version. 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 irida at ims.demokritos.gr Fri Dec 18 18:08:09 2009 From: irida at ims.demokritos.gr (Iris Theofilou) Date: Fri, 18 Dec 2009 19:08:09 +0200 Subject: [Pw_forum] exit status=139 Message-ID: <200912181708.nBIH897a026485@mail.ims.demokritos.gr> Ok thanks for the reply, I will try to use an ifort compiler and see what will happen. In fact I did read the manual and it says that:ifort v.9: The latest (July 2006) 32-bit version of ifort 9.1 works flawlessy. That 's why I asked if this might be appropriate. Thank you all, Iris > > On Dec 18, 2009, at 17:26 , Iris Theofilou wrote: > > > I'm not sure which one it was used > > the one that appears in "make.sys" at line MPIF90=... or F90=... > Presumably, gfortran... > > > running the phonon calculation at Gamma...Segmentation fault > > ...which in fact doesn't produce a correct executable for the phonon > code. Given the type of error, it is very hard to locate what is going > wrong. > > > which compiler should I use? perhaps ifort v.9?? > > you didn't follow Lorenzo's advice ("read the user guide"), did you? > > Use a compiler that is less buggy than the code you want to compile. > G95 works nicely, but the executable it produces is not very fast. > The intel compiler produces faster executables, especially together > with the mkl library, but don't trust too much the first releases of > each > major new version. > > 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 > > From giannozz at democritos.it Fri Dec 18 18:14:06 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 Dec 2009 18:14:06 +0100 Subject: [Pw_forum] exit status=139 In-Reply-To: <200912181708.nBIH897a026485@mail.ims.demokritos.gr> References: <200912181708.nBIH897a026485@mail.ims.demokritos.gr> Message-ID: <05781EAC-7E52-404E-AC66-55F255AA8A4B@democritos.it> On Dec 18, 2009, at 18:08 , Iris Theofilou wrote: > In fact I did read the manual and it says that:ifort v.9: The latest > (July 2006) 32-bit version of ifort 9.1 works flawlessy. or at least, it did with the july 2006 version of the phonon code ... 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 huang87 at purdue.edu Fri Dec 18 21:09:37 2009 From: huang87 at purdue.edu (Zhen Huang) Date: Fri, 18 Dec 2009 15:09:37 -0500 Subject: [Pw_forum] A question about force constants calculation of Graphene nano ribbon Message-ID: <7337ea900912181209j1f0438ffp49ce7e81b9ffd166@mail.gmail.com> Dear Espresso users- I am currently using the software calculating interatomic force constants. I started with a armchair edge graphene nanoribbon of 3^0.5*bondlength width which means two primitive unit cells of graphene are aligned along the axial direction of ribbon and separated by (3^0.5)*bondlength. However, I found the software failed to give some of the force constant. Attached is the structure I am trying to study and below is the script I used for force constants calcualtion. SCF calcualtion ************************************************************************************************** &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='GNR', pseudo_dir = '/scratch/scratch96/h/huang87/espresso-4.1.1/pseudo/', outdir='/scratch/scratch96/h/huang87/espresso-4.1.1/ZhenCalculation/GNRTry2/' / &system ibrav= 0, celldm(1) =8.04, nat= 8, ntyp= 1, nbnd= 20, ecutwfc =16.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 / &electrons diagonalization='cg' conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF CELL_PARAMETERS 7.50746269 0.00000000 0.00000000 0.00000000 2.00000000 0.00000000 0.00000000 0.00000000 1.00000000 ATOMIC_POSITIONS C 0.462 0.5 0.000 C 0.538 0.5 0.000 C 0.462 0.5 0.333 C 0.538 0.5 0.333 C 0.500 0.5 0.500 C 0.577 0.5 0.500 C 0.500 0.5 0.833 C 0.577 0.5 0.833 K_POINTS (automatic) 1 1 32 0 0 0 ***************************************************************************** Phonon calculation phonons of Ti &inputph tr2_ph=1.0d-12, prefix='GNR', ldisp=.true., nq1=1, nq2=1, nq3=16 amass(1)=12.0107, outdir='/scratch/scratch96/h/huang87/espresso-4.1.1/ZhenCalculation/GNRTry2/', fildyn='GNR.dyn', / ************************************************************************* force constants from GNR.dyn1 *************************************************************************** 1 1 252.12788999 0.00000000 -0.00114015 0.00000000 -14.77300805 0.00000000 -0.00114015 0.00000000 ************ 0.00000000 -0.06520954 0.00000000 -14.77300805 0.00000000 -0.06520954 0.00000000 -93.03374039 0.00000000 1 2 ************ 0.00000000 0.09747458 0.00000000 -1.20698824 0.00000000 -0.01665358 0.00000000 113.56482271 0.00000000 -0.00847488 0.00000000 5.45990614 0.00000000 -0.00244794 0.00000000 113.74430800 0.00000000 1 3 0.53138677 0.00000000 0.01284739 0.00000000 -0.00496088 0.00000000 0.00078527 0.00000000 1.10083154 0.00000000 -0.00960997 0.00000000 -0.01328205 0.00000000 -0.13249470 0.00000000 -0.93853159 0.00000000 1 4 -0.36705054 0.00000000 0.00166782 0.00000000 0.03803961 0.00000000 -0.01073043 0.00000000 -0.02005837 0.00000000 0.03032361 0.00000000 -0.33345226 0.00000000 0.12638729 0.00000000 -1.53647444 0.00000000 1 5 -0.36239819 0.00000000 -0.02331924 0.00000000 -0.58155909 0.00000000 -0.03210181 0.00000000 -0.86035688 0.00000000 -0.08297313 0.00000000 1.52018776 0.00000000 0.05112061 0.00000000 0.32584098 0.00000000 *********************************************************************** Best Regards ------- Zhen (Alex) Huang Ph.D. Student Nanoscale Transport Research Group Laboratory for Computational Methods in Emerging Technologies Cooling Technologies Research Center School of Mechanical Engineering Purdue University Tel: 765 722 1113 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091218/e8a56e58/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: ArmchiarRibbon.odg Type: application/vnd.oasis.opendocument.graphics Size: 8322 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091218/e8a56e58/attachment.odg From dimpy.sharma at tyndall.ie Sat Dec 19 20:27:00 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Sat, 19 Dec 2009 19:27:00 -0000 Subject: [Pw_forum] calculating eigenenergy of single atom using QE Message-ID: Hi there, I have tried to calculate the eigen energy of an isolated Hydrogen atom using quantum espresso, however in the output file it is showing me 'charge is wrong'. I guess my input file is correct. I used 1 node to run the calculation. My input file is as given below! &CONTROL calculation ='scf' restart_mode = 'from_scratch' outdir = '/' pseudo_dir = '/' prefix = 'H' tstress = .true. tprnfor = .true. wf_collect =.true. / &SYSTEM ibrav = 0 celldm(1) = 1 nat = 1 ntyp = 1 ecutwfc = 40 ecutrho = 160.0 nbnd = 2 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / &IONS / &CELL cell_dynamics='none' / CELL_PARAMETERS cubic 1.000000000 0.000000000 0.000000000 0.000000000 2.000000000 0.000000000 0.000000000 0.000000000 2.000000000 ATOMIC_SPECIES H 1.00794 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms H 0.0000 0.0000 0.0000 K_POINTS automatic 1 1 1 0 0 0 suggestions welcome! Thanks and regards Dimpy UCC Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091219/8b34bc38/attachment.htm From huang87 at purdue.edu Sat Dec 19 20:33:47 2009 From: huang87 at purdue.edu (Zhen Huang) Date: Sat, 19 Dec 2009 14:33:47 -0500 Subject: [Pw_forum] Ph.x and force constants calculation questions. Message-ID: <7337ea900912191133h671c1595w56c5e471d263350d@mail.gmail.com> Dear Users- This is Alex. I have several beginner questions 1. I wonder if force constants outputs are in the unit of Hartree/bohr^2. 2. For a 2 atoms unit cell, for example, the program (ph.x calcualtion) only gives the force constants between the atoms but any other, say, second and third nearest neighbors interactions. Other than increasing the number and size of unit cell generate non-primitive unit cell, is there a way to obtain the force constants for atoms beyond the atoms in unit cell? 3. On top of the last question, is there a way to control the cutoff number of the nearest neighbors.For example, if I only want to consider upto fourth nearest neighbor based force constants for a certain material which perimeter should I study and adjust to gives a promising dispersion relation based the selected number of force constants from calculation. Best Regards ------- Zhen (Alex) Huang Ph.D. Student Nanoscale Transport Research Group Laboratory for Computational Methods in Emerging Technologies Cooling Technologies Research Center School of Mechanical Engineering Purdue University Tel: 765 237 9733 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091219/5cab1256/attachment.htm From eyvaz_isaev at yahoo.com Sun Dec 20 03:05:53 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 19 Dec 2009 18:05:53 -0800 (PST) Subject: [Pw_forum] A question about force constants calculation of Graphene nano ribbon In-Reply-To: <7337ea900912181209j1f0438ffp49ce7e81b9ffd166@mail.gmail.com> Message-ID: <896543.21082.qm@web65712.mail.ac4.yahoo.com> Dear Huang, --- On Fri, 12/18/09, Zhen Huang wrote: > However, I found the software failed to give some of the > force constant. > 1 1 > 252.12788999 0.00000000 -0.00114015 0.00000000 > -14.77300805 0.00000000 > -0.00114015 0.00000000 ************ 0.00000000 > -0.06520954 0.00000000 > The software, fortunately, did not fail, it just stated that something wrong in your input files which resulted in large IFC components that can not be printed using the f12.8 format. Reasons for this: 1. > ??? ecutwfc =16.0, > ??? degauss=0.05 ecutwfc looks very small, I would use 25Ry. degauss is quite large, usually it is around 0.02 You did not specify ecutrho (8-12 times of ecutwfc) which is important for ultrasoft PsPs (see your PsP below). > ?C? 12.0107? C.pz-rrkjus.UPF 2. > ATOMIC_POSITIONS > ?C 0.462? 0.5? 0.000 > ?C 0.538? 0.5? 0.000 > ?C 0.462? 0.5? 0.333 > ?C 0.538? 0.5? 0.333 > ?C 0.500? 0.5? 0.500 > ?C 0.577? 0.5? 0.500 > ?C 0.500? 0.5? 0.833 > ?C 0.577? 0.5? 0.833 You have mistaken here as you left an important parameter. By default atomic positions are in units of the lattice parameter "a". If you visualize your structure you will find very funny picture. In fact, atomic positions provided are in units of basis vectors, i.e. you should add "crystal" after "ATOMIC_POSITIONS" I think this is the main reason. 3. > ? tr2_ph=1.0d-12, Try -14. 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 Sun Dec 20 03:14:09 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 19 Dec 2009 18:14:09 -0800 (PST) Subject: [Pw_forum] Ph.x and force constants calculation questions. In-Reply-To: <7337ea900912191133h671c1595w56c5e471d263350d@mail.gmail.com> Message-ID: <914566.14548.qm@web65715.mail.ac4.yahoo.com> Dear Alex, --- On Sat, 12/19/09, Zhen Huang wrote: > > 1. I wonder if force constants outputs are in the unit of > Hartree/bohr^2. In QE all quantities are in atomic units, so IFC are in Ry/au^2 > 2. For a 2 atoms unit cell, for example, the program (ph.x > calcualtion) only gives the force constants between the atoms but any > other, say, second and third nearest neighbors interactions. Other > than increasing the number and size of unit cell generate > non-primitive unit cell, is there a way to obtain the force constants > for atoms beyond the atoms in unit cell? > In the Linear Response all calculations are performed inside the unit cell. What you are talking about is intrinsic for the Direct Method. You can increase number of q-points for which dynamical matrices have to be calculated. Calculated force constants F(R) are defined for R=(i-1)*a+(j-1)*b+(k-1)*c where a,b,c are basis vectors, and i,j,k are those from nq1,nq2,nq3. nq1,nq2,nq3 are division numbers from ph.in file. Calculations for a cell within N atoms and nq1,nq2,nq3 set of q-points mimic a supercell containing N*nq1*nq2*nq3 atoms. > 3. On top of the last question, is there a way to control > the cutoff number of the nearest neighbors.For example, if I only > want to consider upto fourth nearest neighbor based force constants > for a certain material which perimeter should I study and adjust to > gives a promising dispersion relation based the selected number of > force constants from calculation. If you know the nearest neighbor distance you are interested in, then just calculate for which nq1,nq2,nq3 you can get this distance and use these nq1,nq2,nq3 set to calculate dynamical matrices. Usually one starts from a reasonable number of q-set (which is different for different systems depending on the atomic bonding, complexity, symmetry) and then gradually increase nq's to see how the phonon dispersion relations are affected. Hope this helps. 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 isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From lanhaiping at gmail.com Sun Dec 20 04:07:13 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sun, 20 Dec 2009 11:07:13 +0800 Subject: [Pw_forum] calculating eigenenergy of single atom using QE In-Reply-To: References: Message-ID: Hi, Your cell parameters are too small, which would result of a hydrogen solid not a single hydrogen atom. Regards On Sun, Dec 20, 2009 at 3:27 AM, Dimpy Sharma wrote: > > Hi there, > > I have tried to calculate the eigen energy of an isolated Hydrogen atom > using quantum espresso, however in the output file it is showing me 'charge > is wrong'. I guess my input file is correct. I used 1 node to run the > calculation. > > My input file is as given below! > &CONTROL > calculation ='scf' > restart_mode = 'from_scratch' > outdir = '/' > pseudo_dir = '/' > prefix = 'H' > tstress = .true. > tprnfor = .true. > wf_collect =.true. > / > &SYSTEM > ibrav = 0 > celldm(1) = 1 > nat = 1 > ntyp = 1 > ecutwfc = 40 > ecutrho = 160.0 > nbnd = 2 > > / > &ELECTRONS > diagonalization ='cg' > mixing_mode = 'plain' > conv_thr = 1.0d-6 > mixing_beta = 0.7 > / > &IONS > / > &CELL > cell_dynamics='none' > / > CELL_PARAMETERS cubic > 1.000000000 0.000000000 0.000000000 > 0.000000000 2.000000000 0.000000000 > 0.000000000 0.000000000 2.000000000 > ATOMIC_SPECIES > H 1.00794 H.pz-vbc.UPF > ATOMIC_POSITIONS angstroms > H 0.0000 0.0000 0.0000 > K_POINTS automatic > 1 1 1 0 0 0 > > suggestions welcome! > > > Thanks and regards > > Dimpy > > UCC > Ireland > > > _______________________________________________ > 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/20091220/51f781b6/attachment.htm From pckboy at gmail.com Sun Dec 20 13:16:52 2009 From: pckboy at gmail.com (E.M.) Date: Sun, 20 Dec 2009 06:16:52 -0600 Subject: [Pw_forum] total all-electron energy Message-ID: <4B2E15B4.7030109@gmail.com> Greetings I am trying to compare the total all-electron energy with results from other codes, unfortunately I can do this only for PAW potentials: Harris-Foulkes estimate = -40.11313279 Ry estimated scf accuracy < 1.8E-10 Ry total all-electron energy = -148.913287 Ry The only energy reported in the other relaxation examples is in the order of the -40 for this example, how to get the total all-electron energy for any other system?. Is there a flag to trigger this calculation? Is the -40 Ry estimate that from the binding energy? Regards Eduardo From paulatto at sissa.it Sun Dec 20 13:43:16 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 20 Dec 2009 13:43:16 +0100 Subject: [Pw_forum] total all-electron energy In-Reply-To: <4B2E15B4.7030109@gmail.com> References: <4B2E15B4.7030109@gmail.com> Message-ID: <20091220134316.mqonjm524g0o4c48@webmail.sissa.it> Quoting "E.M." : > I am trying to compare the total all-electron energy with results from > other codes, > Is there a flag to trigger this calculation? Dear Eduardo, it doesn't make much sense to compute the all-electron energies, even in the PAW case I've put it there for fun, but it's not really meaningful: it has 12 digits, but only a few are really significant. What you should do is compute the binding energy, e.g. energy of the system minus energy of its constituents. The binding energy is universal, while the total energy depends on the pseudopotential (except in the PAW case, in theory). There are plenty of discussions in the forum on how to compute the energy of an isolated atom, there are a few points to keep in mind, but it's not hard at all. chers -- 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 Horde http://www.horde.org/ From njuxuyuehua at gmail.com Sun Dec 20 13:56:35 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Sun, 20 Dec 2009 20:56:35 +0800 Subject: [Pw_forum] inqure about the theory of infrared spectrum calculation Message-ID: hi everyone here: i am seeking some literature or paper about infrared intensity calculation in PWSCF, can anyone tell me where is it available. thank you ! -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/b073799d/attachment.htm From m.abbasnejad at gmail.com Sun Dec 20 15:06:26 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Sun, 20 Dec 2009 17:36:26 +0330 Subject: [Pw_forum] equilibrium volume Message-ID: <7699a1950912200606j709efbbau4a0ed192384fa00e@mail.gmail.com> Dear all When I run an scf calculation for the equilibrium volume obtained by the Murnaghan-fit, the stresses are too far from zero. Should i expect this volume to be zero pressure volume, or there is a problem in the calculation? Thanx for any comment -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/93074f60/attachment.htm From r.golesorkhtabar at gmail.com Sun Dec 20 16:36:03 2009 From: r.golesorkhtabar at gmail.com (rostam golesorkhtabar) Date: Sun, 20 Dec 2009 16:36:03 +0100 Subject: [Pw_forum] Ti Pseudopotential Message-ID: <8622a7010912200736n3f85b226g2d39a6c8052efbcb@mail.gmail.com> Dear All I want to calculate Phonon Phonon interaction on Ti bcc structure by d3.x but it has been employed by norm conserving pseudopotential only. This pseudopotential is not available In pwscf website. I found it (NC-pbe- with 4 valance electron) on FHI website and convert it to UPF format. I tested the pseudopotential but i realized that structural properties is completely wrong. As far as my understanding Ti properties is quite sensitive to number of valence electrons and i checked pseudopotential (van pbe 12 z electron) with 12 valance electrons and the results are reasonable. Kindly, let me to have Ti pseudopotential (Norm Conserving, pbe, with 12 valance electron) if you have it. Thank you very much in advance. Best wishes Rostam Golesorkhtabar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/7401dc1f/attachment.htm From dimpy.sharma at tyndall.ie Sun Dec 20 19:25:59 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Sun, 20 Dec 2009 18:25:59 -0000 Subject: [Pw_forum] too few bands or 'charge is wrong Message-ID: Hi there, I would like to ask one thing,as I face this problem almost in every calculation, it is about 'nbnd ' in quantum espresso input. Actually I use to calculate the nbn as per the rule given in manual i.e I use to take 20% more number of valence bands( actually I calculate total number of electrons and then divide them by 2 and take 20% extra electrons ), but since my last few calculations, if I take this value in nbn, I always get 'too few bands', thus now I am giving a random value in nbn when I get either 'charge is wrong'. My apologise, is it because of nbnd value or is there chance of any other error in my input file?I am running a scf calculation with K_points '2 1 1 0 0 0'. Actually I have tried varying other parameters like mixing beta, but I get the same output? Thanks and regards! Dimpy UCC Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/57121359/attachment.htm From eyvaz_isaev at yahoo.com Mon Dec 21 03:17:03 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 20 Dec 2009 18:17:03 -0800 (PST) Subject: [Pw_forum] too few bands or 'charge is wrong In-Reply-To: Message-ID: <491366.14274.qm@web65708.mail.ac4.yahoo.com> Dear Dimpy, --- On Sun, 12/20/09, Dimpy Sharma wrote: > > too few bands or 'charge is wrong > You can just simply do not specify "nbnd" allowing the code to take it by default. If this does not help, use more nbnd's, say 30-40%, not 20%, additional bands. 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 mohnish.iitk at gmail.com Mon Dec 21 06:17:58 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 21 Dec 2009 10:47:58 +0530 Subject: [Pw_forum] program for converting pwscf output file to crystal maker format Message-ID: Dear QE users, Does anybody have fortran, C or any other program to convert PWSCF output or input file CRYSTALMAKER format. I need that because I want to cleave some plane of the bulk to visualize the surface which I think is not availbale in Xcrysden. Sicere thanks in advance. MOHNISH -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/cf646088/attachment.htm From quantumdft at gmail.com Mon Dec 21 09:10:29 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 21 Dec 2009 16:10:29 +0800 Subject: [Pw_forum] adsorption calculations with spin-polarization Message-ID: <412f6c680912210010i716b02f0p1c93768c290ba99@mail.gmail.com> Dear all, I want to calculate O2 adsorped on certain defect free TiO2 surface. It is well known that the most stable state for O2 is triplet. Test calculations showed that the singlet state of O2 was ~*1.13 eV higher* than triplet state. So we should set nspin = 2, multiplicity = 3, for O2 isolate molecule. When O2 adsorbed on the defect free TiO2 surface in the slab model, we still compared the calculations with or without 'nspin = 2, multiplicity = 3'. The singlet state of the slab model of adsorption is ~*0.82 eV higher *than triplet state. So I think the triplet is suitable for this adsoprtion slab model. However, the singlet state is the most stable sate for the bare surface slab model. The triplet stateis of bare surface model about ~*1.67 eV higher *than singlet state. So I wonder how to determin the adsorption energy for this system. E(adsorption)= E(O2+surface)_triplet - E(surface)_*singlet* - E(isolate O2)_triplet? or E(adsorption)= E(O2+surface)_triplet - E(surface)_*triplet* - E(isolate O2)_triplet? I also confused about when spin-polarization is indispensablethe for the calculation of adsorption behaviours on the surface slab model. Thank you for reading. best wishes, vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091221/259a57aa/attachment.htm From lfhuang at theory.issp.ac.cn Mon Dec 21 09:11:42 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 21 Dec 2009 16:11:42 +0800 Subject: [Pw_forum] =?utf-8?q?inqure_about_the_theory_of_infrared_spectrum?