From cjobrien at ncsu.edu Tue Jun 1 02:05:35 2010 From: cjobrien at ncsu.edu (Christopher O'Brien) Date: Mon, 31 May 2010 20:05:35 -0400 Subject: [Pw_forum] My installation of Espresso 4.1/4.2 is not passing benchmarks Message-ID: <18A04F42-0B07-4089-BEEA-DA28A53A992C@ncsu.edu> To all: I have successfully compiled Quantum Espresso 4.2 with the GCC v4.5 (April 2010) on Mac 10.6.3 (64-bit kernel enabled). I have also installed 4.1 with ifort 9.0 on a red-had linux cluster. After completing the installation, I ran the benchmarks included in the 'test' folder of the distributions but saw many discrepancies. Perhaps the most disturbing were those involving simple SCF calculations such as: > Checking atom-pbe...discrepancy in pressure detected > Reference: -14.44, You got: -14.43 and > Checking atom-sigmapbe...discrepancy in pressure detected > Reference: -15.02, You got: -15.03 Also, large errors were reported for > Checking lda+U_gamma...discrepancy in number of scf iterations detected > Reference: 46, You got: 40 > discrepancy in force detected > Reference: 0.4682, You got: 0.4690 > discrepancy in pressure detected > Reference: 549.51, You got: 551.15 It seems that these discrepancies are due to more than numerical error. Is this a common problem? Is this related to the fact that the reference values are from v4.1a? Detailed error reports and my configuration file can be found at: https://sites.google.com/a/ncsu.edu/cjobrien/tutorials-and-guides/quantum-espresso-install-errors Thanks in advance. =================================================================== Christopher J. O'Brien Ph.D. Candidate Computational Materials Group Department of Materials Science & Engineering North Carolina State University ___________________________________________________________________ Please send all documents in PDF, HTML, RTF, DVI, PS or plain text. For Word documents: Please use the 'Save as PDF' option before sending. =================================================================== From amit99266 at rediffmail.com Tue Jun 1 05:59:49 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 1 Jun 2010 03:59:49 -0000 Subject: [Pw_forum] =?utf-8?q?Is_it_possible_to_calculate_the_phonon_dos_f?= =?utf-8?q?or_each_branch=3F?= In-Reply-To: <904455.56019.qm@web65709.mail.ac4.yahoo.com> Message-ID: <1275322092.S.4400.59607.H.TkV5dmF6IElzYWV2AFJlOiBbUHdfZm9ydW1dIElzIGl0IHBvc3NpYmxlIHRvIGNhbGN1bGF0ZSB0aGUgcGg_.f4-234-204.1275364789.27307@webmail.rediffmail.com> Dear Prof. Eyvaz Could you please upload/email the revised version of QHA? Warm Regards Amit On Mon, 31 May 2010 21:38:12 +0530 wrote >Hi Paolo, Sorry for the confusing note I have written. You are right, now QHA in QE v.4.2. In fact, I was talking about the possibility for branch-resolved phonon DOS, that is not included in the current version of QHA. But you know I am going top upgrade it (QHA), so i will include it, too. One reason for not including of this option was that I had no data (and do not have) to compare. Bests, Eyvaz. --- On Mon, 5/31/10, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Is it possible to calculate the phonon dos for each branch? > To: "PWSCF Forum" > Date: Monday, May 31, 2010, 6:26 PM > Eyvaz Isaev wrote: > > > No. But, in fact, it can be done using QHA, though it > is not included > > in its current version. > > v.4.2 of QE includes QHA, as far as I know > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/f9f22543/attachment-0001.htm From kyin.cn at gmail.com Tue Jun 1 06:34:06 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Tue, 1 Jun 2010 12:34:06 +0800 Subject: [Pw_forum] how to do fixed volume optimization References: <201005302041597969466@gmail.com>, <201005302109318285369@gmail.com>, <201005311614027962613@gmail.com>, <201005312028518289019@gmail.com> Message-ID: <201006011234043907165@gmail.com> Hi, Han It is well known that GGA functionals tend to overestimate lattice parameters, while LDAs underestimate. When performing phonon calculations, using the experimental volume of a crystal will give more accurate frequencies with experimental data than using theoretically predicted volume. So I need this functionality when doing "the volume scaling" computations. But I have a new idea. Maybe this could be done by replacement of "the volume scaling" by "pressure scaling" through an equation of state. ------------------ Kun Yin 2010-06-01 Hello Kun Yin, I'd appreciate if you would let me know why constant-volume vc-relax is "very useful" in high-pressure physics. Here is my response to your question. Do you really need to perform vc-relax at a "constant" volume, or do you just need the final volume to be very close to the initial volume? If the latter, you can do so by properly setting the target pressure (press), usually through good guessing, in your input file. Han > I see. Thanks for giving the answer, Paolo. I hope this easy-to-implement > functionality, doing 'vc-relax' at constant volume, will be done by some > enthusiastic guy, since it is very useful in some research such as the > study of high-pressure materials. > Kun Yin > 2010-05-31 > > > > short answer: no. It should be relatively easy to implement but > it has never been done, to the best of my knowledge. You can > use 'vc-relax' at costant pressure, though, and vary the > pressure, if I remember correctly > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy ******************************************************* Han Hsu, Ph.D. Postdoctoral Associate Department of Chemical Engineering & Materials Science University of Minnesota http://www.cems.umn.edu/~hsuhan ******************************************************* _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From sclauzer at sissa.it Tue Jun 1 08:05:02 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 1 Jun 2010 08:05:02 +0200 Subject: [Pw_forum] calculation with magnetic field In-Reply-To: References: <4C03D031.5090007@democritos.it> Message-ID: <7E9D7F31-A4D4-46D9-90AC-226C0A2E12B1@sissa.it> Il giorno 31/mag/10, alle ore 17:20, Arles V. Gil Rebaza ha scritto: > Hi Paolo.. what about B_field(3) variable in input_parameters.f90 > of QE 4.1.1 ..?? I