= =?utf-8?q?_calculation?= Message-ID: <20091221081142.26380.qmail@ms.hfcas.ac.cn> Dear Y. H. Xu: P. Umari's papers are worthy of being refered to, e.g.: P. Umari, A. Pasquarello, "Infrared and Raman spectra of disordered materials from first principles" Diamond & Related Materials vol 14, p1255-1261 (2005). Or the references therein. The relevent papers citing these papers shall be not hard to trace. Best Wishes Yours Sincerely L.F.Huang Other papers shall be > Date: Sun, 20 Dec 2009 20:56:35 +0800 > From: xu yuehua > Subject: [Pw_forum] inqure about the theory of infrared spectrum > calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > hi everyone here: > > i am seeking some literature or paper about infrared intensity calculation > in PWSCF, can anyone tell me > > where is it available. > > thank you ! > > -- > Yuehua Xu > Group of Computational Condensed Matter Physics, > National Laboratory of Solid State Microstructures and Department of > Physics, > Nanjing University, > Nanjing 210093, > P. R. China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/b073799d/attachment.html > ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== 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/20091221/4d18ecec/attachment.htm From sclauzer at sissa.it Mon Dec 21 10:33:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 21 Dec 2009 10:33:45 +0100 Subject: [Pw_forum] equilibrium volume In-Reply-To: <7699a1950912200606j709efbbau4a0ed192384fa00e@mail.gmail.com> References: <7699a1950912200606j709efbbau4a0ed192384fa00e@mail.gmail.com> Message-ID: <4B2F40F9.5030104@sissa.it> Dear Mohaddeseh mohaddeseh abbasnejad wrote: > > Dear all > When I run an scf calculation for the equilibrium volume obtained by the > Murnaghan-fit, the stresses are too far from zero. What does it mean too far? Please specify some numbers, so that we can have an idea of what's happening. You should also specify some input file of your system. > Should i expect this volume to be zero pressure volume, or there is a > problem in the calculation? I think it will be hardly exactly zero (for obvious numerical reasons) unless you specify the exact equilibrium lattice constant with many significant digits and use very high cutoffs (I think that stress is much harder to converge than total energy differences). You should also keep in mind that the parameters resulting from a fit have an error bar associated with them (though this might be quite small for the equilibrium lattice constant, it may be enough to offset the stress a little bit from zero). Try to sample more points around the minimum and fit with a parabola (such that the chi square of the fit is very low). Gabriele > Thanx for any comment > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 ynwuyang at gmail.com Mon Dec 21 11:17:48 2009 From: ynwuyang at gmail.com (yuning wu) Date: Mon, 21 Dec 2009 05:17:48 -0500 Subject: [Pw_forum] (no subject) Message-ID: <8f1062e50912210217n52de5105mdc03bc5f30a7c745@mail.gmail.com> Dear all, I am doing a phonon spectrum calculation. After got all *.dyn* files, I use the q2r.x to do get *.fc file successfully. However, in phdos calculation, I got an error message: from frc_blk : error # 1 wrong total_weight I am confused that what can cause this error. Thanks. Yuning Wu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/c77ea026/attachment.htm From kazempoor2000 at yahoo.com Mon Dec 21 14:31:21 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 21 Dec 2009 05:31:21 -0800 (PST) Subject: [Pw_forum] EXX compile Message-ID: <983920.96502.qm@web112516.mail.gq1.yahoo.com> Dear All I am success in compilation of cvs version of espresso for using EXX.(first ./configure and then add -DEXX or _D__EXX to DFLAGS). but when i want to run example it get this error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from read_namelists : error # 88 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% what goes wrong? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/e07fa289/attachment.htm From njuxuyuehua at gmail.com Mon Dec 21 14:43:32 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Mon, 21 Dec 2009 21:43:32 +0800 Subject: [Pw_forum] inqure about the theory of infrared spectrum calculation In-Reply-To: <20091221081142.26380.qmail@ms.hfcas.ac.cn> References: <20091221081142.26380.qmail@ms.hfcas.ac.cn> Message-ID: hello L.F.Huang Thank you for your reply. and maybe you have read the reference you give me. and is that theory used in PWSCF code? ---------- Forwarded message ---------- From: lfhuang Date: 2009/12/21 Subject: Re: [Pw_forum] inqure about the theory of infrared spectrum calculation To: pw_forum Dear Y. H. Xu: P. Umari's papers are worthy of being refered to, e.g.: P. Umari, A. Pasquarello, "Infrared and Raman spectra of disordered materials from first principles" Diamond & Related Materials vol 14, p1255-1261 (2005). Or the references therein. The relevent papers citing these papers shall be not hard to trace. Best Wishes Yours Sincerely L.F.Huang Other papers shall be > Date: Sun, 20 Dec 2009 20:56:35 +0800 > From: xu yuehua > Subject: [Pw_forum] inqure about the theory of infrared spectrum > calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > hi everyone here: > > i am seeking some literature or paper about infrared intensity calculation > in PWSCF, can anyone tell me > > where is it available. > > thank you ! > > -- > Yuehua Xu > Group of Computational Condensed Matter Physics, > National Laboratory of Solid State Microstructures and Department of > Physics, > Nanjing University, > Nanjing 210093, > P. R. China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/b073799d/attachment.html> > ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== 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) ====================================================================== _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/b8754900/attachment-0001.htm From giannozz at democritos.it Mon Dec 21 14:51:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Dec 2009 14:51:50 +0100 Subject: [Pw_forum] inqure about the theory of infrared spectrum calculation In-Reply-To: References: <20091221081142.26380.qmail@ms.hfcas.ac.cn> Message-ID: <4B2F7D76.8030009@democritos.it> xu yuehua wrote: > and is that theory used in PWSCF code? http://www.springer.com/physics/book/978-1-4020-3287-5 go to 'Sample pages', download the file. It contains a brief introduction to density-fgunctional perturbation theory, including some essential info on how to calculate IR cross sections P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Dec 21 15:06:19 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Dec 2009 15:06:19 +0100 Subject: [Pw_forum] EXX compile In-Reply-To: <983920.96502.qm@web112516.mail.gq1.yahoo.com> References: <983920.96502.qm@web112516.mail.gq1.yahoo.com> Message-ID: <4B2F80DB.1070105@democritos.it> ali kazempour wrote: > (first ./configure and then add -DEXX or _D__EXX to DFLAGS) it is not the same: -DEXX is the correct option - P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From njuxuyuehua at gmail.com Mon Dec 21 15:11:38 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Mon, 21 Dec 2009 22:11:38 +0800 Subject: [Pw_forum] inqure about the theory of infrared spectrum calculation In-Reply-To: <4B2F7D76.8030009@democritos.it> References: <20091221081142.26380.qmail@ms.hfcas.ac.cn> <4B2F7D76.8030009@democritos.it> Message-ID: thank Paolo Giannozzi as well as L.F.Huang . 2009/12/21 Paolo Giannozzi > xu yuehua wrote: > > > and is that theory used in PWSCF code? > > http://www.springer.com/physics/book/978-1-4020-3287-5 > go to 'Sample pages', download the file. It contains a brief > introduction to density-fgunctional perturbation theory, > including some essential info on how to calculate IR cross > sections > > 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 > -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/c989aaf5/attachment.htm From kazempoor2000 at yahoo.com Mon Dec 21 15:36:17 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 21 Dec 2009 06:36:17 -0800 (PST) Subject: [Pw_forum] EXX compile In-Reply-To: <4B2F80DB.1070105@democritos.it> References: <983920.96502.qm@web112516.mail.gq1.yahoo.com> <4B2F80DB.1070105@democritos.it> Message-ID: <120147.55601.qm@web112503.mail.gq1.yahoo.com> Dear Paolo I did it several time but It didn't work. I just added -DEXX to DFLAGS and make pw, But the errore remains yet. Best Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ________________________________ From: Paolo Giannozzi To: PWSCF Forum Sent: Mon, December 21, 2009 3:06:19 PM Subject: Re: [Pw_forum] EXX compile ali kazempour wrote: > (first ./configure and then add -DEXX or _D__EXX to DFLAGS) it is not the same: -DEXX is the correct option - 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/20091221/d9c456e4/attachment.htm From kazempoor2000 at yahoo.com Mon Dec 21 15:43:09 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 21 Dec 2009 06:43:09 -0800 (PST) Subject: [Pw_forum] EXX compile In-Reply-To: <120147.55601.qm@web112503.mail.gq1.yahoo.com> References: <983920.96502.qm@web112516.mail.gq1.yahoo.com> <4B2F80DB.1070105@democritos.it> <120147.55601.qm@web112503.mail.gq1.yahoo.com> Message-ID: <941359.63829.qm@web112503.mail.gq1.yahoo.com> Sorry I forgot to attach make.sys best Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ________________________________ From: ali kazempour To: PWSCF Forum Sent: Mon, December 21, 2009 3:36:17 PM Subject: Re: [Pw_forum] EXX compile Dear Paolo I did it several time but It didn't work. I just added -DEXX to DFLAGS and make pw, But the errore remains yet. Best Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ________________________________ From: Paolo Giannozzi To: PWSCF Forum Sent: Mon, December 21, 2009 3:06:19 PM Subject: Re: [Pw_forum] EXX compile ali kazempour wrote: > (first ./configure and then add -DEXX or _D__EXX to DFLAGS) it is not the same: -DEXX is the correct option - 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/20091221/61e8683a/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: make.sys Type: application/octet-stream Size: 4420 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091221/61e8683a/attachment.obj From giannozz at democritos.it Mon Dec 21 15:45:32 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Dec 2009 15:45:32 +0100 Subject: [Pw_forum] EXX compile In-Reply-To: <941359.63829.qm@web112503.mail.gq1.yahoo.com> References: <983920.96502.qm@web112516.mail.gq1.yahoo.com> <4B2F80DB.1070105@democritos.it> <120147.55601.qm@web112503.mail.gq1.yahoo.com> <941359.63829.qm@web112503.mail.gq1.yahoo.com> Message-ID: <4B2F8A0C.2000600@democritos.it> ali kazempour wrote: > I forgot to attach make.sys > # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas is it? > DFLAGS = -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA -DEXX > FDFLAGS = -D__AIX,-D__XLF,-D__ESSL,-D__MASS,-D__MPI,-D__PARA P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From nicvok at freenet.de Mon Dec 21 15:04:57 2009 From: nicvok at freenet.de (Nicki Frank Hinsche) Date: Mon, 21 Dec 2009 15:04:57 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations Message-ID: Hi there, I just want to know whether and how it is possible to shift the Fermi energy before constructing the Fermi surface?! See the following scenario: 1. making a scf calculation for a semiconductor - the Fermi energy will be in the energy gap (thats all right) and there will be (of course) no Fermi surface 2. I want to simulate doping for some tests, just by shifting the Fermi energy a bit into either valence or conduction band - there would be a fermi surface - this is what I want ...so,how can I shift the Fermi energy (manually) after a scf calculation to an energy quit near the original one and calculate the Fermi surface afterwards? ..thanks a lot Nicki ------------------------------------------------------------- Nicki Frank Hinsche, Dipl. Phys. Institut f?r Physik - Theoretische Physik, Martin-Luther-Universit?t Halle-Wittenberg, Von-Seckendorff-Platz 1, Raum 1.07 D-06120 Halle/Saale, Germany Tel.: ++49 345 5525460 ------------------------------------------------------------- From majdoub at gmail.com Mon Dec 21 18:00:25 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Mon, 21 Dec 2009 11:00:25 -0600 Subject: [Pw_forum] Graphene on BN : unable to reach convergence Message-ID: Dear Pwscf user, I am trying to achieve relaxation of 1 layer of graphene on bilayer BN. I am using 40 processors. However, I am not able to reach convergence. I tried to increase ecutwfc from 25 to 30, ecutrho from 250 to 300. Also, I tried using 'cg' mode instead of 'david' algorithm, mixing_mode = 'local-TF', and reducing conv_thr from default to 1.D-5 and 1.D-4. But, convergence is not achieved. Either it stays running for ever, or stop after a while. Could you pleas help with this calculation. Your suggestions and help are highly appreciated. Thank you inadvance. Here is a sample of the output file: --------------------------------------------------------------------------------------------------------------------------------------------------------------------- ............................................. the Fermi energy is 0.6876 ev ! total energy = -869.39400388 Ry Harris-Foulkes estimate = -869.39395818 Ry estimated scf accuracy < 0.00000005 Ry The total energy is the sum of the following terms: one-electron contribution =-11231.22009619 Ry hartree contribution = 5691.19012576 Ry xc contribution = -255.73750085 Ry ewald contribution = 4926.37346740 Ry smearing contrib. (-TS) = 0.00000000 Ry convergence has been achieved in 9 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00011088 -0.00065304 -0.00103877 atom 2 type 1 force = -0.00022395 0.00081219 -0.00104134 atom 3 type 1 force = 0.00021000 -0.00084527 -0.00105019 atom 4 type 1 force = 0.00119892 -0.00035183 -0.00104665 atom 5 type 1 force = -0.00184192 -0.00038828 -0.00113477 atom 6 type 1 force = -0.00038293 -0.00112440 -0.00114180 atom 7 type 1 force = 0.00005921 0.00071395 -0.00114073 atom 8 type 1 force = 0.00049597 0.00059147 -0.00104299 atom 9 type 1 force = -0.00034360 -0.00081840 -0.00105115 atom 10 type 1 force = -0.00003603 0.00063828 -0.00104436 atom 11 type 1 force = 0.00103004 0.00039896 -0.00105379 atom 12 type 1 force = -0.00011365 0.00086060 -0.00104572 atom 13 type 1 force = 0.00155737 0.00035585 -0.00105257 atom 14 type 1 force = 0.00129408 -0.00035678 -0.00105119 atom 15 type 1 force = 0.00020134 -0.00058471 -0.00104354 atom 16 type 1 force = 0.00008227 -0.00073252 -0.00115227 atom 17 type 1 force = 0.00010912 0.00073818 -0.00114516 atom 18 type 1 force = -0.00033300 -0.00104104 -0.00114566 atom 19 type 1 force = -0.00180151 -0.00037723 -0.00113755 atom 20 type 1 force = -0.00027782 0.00100537 -0.00114916 atom 21 type 1 force = -0.00021158 -0.00071913 -0.00115459 atom 22 type 1 force = -0.00061506 0.00109819 -0.00115210 atom 23 type 1 force = -0.00172302 0.00037700 -0.00113522 atom 24 type 1 force = -0.00201534 0.00037864 -0.00113601 atom 25 type 2 force = 0.00266334 -0.00082256 0.00141953 atom 26 type 2 force = 0.00354500 -0.00004336 0.00141302 atom 27 type 2 force = 0.00354161 0.00041848 0.00141361 atom 28 type 2 force = 0.00174673 0.00085406 0.00141868 atom 29 type 2 force = 0.00263899 0.00014396 0.00141397 atom 30 type 2 force = 0.00266108 -0.00034465 0.00141502 atom 31 type 2 force = -0.00319859 0.00037610 0.00045810 atom 32 type 2 force = -0.00317599 -0.00016845 0.00045961 atom 33 type 2 force = -0.00228049 -0.00087344 0.00045818 atom 34 type 2 force = 0.00326060 -0.00013378 0.00141700 atom 35 type 2 force = 0.00238518 -0.00083037 0.00141978 atom 36 type 2 force = -0.00362994 0.00044169 0.00045646 atom 37 type 2 force = 0.00328935 0.00035247 0.00141514 atom 38 type 2 force = -0.00176990 0.00085166 0.00045815 atom 39 type 2 force = -0.00267409 0.00014749 0.00045626 atom 40 type 2 force = -0.00269243 -0.00040253 0.00045489 atom 41 type 2 force = -0.00362727 -0.00006198 0.00045778 atom 42 type 2 force = -0.00327950 0.00084940 0.00045779 atom 43 type 2 force = -0.00414992 0.00005688 0.00045823 atom 44 type 2 force = -0.00417525 -0.00044357 0.00045652 atom 45 type 2 force = 0.00420469 -0.00041238 0.00141471 atom 46 type 2 force = -0.00275647 -0.00085117 0.00045939 atom 47 type 2 force = 0.00331631 0.00084650 0.00141767 atom 48 type 2 force = 0.00417437 0.00005078 0.00141584 atom 49 type 3 force = -0.00088022 -0.00023100 0.00063786 atom 50 type 3 force = -0.00019195 0.00024496 0.00062889 atom 51 type 3 force = 0.00033221 0.00013013 0.00063784 atom 52 type 3 force = -0.00008497 0.00055599 -0.00031675 atom 53 type 3 force = 0.00050558 0.00049650 -0.00032468 atom 54 type 3 force = 0.00146339 -0.00045612 -0.00031558 atom 55 type 3 force = 0.00004674 -0.00051090 -0.00031838 atom 56 type 3 force = 0.00067836 -0.00045754 -0.00031539 atom 57 type 3 force = 0.00163709 0.00041107 -0.00031095 atom 58 type 3 force = 0.00175006 -0.00045164 -0.00031617 atom 59 type 3 force = 0.00086604 0.00056530 -0.00032391 atom 60 type 3 force = 0.00021240 0.00059253 -0.00031733 atom 61 type 3 force = 0.00150146 0.00042748 -0.00030823 atom 62 type 3 force = 0.00057028 -0.00053586 -0.00031293 atom 63 type 3 force = -0.00012902 -0.00056852 -0.00031301 atom 64 type 3 force = 0.00041895 -0.00015221 0.00063305 atom 65 type 3 force = -0.00012048 -0.00020963 0.00063052 atom 66 type 3 force = -0.00080908 0.00018092 0.00063740 atom 67 type 3 force = -0.00014421 -0.00009401 0.00062955 atom 68 type 3 force = -0.00066194 -0.00016966 0.00062806 atom 69 type 3 force = -0.00136062 0.00021334 0.00063441 atom 70 type 3 force = -0.00129838 -0.00022836 0.00063582 atom 71 type 3 force = -0.00061758 0.00016207 0.00062794 atom 72 type 3 force = -0.00013128 0.00010786 0.00063396 Total force = 0.019204 Total SCF correction = 0.003942 SCF correction compared to forces is too large, reduce conv_thr number of scf cycles = 14 number of bfgs steps = 10 energy old = -869.3937346680 Ry energy new = -869.3940038837 Ry CASE: energy _new < energy _old new trust radius = 0.0460818304 bohr new conv_thr = 0.0000002692 Ry ATOMIC_POSITIONS (angstrom) B 0.710238954 8.607144248 11.274646121 B 0.710189658 11.065254747 11.274653416 B 2.840139961 7.377767735 11.274662357 B 0.710003498 6.148338558 11.274660830 B 6.389874581 6.148447299 7.975298562 B 6.389694310 8.607201677 7.975281894 B 6.389730015 11.065514141 7.975299602 B 2.840191056 9.835876709 11.274657002 B 7.099545998 7.377769839 11.274689692 B 7.099599100 9.835868309 11.274678490 B 7.099362158 12.294682727 11.274692097 B 4.969987784 11.065251631 11.274659162 B 2.839951415 12.294679179 11.274672405 B 4.969811953 6.148349478 11.274658687 B 4.970048734 8.607141050 11.274647348 B 4.259776451 7.377516545 7.975309501 B 2.129891520 11.065515297 7.975282179 B 2.129842847 8.607205772 7.975262478 B 2.130025127 6.148453706 7.975275500 B 4.259735938 9.835817945 7.975300165 B 0.000285812 7.377523468 7.975298224 B 0.000244054 9.835819979 7.975293909 B 4.259922871 12.294590418 7.975303472 B 0.000423122 12.294596884 7.975294114 C 2.129634203 6.148890372 14.670766572 C 2.129256615 8.606951473 14.670776369 C 2.129926206 11.064961183 14.670777896 C 0.000207950 12.294075989 14.670756205 C -0.000148110 9.835992828 14.670765477 C 0.000493248 7.377989412 14.670762573 C 0.710340292 11.064953696 14.672139091 C 0.710994208 8.606967109 14.672133164 C 0.710632246 6.148877778 14.672127260 C 6.389121270 8.606962975 14.670760178 C 6.389493703 6.148878001 14.670752431 C 4.970228330 11.064955212 14.672130196 C 6.389782767 11.064958283 14.670765658 C 7.099924988 12.294066685 14.672121322 C 7.100274852 9.835992897 14.672124845 C 7.099632661 7.377986551 14.672124547 C 4.970896506 8.606948139 14.672124019 C 2.840688593 12.294053703 14.672126654 C 2.841064052 9.835998132 14.672130891 C 2.840395045 7.377985542 14.672134207 C 4.259743827 7.377985914 14.670761100 C 4.970520412 6.148887268 14.672120730 C 4.259452927 12.294061978 14.670750182 C 4.259074950 9.836003379 14.670756904 N 0.000343961 12.294490660 11.274489476 N 0.000060685 9.835744446 11.274473641 N 0.000031953 7.378176055 11.274499102 N 2.840479804 7.378131693 7.968594027 N 2.840459610 9.835679843 7.968670941 N 2.840178358 12.294324967 7.968663142 N 4.970396710 11.064897346 7.968622809 N 4.970391015 8.607371192 7.968652183 N 4.970115668 6.148687554 7.968667860 N 7.099707812 12.294333396 7.968672304 N 7.099982646 9.835676642 7.968676968 N 7.099995825 7.378144315 7.968604107 N 0.710270006 6.148679123 7.968653703 N 0.710539826 8.607361686 7.968641382 N 0.710541147 11.064889755 7.968612889 N 6.389440690 11.064847790 11.274567333 N 6.389486158 8.607276250 11.274503293 N 6.389761122 6.148516618 11.274566266 N 2.129515407 11.064847507 11.274562347 N 2.129541822 8.607279997 11.274491068 N 2.129822637 6.148522233 11.274556890 N 4.259798907 12.294488325 11.274468720 N 4.259518456 9.835749258 11.274454242 N 4.259471118 7.378171507 11.274469629 Writing output data file GphBN.save Check: negative starting charge= -0.070546 NEW-OLD atomic charge density approx. for the potential Check: negative starting charge= -0.070364 negative rho (up, down): 0.748E-03 0.000E+00 total cpu time spent up to now is 57670.72 secs per-process dynamical memory: 103.8 Mb Self-consistent Calculation iteration # 1 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.00E-06, avg # of iterations = 3.3 negative rho (up, down): 0.649E-03 0.000E+00 total cpu time spent up to now is 58356.91 secs total energy = -869.39427487 Ry Harris-Foulkes estimate = -869.39428822 Ry estimated scf accuracy < 0.00034068 Ry iteration # 2 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.18E-07, avg # of iterations = 1.1 negative rho (up, down): 0.827E-03 0.000E+00 total cpu time spent up to now is 58701.26 secs total energy = -869.39419485 Ry Harris-Foulkes estimate = -869.39427958 Ry estimated scf accuracy < 0.00027476 Ry iteration # 3 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 9.54E-08, avg # of iterations = 2.0 negative rho (up, down): 0.717E-03 0.000E+00 total cpu time spent up to now is 59124.23 secs total energy = -869.39423763 Ry Harris-Foulkes estimate = -869.39423514 Ry estimated scf accuracy < 0.00005408 Ry iteration # 4 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.88E-08, avg # of iterations = 1.0 negative rho (up, down): 0.170E-02 0.000E+00 total cpu time spent up to now is 59452.62 secs total energy = -869.39423735 Ry Harris-Foulkes estimate = -869.39423817 Ry estimated scf accuracy < 0.00004506 Ry iteration # 5 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.56E-08, avg # of iterations = 2.0 negative rho (up, down): 0.153E-02 0.000E+00 total cpu time spent up to now is 59842.36 secs total energy = -869.39424453 Ry Harris-Foulkes estimate = -869.39424150 Ry estimated scf accuracy < 0.00000187 Ry iteration # 6 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 6.50E-10, avg # of iterations = 3.0 negative rho (up, down): 0.139E-02 0.000E+00 total cpu time spent up to now is 60284.73 secs total energy = -869.39424753 Ry Harris-Foulkes estimate = -869.39424469 Ry estimated scf accuracy < 0.00000170 Ry iteration # 7 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 5.90E-10, avg # of iterations = 1.0 negative rho (up, down): 0.135E-02 0.000E+00 total cpu time spent up to now is 60613.51 secs total energy = -869.39425010 Ry Harris-Foulkes estimate = -869.39424756 Ry estimated scf accuracy < 0.00000101 Ry iteration # 8 ecut= 25.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 3.50E-10, avg # of iterations = 2.0 total cpu time spent up to now is 61035.01 secs End of self-consistent calculation k = 0.0059 0.0068 0.0000 ( 20180 PWs) bands (ev): -20.3140 -20.1796 -19.2251 -19.1767 -19.0882 -18.9982 -18.8876 -18.8671 .......................... Here the input file: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- &control title = 'GphBNcapa' calculation = 'relax' outdir = '/pwscf/pwscftemp/GphBN' prefix = 'GphBN' pseudo_dir = '/input/Gph-BN/pseudopot-C-B-N' tprnfor = .t. restart_mode = 'from_scratch' / &system ibrav = 0, celldm(1) = 1.8897261 nat = 72, ntyp = 3, ecutwfc = 30.0 ecutrho = 300.0 occupations = 'smearing' smearing = 'gaussian' degauss = 0.003675 / &electrons mixing_beta = 0.05 diagonalization = 'david' / &ions trust_radius_ini = 0.10 / &cell ATOMIC_SPECIES B 10.81100 B.pz-vbc.UPF C 12.01070 C.pz-vbc.UPF N 14.00674 N.pz-vbc.UPF ATOMIC_POSITIONS angstrom B 0.710000 8.607000 11.306000 B 0.710000 11.066000 11.306000 B 2.840000 7.377000 11.306000 B 0.710000 6.148000 11.306000 B 6.390000 6.148000 8.000000 B 6.390000 8.607000 8.000000 B 6.390000 11.066000 8.000000 B 2.840000 9.836000 11.306000 B 7.100000 7.377000 11.306000 B 7.100000 9.836000 11.306000 B 7.100000 12.295000 11.306000 B 4.970000 11.066000 11.306000 B 2.840000 12.295000 11.306000 B 4.970000 6.148000 11.306000 B 4.970000 8.607000 11.306000 B 4.260000 7.377000 8.000000 B 2.130000 11.066000 8.000000 B 2.130000 8.607000 8.000000 B 2.130000 6.148000 8.000000 B 4.260000 9.836000 8.000000 B 0.000000 7.377000 8.000000 B 0.000000 9.836000 8.000000 B 4.260000 12.295000 8.000000 B 0.000000 12.295000 8.000000 C 2.130000 6.148000 14.612000 C 2.130000 8.607000 14.612000 C 2.130000 11.066000 14.612000 C 0.000000 12.295000 14.612000 C 0.000000 9.836000 14.612000 C 0.000000 7.377000 14.612000 C 0.710000 11.066000 14.612000 C 0.710000 8.607000 14.612000 C 0.710000 6.148000 14.612000 C 6.390000 8.607000 14.612000 C 6.390000 6.148000 14.612000 C 4.970000 11.066000 14.612000 C 6.390000 11.066000 14.612000 C 7.100000 12.295000 14.612000 C 7.100000 9.836000 14.612000 C 7.100000 7.377000 14.612000 C 4.970000 8.607000 14.612000 C 2.840000 12.295000 14.612000 C 2.840000 9.836000 14.612000 C 2.840000 7.377000 14.612000 C 4.260000 7.377000 14.612000 C 4.970000 6.148000 14.612000 C 4.260000 12.295000 14.612000 C 4.260000 9.836000 14.612000 N 0.000000 12.295000 11.306000 N 0.000000 9.836000 11.306000 N 0.000000 7.377000 11.306000 N 2.840000 7.377000 8.000000 N 2.840000 9.836000 8.000000 N 2.840000 12.295000 8.000000 N 4.970000 11.066000 8.000000 N 4.970000 8.607000 8.000000 N 4.970000 6.148000 8.000000 N 7.100000 12.295000 8.000000 N 7.100000 9.836000 8.000000 N 7.100000 7.377000 8.000000 N 0.710000 6.148000 8.000000 N 0.710000 8.607000 8.000000 N 0.710000 11.066000 8.000000 N 6.390000 11.066000 11.306000 N 6.390000 8.607000 11.306000 N 6.390000 6.148000 11.306000 N 2.130000 11.066000 11.306000 N 2.130000 8.607000 11.306000 N 2.130000 6.148000 11.306000 N 4.260000 12.295000 11.306000 N 4.260000 9.836000 11.306000 N 4.260000 7.377000 11.306000 K_POINTS automatic 10 10 1 1 1 0 CELL_PARAMETERS 8.51980 0.00000 0.00000 0.00000 7.37600 0.00000 0.00000 0.00000 22.6120 Departement of Mechanical Engineering University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/20dcedfa/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Mon Dec 21 17:59:09 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 21 Dec 2009 17:59:09 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: References: Message-ID: <200912211759.10048.giuseppe.mattioli@mlib.ism.cnr.it> Dear Nicki You could add (or remove) some fraction of electronic charge and perform a new scf calculation. Giuseppe On Monday 21 December 2009 15:04:57 Nicki Frank Hinsche wrote: > Hi there, > > I just want to know whether and how it is possible to shift the Fermi > energy before constructing the Fermi surface?! See the following > scenario: > > 1. making a scf calculation for a semiconductor - the Fermi energy > will be in the energy gap (thats all right) and there will be (of > course) no Fermi surface > 2. I want to simulate doping for some tests, just by shifting the > Fermi energy a bit into either valence or conduction band - there > would be a fermi surface - this is what I want > > ...so,how can I shift the Fermi energy (manually) after a scf > calculation to an energy quit near the original one and calculate the > Fermi surface afterwards? > > ..thanks a lot > > Nicki > ------------------------------------------------------------- > Nicki Frank Hinsche, Dipl. Phys. > Institut f?r Physik - Theoretische Physik, > Martin-Luther-Universit?t Halle-Wittenberg, > Von-Seckendorff-Platz 1, Raum 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > ------------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091221/9aefbf60/attachment.htm From kondor.jess at gmail.com Mon Dec 21 18:32:29 2009 From: kondor.jess at gmail.com (Jess Kondor) Date: Mon, 21 Dec 2009 12:32:29 -0500 Subject: [Pw_forum] Graphene on BN : unable to reach convergence In-Reply-To: References: Message-ID: <1d9d5d9d0912210932o22d3fd5bta27308e1e33a1bbf@mail.gmail.com> Hi, you use norm-conserving pseudos, therefore your ecut/ecutwfc are not correct. (ecut is very low, ecutrho should not be set by hand). On Mon, Dec 21, 2009 at 12:00 PM, mohamed sabri majdoub wrote: > Dear Pwscf user, > > I am trying to achieve relaxation of 1 layer of graphene on bilayer BN. I am > using 40 processors. > However, I am not able to reach convergence. I tried to increase ecutwfc > from 25 to 30, ecutrho from 250 to 300. Also, I tried using 'cg' mode > instead of 'david' algorithm, mixing_mode = 'local-TF', and reducing > conv_thr from default to 1.D-5 and 1.D-4. But, convergence is not achieved. > Either it stays running for ever, or stop after a while. > Could you pleas help with this calculation. Your suggestions and help are > highly appreciated. Thank you inadvance. > > Here is a sample of the output file: > --------------------------------------------------------------------------------------------------------------------------------------------------------------------- > ............................................. > > ?the Fermi energy is???? 0.6876 ev > > !??? total energy????????????? =? -869.39400388 Ry > ???? Harris-Foulkes estimate?? =? -869.39395818 Ry > ???? estimated scf accuracy??? > ???? The total energy is the sum of the following terms: > > ???? one-electron contribution =-11231.22009619 Ry > ???? hartree contribution????? =? 5691.19012576 Ry > ???? xc contribution?????????? =? -255.73750085 Ry > ???? ewald contribution??????? =? 4926.37346740 Ry > ???? smearing contrib. (-TS)?? =???? 0.00000000 Ry > > ???? convergence has been achieved in?? 9 iterations > > ???? Forces acting on atoms (Ry/au): > > ???? atom?? 1 type? 1?? force =???? 0.00011088?? -0.00065304?? -0.00103877 > ???? atom?? 2 type? 1?? force =??? -0.00022395??? 0.00081219?? -0.00104134 > ???? atom?? 3 type? 1?? force =???? 0.00021000?? -0.00084527?? -0.00105019 > ???? atom?? 4 type? 1?? force =???? 0.00119892?? -0.00035183?? -0.00104665 > ???? atom?? 5 type? 1?? force =??? -0.00184192?? -0.00038828?? -0.00113477 > ???? atom?? 6 type? 1?? force =??? -0.00038293?? -0.00112440?? -0.00114180 > ???? atom?? 7 type? 1?? force =???? 0.00005921??? 0.00071395?? -0.00114073 > ???? atom?? 8 type? 1?? force =???? 0.00049597??? 0.00059147?? -0.00104299 > ???? atom?? 9 type? 1?? force =??? -0.00034360?? -0.00081840?? -0.00105115 > ???? atom? 10 type? 1?? force =??? -0.00003603??? 0.00063828?? -0.00104436 > ???? atom? 11 type? 1?? force =???? 0.00103004??? 0.00039896?? -0.00105379 > ???? atom? 12 type? 1?? force =??? -0.00011365??? 0.00086060?? -0.00104572 > ???? atom? 13 type? 1?? force =???? 0.00155737??? 0.00035585?? -0.00105257 > ???? atom? 14 type? 1?? force =???? 0.00129408?? -0.00035678?? -0.00105119 > ???? atom? 15 type? 1?? force =???? 0.00020134?? -0.00058471?? -0.00104354 > ???? atom? 16 type? 1?? force =???? 0.00008227?? -0.00073252?? -0.00115227 > ???? atom? 17 type? 1?? force =???? 0.00010912??? 0.00073818?? -0.00114516 > ???? atom? 18 type? 1?? force =??? -0.00033300?? -0.00104104?? -0.00114566 > ???? atom? 19 type? 1?? force =??? -0.00180151?? -0.00037723?? -0.00113755 > ???? atom? 20 type? 1?? force =??? -0.00027782??? 0.00100537?? -0.00114916 > ???? atom? 21 type? 1?? force =??? -0.00021158?? -0.00071913?? -0.00115459 > ???? atom? 22 type? 1?? force =??? -0.00061506??? 0.00109819?? -0.00115210 > ???? atom? 23 type? 1?? force =??? -0.00172302??? 0.00037700?? -0.00113522 > ???? atom? 24 type? 1?? force =??? -0.00201534??? 0.00037864?? -0.00113601 > ???? atom? 25 type? 2?? force =???? 0.00266334?? -0.00082256??? 0.00141953 > ???? atom? 26 type? 2?? force =???? 0.00354500?? -0.00004336??? 0.00141302 > ???? atom? 27 type? 2?? force =???? 0.00354161??? 0.00041848??? 0.00141361 > ???? atom? 28 type? 2?? force =???? 0.00174673??? 0.00085406??? 0.00141868 > ???? atom? 29 type? 2?? force =???? 0.00263899??? 0.00014396??? 0.00141397 > ???? atom? 30 type? 2?? force =???? 0.00266108?? -0.00034465??? 0.00141502 > ???? atom? 31 type? 2?? force =??? -0.00319859??? 0.00037610??? 0.00045810 > ???? atom? 32 type? 2?? force =??? -0.00317599?? -0.00016845??? 0.00045961 > ???? atom? 33 type? 2?? force =??? -0.00228049?? -0.00087344??? 0.00045818 > ???? atom? 34 type? 2?? force =???? 0.00326060?? -0.00013378??? 0.00141700 > ???? atom? 35 type? 2?? force =???? 0.00238518?? -0.00083037??? 0.00141978 > ???? atom? 36 type? 2?? force =??? -0.00362994??? 0.00044169??? 0.00045646 > ???? atom? 37 type? 2?? force =???? 0.00328935??? 0.00035247??? 0.00141514 > ???? atom? 38 type? 2?? force =??? -0.00176990??? 0.00085166??? 0.00045815 > ???? atom? 39 type? 2?? force =??? -0.00267409??? 0.00014749??? 0.00045626 > ???? atom? 40 type? 2?? force =??? -0.00269243?? -0.00040253??? 0.00045489 > ???? atom? 41 type? 2?? force =??? -0.00362727?? -0.00006198??? 0.00045778 > ???? atom? 42 type? 2?? force =??? -0.00327950??? 0.00084940??? 0.00045779 > ???? atom? 43 type? 2?? force =??? -0.00414992??? 0.00005688??? 0.00045823 > ???? atom? 44 type? 2?? force =??? -0.00417525?? -0.00044357??? 0.00045652 > ???? atom? 45 type? 2?? force =???? 0.00420469?? -0.00041238??? 0.00141471 > ???? atom? 46 type? 2?? force =??? -0.00275647?? -0.00085117??? 0.00045939 > ???? atom? 47 type? 2?? force =???? 0.00331631??? 0.00084650??? 0.00141767 > ???? atom? 48 type? 2?? force =???? 0.00417437??? 0.00005078??? 0.00141584 > ???? atom? 49 type? 3?? force =??? -0.00088022?? -0.00023100??? 0.00063786 > ???? atom? 50 type? 3?? force =??? -0.00019195??? 0.00024496??? 0.00062889 > ???? atom? 51 type? 3?? force =???? 0.00033221??? 0.00013013??? 0.00063784 > ???? atom? 52 type? 3?? force =??? -0.00008497??? 0.00055599?? -0.00031675 > ???? atom? 53 type? 3?? force =???? 0.00050558??? 0.00049650?? -0.00032468 > ???? atom? 54 type? 3?? force =???? 0.00146339?? -0.00045612?? -0.00031558 > ???? atom? 55 type? 3?? force =???? 0.00004674?? -0.00051090?? -0.00031838 > ???? atom? 56 type? 3?? force =???? 0.00067836?? -0.00045754?? -0.00031539 > ???? atom? 57 type? 3?? force =???? 0.00163709??? 0.00041107?? -0.00031095 > ???? atom? 58 type? 3?? force =???? 0.00175006?? -0.00045164?? -0.00031617 > ???? atom? 59 type? 3?? force =???? 0.00086604??? 0.00056530?? -0.00032391 > ???? atom? 60 type? 3?? force =???? 0.00021240??? 0.00059253?? -0.00031733 > ???? atom? 61 type? 3?? force =???? 0.00150146??? 0.00042748?? -0.00030823 > ???? atom? 62 type? 3?? force =???? 0.00057028?? -0.00053586?? -0.00031293 > ???? atom? 63 type? 3?? force =??? -0.00012902?? -0.00056852?? -0.00031301 > ???? atom? 64 type? 3?? force =???? 0.00041895?? -0.00015221??? 0.00063305 > ???? atom? 65 type? 3?? force =??? -0.00012048?? -0.00020963??? 0.00063052 > ???? atom? 66 type? 3?? force =??? -0.00080908??? 0.00018092??? 0.00063740 > ???? atom? 67 type? 3?? force =??? -0.00014421?? -0.00009401??? 0.00062955 > ???? atom? 68 type? 3?? force =??? -0.00066194?? -0.00016966??? 0.00062806 > ???? atom? 69 type? 3?? force =??? -0.00136062??? 0.00021334??? 0.00063441 > ???? atom? 70 type? 3?? force =??? -0.00129838?? -0.00022836??? 0.00063582 > ???? atom? 71 type? 3?? force =??? -0.00061758??? 0.00016207??? 0.00062794 > ???? atom? 72 type? 3?? force =??? -0.00013128??? 0.00010786??? 0.00063396 > > ???? Total force =???? 0.019204???? Total SCF correction =???? 0.003942 > ???? SCF correction compared to forces is too large, reduce conv_thr > > ???? number of scf cycles??? =? 14 > ???? number of bfgs steps??? =? 10 > > ???? energy?? old??????????? =??? -869.3937346680 Ry > ???? energy?? new??????????? =??? -869.3940038837 Ry > > ???? CASE: energy? _new < energy? _old > > ???? new trust radius??????? =?????? 0.0460818304 bohr > ???? new conv_thr??????????? =?????? 0.0000002692 Ry > > > ATOMIC_POSITIONS (angstrom) > B??????? 0.710238954?? 8.607144248? 11.274646121 > B??????? 0.710189658? 11.065254747? 11.274653416 > B??????? 2.840139961?? 7.377767735? 11.274662357 > B??????? 0.710003498?? 6.148338558? 11.274660830 > B??????? 6.389874581?? 6.148447299?? 7.975298562 > B??????? 6.389694310?? 8.607201677?? 7.975281894 > B??????? 6.389730015? 11.065514141?? 7.975299602 > B??????? 2.840191056?? 9.835876709? 11.274657002 > B??????? 7.099545998?? 7.377769839? 11.274689692 > B??????? 7.099599100?? 9.835868309? 11.274678490 > B??????? 7.099362158? 12.294682727? 11.274692097 > B??????? 4.969987784? 11.065251631? 11.274659162 > B??????? 2.839951415? 12.294679179? 11.274672405 > B??????? 4.969811953?? 6.148349478? 11.274658687 > B??????? 4.970048734?? 8.607141050? 11.274647348 > B??????? 4.259776451?? 7.377516545?? 7.975309501 > B??????? 2.129891520? 11.065515297?? 7.975282179 > B??????? 2.129842847?? 8.607205772?? 7.975262478 > B??????? 2.130025127?? 6.148453706?? 7.975275500 > B??????? 4.259735938?? 9.835817945?? 7.975300165 > B??????? 0.000285812?? 7.377523468?? 7.975298224 > B??????? 0.000244054?? 9.835819979?? 7.975293909 > B??????? 4.259922871? 12.294590418?? 7.975303472 > B??????? 0.000423122? 12.294596884?? 7.975294114 > C??????? 2.129634203?? 6.148890372? 14.670766572 > C??????? 2.129256615?? 8.606951473? 14.670776369 > C??????? 2.129926206? 11.064961183? 14.670777896 > C??????? 0.000207950? 12.294075989? 14.670756205 > C?????? -0.000148110?? 9.835992828? 14.670765477 > C??????? 0.000493248?? 7.377989412? 14.670762573 > C??????? 0.710340292? 11.064953696? 14.672139091 > C??????? 0.710994208?? 8.606967109? 14.672133164 > C??????? 0.710632246?? 6.148877778? 14.672127260 > C??????? 6.389121270?? 8.606962975? 14.670760178 > C??????? 6.389493703?? 6.148878001? 14.670752431 > C??????? 4.970228330? 11.064955212? 14.672130196 > C??????? 6.389782767? 11.064958283? 14.670765658 > C??????? 7.099924988? 12.294066685? 14.672121322 > C??????? 7.100274852?? 9.835992897? 14.672124845 > C??????? 7.099632661?? 7.377986551? 14.672124547 > C??????? 4.970896506?? 8.606948139? 14.672124019 > C??????? 2.840688593? 12.294053703? 14.672126654 > C??????? 2.841064052?? 9.835998132? 14.672130891 > C??????? 2.840395045?? 7.377985542? 14.672134207 > C??????? 4.259743827?? 7.377985914? 14.670761100 > C??????? 4.970520412?? 6.148887268? 14.672120730 > C??????? 4.259452927? 12.294061978? 14.670750182 > C??????? 4.259074950?? 9.836003379? 14.670756904 > N??????? 0.000343961? 12.294490660? 11.274489476 > N??????? 0.000060685?? 9.835744446? 11.274473641 > N??????? 0.000031953?? 7.378176055? 11.274499102 > N??????? 2.840479804?? 7.378131693?? 7.968594027 > N??????? 2.840459610?? 9.835679843?? 7.968670941 > N??????? 2.840178358? 12.294324967?? 7.968663142 > N??????? 4.970396710? 11.064897346?? 7.968622809 > N??????? 4.970391015?? 8.607371192?? 7.968652183 > N??????? 4.970115668?? 6.148687554?? 7.968667860 > N??????? 7.099707812? 12.294333396?? 7.968672304 > N??????? 7.099982646?? 9.835676642?? 7.968676968 > N??????? 7.099995825?? 7.378144315?? 7.968604107 > N??????? 0.710270006?? 6.148679123?? 7.968653703 > N??????? 0.710539826?? 8.607361686?? 7.968641382 > N??????? 0.710541147? 11.064889755?? 7.968612889 > N??????? 6.389440690? 11.064847790? 11.274567333 > N??????? 6.389486158?? 8.607276250? 11.274503293 > N??????? 6.389761122?? 6.148516618? 11.274566266 > N??????? 2.129515407? 11.064847507? 11.274562347 > N??????? 2.129541822?? 8.607279997? 11.274491068 > N??????? 2.129822637?? 6.148522233? 11.274556890 > N??????? 4.259798907? 12.294488325? 11.274468720 > N??????? 4.259518456?? 9.835749258? 11.274454242 > N??????? 4.259471118?? 7.378171507? 11.274469629 > > > > ???? Writing output data file GphBN.save > ???? Check: negative starting charge=?? -0.070546 > ???? NEW-OLD atomic charge density approx. for the potential > ???? Check: negative starting charge=?? -0.070364 > > ???? negative rho (up, down):? 0.748E-03 0.000E+00 > > ???? total cpu time spent up to now is? 57670.72 secs > > ???? per-process dynamical memory:?? 103.8 Mb > > ???? Self-consistent Calculation > > ???? iteration #? 1???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 1.00E-06,? avg # of iterations =? 3.3 > > ???? negative rho (up, down):? 0.649E-03 0.000E+00 > > ???? total cpu time spent up to now is? 58356.91 secs > > ???? total energy????????????? =? -869.39427487 Ry > ???? Harris-Foulkes estimate?? =? -869.39428822 Ry > ???? estimated scf accuracy??? > ???? iteration #? 2???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 1.18E-07,? avg # of iterations =? 1.1 > > ???? negative rho (up, down):? 0.827E-03 0.000E+00 > > ???? total cpu time spent up to now is? 58701.26 secs > > ???? total energy????????????? =? -869.39419485 Ry > ???? Harris-Foulkes estimate?? =? -869.39427958 Ry > ???? estimated scf accuracy??? > ???? iteration #? 3???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 9.54E-08,? avg # of iterations =? 2.0 > > ???? negative rho (up, down):? 0.717E-03 0.000E+00 > > ???? total cpu time spent up to now is? 59124.23 secs > > ???? total energy????????????? =? -869.39423763 Ry > ???? Harris-Foulkes estimate?? =? -869.39423514 Ry > ???? estimated scf accuracy??? > ???? iteration #? 4???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 1.88E-08,? avg # of iterations =? 1.0 > > ???? negative rho (up, down):? 0.170E-02 0.000E+00 > > ???? total cpu time spent up to now is? 59452.62 secs > > ???? total energy????????????? =? -869.39423735 Ry > ???? Harris-Foulkes estimate?? =? -869.39423817 Ry > ???? estimated scf accuracy??? > ???? iteration #? 5???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 1.56E-08,? avg # of iterations =? 2.0 > > ???? negative rho (up, down):? 0.153E-02 0.000E+00 > > ???? total cpu time spent up to now is? 59842.36 secs > > ???? total energy????????????? =? -869.39424453 Ry > ???? Harris-Foulkes estimate?? =? -869.39424150 Ry > ???? estimated scf accuracy??? > ???? iteration #? 6???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 6.50E-10,? avg # of iterations =? 3.0 > > ???? negative rho (up, down):? 0.139E-02 0.000E+00 > > ???? total cpu time spent up to now is? 60284.73 secs > > ???? total energy????????????? =? -869.39424753 Ry > ???? Harris-Foulkes estimate?? =? -869.39424469 Ry > ???? estimated scf accuracy??? > ???? iteration #? 7???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 5.90E-10,? avg # of iterations =? 1.0 > > ???? negative rho (up, down):? 0.135E-02 0.000E+00 > > ???? total cpu time spent up to now is? 60613.51 secs > > ???? total energy????????????? =? -869.39425010 Ry > ???? Harris-Foulkes estimate?? =? -869.39424756 Ry > ???? estimated scf accuracy??? > ???? iteration #? 8???? ecut=??? 25.00 Ry???? beta=0.05 > ???? Davidson diagonalization with overlap > ???? ethr =? 3.50E-10,? avg # of iterations =? 2.0 > > ???? total cpu time spent up to now is? 61035.01 secs > > ???? End of self-consistent calculation > > ????????? k = 0.0059 0.0068 0.0000 ( 20180 PWs)?? bands (ev): > > ?? -20.3140 -20.1796 -19.2251 -19.1767 -19.0882 -18.9982 -18.8876 -18.8671 > .......................... > > > > Here the input file: > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > ?&control > ???????????? title = 'GphBNcapa' > ?????? calculation = 'relax' > ??????????? outdir = '/pwscf/pwscftemp/GphBN' > ??????????? prefix = 'GphBN' > ??????? pseudo_dir = '/input/Gph-BN/pseudopot-C-B-N' > ????????? tprnfor? = .t. > ????? restart_mode = 'from_scratch' > > ?/ > ?&system > ???????????? ibrav = 0, > ???????? celldm(1) = 1.8897261 > ?????????????? nat = 72, > ????????????? ntyp = 3, > ?????????? ecutwfc = 30.0 > ?????????? ecutrho = 300.0 > ???????? occupations = 'smearing' > ????????? smearing = 'gaussian' > ?????????? degauss = 0.003675 > > ?/ > ?&electrons > ??? mixing_beta = 0.05 > ??? diagonalization = 'david' > ?/ > ?&ions > ? trust_radius_ini = 0.10 > > ?/ > ?&cell > > ATOMIC_SPECIES > ?B??? 10.81100?? B.pz-vbc.UPF > ?C??? 12.01070?? C.pz-vbc.UPF > ?N??? 14.00674?? N.pz-vbc.UPF > ATOMIC_POSITIONS angstrom > ?B???????? 0.710000??????? 8.607000?????? 11.306000 > ?B???????? 0.710000?????? 11.066000?????? 11.306000 > ?B???????? 2.840000??????? 7.377000?????? 11.306000 > ?B???????? 0.710000??????? 6.148000?????? 11.306000 > ?B???????? 6.390000??????? 6.148000??????? 8.000000 > ?B???????? 6.390000??????? 8.607000??????? 8.000000 > ?B???????? 6.390000?????? 11.066000??????? 8.000000 > ?B???????? 2.840000??????? 9.836000?????? 11.306000 > ?B???????? 7.100000??????? 7.377000?????? 11.306000 > ?B???????? 7.100000??????? 9.836000?????? 11.306000 > ?B???????? 7.100000?????? 12.295000?????? 11.306000 > ?B???????? 4.970000?????? 11.066000?????? 11.306000 > ?B???????? 2.840000?????? 12.295000?????? 11.306000 > ?B???????? 4.970000??????? 6.148000?????? 11.306000 > ?B???????? 4.970000??????? 8.607000?????? 11.306000 > ?B???????? 4.260000??????? 7.377000??????? 8.000000 > ?B???????? 2.130000?????? 11.066000??????? 8.000000 > ?B???????? 2.130000??????? 8.607000??????? 8.000000 > ?B???????? 2.130000??????? 6.148000??????? 8.000000 > ?B???????? 4.260000??????? 9.836000??????? 8.000000 > ?B???????? 0.000000??????? 7.377000??????? 8.000000 > ?B???????? 0.000000??????? 9.836000??????? 8.000000 > ?B???????? 4.260000?????? 12.295000??????? 8.000000 > ?B???????? 0.000000?????? 12.295000??????? 8.000000 > ?C???????? 2.130000??????? 6.148000?????? 14.612000 > ?C???????? 2.130000??????? 8.607000?????? 14.612000 > ?C???????? 2.130000?????? 11.066000?????? 14.612000 > ?C???????? 0.000000?????? 12.295000?????? 14.612000 > ?C???????? 0.000000??????? 9.836000?????? 14.612000 > ?C???????? 0.000000??????? 7.377000?????? 14.612000 > ?C???????? 0.710000?????? 11.066000?????? 14.612000 > ?C???????? 0.710000??????? 8.607000?????? 14.612000 > ?C???????? 0.710000??????? 6.148000?????? 14.612000 > ?C???????? 6.390000??????? 8.607000?????? 14.612000 > ?C???????? 6.390000??????? 6.148000?????? 14.612000 > ?C???????? 4.970000?????? 11.066000?????? 14.612000 > ?C???????? 6.390000?????? 11.066000?????? 14.612000 > ?C???????? 7.100000?????? 12.295000?????? 14.612000 > ?C???????? 7.100000??????? 9.836000?????? 14.612000 > ?C???????? 7.100000??????? 7.377000?????? 14.612000 > ?C???????? 4.970000??????? 8.607000?????? 14.612000 > ?C???????? 2.840000?????? 12.295000?????? 14.612000 > ?C???????? 2.840000??????? 9.836000?????? 14.612000 > ?C???????? 2.840000??????? 7.377000?????? 14.612000 > ?C???????? 4.260000??????? 7.377000?????? 14.612000 > ?C???????? 4.970000??????? 6.148000?????? 14.612000 > ?C???????? 4.260000?????? 12.295000?????? 14.612000 > ?C???????? 4.260000??????? 9.836000?????? 14.612000 > ?N???????? 0.000000?????? 12.295000?????? 11.306000 > ?N???????? 0.000000??????? 9.836000?????? 11.306000 > ?N???????? 0.000000??????? 7.377000?????? 11.306000 > ?N???????? 2.840000??????? 7.377000??????? 8.000000 > ?N???????? 2.840000??????? 9.836000??????? 8.000000 > ?N???????? 2.840000?????? 12.295000??????? 8.000000 > ?N???????? 4.970000?????? 11.066000??????? 8.000000 > ?N???????? 4.970000??????? 8.607000??????? 8.000000 > ?N???????? 4.970000??????? 6.148000??????? 8.000000 > ?N???????? 7.100000?????? 12.295000??????? 8.000000 > ?N???????? 7.100000??????? 9.836000??????? 8.000000 > ?N???????? 7.100000??????? 7.377000??????? 8.000000 > ?N???????? 0.710000??????? 6.148000??????? 8.000000 > ?N???????? 0.710000??????? 8.607000??????? 8.000000 > ?N???????? 0.710000?????? 11.066000??????? 8.000000 > ?N???????? 6.390000?????? 11.066000?????? 11.306000 > ?N???????? 6.390000??????? 8.607000?????? 11.306000 > ?N???????? 6.390000??????? 6.148000?????? 11.306000 > ?N???????? 2.130000?????? 11.066000?????? 11.306000 > ?N???????? 2.130000??????? 8.607000?????? 11.306000 > ?N???????? 2.130000??????? 6.148000?????? 11.306000 > ?N???????? 4.260000?????? 12.295000?????? 11.306000 > ?N???????? 4.260000??????? 9.836000?????? 11.306000 > ?N???????? 4.260000??????? 7.377000?????? 11.306000 > K_POINTS automatic > 10 10 1 1 1 0 > CELL_PARAMETERS > 8.51980 0.00000 0.00000 > 0.00000 7.37600 0.00000 > 0.00000 0.00000 22.6120 > > Departement of Mechanical Engineering > University of Houston > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ===================================== Jess Kondor NSTI ===================================== From majdoub at gmail.com Mon Dec 21 20:00:44 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Mon, 21 Dec 2009 13:00:44 -0600 Subject: [Pw_forum] Graphene on BN : unable to reach convergence In-Reply-To: <1d9d5d9d0912210932o22d3fd5bta27308e1e33a1bbf@mail.gmail.com> References: <1d9d5d9d0912210932o22d3fd5bta27308e1e33a1bbf@mail.gmail.com> Message-ID: Dear Jess, Thank you for your response. Could you elaborate please more by my ecut/ecutwfc are not correct because I am using norm conserving pseudos. I am a beginner with pwscf. How would I know which values of ecutwfc I should use? In case I would change pseudo type what I should do? Thank you again for your help. On Mon, Dec 21, 2009 at 11:32 AM, Jess Kondor wrote: > Hi, > > you use norm-conserving pseudos, therefore your ecut/ecutwfc are not > correct. (ecut is very low, ecutrho should not be set by hand). > > > > On Mon, Dec 21, 2009 at 12:00 PM, mohamed sabri majdoub > wrote: > > Dear Pwscf user, > > > > I am trying to achieve relaxation of 1 layer of graphene on bilayer BN. I > am > > using 40 processors. > > However, I am not able to reach convergence. I tried to increase ecutwfc > > from 25 to 30, ecutrho from 250 to 300. Also, I tried using 'cg' mode > > instead of 'david' algorithm, mixing_mode = 'local-TF', and reducing > > conv_thr from default to 1.D-5 and 1.D-4. But, convergence is not > achieved. > > Either it stays running for ever, or stop after a while. > > Could you pleas help with this calculation. Your suggestions and help are > > highly appreciated. Thank you inadvance. > > > > Here is a sample of the output file: > > > --------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > ............................................. > > > > the Fermi energy is 0.6876 ev > > > > ! total energy = -869.39400388 Ry > > Harris-Foulkes estimate = -869.39395818 Ry > > estimated scf accuracy < 0.00000005 Ry > > > > The total energy is the sum of the following terms: > > > > one-electron contribution =-11231.22009619 Ry > > hartree contribution = 5691.19012576 Ry > > xc contribution = -255.73750085 Ry > > ewald contribution = 4926.37346740 Ry > > smearing contrib. (-TS) = 0.00000000 Ry > > > > convergence has been achieved in 9 iterations > > > > Forces acting on atoms (Ry/au): > > > > atom 1 type 1 force = 0.00011088 -0.00065304 > -0.00103877 > > atom 2 type 1 force = -0.00022395 0.00081219 > -0.00104134 > > atom 3 type 1 force = 0.00021000 -0.00084527 > -0.00105019 > > atom 4 type 1 force = 0.00119892 -0.00035183 > -0.00104665 > > atom 5 type 1 force = -0.00184192 -0.00038828 > -0.00113477 > > atom 6 type 1 force = -0.00038293 -0.00112440 > -0.00114180 > > atom 7 type 1 force = 0.00005921 0.00071395 > -0.00114073 > > atom 8 type 1 force = 0.00049597 0.00059147 > -0.00104299 > > atom 9 type 1 force = -0.00034360 -0.00081840 > -0.00105115 > > atom 10 type 1 force = -0.00003603 0.00063828 > -0.00104436 > > atom 11 type 1 force = 0.00103004 0.00039896 > -0.00105379 > > atom 12 type 1 force = -0.00011365 0.00086060 > -0.00104572 > > atom 13 type 1 force = 0.00155737 0.00035585 > -0.00105257 > > atom 14 type 1 force = 0.00129408 -0.00035678 > -0.00105119 > > atom 15 type 1 force = 0.00020134 -0.00058471 > -0.00104354 > > atom 16 type 1 force = 0.00008227 -0.00073252 > -0.00115227 > > atom 17 type 1 force = 0.00010912 0.00073818 > -0.00114516 > > atom 18 type 1 force = -0.00033300 -0.00104104 > -0.00114566 > > atom 19 type 1 force = -0.00180151 -0.00037723 > -0.00113755 > > atom 20 type 1 force = -0.00027782 0.00100537 > -0.00114916 > > atom 21 type 1 force = -0.00021158 -0.00071913 > -0.00115459 > > atom 22 type 1 force = -0.00061506 0.00109819 > -0.00115210 > > atom 23 type 1 force = -0.00172302 0.00037700 > -0.00113522 > > atom 24 type 1 force = -0.00201534 0.00037864 > -0.00113601 > > atom 25 type 2 force = 0.00266334 -0.00082256 > 0.00141953 > > atom 26 type 2 force = 0.00354500 -0.00004336 > 0.00141302 > > atom 27 type 2 force = 0.00354161 0.00041848 > 0.00141361 > > atom 28 type 2 force = 0.00174673 0.00085406 > 0.00141868 > > atom 29 type 2 force = 0.00263899 0.00014396 > 0.00141397 > > atom 30 type 2 force = 0.00266108 -0.00034465 > 0.00141502 > > atom 31 type 2 force = -0.00319859 0.00037610 > 0.00045810 > > atom 32 type 2 force = -0.00317599 -0.00016845 > 0.00045961 > > atom 33 type 2 force = -0.00228049 -0.00087344 > 0.00045818 > > atom 34 type 2 force = 0.00326060 -0.00013378 > 0.00141700 > > atom 35 type 2 force = 0.00238518 -0.00083037 > 0.00141978 > > atom 36 type 2 force = -0.00362994 0.00044169 > 0.00045646 > > atom 37 type 2 force = 0.00328935 0.00035247 > 0.00141514 > > atom 38 type 2 force = -0.00176990 0.00085166 > 0.00045815 > > atom 39 type 2 force = -0.00267409 0.00014749 > 0.00045626 > > atom 40 type 2 force = -0.00269243 -0.00040253 > 0.00045489 > > atom 41 type 2 force = -0.00362727 -0.00006198 > 0.00045778 > > atom 42 type 2 force = -0.00327950 0.00084940 > 0.00045779 > > atom 43 type 2 force = -0.00414992 0.00005688 > 0.00045823 > > atom 44 type 2 force = -0.00417525 -0.00044357 > 0.00045652 > > atom 45 type 2 force = 0.00420469 -0.00041238 > 0.00141471 > > atom 46 type 2 force = -0.00275647 -0.00085117 > 0.00045939 > > atom 47 type 2 force = 0.00331631 0.00084650 > 0.00141767 > > atom 48 type 2 force = 0.00417437 0.00005078 > 0.00141584 > > atom 49 type 3 force = -0.00088022 -0.00023100 > 0.00063786 > > atom 50 type 3 force = -0.00019195 0.00024496 > 0.00062889 > > atom 51 type 3 force = 0.00033221 0.00013013 > 0.00063784 > > atom 52 type 3 force = -0.00008497 0.00055599 > -0.00031675 > > atom 53 type 3 force = 0.00050558 0.00049650 > -0.00032468 > > atom 54 type 3 force = 0.00146339 -0.00045612 > -0.00031558 > > atom 55 type 3 force = 0.00004674 -0.00051090 > -0.00031838 > > atom 56 type 3 force = 0.00067836 -0.00045754 > -0.00031539 > > atom 57 type 3 force = 0.00163709 0.00041107 > -0.00031095 > > atom 58 type 3 force = 0.00175006 -0.00045164 > -0.00031617 > > atom 59 type 3 force = 0.00086604 0.00056530 > -0.00032391 > > atom 60 type 3 force = 0.00021240 0.00059253 > -0.00031733 > > atom 61 type 3 force = 0.00150146 0.00042748 > -0.00030823 > > atom 62 type 3 force = 0.00057028 -0.00053586 > -0.00031293 > > atom 63 type 3 force = -0.00012902 -0.00056852 > -0.00031301 > > atom 64 type 3 force = 0.00041895 -0.00015221 > 0.00063305 > > atom 65 type 3 force = -0.00012048 -0.00020963 > 0.00063052 > > atom 66 type 3 force = -0.00080908 0.00018092 > 0.00063740 > > atom 67 type 3 force = -0.00014421 -0.00009401 > 0.00062955 > > atom 68 type 3 force = -0.00066194 -0.00016966 > 0.00062806 > > atom 69 type 3 force = -0.00136062 0.00021334 > 0.00063441 > > atom 70 type 3 force = -0.00129838 -0.00022836 > 0.00063582 > > atom 71 type 3 force = -0.00061758 0.00016207 > 0.00062794 > > atom 72 type 3 force = -0.00013128 0.00010786 > 0.00063396 > > > > Total force = 0.019204 Total SCF correction = 0.003942 > > SCF correction compared to forces is too large, reduce conv_thr > > > > number of scf cycles = 14 > > number of bfgs steps = 10 > > > > energy old = -869.3937346680 Ry > > energy new = -869.3940038837 Ry > > > > CASE: energy _new < energy _old > > > > new trust radius = 0.0460818304 bohr > > new conv_thr = 0.0000002692 Ry > > > > > > ATOMIC_POSITIONS (angstrom) > > B 0.710238954 8.607144248 11.274646121 > > B 0.710189658 11.065254747 11.274653416 > > B 2.840139961 7.377767735 11.274662357 > > B 0.710003498 6.148338558 11.274660830 > > B 6.389874581 6.148447299 7.975298562 > > B 6.389694310 8.607201677 7.975281894 > > B 6.389730015 11.065514141 7.975299602 > > B 2.840191056 9.835876709 11.274657002 > > B 7.099545998 7.377769839 11.274689692 > > B 7.099599100 9.835868309 11.274678490 > > B 7.099362158 12.294682727 11.274692097 > > B 4.969987784 11.065251631 11.274659162 > > B 2.839951415 12.294679179 11.274672405 > > B 4.969811953 6.148349478 11.274658687 > > B 4.970048734 8.607141050 11.274647348 > > B 4.259776451 7.377516545 7.975309501 > > B 2.129891520 11.065515297 7.975282179 > > B 2.129842847 8.607205772 7.975262478 > > B 2.130025127 6.148453706 7.975275500 > > B 4.259735938 9.835817945 7.975300165 > > B 0.000285812 7.377523468 7.975298224 > > B 0.000244054 9.835819979 7.975293909 > > B 4.259922871 12.294590418 7.975303472 > > B 0.000423122 12.294596884 7.975294114 > > C 2.129634203 6.148890372 14.670766572 > > C 2.129256615 8.606951473 14.670776369 > > C 2.129926206 11.064961183 14.670777896 > > C 0.000207950 12.294075989 14.670756205 > > C -0.000148110 9.835992828 14.670765477 > > C 0.000493248 7.377989412 14.670762573 > > C 0.710340292 11.064953696 14.672139091 > > C 0.710994208 8.606967109 14.672133164 > > C 0.710632246 6.148877778 14.672127260 > > C 6.389121270 8.606962975 14.670760178 > > C 6.389493703 6.148878001 14.670752431 > > C 4.970228330 11.064955212 14.672130196 > > C 6.389782767 11.064958283 14.670765658 > > C 7.099924988 12.294066685 14.672121322 > > C 7.100274852 9.835992897 14.672124845 > > C 7.099632661 7.377986551 14.672124547 > > C 4.970896506 8.606948139 14.672124019 > > C 2.840688593 12.294053703 14.672126654 > > C 2.841064052 9.835998132 14.672130891 > > C 2.840395045 7.377985542 14.672134207 > > C 4.259743827 7.377985914 14.670761100 > > C 4.970520412 6.148887268 14.672120730 > > C 4.259452927 12.294061978 14.670750182 > > C 4.259074950 9.836003379 14.670756904 > > N 0.000343961 12.294490660 11.274489476 > > N 0.000060685 9.835744446 11.274473641 > > N 0.000031953 7.378176055 11.274499102 > > N 2.840479804 7.378131693 7.968594027 > > N 2.840459610 9.835679843 7.968670941 > > N 2.840178358 12.294324967 7.968663142 > > N 4.970396710 11.064897346 7.968622809 > > N 4.970391015 8.607371192 7.968652183 > > N 4.970115668 6.148687554 7.968667860 > > N 7.099707812 12.294333396 7.968672304 > > N 7.099982646 9.835676642 7.968676968 > > N 7.099995825 7.378144315 7.968604107 > > N 0.710270006 6.148679123 7.968653703 > > N 0.710539826 8.607361686 7.968641382 > > N 0.710541147 11.064889755 7.968612889 > > N 6.389440690 11.064847790 11.274567333 > > N 6.389486158 8.607276250 11.274503293 > > N 6.389761122 6.148516618 11.274566266 > > N 2.129515407 11.064847507 11.274562347 > > N 2.129541822 8.607279997 11.274491068 > > N 2.129822637 6.148522233 11.274556890 > > N 4.259798907 12.294488325 11.274468720 > > N 4.259518456 9.835749258 11.274454242 > > N 4.259471118 7.378171507 11.274469629 > > > > > > > > Writing output data file GphBN.save > > Check: negative starting charge= -0.070546 > > NEW-OLD atomic charge density approx. for the potential > > Check: negative starting charge= -0.070364 > > > > negative rho (up, down): 0.748E-03 0.000E+00 > > > > total cpu time spent up to now is 57670.72 secs > > > > per-process dynamical memory: 103.8 Mb > > > > Self-consistent Calculation > > > > iteration # 1 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 1.00E-06, avg # of iterations = 3.3 > > > > negative rho (up, down): 0.649E-03 0.000E+00 > > > > total cpu time spent up to now is 58356.91 secs > > > > total energy = -869.39427487 Ry > > Harris-Foulkes estimate = -869.39428822 Ry > > estimated scf accuracy < 0.00034068 Ry > > > > iteration # 2 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 1.18E-07, avg # of iterations = 1.1 > > > > negative rho (up, down): 0.827E-03 0.000E+00 > > > > total cpu time spent up to now is 58701.26 secs > > > > total energy = -869.39419485 Ry > > Harris-Foulkes estimate = -869.39427958 Ry > > estimated scf accuracy < 0.00027476 Ry > > > > iteration # 3 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 9.54E-08, avg # of iterations = 2.0 > > > > negative rho (up, down): 0.717E-03 0.000E+00 > > > > total cpu time spent up to now is 59124.23 secs > > > > total energy = -869.39423763 Ry > > Harris-Foulkes estimate = -869.39423514 Ry > > estimated scf accuracy < 0.00005408 Ry > > > > iteration # 4 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 1.88E-08, avg # of iterations = 1.0 > > > > negative rho (up, down): 0.170E-02 0.000E+00 > > > > total cpu time spent up to now is 59452.62 secs > > > > total energy = -869.39423735 Ry > > Harris-Foulkes estimate = -869.39423817 Ry > > estimated scf accuracy < 0.00004506 Ry > > > > iteration # 5 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 1.56E-08, avg # of iterations = 2.0 > > > > negative rho (up, down): 0.153E-02 0.000E+00 > > > > total cpu time spent up to now is 59842.36 secs > > > > total energy = -869.39424453 Ry > > Harris-Foulkes estimate = -869.39424150 Ry > > estimated scf accuracy < 0.00000187 Ry > > > > iteration # 6 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 6.50E-10, avg # of iterations = 3.0 > > > > negative rho (up, down): 0.139E-02 0.000E+00 > > > > total cpu time spent up to now is 60284.73 secs > > > > total energy = -869.39424753 Ry > > Harris-Foulkes estimate = -869.39424469 Ry > > estimated scf accuracy < 0.00000170 Ry > > > > iteration # 7 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 5.90E-10, avg # of iterations = 1.0 > > > > negative rho (up, down): 0.135E-02 0.000E+00 > > > > total cpu time spent up to now is 60613.51 secs > > > > total energy = -869.39425010 Ry > > Harris-Foulkes estimate = -869.39424756 Ry > > estimated scf accuracy < 0.00000101 Ry > > > > iteration # 8 ecut= 25.00 Ry beta=0.05 > > Davidson diagonalization with overlap > > ethr = 3.50E-10, avg # of iterations = 2.0 > > > > total cpu time spent up to now is 61035.01 secs > > > > End of self-consistent calculation > > > > k = 0.0059 0.0068 0.0000 ( 20180 PWs) bands (ev): > > > > -20.3140 -20.1796 -19.2251 -19.1767 -19.0882 -18.9982 -18.8876 > -18.8671 > > .......................... > > > > > > > > Here the input file: > > > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > &control > > title = 'GphBNcapa' > > calculation = 'relax' > > outdir = '/pwscf/pwscftemp/GphBN' > > prefix = 'GphBN' > > pseudo_dir = '/input/Gph-BN/pseudopot-C-B-N' > > tprnfor = .t. > > restart_mode = 'from_scratch' > > > > / > > &system > > ibrav = 0, > > celldm(1) = 1.8897261 > > nat = 72, > > ntyp = 3, > > ecutwfc = 30.0 > > ecutrho = 300.0 > > occupations = 'smearing' > > smearing = 'gaussian' > > degauss = 0.003675 > > > > / > > &electrons > > mixing_beta = 0.05 > > diagonalization = 'david' > > / > > &ions > > trust_radius_ini = 0.10 > > > > / > > &cell > > > > ATOMIC_SPECIES > > B 10.81100 B.pz-vbc.UPF > > C 12.01070 C.pz-vbc.UPF > > N 14.00674 N.pz-vbc.UPF > > ATOMIC_POSITIONS angstrom > > B 0.710000 8.607000 11.306000 > > B 0.710000 11.066000 11.306000 > > B 2.840000 7.377000 11.306000 > > B 0.710000 6.148000 11.306000 > > B 6.390000 6.148000 8.000000 > > B 6.390000 8.607000 8.000000 > > B 6.390000 11.066000 8.000000 > > B 2.840000 9.836000 11.306000 > > B 7.100000 7.377000 11.306000 > > B 7.100000 9.836000 11.306000 > > B 7.100000 12.295000 11.306000 > > B 4.970000 11.066000 11.306000 > > B 2.840000 12.295000 11.306000 > > B 4.970000 6.148000 11.306000 > > B 4.970000 8.607000 11.306000 > > B 4.260000 7.377000 8.000000 > > B 2.130000 11.066000 8.000000 > > B 2.130000 8.607000 8.000000 > > B 2.130000 6.148000 8.000000 > > B 4.260000 9.836000 8.000000 > > B 0.000000 7.377000 8.000000 > > B 0.000000 9.836000 8.000000 > > B 4.260000 12.295000 8.000000 > > B 0.000000 12.295000 8.000000 > > C 2.130000 6.148000 14.612000 > > C 2.130000 8.607000 14.612000 > > C 2.130000 11.066000 14.612000 > > C 0.000000 12.295000 14.612000 > > C 0.000000 9.836000 14.612000 > > C 0.000000 7.377000 14.612000 > > C 0.710000 11.066000 14.612000 > > C 0.710000 8.607000 14.612000 > > C 0.710000 6.148000 14.612000 > > C 6.390000 8.607000 14.612000 > > C 6.390000 6.148000 14.612000 > > C 4.970000 11.066000 14.612000 > > C 6.390000 11.066000 14.612000 > > C 7.100000 12.295000 14.612000 > > C 7.100000 9.836000 14.612000 > > C 7.100000 7.377000 14.612000 > > C 4.970000 8.607000 14.612000 > > C 2.840000 12.295000 14.612000 > > C 2.840000 9.836000 14.612000 > > C 2.840000 7.377000 14.612000 > > C 4.260000 7.377000 14.612000 > > C 4.970000 6.148000 14.612000 > > C 4.260000 12.295000 14.612000 > > C 4.260000 9.836000 14.612000 > > N 0.000000 12.295000 11.306000 > > N 0.000000 9.836000 11.306000 > > N 0.000000 7.377000 11.306000 > > N 2.840000 7.377000 8.000000 > > N 2.840000 9.836000 8.000000 > > N 2.840000 12.295000 8.000000 > > N 4.970000 11.066000 8.000000 > > N 4.970000 8.607000 8.000000 > > N 4.970000 6.148000 8.000000 > > N 7.100000 12.295000 8.000000 > > N 7.100000 9.836000 8.000000 > > N 7.100000 7.377000 8.000000 > > N 0.710000 6.148000 8.000000 > > N 0.710000 8.607000 8.000000 > > N 0.710000 11.066000 8.000000 > > N 6.390000 11.066000 11.306000 > > N 6.390000 8.607000 11.306000 > > N 6.390000 6.148000 11.306000 > > N 2.130000 11.066000 11.306000 > > N 2.130000 8.607000 11.306000 > > N 2.130000 6.148000 11.306000 > > N 4.260000 12.295000 11.306000 > > N 4.260000 9.836000 11.306000 > > N 4.260000 7.377000 11.306000 > > K_POINTS automatic > > 10 10 1 1 1 0 > > CELL_PARAMETERS > > 8.51980 0.00000 0.00000 > > 0.00000 7.37600 0.00000 > > 0.00000 0.00000 22.6120 > > > > Departement of Mechanical Engineering > > University of Houston > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > -- > ===================================== > Jess Kondor > > NSTI > ===================================== > _______________________________________________ > 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/20091221/09f320fa/attachment-0001.htm From dekura at cmp.sanken.osaka-u.ac.jp Tue Dec 22 03:43:45 2009 From: dekura at cmp.sanken.osaka-u.ac.jp (dekura at cmp.sanken.osaka-u.ac.jp) Date: Tue, 22 Dec 2009 11:43:45 +0900 (JST) Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: References: Message-ID: <38456.118.240.158.9.1261449825.squirrel@lucy.cmp.sanken.osaka-u.ac.jp> Hi Nicki. I think you can do it with manipulating input file " input_FS " which is read in running "bands_FS.x", after scf and nscf calculation, as below strategy. #-- input_FS--- nband_min nband_max EF <----- YOU change this value title ..... ..... #---------------- and you run bands_FS.x < Bands_SP.out , then you can see the information about Fermi-surface and modified the Fermi level you input. Best Regards Haruhiko Dekura PH.D. student Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan > Hi there, > > I just want to know whether and how it is possible to shift the Fermi > energy before constructing the Fermi surface?! See the following > scenario: > > 1. making a scf calculation for a semiconductor - the Fermi energy > will be in the energy gap (thats all right) and there will be (of > course) no Fermi surface > 2. I want to simulate doping for some tests, just by shifting the > Fermi energy a bit into either valence or conduction band - there > would be a fermi surface - this is what I want > > ...so,how can I shift the Fermi energy (manually) after a scf > calculation to an energy quit near the original one and calculate the > Fermi surface afterwards? > > ..thanks a lot > > Nicki > ------------------------------------------------------------- > Nicki Frank Hinsche, Dipl. Phys. > Institut fr Physik - Theoretische Physik, > Martin-Luther-Universitt Halle-Wittenberg, > Von-Seckendorff-Platz 1, Raum 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > ------------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Dec 22 09:24:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 22 Dec 2009 09:24:25 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: <8f1062e50912210217n52de5105mdc03bc5f30a7c745@mail.gmail.com> References: <8f1062e50912210217n52de5105mdc03bc5f30a7c745@mail.gmail.com> Message-ID: <4B308239.60709@sissa.it> There have been a request similar to yours some time ago http://www.democritos.it/pipermail/pw_forum/2008-November/010604.html you can try to see if it has been solved by following the thread. Most probably, the problem was caused by your choice of the q-point grid. From the very little information you provide, it is difficult to say more than this. Gabriele yuning wu wrote: > Dear all, > > I am doing a phonon spectrum calculation. After got all *.dyn* files, I > use the q2r.x to do get *.fc file successfully. However, in phdos > calculation, I got an error message: > > from frc_blk : error # 1 > wrong total_weight > > I am confused that what can cause this error. Thanks. > > Yuning Wu > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Tue Dec 22 12:13:30 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 22 Dec 2009 03:13:30 -0800 (PST) Subject: [Pw_forum] pbe0 problem Message-ID: <36725.93903.qm@web112510.mail.gq1.yahoo.com> Dear all for noncubic cell ,in EXX calculation How we can choose the nq points? For TiO2 I used this input file but the code stop in midway without any message? and it didn't print total energy? &control calculation='scf' restart_mode='from_scratch', pseudo_dir = './', prefix='tio2' outdir='/p5/batch/kazempou/' / &system ibrav = 6, celldm(1) = 8.79, celldm(3) = 0.639, nat = 6, ntyp = 2, ecutwfc = 25 , ecutrho = 400 , input_dft='pbe0', nqx1 = 2, nqx2 = 2, nqx3 = 4, / &electrons diagonalization='david', conv_thr = 1.0d-4 mixing_beta = 0.5, / ATOMIC_SPECIES Ti 47.86700 ti.optgga2.fhi.UPF O 15.99940 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.305131381 0.305131381 0.000000000 O -0.305131381 -0.305131381 0.000000000 O 0.805131381 0.194868619 0.5 O 0.194868619 0.805131381 0.5 K_POINTS automatic 2 2 4 1 1 1 ------------------------------ output file total cpu time spent up to now is 1.60 secs total energy = -355.97704102 Ry Harris-Foulkes estimate = -355.97835356 Ry estimated scf accuracy < 0.00523443 Ry iteration # 5 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 1.09E-05, avg # of iterations = 4.0 total cpu time spent up to now is 1.84 secs total energy = -355.97795182 Ry Harris-Foulkes estimate = -355.97903987 Ry estimated scf accuracy < 0.00242696 Ry iteration # 6 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 5.06E-06, avg # of iterations = 3.0 total cpu time spent up to now is 2.02 secs End of self-consistent calculation k = 0.2500 0.2500 0.1956 ( 920 PWs) bands (ev): -50.3131 -50.2750 -26.6056 -26.5256 -26.5170 -26.5064 -26.4805 -26.4632 -9.2828 -8.6924 -8.2771 -8.1594 4.0836 4.7890 5.3145 5.8431 6.1571 6.8145 7.1870 7.4771 7.7110 8.6006 8.7972 9.2575 k = 0.2500 0.2500 0.5869 ( 908 PWs) bands (ev): -50.2617 -50.2509 -26.7111 -26.6144 -26.5061 -26.4959 -26.4896 -26.4409 -8.7021 -8.4646 -8.4175 -8.2262 4.7053 5.0674 5.0763 5.4017 6.0629 6.5874 7.1698 7.2399 7.5577 8.4242 8.4760 9.0196 0.892062058076385500 0.892062058076385500 EXX divergence ( 2)= -108.3050 0.4000 exx_div : 0.01s CPU ! EXXALFA SET TO 0.250000000000000000 thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091222/ddac73ba/attachment.html From kazempoor2000 at yahoo.com Tue Dec 22 12:25:06 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 22 Dec 2009 03:25:06 -0800 (PST) Subject: [Pw_forum] pbe0 problem Message-ID: <939640.53868.qm@web112502.mail.gq1.yahoo.com> Dear all for noncubic cell ,in EXX calculation How we can choose the nq points? For TiO2 I used this input file but the code stop in midway without any message? and it didn't print total energy? &control calculation='scf' restart_mode='from_scratch', pseudo_dir = './', prefix='tio2' outdir='/p5/batch/kazempou/' / &system ibrav = 6, celldm(1) = 8.79, celldm(3) = 0.639, nat = 6, ntyp = 2, ecutwfc = 25 , ecutrho = 400 , input_dft='pbe0', nqx1 = 2, nqx2 = 2, nqx3 = 4, / &electrons diagonalization='david', conv_thr = 1.0d-4 mixing_beta = 0.5, / ATOMIC_SPECIES Ti 47.86700 ti.optgga2.fhi.UPF O 15.99940 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.305131381 0.305131381 0.000000000 O -0.305131381 -0.305131381 0.000000000 O 0.805131381 0.194868619 0.5 O 0.194868619 0.805131381 0.5 K_POINTS automatic 2 2 4 1 1 1 ------------------------------ output file total cpu time spent up to now is 1.60 secs total energy = -355.97704102 Ry Harris-Foulkes estimate = -355.97835356 Ry estimated scf accuracy < 0.00523443 Ry iteration # 5 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 1.09E-05, avg # of iterations = 4.0 total cpu time spent up to now is 1.84 secs total energy = -355.97795182 Ry Harris-Foulkes estimate = -355.97903987 Ry estimated scf accuracy < 0.00242696 Ry iteration # 6 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 5.06E-06, avg # of iterations = 3.0 total cpu time spent up to now is 2.02 secs End of self-consistent calculation k = 0.2500 0.2500 0.1956 ( 920 PWs) bands (ev): -50.3131 -50.2750 -26.6056 -26.5256 -26.5170 -26.5064 -26.4805 -26.4632 -9.2828 -8.6924 -8.2771 -8.1594 4.0836 4.7890 5.3145 5.8431 6.1571 6.8145 7.1870 7.4771 7.7110 8.6006 8.7972 9.2575 k = 0.2500 0.2500 0.5869 ( 908 PWs) bands (ev): -50.2617 -50.2509 -26.7111 -26.6144 -26.5061 -26.4959 -26.4896 -26.4409 -8.7021 -8.4646 -8.4175 -8.2262 4.7053 5.0674 5.0763 5.4017 6.0629 6.5874 7.1698 7.2399 7.5577 8.4242 8.4760 9.0196 0.892062058076385500 0.892062058076385500 EXX divergence ( 2)= -108.3050 0.4000 exx_div : 0.01s CPU ! EXXALFA SET TO 0.250000000000000000 thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091222/3f9e39dd/attachment.htm From xomiakk at gmail.com Tue Dec 22 12:34:18 2009 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Tue, 22 Dec 2009 17:34:18 +0600 Subject: [Pw_forum] epsilon.x Message-ID: Dear PWscf Users, I have a question about epsilon.x PP. How should I chose the values for the broading parameters (intersmear and intrasmear)? From experiment? Thank you, O.Sedelnikova -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091222/cf232e59/attachment.htm From daijiayu at nudt.edu.cn Tue Dec 22 13:22:16 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Tue, 22 Dec 2009 20:22:16 +0800 Subject: [Pw_forum] problem in the local inversion. Message-ID: <461484536.25860@nudt.edu.cn> Dear Users, Did anybody meet this problem: the hint of "problem in the local inversion" appears when the molecular dynamics calculation at high pressure was doing. Sometimes, when i changed the Pseudopotentials, this problem can be solved. But it appreared occasionally. And is it the problem of the code? Or the problem in my computer? Thanks in advance. Jiayu ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From kazempoor2000 at yahoo.com Tue Dec 22 15:50:58 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 22 Dec 2009 06:50:58 -0800 (PST) Subject: [Pw_forum] pbe0 problem Message-ID: <502557.11260.qm@web112513.mail.gq1.yahoo.com> Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ----- Forwarded Message ---- From: ali kazempour To: pw Sent: Tue, December 22, 2009 12:13:30 PM Subject: pbe0 problem Dear all for noncubic cell ,in EXX calculation How we can choose the nq points? For TiO2 I used this input file but the code stop in midway without any message? and it didn't print total energy? &control calculation='scf' restart_mode='from_scratch', pseudo_dir = './', prefix='tio2' outdir='/p5/batch/kazempou/' / &system ibrav = 6, celldm(1) = 8.79, celldm(3) = 0.639, nat = 6, ntyp = 2, ecutwfc = 25 , ecutrho = 400 , input_dft='pbe0', nqx1 = 2, nqx2 = 2, nqx3 = 4, / &electrons diagonalization='david', conv_thr = 1.0d-4 mixing_beta = 0.5, / ATOMIC_SPECIES Ti 47.86700 ti.optgga2.fhi.UPF O 15.99940 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.305131381 0.305131381 0.000000000 O -0.305131381 -0.305131381 0.000000000 O 0.805131381 0.194868619 0.5 O 0.194868619 0.805131381 0.5 K_POINTS automatic 2 2 4 1 1 1 ------------------------------ output file total cpu time spent up to now is 1.60 secs total energy = -355.97704102 Ry Harris-Foulkes estimate = -355.97835356 Ry estimated scf accuracy < 0.00523443 Ry iteration # 5 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 1.09E-05, avg # of iterations = 4.0 total cpu time spent up to now is 1.84 secs total energy = -355.97795182 Ry Harris-Foulkes estimate = -355.97903987 Ry estimated scf accuracy < 0.00242696 Ry iteration # 6 ecut= 25.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 5.06E-06, avg # of iterations = 3.0 total cpu time spent up to now is 2.02 secs End of self-consistent calculation k = 0.2500 0.2500 0.1956 ( 920 PWs) bands (ev): -50.3131 -50.2750 -26.6056 -26.5256 -26.5170 -26.5064 -26.4805 -26.4632 -9.2828 -8.6924 -8.2771 -8.1594 4.0836 4.7890 5.3145 5.8431 6.1571 6.8145 7.1870 7.4771 7.7110 8.6006 8.7972 9.2575 k = 0.2500 0.2500 0.5869 ( 908 PWs) bands (ev): -50.2617 -50.2509 -26.7111 -26.6144 -26.5061 -26.4959 -26.4896 -26.4409 -8.7021 -8.4646 -8.4175 -8.2262 4.7053 5.0674 5.0763 5.4017 6.0629 6.5874 7.1698 7.2399 7.5577 8.4242 8.4760 9.0196 0.892062058076385500 0.892062058076385500 EXX divergence ( 2)= -108.3050 0.4000 exx_div : 0.01s CPU ! EXXALFA SET TO 0.250000000000000000 thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091222/ca5ce811/attachment.htm From dimpy.sharma at tyndall.ie Tue Dec 22 21:41:52 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 22 Dec 2009 20:41:52 -0000 Subject: [Pw_forum] too many bands are not converging Message-ID: Hi there, I have been trying to run a nscf calculation, after finishing my scsf calculation, howvever I am getting the following error 'too many bands are not converged', what I can get from previous question that 'changing mixing beta or diagonalisation ' will run it.I have tried that but it wonnt work.I have even number of electrons , so I ignored occupation. Also due to memory problem I have decided to take less number of k points, I mean I will break my kpoints in parts and will continue my calculations. Can anybody please help me! &CONTROL calculation ='nscf' restart_mode ='from_scratch' outdir = '/' pseudo_dir = '/' prefix = 'Kpoint4' tstress = .true. tprnfor = .true. forc_conv_thr=2.D-4 etot_conv_thr=1.D-8 nstep=600 / &SYSTEM ibrav = 0 celldm(1) =14.5152 nat = 321 ntyp = 3 ecutwfc = 35 ecutrho = 120 nbnd = 742 nosym=.true. smearing='gaussian' / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-8 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.000000000 0.000000000 0.000000000 0.000000000 5.800000000 0.000000000 0.000000000 0.000000000 5.800000000 ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPF O 15.9994 O.pz-rrkjus.UPF H 1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 7.4734 12.9443 16.0594 Si 0.9063 12.9082 11.9628 ................ K_POINTS crystal 2 -0.500000000 -0.500000000 -0.500000000 1.00000000 -0.460000000 -0.500000000 -0.500000000 1.00000000 Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091222/c12c1f68/attachment.htm From giannozz at democritos.it Tue Dec 22 22:56:51 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Dec 2009 22:56:51 +0100 Subject: [Pw_forum] Graphene on BN : unable to reach convergence In-Reply-To: References: <1d9d5d9d0912210932o22d3fd5bta27308e1e33a1bbf@mail.gmail.com> Message-ID: <5F6BC106-D3EE-451D-B2AE-F5C3BFD1EF48@democritos.it> On Dec 21, 2009, at 20:00 , mohamed sabri majdoub wrote: > I am a beginner with pwscf beginners shouldn't start with a 40-processor job. They should from here: http://www.quantum-espresso.org/learn.php . By the way, there wasn't anything especially wrong in the snapshot of output you sent. 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 Tue Dec 22 23:04:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Dec 2009 23:04:29 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: <8f1062e50912210217n52de5105mdc03bc5f30a7c745@mail.gmail.com> References: <8f1062e50912210217n52de5105mdc03bc5f30a7c745@mail.gmail.com> Message-ID: <9221F54B-A2BE-4B8F-A242-FEECC13BCC98@democritos.it> On Dec 21, 2009, at 11:17 , yuning wu wrote: > After got all *.dyn* files, I use the q2r.x to do get *.fc file > successfully. However, in phdos calculation, I got an error message: > > from frc_blk : error # 1 > wrong total_weight > > I am confused that what can cause this error. this is something that may occur when the grid of wavevectors used to calculate the force constant matrix is "strange", i.e. very small or very elongated. In PH/matdyn.f90, locate the following line: ! SUM OVER R VECTORS IN THE SUPERCELL - VERY VERY SAFE RANGE! In some cases, it turns out that the VERY VERY SAFE RANGE is not that safe. Try to increase the coefficients in the preceding lines: DO n1=-2*nr1,2*nr1 DO n2=-2*nr2,2*nr2 DO n3=-2*nr3,2*nr3 to something larger, e.g. -4*nr1,4*nr1 and so on. No warranty this is related to your problem, but it might be 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 Tue Dec 22 23:06:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Dec 2009 23:06:12 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: References: Message-ID: <2B9C1754-74AC-4D73-A78E-5C3DA971CF3B@democritos.it> On Dec 21, 2009, at 15:04 , Nicki Frank Hinsche wrote: > I just want to know whether and how it is possible to shift the Fermi > energy before constructing the Fermi surface?! In order to plot it, or in order to do something else? 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 shrek_826 at yahoo.com.cn Wed Dec 23 03:51:21 2009 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Wed, 23 Dec 2009 10:51:21 +0800 (CST) Subject: [Pw_forum] grid shift Message-ID: <197357.47438.qm@web15307.mail.cnb.yahoo.com> Dear?everyone: I have some questions about grid offsets. In?our input file, the k-points are automatically generated with uniform grid,?and the grid offsets?are either set as 0 (no offset) or 1 (grid displaced by 1/2 step). But the problem is that?we got different results with different offsets. For example, we tested the adsorption of?one oxygen atom on three low-index Pt crystal planes, namely, Pt(100), Pt(110) and Pt(111).?With grid shift (0 0 0), the adsorption energy of O on Pt(110) is slightly larger than on Pt(100), but much larger than on Pt(111). However, with grid shift (1 1 1), the order of adsorption energy is Pt(110)>Pt(111)>Pt(100). Which result is more reasonable? Best Regards & Merry Christmas, Fan Yang ******************************************* Fan Yang PH.D Candidate?in Electrochemistry College of Chemistry and Molecular Science Wuhan University, 430072, Hubei Province, China E-mail:shrek_826 at yahoo.com.cn ******************************************* ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091223/7945eff9/attachment-0001.htm From eyvaz_isaev at yahoo.com Wed Dec 23 12:27:05 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 23 Dec 2009 03:27:05 -0800 (PST) Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: Message-ID: <765007.69672.qm@web65710.mail.ac4.yahoo.com> Dear Nicki, > I just want to know whether and how it is possible to shift > the Fermi energy before constructing the Fermi surface?! > I just want to know whether and how it is possible to shift > the Fermi energy before constructing the Fermi surface?! I should note there is NO Fermi level, thus, no Fermi surface for semiconductors!!! Please think about why. 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 Mon, 12/21/09, Nicki Frank Hinsche wrote: > From: Nicki Frank Hinsche > Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations > To: pw_forum at pwscf.org > Date: Monday, December 21, 2009, 5:04 PM > Hi there, > > I just want to know whether and how it is possible to shift > the Fermi? > energy before constructing the Fermi surface?! See the > following? > scenario: > > 1. making a scf calculation for a semiconductor - the Fermi > energy? > will be in the energy gap (thats all right) and there will > be (of? > course) no Fermi surface > 2. I want to simulate doping for some tests, just by > shifting the? > Fermi energy a bit into either valence or conduction band - > there? > would be a fermi surface - this is what I want > > ...so,how can I shift the Fermi energy (manually) after a > scf? > calculation to an energy quit near the original one and > calculate the? > Fermi surface afterwards? > > ..thanks a lot > > Nicki > ------------------------------------------------------------- > Nicki Frank Hinsche, Dipl. Phys. > Institut f?r Physik - Theoretische Physik, > Martin-Luther-Universit?t Halle-Wittenberg, > Von-Seckendorff-Platz 1, Raum 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > ------------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Dec 22 09:35:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 22 Dec 2009 09:35:47 +0100 Subject: [Pw_forum] Graphene on BN : unable to reach convergence In-Reply-To: References: <1d9d5d9d0912210932o22d3fd5bta27308e1e33a1bbf@mail.gmail.com> Message-ID: <4B3084E3.6020809@sissa.it> mohamed sabri majdoub wrote: > Dear Jess, > > Thank you for your response. > Could you elaborate please more by my ecut/ecutwfc are not correct > because I am using norm conserving pseudos. > I am a beginner with pwscf. You can start having a look at lecture slides and sample files from hands on sessions available online here: http://media.quantum-espresso.org/santa_barbara_2009_07/index.php > How would I know which values of ecutwfc I > should use? Testing for convergence of total energy and other quantities of your interest (magnetization for instance), by increasing the cutoff ecutwfc and monitoring the behavior of those quantities. > In case I would change pseudo type what I should do? Download the file, put in pseudo_dir and change your input file accordingly. Test again for convergence. Normconserving pseudopotentials always need ecutrho=4*ecutwfc (which is the default, so that you should not specify a value for it), while ultrasoft need ecutrho > 4*ecutwfc (usually ecutrho ~ 8*ecutwfc or bigger). Regards, Gabriele > Thank you again for your help. > > -- 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 nicvok at freenet.de Wed Dec 23 14:32:34 2009 From: nicvok at freenet.de (Nicki Frank Hinsche) Date: Wed, 23 Dec 2009 14:32:34 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: References: Message-ID: <354D3CE3-4D5E-40B1-918C-675304398E27@freenet.de> Dear Paolo, plotting the fermi surface for the shifted energy would be the last stage... > On Dec 21, 2009, at 15:04 , Nicki Frank Hinsche wrote: > >> I just want to know whether and how it is possible to shift the Fermi >> energy before constructing the Fermi surface?! > > In order to plot it, or in order to do something else? > > 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 Haruhiko, I've tried this out but the the fermi surface was 'invisible' as I would have expected for the non shifted Fermi energy right in the gap. But I'll try on this again... thanks a lot on both of you Nicki > Hi Nicki. > > I think you can do it with manipulating input file " input_FS " > which is > read in running "bands_FS.x", after scf and nscf calculation, as below > strategy. > > #-- input_FS--- > nband_min nband_max > EF <----- YOU change this value > title > ..... > ..... > #---------------- > > and you run > > bands_FS.x < Bands_SP.out , > > then you can see the information about Fermi-surface and modified the > Fermi level you input. > > > Best Regards > Haruhiko Dekura ------------------------------------------------------------- Nicki Frank Hinsche, Dipl. Phys. Institut f?r Physik - Theoretische Physik, Martin-Luther-Universit?t Halle-Wittenberg, Von-Seckendorff-Platz 1, Raum 1.07 D-06120 Halle/Saale, Germany Tel.: ++49 345 5525460 ------------------------------------------------------------- From giannozz at democritos.it Wed Dec 23 14:42:56 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Dec 2009 14:42:56 +0100 Subject: [Pw_forum] problem in the local inversion. In-Reply-To: <461484536.25860@nudt.edu.cn> References: <461484536.25860@nudt.edu.cn> Message-ID: <29D3533B-A3F3-4FC7-A027-104F02E52EA7@democritos.it> On Dec 22, 2009, at 13:22 , Jiayu Dai wrote: > Did anybody meet this problem: the hint of "problem in the local > inversion" > appears when the molecular dynamics calculation at high pressure > was doing. > Sometimes, when i changed the Pseudopotentials, this problem can be > solved. > But it appreared occasionally. And is it the problem of the code? > Or the problem > in my computer? hard to say. The problem is in subspace parallel diagonalization (or in iterative orthonormalization for Car-Parrinello dynamics). It means that one of the LAPACK algorithms used in the parallel algorithm returns an error message. It may be due to an ill-conceived algorithm that fails in some cases, to an ill- conditioned matrix, to the quality of mathematical libraries...hard to say 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 Wed Dec 23 14:47:03 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Dec 2009 14:47:03 +0100 Subject: [Pw_forum] grid shift In-Reply-To: <197357.47438.qm@web15307.mail.cnb.yahoo.com> References: <197357.47438.qm@web15307.mail.cnb.yahoo.com> Message-ID: On Dec 23, 2009, at 3:51 , Fan Yang wrote: > Which result is more reasonable? this is not the correct answer. The correct answer is "which result is closer to convergence (assuming that I did things properly)"? 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 Wed Dec 23 14:47:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Dec 2009 14:47:57 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: <354D3CE3-4D5E-40B1-918C-675304398E27@freenet.de> References: <354D3CE3-4D5E-40B1-918C-675304398E27@freenet.de> Message-ID: On Dec 23, 2009, at 14:32 , Nicki Frank Hinsche wrote: > plotting the fermi surface for the shifted energy would be the last > stage... and what are the previous stages? 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 dekura at cmp.sanken.osaka-u.ac.jp Wed Dec 23 14:56:30 2009 From: dekura at cmp.sanken.osaka-u.ac.jp (dekura at cmp.sanken.osaka-u.ac.jp) Date: Wed, 23 Dec 2009 22:56:30 +0900 (JST) Subject: [Pw_forum] grid shift In-Reply-To: <197357.47438.qm@web15307.mail.cnb.yahoo.com> References: <197357.47438.qm@web15307.mail.cnb.yahoo.com> Message-ID: <44936.118.240.158.9.1261576590.squirrel@lucy.cmp.sanken.osaka-u.ac.jp> Dear Fan I think it is reasonable that use of different grid gives different total energy because the calculated KS energies are different, and hence averaged total energy is different in each selected grid if you don't have sufficient grid for k-points leading to converged energy. So that I think you should check the convergency of total energy with increasing mesh of k-point. In my guess, If you have dense grid, you can have same energy not depending on grid offsets. Best Regards Haruhiko Dekura > Dear?everyone: > > I have some questions about grid offsets. > > In?our input file, the k-points are automatically generated with uniform > grid,?and the grid offsets?are either set as 0 (no offset) or 1 (grid > displaced by 1/2 step). But the problem is that?we got different results > with different offsets. > > For example, we tested the adsorption of?one oxygen atom on three > low-index Pt crystal planes, namely, Pt(100), Pt(110) and Pt(111).?With > grid shift (0 0 0), the adsorption energy of O on Pt(110) is slightly > larger than on Pt(100), but much larger than on Pt(111). However, with > grid shift (1 1 1), the order of adsorption energy is > Pt(110)>Pt(111)>Pt(100). > > Which result is more reasonable? > > Best Regards & Merry Christmas, > > Fan Yang > ******************************************* > Fan Yang > PH.D Candidate?in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University, 430072, Hubei Province, China > E-mail:shrek_826 at yahoo.com.cn > ******************************************* > > > ___________________________________________________________ > ???�?�?????�????? > http://card.mail.cn.yahoo.com/_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From dekura at cmp.sanken.osaka-u.ac.jp Wed Dec 23 16:11:00 2009 From: dekura at cmp.sanken.osaka-u.ac.jp (dekura at cmp.sanken.osaka-u.ac.jp) Date: Thu, 24 Dec 2009 00:11:00 +0900 (JST) Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: <354D3CE3-4D5E-40B1-918C-675304398E27@freenet.de> References: <354D3CE3-4D5E-40B1-918C-675304398E27@freenet.de> Message-ID: <45234.118.240.158.9.1261581060.squirrel@lucy.cmp.sanken.osaka-u.ac.jp> Dear Nicki I think you want to change chemical potential in semiconductor and you want to plot "iso-energy surface" ( not Fermi surface, of course) in order to the study of impurity dope, is it correct? If so, please try an example attached in this mail. This example shows how to plot "iso-energy surface" in Diamond. (1) you run fs.sh after modifying environmental variables in fs.sh. (2) you can change the value of EF ( means chemical potential in our case exactly) I put also reference files, and please compare your result with mine after the calculation. Hoping this help you. Best Regards Haruhiko Dekura > > Dear Haruhiko, > > I've tried this out but the the fermi surface was 'invisible' as I > would have expected for the non shifted Fermi energy right in the gap. > But I'll try on this again... > > thanks a lot on both of you > > Nicki > >> Hi Nicki. >> >> I think you can do it with manipulating input file " input_FS " >> which is >> read in running "bands_FS.x", after scf and nscf calculation, as below >> strategy. >> >> #-- input_FS--- >> nband_min nband_max >> EF <----- YOU change this value >> title >> ..... >> ..... >> #---------------- >> >> and you run >> >> bands_FS.x < Bands_SP.out , >> >> then you can see the information about Fermi-surface and modified the >> Fermi level you input. >> >> >> Best Regards >> Haruhiko Dekura > ------------------------------------------------------------- > Nicki Frank Hinsche, Dipl. Phys. > Institut fr Physik - Theoretische Physik, > Martin-Luther-Universitt Halle-Wittenberg, > Von-Seckendorff-Platz 1, Raum 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > ------------------------------------------------------------- > _______________________________________________ > 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: example_Haru.tar.gz Type: application/x-gzip Size: 14343 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091224/5547df3e/attachment-0001.bin From nicvok at freenet.de Wed Dec 23 20:52:31 2009 From: nicvok at freenet.de (Nicki Frank Hinsche) Date: Wed, 23 Dec 2009 20:52:31 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: References: Message-ID: <1F8BE3F7-6ABC-416F-B33D-E1D9088787BE@freenet.de> Dear Eyvaz, You are right. I already mentioned this in my first post. In the right physical way I want to simulate doping by shifting the chemical potential to an energy near the original Fermi energy for the charge neutral, isolating system. In any case the chemical potential has to be shifted in either valence- or conduction band and therefore there would be an iso-energy surface (what I sloppy called Fermi surface...). in any case, thank you Nicki > Dear Nicki, > >> I just want to know whether and how it is possible to shift >> the Fermi energy before constructing the Fermi surface?! > >> I just want to know whether and how it is possible to shift >> the Fermi energy before constructing the Fermi surface?! > > I should note there is NO Fermi level, thus, no Fermi surface for > semiconductors!!! Please think about why. > > 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 Dear Paolo, The previous stages are the formal ones: -making a proper scf calculation for the isolating system -calculate the total DOS to obtain the size of the gap and the possible energetic positions of valence/conduction band edge, where later on the chemical potential should be shifted into. -generating a k-point grid in the BZ with kvecs_FS.x -afterwards the eigenvalues are calculated on this grid for one special energy -> this is the Fermi energy, but: For my isolating system the Fermi energy would be in the gap, therefore there wont be an eigenvalue for given k-points at the Fermi energy. If I shift the energy to a value right where states are, then I would expect of course some contribution to an iso-energetic surface. But how to change this 'Fermi energy' in the right way. Is it enough to change the parameter in input_FS? Of course I know, that the system isn't charge-neutral anymore after artificially shifting the Fermi energy. Thanks a lot, Nicki > On Dec 23, 2009, at 14:32 , Nicki Frank Hinsche wrote: > >> plotting the fermi surface for the shifted energy would be the last >> stage... > > and what are the previous stages? P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 ------------------------------------------------------------- Nicki Frank Hinsche, Dipl. Phys. Institut f?r Physik - Theoretische Physik, Martin-Luther-Universit?t Halle-Wittenberg, Von-Seckendorff-Platz 1, Raum 1.07 D-06120 Halle/Saale, Germany Tel.: ++49 345 5525460 nicki.hinsche at physik.uni-halle.de ------------------------------------------------------------- From giannozz at democritos.it Wed Dec 23 21:09:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Dec 2009 21:09:29 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: <1F8BE3F7-6ABC-416F-B33D-E1D9088787BE@freenet.de> References: <1F8BE3F7-6ABC-416F-B33D-E1D9088787BE@freenet.de> Message-ID: <20773FCE-118C-45DB-BA58-5CD1CA53B4B1@democritos.it> On Dec 23, 2009, at 20:52 , Nicki Frank Hinsche wrote: > For my isolating system the Fermi energy would be in the gap, > therefore there wont be an eigenvalue for given k-points at the Fermi > energy. If I shift the energy to a value right where states are, then > I would expect of course some contribution to an iso-energetic > surface. But how to change this 'Fermi energy' in the right way. Is it > enough to change the parameter in input_FS? Of course I know, that the > system isn't charge-neutral anymore after artificially shifting the > Fermi energy. input_FS is the file containing input data for the program (written by Eyvaz) that calculates the Fermi surface, given the band structure calculated in a previous run, IIRC. That code requires in input the Fermi energy (it might read it from the bands data, but apparently it doesn't). If this is your problem: you can change the Fermi at will, since the band structure is fixed. You can change the Fermi energy in a self-consistent way by adding or removing charge to the system (variable "nelec"). This will modify the band structure wrt the neutral case, but not by much if you add or remove just a fraction of an electron. The code will take care of adding a neutralizing background (needed in order to have a finite value of the energy). 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 eyvaz_isaev at yahoo.com Wed Dec 23 22:17:24 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 23 Dec 2009 13:17:24 -0800 (PST) Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations and X-mas In-Reply-To: <20773FCE-118C-45DB-BA58-5CD1CA53B4B1@democritos.it> Message-ID: <776519.72384.qm@web65705.mail.ac4.yahoo.com> Hi, >That code requires in input the Fermi energy (it might >read it from the bands data, but apparently it doesn't). Well, it is my pleasure telling you that I will fix this small problem soon. By the way, why we are discussing such kind serious problems, when X-mas is approaching? Merry X-mas and Happy New Year to all q-ESPRESSO Developers and Users! 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 Wed, 12/23/09, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Shifting Fermi energy for Fermi surface calculations > To: "PWSCF Forum" > Date: Wednesday, December 23, 2009, 11:09 PM > > On Dec 23, 2009, at 20:52 , Nicki Frank Hinsche wrote: > > > For my isolating system the Fermi energy would be in > the gap, therefore there wont be an eigenvalue for given > k-points at the Fermi energy. If I shift the energy to a value right > where states are, then I would expect of course some contribution to an > iso-energetic surface. But how to change this 'Fermi energy' in the > right way. Is it enough to change the parameter in input_FS? Of course > I know, that the system isn't charge-neutral anymore after artificially > shifting the Fermi energy. > > input_FS is the file containing input data for the program > (written? by Eyvaz) > that calculates the Fermi surface, given the band > structure?calculated in a previous run, IIRC. That code requires in input the Fermi energy (it might > read it from the bands data, but apparently it doesn't). If > this is? your problem: you can change the Fermi at will, since the band structure is fixed. > > You can change the Fermi energy in a self-consistent way by > adding or removing charge to the system (variable "nelec"). This will > modify the band?structure wrt the neutral case, but not by much if you add or remove just a fraction of an electron. The code will take care of adding a neutralizing background (needed in order to have a finite value of the energy). > > 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 daijiayu at nudt.edu.cn Thu Dec 24 09:29:02 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Thu, 24 Dec 2009 16:29:02 +0800 Subject: [Pw_forum] problem in the local inversion. Message-ID: <461643342.19581@nudt.edu.cn> Thanks for your reply, professor. I found it is dependent on the PPs i chose. For Fe system, if i used the PP: Fe.pbe-nd-rrkjus.UPF, the calculation would stop in this case. But if i used Fe.pbe-sp-van.UPF, it was always going. Then, i think the PPs has significant influence. Merry Christmas and happy new year. :) Jiayu > hard to say. The problem is in subspace parallel diagonalization (or > in iterative > orthonormalization for Car-Parrinello dynamics). It means that one of > the LAPACK > algorithms used in the parallel algorithm returns an error message. > It may be due > to an ill-conceived algorithm that fails in some cases, to an ill- > conditioned matrix, to > the quality of mathematical libraries...hard to say > ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From nicvok at freenet.de Thu Dec 24 10:54:10 2009 From: nicvok at freenet.de (Nicki Frank Hinsche) Date: Thu, 24 Dec 2009 10:54:10 +0100 Subject: [Pw_forum] Shifting Fermi energy for Fermi surface calculations In-Reply-To: References: Message-ID: <23383246-A65E-4132-B996-B289517FF1D3@freenet.de> Dear Paolo, Eyvaz, Haruhiko thanks for your effort. The description of Paolo and Haruhiko solved my problem... > input_FS is the file containing input data for the program (written > by Eyvaz) > that calculates the Fermi surface, given the band structure > calculated in a > previous run, IIRC. That code requires in input the Fermi energy (it > might > read it from the bands data, but apparently it doesn't). If this is > your problem: > you can change the Fermi at will, since the band structure is fixed. > > You can change the Fermi energy in a self-consistent way by adding or > removing > charge to the system (variable "nelec"). This will modify the band > structure wrt the > neutral case, but not by much if you add or remove just a fraction of > an electron. > The code will take care of adding a neutralizing background (needed > in order to > have a finite value of the energy). right now, christmas can start. Relaxing days to all of you! Best regards, Nicki. From josepht at chips.ncsu.edu Thu Dec 24 15:11:44 2009 From: josepht at chips.ncsu.edu (josepht at chips.ncsu.edu) Date: Thu, 24 Dec 2009 09:11:44 -0500 (EST) Subject: [Pw_forum] problem in the local inversion. In-Reply-To: <461643342.19581@nudt.edu.cn> References: <461643342.19581@nudt.edu.cn> Message-ID: <49381.64.134.182.0.1261663904.squirrel@chips.ncsu.edu> Jiayu, I have found that several PP in the repository have been loaded/modified and saved in Windows/MS-DOS, imbuing the files with non-standard characters (like ^M at linebreaks) which cannot be subsequently read. Though it may not be the case for the PP you are using here, it is worthwhile to check for this "converting" the file using sed or tr (like tr -d '\015' < PP_OLD.UPF > PP_NEW.UPF), or by using the dos2unix command. I believe this is the case for the Si rrkjus PP (or at least it was for the version I downloaded). Joe Turnbull North Carolina State University Department of Physics > Thanks for your reply, professor. I found it is dependent on the PPs i chose. For > Fe system, if i used the PP: Fe.pbe-nd-rrkjus.UPF, the calculation would stop in > this case. But if i used Fe.pbe-sp-van.UPF, it was always going. Then, i think the > PPs has significant influence. > > Merry Christmas and happy new year. :) > > Jiayu > > >> hard to say. The problem is in subspace parallel diagonalization (or >> in iterative >> orthonormalization for Car-Parrinello dynamics). It means that one of >> the LAPACK >> algorithms used in the parallel algorithm returns an error message. >> It may be due >> to an ill-conceived algorithm that fails in some cases, to an ill- >> conditioned matrix, to >> the quality of mathematical libraries...hard to say >> > > > > > ------------------------------ > ------------------------------------------- > 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 > From baroni at sissa.it Thu Dec 24 16:45:19 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 24 Dec 2009 16:45:19 +0100 Subject: [Pw_forum] greetings Message-ID: Not sure what would be worse: not to greet anybody, or send non-Christians (like myself) greetings for the most important Christian festivity? Don't know about you, but I love to be greeted on Christmas even if I am no Christian. So, please all accept my humble greetings for a Merry Christmas and a Happy New Year Stefano PS - the bottom line is political correctness is a rather pedantic exercise! --- 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/20091224/8f9c4dd7/attachment.htm From meisam_a84 at yahoo.com Thu Dec 24 17:35:14 2009 From: meisam_a84 at yahoo.com (meisam aghtar) Date: Thu, 24 Dec 2009 08:35:14 -0800 (PST) Subject: [Pw_forum] greetings In-Reply-To: References: Message-ID: <597540.2068.qm@web30601.mail.mud.yahoo.com> I also wish a merry Christmas and a happy New Year to you and all other users. Meisam __ Isfahan, Iran ________________________________ From: Stefano Baroni To: PWSCF Forum Sent: Thu, December 24, 2009 7:45:19 AM Subject: [Pw_forum] greetings Not sure what would be worse: not to greet anybody, or send non-Christians (like myself) greetings for the most important Christian festivity? Don't know about you, but I love to be greeted on Christmas even if I am no Christian. So, please all accept my humble greetings for a? Merry Christmas and a Happy New Year Stefano PS - the bottom line is political correctness is a rather pedantic exercise! --- 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/20091224/9ced0e54/attachment.htm From majdoub at gmail.com Fri Dec 25 05:14:06 2009 From: majdoub at gmail.com (mohamed sabri majdoub) Date: Thu, 24 Dec 2009 22:14:06 -0600 Subject: [Pw_forum] problem with saw like potential calculation on Graphene BN system Message-ID: Dear PWSCF users, I want to plot the electric potential difference between 2 configurations of Graphene on BN system. One in the presence of sawlike potential and one without. The calculation without saw like potential did converge. Here a snapshot of the end of the output : ---------------------------------------------------------------------------------------- the Fermi energy is 0.5431 ev ! total energy = -876.50130984 Ry Harris-Foulkes estimate = -876.50131070 Ry estimated scf accuracy < 0.00000098 Ry The total energy is the sum of the following terms: one-electron contribution =-11420.47672354 Ry hartree contribution = 5787.16715122 Ry xc contribution = -257.10494832 Ry ewald contribution = 5013.91321080 Ry smearing contrib. (-TS) = 0.00000000 Ry convergence has been achieved in 8 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00004991 0.00023487 0.00013847 atom 2 type 1 force = -0.00000850 0.00023513 0.00011854 atom 3 type 1 force = 0.00004362 -0.00023146 0.00012581 atom 4 type 1 force = 0.00004572 0.00006253 0.00014587 atom 5 type 1 force = -0.00004755 0.00008873 -0.00029256 atom 6 type 1 force = -0.00007509 0.00026086 -0.00026676 atom 7 type 1 force = -0.00001273 0.00026096 -0.00023962 atom 8 type 1 force = 0.00009831 -0.00024159 0.00014046 atom 9 type 1 force = 0.00011792 -0.00023203 0.00013144 atom 10 type 1 force = 0.00016918 -0.00023359 0.00015208 atom 11 type 1 force = 0.00015964 -0.00005540 0.00016279 atom 12 type 1 force = 0.00000416 0.00023161 0.00013408 atom 13 type 1 force = 0.00010353 -0.00005959 0.00014542 atom 14 type 1 force = 0.00005981 0.00005922 0.00016221 atom 15 type 1 force = 0.00006131 0.00022791 0.00015555 atom 16 type 1 force = -0.00003569 -0.00025848 -0.00024195 atom 17 type 1 force = -0.00001015 0.00025569 -0.00025872 atom 18 type 1 force = -0.00006646 0.00025363 -0.00028531 atom 19 type 1 force = -0.00004477 0.00008710 -0.00030934 atom 20 type 1 force = -0.00009101 -0.00027172 -0.00027002 atom 21 type 1 force = -0.00014921 -0.00025552 -0.00025789 atom 22 type 1 force = -0.00020251 -0.00026290 -0.00028407 atom 23 type 1 force = -0.00007504 -0.00008404 -0.00029430 atom 24 type 1 force = -0.00016627 -0.00008191 -0.00031347 atom 25 type 2 force = 0.00051603 -0.00031111 0.00031922 atom 26 type 2 force = 0.00066795 0.00017652 0.00031399 atom 27 type 2 force = 0.00052005 -0.00017951 0.00026165 atom 28 type 2 force = 0.00007573 0.00032942 0.00032267 atom 29 type 2 force = 0.00020909 -0.00017517 0.00031074 atom 30 type 2 force = 0.00004563 0.00020570 0.00026529 atom 31 type 2 force = -0.00030754 -0.00020609 -0.00000963 atom 32 type 2 force = -0.00045660 0.00016711 0.00003189 atom 33 type 2 force = -0.00030679 -0.00035495 0.00003254 atom 34 type 2 force = 0.00046005 0.00018799 0.00031787 atom 35 type 2 force = 0.00031926 -0.00032862 0.00031348 atom 36 type 2 force = -0.00050536 -0.00019000 -0.00000976 atom 37 type 2 force = 0.00029818 -0.00018842 0.00025352 atom 38 type 2 force = -0.00007132 0.00034273 0.00002266 atom 39 type 2 force = -0.00021836 -0.00016861 0.00002478 atom 40 type 2 force = -0.00004970 0.00020543 -0.00000631 atom 41 type 2 force = -0.00068094 0.00015822 0.00002829 atom 42 type 2 force = -0.00059726 0.00032077 0.00003622 atom 43 type 2 force = -0.00075121 -0.00017896 0.00002988 atom 44 type 2 force = -0.00061187 0.00020308 -0.00000938 atom 45 type 2 force = 0.00061125 0.00019187 0.00025788 atom 46 type 2 force = -0.00052473 -0.00032891 0.00002424 atom 47 type 2 force = 0.00059689 0.00030997 0.00032171 atom 48 type 2 force = 0.00074993 -0.00018601 0.00031044 atom 49 type 3 force = -0.00021629 0.00013637 -0.00002211 atom 50 type 3 force = -0.00012927 -0.00004552 -0.00003957 atom 51 type 3 force = -0.00014022 -0.00007112 -0.00014479 atom 52 type 3 force = 0.00003567 -0.00002637 -0.00004582 atom 53 type 3 force = 0.00001837 -0.00001681 -0.00013369 atom 54 type 3 force = 0.00014761 0.00017594 -0.00012332 atom 55 type 3 force = 0.00008922 0.00003087 -0.00005261 atom 56 type 3 force = 0.00006341 0.00001675 -0.00016291 atom 57 type 3 force = 0.00019014 -0.00019338 -0.00013489 atom 58 type 3 force = 0.00025998 0.00019164 -0.00013950 atom 59 type 3 force = 0.00012773 -0.00000666 -0.00014741 atom 60 type 3 force = 0.00016931 -0.00001882 -0.00003757 atom 61 type 3 force = 0.00007519 -0.00019259 -0.00010957 atom 62 type 3 force = -0.00005198 0.00001843 -0.00013946 atom 63 type 3 force = -0.00003895 0.00002506 -0.00004626 atom 64 type 3 force = 0.00005318 0.00007782 -0.00012175 atom 65 type 3 force = 0.00004722 0.00005668 -0.00005446 atom 66 type 3 force = -0.00004209 -0.00013570 -0.00006567 atom 67 type 3 force = -0.00008733 0.00007755 -0.00012696 atom 68 type 3 force = -0.00008666 0.00005408 -0.00003186 atom 69 type 3 force = -0.00017176 -0.00013583 -0.00004644 atom 70 type 3 force = -0.00014236 0.00012217 -0.00005216 atom 71 type 3 force = -0.00004416 -0.00005654 -0.00005829 atom 72 type 3 force = -0.00004246 -0.00007653 -0.00012550 Total force = 0.003351 Total SCF correction = 0.002631 SCF correction compared to forces is too large, reduce conv_thr bfgs converged in 13 scf cycles and 9 bfgs steps End of BFGS Geometry Optimization Final energy = -876.5013098370 Ry CELL_PARAMETERS (alat) 8.519800000 0.000000000 0.000000000 0.000000000 7.376000000 0.000000000 0.000000000 0.000000000 22.612000000 ATOMIC_POSITIONS (angstrom) B 0.709950650 8.606569870 11.178365426 B 0.710024516 11.065188378 11.178196366 B 2.839938440 7.377781874 11.178319218 B 0.710003828 6.148025709 11.178218236 B 6.389924656 6.147964138 8.062298249 B 6.390045708 8.606511929 8.062245112 B 6.389941890 11.065116918 8.062198735 B 2.839865957 9.836415504 11.178333535 B 7.099785762 7.377773800 11.178462669 B 7.099706769 9.836400737 11.178246106 B 7.099765193 12.294941516 11.178080685 B 4.969848766 11.065215568 11.178307441 B 2.839916149 12.294955434 11.178236791 B 4.969832821 6.148051719 11.178244158 B 4.969772362 8.606593646 11.178348415 B 4.260019659 7.377879436 8.062200371 B 2.130114662 11.065151536 8.062160115 B 2.130210597 8.606534945 8.062244345 B 2.130093260 6.147990069 8.062272651 B 4.260115164 9.836500060 8.062243629 B 0.000180549 7.377867664 8.062111429 B 0.000292205 9.836490209 8.062287258 B 4.260009665 12.295042075 8.062285335 B 0.000162547 12.295032239 8.062347953 C 2.129922912 6.148297792 14.677832647 C 2.129898772 8.606705408 14.677897532 C 2.129914411 11.065574848 14.677963367 C 0.000068718 12.294705904 14.677868648 C 0.000053160 9.836298362 14.677932899 C 0.000073932 7.377414454 14.677964666 C 0.710227438 11.065590534 14.678750754 C 0.710251453 8.606714593 14.678702525 C 0.710221997 6.148318211 14.678645264 C 6.389834558 8.606693656 14.677924270 C 6.389852550 6.148292755 14.677908278 C 4.970160509 11.065589647 14.678773294 C 6.389855501 11.065564265 14.678043187 C 7.100003923 12.294682839 14.678727191 C 7.100037940 9.836278772 14.678753690 C 7.100008554 7.377395526 14.678751306 C 4.970190603 8.606726322 14.678729152 C 2.840223138 12.294698795 14.678638311 C 2.840251568 9.836294701 14.678705275 C 2.840237809 7.377407509 14.678730745 C 4.259849922 7.377427143 14.677992752 C 4.970158608 6.148316286 14.678700531 C 4.259855357 12.294715913 14.677865997 C 4.259828430 9.836309885 14.677925676 N 0.000002933 12.294522833 11.177753922 N -0.000114976 9.836059259 11.178044619 N -0.000089035 7.377375641 11.178758586 N 2.840197587 7.377329909 8.060087341 N 2.840244711 9.836019456 8.060785586 N 2.840070287 12.294499078 8.060835649 N 4.970091529 11.065685303 8.060080269 N 4.970143219 8.607015481 8.060979848 N 4.969965790 6.148541676 8.060878366 N 7.099915340 12.294465358 8.060960245 N 7.100108356 9.835990065 8.060871705 N 7.100041209 7.377303136 8.060015919 N 0.710167780 6.148535741 8.060734949 N 0.710348552 8.607004732 8.060847766 N 0.710306279 11.065688042 8.060132335 N 6.389651783 11.065583541 11.178411967 N 6.389636917 8.606910547 11.178226850 N 6.389756113 6.148451575 11.178145965 N 2.129867804 11.065590918 11.178559562 N 2.129852170 8.606920005 11.178062941 N 2.129961474 6.148457117 11.178029406 N 4.259863960 12.294553821 11.178043095 N 4.259744575 9.836088605 11.178207224 N 4.259762106 7.377399069 11.178563700 Writing output data file GphBN.save PWSCF : 0d 21h55m CPU time, 1d 0h16m wall time init_run : 1392.70s CPU electrons : 77427.55s CPU ( 13 calls,5955.966 s avg) update_pot : 5.78s CPU ( 12 calls, 0.481 s avg) forces : 56.54s CPU ( 13 calls, 4.349 s avg) Called by init_run: wfcinit : 1387.88s CPU potinit : 0.11s CPU Called by electrons: c_bands : 73400.15s CPU ( 131 calls, 560.307 s avg) sum_band : 3619.03s CPU ( 131 calls, 27.626 s avg) v_of_rho : 1.66s CPU ( 144 calls, 0.012 s avg) mix_rho : 374.82s CPU ( 131 calls, 2.861 s avg) Called by c_bands: init_us_2 : 16.43s CPU ( 13800 calls, 0.001 s avg) cegterg : 73387.98s CPU ( 6550 calls, 11.204 s avg) Called by *egterg: h_psi : 33317.15s CPU ( 28811 calls, 1.156 s avg) g_psi : 12.33s CPU ( 22211 calls, 0.001 s avg) cdiaghg : 36250.93s CPU ( 28161 calls, 1.287 s avg) Called by h_psi: add_vuspsi : 233.57s CPU ( 28811 calls, 0.008 s avg) General routines calbec : 412.35s CPU ( 29461 calls, 0.014 s avg) cft3s : 36152.87s CPU ( 6702434 calls, 0.005 s avg) davcio : 1.12s CPU ( 20350 calls, 0.000 s avg) Parallel routines fft_scatter : 26097.00s CPU ( 6702434 calls, 0.004 s avg) --------------------------------------------------------------------------------------------------------------------------------- For the second simulation in the presence of sawlike potential I had to add the corresponding keyword to the same input file without changing the cutoff energy,... Here is the input : ----------------------------------------------------------------------------------------------------------------------------------- &control title = 'GphBNcapa' calculation = 'relax' outdir = '/pwscf/pwscftemp/GphBN' prefix = 'GphBN' pseudo_dir = '/pwscf/input/Gph-BN/pseudopot-C-B-N' tprnfor = .t. restart_mode = 'from_scratch' tefield = .true. dipfield = .true. / &system ibrav = 0, celldm(1) = 1.8897261 nat = 72, ntyp = 3, ecutwfc = 30.0 occupations = 'smearing' smearing = 'gaussian' degauss = 0.003675 edir = 3 ! This is the direction of applied field eamp = 0.002 ! Amplitude of e-field-should be small emaxpos = 0.9 eopreg = 0.2 / &electrons mixing_mode = 'local-TF' mixing_beta = 0.05 diagonalization = 'david' conv_thr = 1.D-5 / &ions trust_radius_ini = 0.10 / &cell ATOMIC_SPECIES B 10.81100 B.pz-vbc.UPF C 12.01070 C.pz-vbc.UPF N 14.00674 N.pz-vbc.UPF ATOMIC_POSITIONS angstrom B 0.710000 8.607000 11.306000 B 0.710000 11.066000 11.306000 B 2.840000 7.377000 11.306000 B 0.710000 6.148000 11.306000 B 6.390000 6.148000 8.000000 B 6.390000 8.607000 8.000000 B 6.390000 11.066000 8.000000 B 2.840000 9.836000 11.306000 B 7.100000 7.377000 11.306000 B 7.100000 9.836000 11.306000 B 7.100000 12.295000 11.306000 B 4.970000 11.066000 11.306000 B 2.840000 12.295000 11.306000 B 4.970000 6.148000 11.306000 B 4.970000 8.607000 11.306000 B 4.260000 7.377000 8.000000 B 2.130000 11.066000 8.000000 B 2.130000 8.607000 8.000000 B 2.130000 6.148000 8.000000 B 4.260000 9.836000 8.000000 B 0.000000 7.377000 8.000000 B 0.000000 9.836000 8.000000 B 4.260000 12.295000 8.000000 B 0.000000 12.295000 8.000000 C 2.130000 6.148000 14.612000 C 2.130000 8.607000 14.612000 C 2.130000 11.066000 14.612000 C 0.000000 12.295000 14.612000 C 0.000000 9.836000 14.612000 C 0.000000 7.377000 14.612000 C 0.710000 11.066000 14.612000 C 0.710000 8.607000 14.612000 C 0.710000 6.148000 14.612000 C 6.390000 8.607000 14.612000 C 6.390000 6.148000 14.612000 C 4.970000 11.066000 14.612000 C 6.390000 11.066000 14.612000 C 7.100000 12.295000 14.612000 C 7.100000 9.836000 14.612000 C 7.100000 7.377000 14.612000 C 4.970000 8.607000 14.612000 C 2.840000 12.295000 14.612000 C 2.840000 9.836000 14.612000 C 2.840000 7.377000 14.612000 C 4.260000 7.377000 14.612000 C 4.970000 6.148000 14.612000 C 4.260000 12.295000 14.612000 C 4.260000 9.836000 14.612000 N 0.000000 12.295000 11.306000 N 0.000000 9.836000 11.306000 N 0.000000 7.377000 11.306000 N 2.840000 7.377000 8.000000 N 2.840000 9.836000 8.000000 N 2.840000 12.295000 8.000000 N 4.970000 11.066000 8.000000 N 4.970000 8.607000 8.000000 N 4.970000 6.148000 8.000000 N 7.100000 12.295000 8.000000 N 7.100000 9.836000 8.000000 N 7.100000 7.377000 8.000000 N 0.710000 6.148000 8.000000 N 0.710000 8.607000 8.000000 N 0.710000 11.066000 8.000000 N 6.390000 11.066000 11.306000 N 6.390000 8.607000 11.306000 N 6.390000 6.148000 11.306000 N 2.130000 11.066000 11.306000 N 2.130000 8.607000 11.306000 N 2.130000 6.148000 11.306000 N 4.260000 12.295000 11.306000 N 4.260000 9.836000 11.306000 N 4.260000 7.377000 11.306000 K_POINTS automatic 10 10 1 1 1 0 CELL_PARAMETERS 8.51980 0.00000 0.00000 0.00000 7.37600 0.00000 0.00000 0.00000 22.6120 ------------------------------------------------------------------------------------------------------------------------------------------- However, as calculation are running I noticed that they are not converging properly. Too many eigenvalues are not converging. I might be wrong but this is the output at the current step of the calculation: ------------------------------------------------------------------------------------------------------------------------------------------- iteration # 20 ecut= 30.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 5.1 negative rho (up, down): 0.590E+03 0.000E+00 Computed dipoles : electron 22.15751 -1.62036********** ion 1932.056005018.71955 82.04264 total 1909.898495020.339906342.69519 Dipole field [a.u.]: 8.3119 total cpu time spent up to now is 84515.55 secs total energy = 85279.52921091 Ry Harris-Foulkes estimate = 85603.57307858 Ry estimated scf accuracy < 5376.92087915 Ry iteration # 21 ecut= 30.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 5.1 negative rho (up, down): 0.528E+03 0.000E+00 Computed dipoles : electron 25.23753 -1.17788********** ion 1932.056005018.71955 82.04264 total 1906.818475019.897436406.06262 Dipole field [a.u.]: 8.3949 total cpu time spent up to now is 85450.41 secs total energy = 93168.49098676 Ry Harris-Foulkes estimate = 86319.02586649 Ry estimated scf accuracy < 4531.24319133 Ry iteration # 22 ecut= 30.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 1.0 negative rho (up, down): 0.381E+03 0.000E+00 Computed dipoles : electron 1.09245 -0.07341********** ion 1932.056005018.71955 82.04264 total 1930.963555018.792966652.29113 Dipole field [a.u.]: 8.7176 total cpu time spent up to now is 85733.13 secs total energy = 99660.57900635 Ry Harris-Foulkes estimate = 97379.26494465 Ry estimated scf accuracy < 3775.34065180 Ry iteration # 23 ecut= 30.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 23 eigenvalues not converged c_bands: 13 eigenvalues not converged ethr = 1.00E-02, avg # of iterations = 11.7 negative rho (up, down): 0.496E+03 0.000E+00 Computed dipoles : electron -13.76337 0.04670********** ion 1932.056005018.71955 82.04264 total 1945.819375018.672856746.79870 Dipole field [a.u.]: 8.8414 total cpu time spent up to now is 87071.95 secs total energy =102491.23930709 Ry Harris-Foulkes estimate =101273.97736718 Ry estimated scf accuracy < 2033.03849554 Ry iteration # 24 ecut= 30.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 24 eigenvalues not converged c_bands: 17 eigenvalues not converged c_bands: 20 eigenvalues not converged c_bands: 13 eigenvalues not converged c_bands: 7 eigenvalues not converged c_bands: 15 eigenvalues not converged c_bands: 15 eigenvalues not converged c_bands: 16 eigenvalues not converged c_bands: 19 eigenvalues not converged c_bands: 25 eigenvalues not converged c_bands: 8 eigenvalues not converged c_bands: 15 eigenvalues not converged c_bands: 18 eigenvalues not converged c_bands: 23 eigenvalues not converged c_bands: 36 eigenvalues not converged c_bands: 9 eigenvalues not converged c_bands: 10 eigenvalues not converged c_bands: 20 eigenvalues not converged c_bands: 18 eigenvalues not converged c_bands: 21 eigenvalues not converged c_bands: 14 eigenvalues not converged c_bands: 17 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 22 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 14 eigenvalues not converged c_bands: 15 eigenvalues not converged c_bands: 23 eigenvalues not converged c_bands: 15 eigenvalues not converged c_bands: 21 eigenvalues not converged c_bands: 14 eigenvalues not converged c_bands: 12 eigenvalues not converged c_bands: 15 eigenvalues not converged c_bands: 19 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 16 eigenvalues not converged c_bands: 22 eigenvalues not converged c_bands: 21 eigenvalues not converged c_bands: 8 eigenvalues not converged c_bands: 20 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 14 eigenvalues not converged c_bands: 19 eigenvalues not converged c_bands: 29 eigenvalues not converged c_bands: 23 eigenvalues not converged c_bands: 20 eigenvalues not converged ethr = 1.00E-02, avg # of iterations =106.4 negative rho (up, down): 0.448E+03 0.000E+00 Computed dipoles : electron -22.55060 0.08222********** ion 1932.056005018.71955 82.04264 total 1954.606605018.637336715.54551 Dipole field [a.u.]: 8.8005 total cpu time spent up to now is 98870.22 secs total energy = 88277.44897680 Ry Harris-Foulkes estimate =101483.98218627 Ry estimated scf accuracy < 3047.32661549 Ry iteration # 25 ecut= 30.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 4 eigenvalues not converged -------------------------------------------------------------------------------------------------------------- I might need to increase the ecutwfc value to reach convergence. But, if this is right how can I compare the 2 calcualtions with and without sawlike potential at different cutoff energies. Do you have any suggestions to reach convergence in presence of the applied potential. I am planning to use the postprocessing tool pp.x to extract the total potential and plot the potential diffrence between the 2 configurations. I beleive I should use plot_num=1 (total potential V_bare+V_H + V_xc). But, how about plot_num=12 (the electric field potential) is it the external potential or the total electric response? Or do I need to add both potential 1+12? Thank you in advance for your suggestions and help on this problem. Regards, Mohamed Sabri Majdoub Department of Mechanical Engineering University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091224/12c54943/attachment-0001.htm From mohnish.iitk at gmail.com Fri Dec 25 10:44:18 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 25 Dec 2009 15:14:18 +0530 Subject: [Pw_forum] greetings In-Reply-To: References: Message-ID: Merry Christmas to all users :) On Thu, Dec 24, 2009 at 9:15 PM, Stefano Baroni wrote: > Not sure what would be worse: not to greet anybody, or send non-Christians > (like myself) greetings for the most important Christian festivity? Don't > know about you, but I love to be greeted on Christmas even if I am no > Christian. So, please all accept my humble greetings for a > > Merry Christmas and a Happy New Year > > Stefano > > PS - the bottom line is political correctness is a rather pedantic > exercise! > > --- > 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 > > -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091225/dafde2b8/attachment.htm From CAPerott at ucs.br Fri Dec 25 12:30:24 2009 From: CAPerott at ucs.br (Claudio Antonio Perottoni) Date: Fri, 25 Dec 2009 09:30:24 -0200 Subject: [Pw_forum] pbe0 problem Message-ID: <20091225093024.70598yiv1126aamo@webmail.ucs.br> Dear Ali, I have faced the same problem. The solution I've found was to set ecutrho = 4*ecutwfc. Hope this helps! Claudio -- ****************************************************************** Cl?udio A. Perottoni Universidade de Caxias do Sul Centro de Ci?ncias Exatas e Tecnologia Rua Francisco Get?lio Vargas, 1130 95070-560 Caxias do Sul - RS - Brazil Phone: +55 54 3218 2100 ext. 2607 http://www.ucs.br/ccet/defq/caperott/ ***************************************************************** On 12/22/2009 12:50 PM, ali kazempour wrote: > > Ali Kazempour > > > > > Fritz-Haber-Institut fax : ++49-30-8413 4701 > der Max-Planck-Gesellschaft > Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de > D-14 195 Berlin-Dahlem / German > > > ----- Forwarded Message ---- > *From:* ali kazempour > *To:* pw > *Sent:* Tue, December 22, 2009 12:13:30 PM > *Subject:* pbe0 problem > > > Dear all > for noncubic cell ,in EXX calculation How we can choose the nq points? > For TiO2 I used this input file but the code stop in midway without > any message? and it didn't print total energy? > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = './', > prefix='tio2' > outdir='/p5/batch/kazempou/' > / > &system > ibrav = 6, > celldm(1) = 8.79, > celldm(3) = 0.639, > nat = 6, > ntyp = 2, > ecutwfc = 25 , > ecutrho = 400 , input_dft='pbe0', nqx1 = 2, nqx2 = 2, nqx3 = 4, > / > &electrons > diagonalization='david', > conv_thr = 1.0d-4 > mixing_beta = 0.5, > / > ATOMIC_SPECIES > Ti 47.86700 ti.optgga2.fhi.UPF > O 15.99940 o.optgga1.fhi.UPF > ATOMIC_POSITIONS crystal > Ti 0.000000000 0.000000000 0.000000000 > Ti 0.500000000 0.500000000 0.500000000 > O 0.305131381 0.305131381 0.000000000 > O -0.305131381 -0.305131381 0.000000000 > O 0.805131381 0.194868619 0.5 > O 0.194868619 0.805131381 0.5 > K_POINTS automatic > 2 2 4 1 1 1 > ------------------------------ > output file > > > > > > > total cpu time spent up to now is 1.60 secs > > total energy = -355.97704102 Ry > Harris-Foulkes estimate = -355.97835356 Ry > estimated scf accuracy < 0.00523443 Ry > > iteration # 5 ecut= 25.00 Ry beta=0.50 > Davidson diagonalization with overlap > ethr = 1.09E-05, avg # of iterations = 4.0 > > total cpu time spent up to now is 1.84 secs > > total energy = -355.97795182 Ry > Harris-Foulkes estimate = -355.97903987 Ry > estimated scf accuracy < 0.00242696 Ry > > iteration # 6 ecut= 25.00 Ry beta=0.50 > Davidson diagonalization with overlap > ethr = 5.06E-06, avg # of iterations = 3.0 > > total cpu time spent up to now is 2.02 secs > > End of self-consistent calculation > > k = 0.2500 0.2500 0.1956 ( 920 PWs) bands (ev): > > -50.3131 -50.2750 -26.6056 -26.5256 -26.5170 -26.5064 -26.4805 -26.4632 > -9.2828 -8.6924 -8.2771 -8.1594 4.0836 4.7890 5.3145 5.8431 > 6.1571 6.8145 7.1870 7.4771 7.7110 8.6006 8.7972 9.2575 > > k = 0.2500 0.2500 0.5869 ( 908 PWs) bands (ev): > > -50.2617 -50.2509 -26.7111 -26.6144 -26.5061 -26.4959 -26.4896 -26.4409 > -8.7021 -8.4646 -8.4175 -8.2262 4.7053 5.0674 5.0763 5.4017 > 6.0629 6.5874 7.1698 7.2399 7.5577 8.4242 8.4760 9.0196 > 0.892062058076385500 0.892062058076385500 > EXX divergence ( 2)= -108.3050 0.4000 > exx_div : 0.01s CPU > ! EXXALFA SET TO 0.250000000000000000 > > > > > > thanks a lot > > > > > Ali Kazempour > > > Fritz-Haber-Institut fax : ++49-30-8413 4701 > der Max-Planck-Gesellschaft > Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de > D-14 195 Berlin-Dahlem / German > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --------------------------------------- Essa mensagem foi enviada pelo UCS Mail From mohnish.iitk at gmail.com Sun Dec 27 14:57:33 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 27 Dec 2009 19:27:33 +0530 Subject: [Pw_forum] problem in making monoclinic supercell Message-ID: Dear PWSCF users, I am using PWSCF for BaTiO3 thin films calculation, I just wanted to visualize the (110) surface of the same by xcrysden. I am pasting the input PWSCF file for the same, the problem is my system is monoclinic but xcrysden is showing it to be cubic, may be I am doing some mistake. Please anybody help me out to fix the problem. The calcualtin is for one layer. Sincere thanks in advance, Mohnish &control calculation = 'relax' prefix='BaTiO3' outdir='/home/rajpala/Desktop/BaTiO3' pseudo_dir="/home/rajpala/Desktop/BaTiO3" / &system ibrav=12,a =5.629,b=4.875,c=20,celldm(4)=0.577344716 ,nat=5, ntyp= 3, ecutwfc = 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'local-TF' mixing_beta = 0.7 conv_thr = 1.0d-6 / &IONS ion_dynamics='bfgs' trust_radius_min=1.D-4 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS (crystal) Ba 0.5 0.5 0.070375 Ti 0.25 0.0 0.070375 O 0.0 0.0 0.0 O 0.5 0.0 0.0 O 0.0 0.5 0.070375 K_POINTS (automatic) 5 5 1 0 0 0 -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091227/bb985642/attachment.htm From dekura at cmp.sanken.osaka-u.ac.jp Sun Dec 27 15:10:57 2009 From: dekura at cmp.sanken.osaka-u.ac.jp (dekura at cmp.sanken.osaka-u.ac.jp) Date: Sun, 27 Dec 2009 23:10:57 +0900 (JST) Subject: [Pw_forum] problem in making monoclinic supercell In-Reply-To: References: Message-ID: <46958.118.240.158.9.1261923057.squirrel@lucy.cmp.sanken.osaka-u.ac.jp> Dear Mohnish How about modifying manually in part of "PRIMVEC" and "CONVVEC" in xcrysden file as a first aid? Sorry for not letting you know the exact solution. Best Regards Haruhiko Dekura Ph.D. student ISIR, Osaka university. > Dear PWSCF users, > > I am using PWSCF for BaTiO3 thin films calculation, I just wanted to > visualize the (110) surface of the same by xcrysden. I am pasting the > input > PWSCF file for the same, the problem is my system is monoclinic but > xcrysden > is showing it to be cubic, may be I am doing some mistake. Please anybody > help me out to fix the problem. The calcualtin is for one layer. > > Sincere thanks in advance, > Mohnish > > &control > calculation = 'relax' > prefix='BaTiO3' > outdir='/home/rajpala/Desktop/BaTiO3' > pseudo_dir="/home/rajpala/Desktop/BaTiO3" > / > &system > ibrav=12,a =5.629,b=4.875,c=20,celldm(4)=0.577344716 ,nat=5, ntyp= 3, > ecutwfc = > 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' > / > &electrons > diagonalization='david' > mixing_mode = 'local-TF' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > &IONS > ion_dynamics='bfgs' > trust_radius_min=1.D-4 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Ba 0.5 0.5 0.070375 > Ti 0.25 0.0 0.070375 > O 0.0 0.0 0.0 > O 0.5 0.0 0.0 > O 0.0 0.5 0.070375 > K_POINTS (automatic) > 5 5 1 0 0 0 > > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From dimpy.sharma at tyndall.ie Sun Dec 27 15:15:33 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Sun, 27 Dec 2009 14:15:33 -0000 Subject: [Pw_forum] Calculation is crashing without any error message Message-ID: i there, I have tried to run my scf calculation in 80 cpu, howeevr it is crashing without giving me any error message.It finished 17 iterations.Can anybody give any advice. I have checked it in Forum earlier and modified my input still I am getting similar error. Here is my input file is &CONTROL calculation ='scf' restart_mode ='from_scratch' outdir = '/' pseudo_dir = '/' prefix = 'Input2' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-8 forc_conv_thr = 1.D-8 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =14.5152 nat = 518 ntyp = 3 ecutwfc = 35 ecutrho = 120 nbnd = 1618 / &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 7.000000000 0.000000000 0.000000000 0.000000000 7.000000000 ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPF O 15.9994 O.pz-rrkjus.UPF H 1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 1.3859 18.2956 15.1401 ..... .. K_POINTS automatic 2 1 1 0 0 0 My file is too big. I am sorry for this ! Thanks and regards! Dimpy UCC Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091227/2ce39f30/attachment.htm From yoshioka at simulatio.jp Mon Dec 28 04:35:27 2009 From: yoshioka at simulatio.jp (Yoshioka) Date: Mon, 28 Dec 2009 12:35:27 +0900 Subject: [Pw_forum] problem in making monoclinic supercell In-Reply-To: References: Message-ID: <000c01ca876e$cde32c10$69a98430$@jp> Hi, Mohnish, You can not mix two ways for describing crystal. Either you can describe symmetry in a,b,c,cosab,cosbc,cosac or you can set celldm(n) n=1.6, Since you give a,b,c first, program will automatically expect cosab.. et al., When program can not find it, it will think cosab. are zero. Yoshioka Makoto Simulatio Company Yokohama-shi, shi-yokohama From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of mohnish pandey Sent: Sunday, December 27, 2009 10:58 PM To: PWSCF Forum Subject: [Pw_forum] problem in making monoclinic supercell Dear PWSCF users, I am using PWSCF for BaTiO3 thin films calculation, I just wanted to visualize the (110) surface of the same by xcrysden. I am pasting the input PWSCF file for the same, the problem is my system is monoclinic but xcrysden is showing it to be cubic, may be I am doing some mistake. Please anybody help me out to fix the problem. The calcualtin is for one layer. Sincere thanks in advance, Mohnish &control calculation = 'relax' prefix='BaTiO3' outdir='/home/rajpala/Desktop/BaTiO3' pseudo_dir="/home/rajpala/Desktop/BaTiO3" / &system ibrav=12,a =5.629,b=4.875,c=20,celldm(4)=0.577344716 ,nat=5, ntyp= 3, ecutwfc = 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'local-TF' mixing_beta = 0.7 conv_thr = 1.0d-6 / &IONS ion_dynamics='bfgs' trust_radius_min=1.D-4 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS (crystal) Ba 0.5 0.5 0.070375 Ti 0.25 0.0 0.070375 O 0.0 0.0 0.0 O 0.5 0.0 0.0 O 0.0 0.5 0.070375 K_POINTS (automatic) 5 5 1 0 0 0 -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091228/8816d944/attachment.htm From mohnish.iitk at gmail.com Mon Dec 28 05:16:58 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 28 Dec 2009 09:46:58 +0530 Subject: [Pw_forum] problem in making monoclinic supercell In-Reply-To: <000c01ca876e$cde32c10$69a98430$@jp> References: <000c01ca876e$cde32c10$69a98430$@jp> Message-ID: Thank you so much dear Yoshioka for your help. I fixed the problem. Now everything is fine. On Mon, Dec 28, 2009 at 9:05 AM, Yoshioka wrote: > Hi, Mohnish, > > > > You can not mix two ways for describing crystal. Either you can describe > symmetry in a,b,c,cosab,cosbc,cosac or you can set celldm(n) n=1?6, > > > > Since you give a,b,c first, program will automatically expect cosab?. et > al., When program can not find it, it will think cosab? are zero. > > > > Yoshioka Makoto > > > > Simulatio Company > > Yokohama-shi, shi-yokohama > > > > > > *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] *On > Behalf Of *mohnish pandey > *Sent:* Sunday, December 27, 2009 10:58 PM > *To:* PWSCF Forum > *Subject:* [Pw_forum] problem in making monoclinic supercell > > > > Dear PWSCF users, > > > I am using PWSCF for BaTiO3 thin films calculation, I just wanted to > visualize the (110) surface of the same by xcrysden. I am pasting the input > PWSCF file for the same, the problem is my system is monoclinic but xcrysden > is showing it to be cubic, may be I am doing some mistake. Please anybody > help me out to fix the problem. The calcualtin is for one layer. > > Sincere thanks in advance, > Mohnish > > &control > calculation = 'relax' > prefix='BaTiO3' > outdir='/home/rajpala/Desktop/BaTiO3' > pseudo_dir="/home/rajpala/Desktop/BaTiO3" > / > &system > ibrav=12,a =5.629,b=4.875,c=20,celldm(4)=0.577344716 ,nat=5, ntyp= 3, > ecutwfc = > 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' > / > &electrons > diagonalization='david' > mixing_mode = 'local-TF' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > &IONS > ion_dynamics='bfgs' > trust_radius_min=1.D-4 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Ba 0.5 0.5 0.070375 > Ti 0.25 0.0 0.070375 > O 0.0 0.0 0.0 > O 0.5 0.0 0.0 > O 0.0 0.5 0.070375 > K_POINTS (automatic) > 5 5 1 0 0 0 > > > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091228/d74887eb/attachment-0001.htm From cristian.degliesposti at unibo.it Mon Dec 28 16:29:20 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Mon, 28 Dec 2009 16:29:20 +0100 Subject: [Pw_forum] greetintgs In-Reply-To: References: Message-ID: <4B38CED0.5070909@unibo.it> Thanks for the really nice message. Simply I point out that most of the Christians (like myself) would agree that the most important Christian festivity is Easter, the resurrection day. So, having passed Christmas, let me wish you all a great 2010! Cristian > Message: 4 > Date: Thu, 24 Dec 2009 16:45:19 +0100 > From: Stefano Baroni > Subject: [Pw_forum] greetings > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Not sure what would be worse: not to greet anybody, or send non-Christians (like myself) greetings for the most important Christian festivity? Don't know about you, but I love to be greeted on Christmas even if I am no Christian. So, please all accept my humble greetings for a > > Merry Christmas and a Happy New Year > > Stefano > > PS - the bottom line is political correctness is a rather pedantic exercise! > > --- > 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 -- ___________________________________________________ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web: http://www.df.unibo.it/fismat/theory ___________________________________________________ From lhuang4 at ncsu.edu Mon Dec 28 18:55:26 2009 From: lhuang4 at ncsu.edu (Liangliang HUANG) Date: Mon, 28 Dec 2009 12:55:26 -0500 Subject: [Pw_forum] NEB convergence problem, how to clean up extrapolation files? Message-ID: Hi, One of my neb calculations failed with the warning message in the out file, saying: "WARNING: scf convergence NOT achieved on image 5 cleaning-up extrapolation files" I assume that I shall delete some files from the outdir folder where all intermediate files are stored. But what files I shall delete in order to restart the neb calculation? The image number in that calculation is 7, so in the outdir folder I have subfolders named top_1, top_2, top_3, top_4, top_5, top_6, top_7, and also some other files, namely, top.broyden, top.path0, top.path1, top.path2, top.path3. Here 'top' is the prefix I set in the input control file. Thanks a lot in advance. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091228/fafc9222/attachment.htm From wangqj1 at 126.com Tue Dec 29 15:51:54 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Tue, 29 Dec 2009 22:51:54 +0800 (CST) Subject: [Pw_forum] about fermi level Message-ID: <3114153.572271262098314088.JavaMail.coremail@bj126app106.126.com> Dear all After I run scf(k-points,3*3*3)with 'smearing' , I increase the k-points (5*5*5)and run nscf with 'tetrahedra' in order to get DOS,but the fermi levels have little difference between the scf.out and nscf.out . Which I should select when plot DOS pictuce ? I have search in the forum ,but still haven't the correct answer . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091229/4c74a57e/attachment.htm From nkxirainbow at gmail.com Tue Dec 29 16:41:52 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 29 Dec 2009 23:41:52 +0800 Subject: [Pw_forum] about fermi level In-Reply-To: <3114153.572271262098314088.JavaMail.coremail@bj126app106.126.com> References: <3114153.572271262098314088.JavaMail.coremail@bj126app106.126.com> Message-ID: <21fbc4790912290741g3c89aaf9yaa3b9cab0517e42e@mail.gmail.com> Dear Wang: I think the fermi level of scf is more believable than that of nscf?? 2009/12/29 Q.J.Wang > Dear all > After I run scf(k-points,3*3*3)with 'smearing' , I increase the > k-points (5*5*5)and run nscf with 'tetrahedra' in order to get DOS,but the > fermi levels have little difference between the scf.out and nscf.out . > Which I should select when plot DOS pictuce ? > I have search in the forum ,but still haven't the correct answer . > -- > Best regards > > Q.J.Wang > > XiangTan University > > ____________________________________ 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/20091229/a903e87a/attachment.htm From dekura at cmp.sanken.osaka-u.ac.jp Tue Dec 29 17:30:28 2009 From: dekura at cmp.sanken.osaka-u.ac.jp (Haruhiko Dekura) Date: Wed, 30 Dec 2009 01:30:28 +0900 Subject: [Pw_forum] about fermi level In-Reply-To: <3114153.572271262098314088.JavaMail.coremail@bj126app106.126.com> References: <3114153.572271262098314088.JavaMail.coremail@bj126app106.126.com> Message-ID: Dear Wang I think that the Fermi-level obtained with nscf run reaches sufficient value only when the KS energy spectrum ( hence, also scf-potential ) is well converged in scf calculation. Therefore, in my guess, if you can see the convergence of KS levels as well as total energy against the increase of k-point (and width of smearing), the Fermi-level obtained with DOS calculation is more reliable value. So, I think the problem is depending on the convergency of your scf-potential after scf calculation. If you don't have converged one, both Fermi-levels ( obtained by scf or nscf run) so obtained are both not sufficient. What do you think ? Haruhiko Dekura PH.D. student Osaka university On 2009/12/29, at 23:51, Q.J.Wang wrote: > Dear all > After I run scf(k-points,3*3*3)with 'smearing' , I increase the k-points (5*5*5)and run nscf with 'tetrahedra' in order to get DOS,but the fermi levels have little difference between the scf.out and nscf.out . Which I should select when plot DOS pictuce ? > I have search in the forum ,but still haven't the correct answer . > -- > Best regards > > Q.J.Wang > > XiangTan University > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From quantumdft at gmail.com Wed Dec 30 02:56:35 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 30 Dec 2009 09:56:35 +0800 Subject: [Pw_forum] NEB convergence problem, how to clean up extrapolation files? In-Reply-To: References: Message-ID: <412f6c680912291756tc10ab82oec3b9a4ac255744d@mail.gmail.com> Dear paul, Is your system metallic or nonmetallic? I think your convergence problem is same as the the one of ordinary electronic structrue calculations. please check the PW.out in ./tmp folder to see more detail of your scf calculations for that image. you may change some parameters like k-points, occupations, smearing, nband, nspin etc. to overcome the convergence problem. hope helps by the way, please add your affiliation at the end of your mail. vega On Tue, Dec 29, 2009 at 1:55 AM, Liangliang HUANG wrote: > Hi, > > One of my neb calculations failed with the warning message in the out file, > saying: > "WARNING: scf convergence NOT achieved on image 5 > cleaning-up extrapolation files" > > I assume that I shall delete some files from the outdir folder where all > intermediate files are stored. But what files I shall delete in order to > restart the neb calculation? > > The image number in that calculation is 7, so in the outdir folder I have > subfolders named top_1, top_2, top_3, top_4, top_5, top_6, top_7, and also > some other files, namely, top.broyden, top.path0, top.path1, top.path2, > top.path3. Here 'top' is the prefix I set in the input control file. > > Thanks a lot in advance. > > Paul > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091230/e7a553c8/attachment.htm From wangqj1 at 126.com Wed Dec 30 09:43:01 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Wed, 30 Dec 2009 16:43:01 +0800 (CST) Subject: [Pw_forum] about fermi level In-Reply-To: References: Message-ID: <22034669.980261262162581312.JavaMail.coremail@bj126app104.126.com> Dear Haruhiko Dekura >Message: 3 >Date: Wed, 30 Dec 2009 01:30:28 +0900 >From: Haruhiko Dekura >Subject: Re: [Pw_forum] about fermi level >To: PWSCF Forum >Message-ID: > >Content-Type: text/plain; charset=us-ascii > >Dear Wang > >I think that the Fermi level obtained with nscf run reaches sufficient value only when the KS energy spectrum ( hence, also scf-potential ) is well converged in scf calculation. How to judge the KS energy spectrum is well converged or not in scf calculation ? Can you give me special examples or make some elaborate on this ? what should I do when encounter this problem ? I found many pwscf users encounter the same problem and they don't know which fermi level is used to plot DOS when fermi level is different between scf.out and nscf.out. Thank you very much for you help ! >Therefore, in my guess, if you can see the convergence of KS levels as well as total energy against the increase of k-point (and width of smearing), the Fermi-level obtained with DOS calculation is more reliable value. So, I think the problem is depending on the convergency of your scf-potential after scf calculation. If you don't have converged one, both Fermi-levels ( obtained by scf or nscf run) so obtained are both not sufficient. >What do you think ? > > >Haruhiko Dekura > >PH.D. student >Osaka university > > >On 2009/12/29, at 23:51, Q.J.Wang wrote: > >> Dear all >> After I run scf(k-points,3*3*3)with 'smearing' , I increase the k-points (5*5*5)and run nscf with 'tetrahedra' in order to get DOS,but the fermi levels have little difference between the scf.out and nscf.out . Which I should select when plot DOS pictuce ? >> I have search in the forum ,but still haven't the correct answer . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091230/a00b28b0/attachment.htm From siyouber at yahoo.fr Wed Dec 30 10:56:17 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Wed, 30 Dec 2009 09:56:17 +0000 (GMT) Subject: [Pw_forum] selection in XcrysDen Message-ID: <621883.71693.qm@web26507.mail.ukl.yahoo.com> Dear all, Happy new year in advance, I would like to know if it is possible to select only one part of the structure displayed by Xcrysden and print only this, instead of a certain number of unit cell? Thanks very much for your kind help ******************************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaound? I-Cameroon ***************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091230/21268a14/attachment.htm From huang87 at purdue.edu Wed Dec 30 19:16:39 2009 From: huang87 at purdue.edu (Zhen Huang) Date: Wed, 30 Dec 2009 13:16:39 -0500 Subject: [Pw_forum] A question about force constants calculation output Message-ID: <7337ea900912301016p45fc5b1if734acd3a42f3a1@mail.gmail.com> Dear PWSCF users- I am a little bit confused by the output from example06. ph.x calculation generated files alas.dynX where X goes from 0 to 8. In the file alas.dyn0 it gives the k points. Seems in the other dynX files for example .dyn1 it gives force constants of q=(0.0, 0.0, 0.0) and .dyn2 gives force constants of q=(-0.25 0.25 -0.25), (0.25 0.25 0.25), ( 0.25 -0.25 -0.25), and such. One of the dynmical matrix is shown below. On the other hand, matdyn.x also give force constants file alas444.fc which is also partialy attached. What is the T matrix and Matrix 1 and 2 labeled below. Also, the questions are what is 4 4 4 representing the the force constants information part labeled below, what does the 1 1 1 1 mean on the second line and also what is the meaning of the index 2 1 1 -6.26636620736E-03 (for example), I assume -6.266e-03 is the force constants but what is 2 1 1. If the forth column is the force constants why it is different from Ph.x calcualtion's output. One more question, if I want to look at the force constants between a unit cell and its closest nearest neibhor unit cell do I look at the dynX output with k=(0, -1, 0), (-1, 0, 0) and such and second nearest unit cells will be in dynX of k=(0, -.5, 0), (-.5, 0, 0)? Thanks for your help. Have a merry christmas and happy new year. $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Dynamical Matrix from Ph.x calcualtion of example06 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Dynamical Matrix in cartesian axes q = ( 0.000000000 0.000000000 0.000000000 ) 1 1 0.21172298 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21172298 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21172298 0.00000000 1 2 -0.21171370 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.21171370 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.21171370 0.00000000 2 1 -0.21171370 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.21171370 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.21171370 0.00000000 2 2 0.21201035 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21201035 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21201035 0.00000000 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ alas444.fc $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ T Matrix T 13.7429074 0.0000000 0.0000000 0.0000000 13.7429074 0.0000000 0.0000000 0.0000000 13.7429074 $$$$$$$$$$$$$$$$$$$$$ Matrix 1 and 2 1 2.5582692 0.0000000 0.0000000 0.0000000 2.5582692 0.0000000 0.0000000 0.0000000 2.5582692 2 -2.5582692 0.0000000 0.0000000 0.0000000 -2.5582692 0.0000000 0.0000000 0.0000000 -2.5582692 $$$$$$$$$$$$$$$$$$$$$ Force Constants Infromation 4 4 4 1 1 1 1 1 1 1 2.24392881916E-01 2 1 1 -6.26636620736E-03 3 1 1 6.76999450859E-05 4 1 1 -6.26636620736E-03 1 2 1 1.16718256113E-02 2 2 1 -6.20697521626E-04 3 2 1 -2.58577048375E-04 4 2 1 -6.26636620736E-03 1 3 1 4.19167726130E-03 2 3 1 -6.20697521626E-04 3 3 1 6.76999450859E-05 4 3 1 -6.20697521626E-04 1 4 1 1.16718256113E-02 2 4 1 -6.26636620736E-03 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Best Regards ------- Zhen (Alex) Huang Ph.D. Student Nanoscale Transport Research Group Laboratory for Computational Methods in Emerging Technologies Cooling Technologies Research Center School of Mechanical Engineering Purdue University Tel: 765 237 9733 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091230/08ad3d95/attachment.htm From m.abbasnejad at gmail.com Wed Dec 30 21:23:13 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 30 Dec 2009 23:53:13 +0330 Subject: [Pw_forum] question about matdyn.x Message-ID: <7699a1950912301223s76b358c9i34ec7ba372586e2a@mail.gmail.com> Dear all, Would you please tell me what the coordination is for the vibrating atoms in the output file of matdyn.x (matdyn.mode) and also those in the dynmat.out of dynmat.x. In fact I searched through the forum but I couldn't find my answer exactly. Thanks in advance. Merry Christmas and happy new year! **** -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091230/438ba936/attachment.htm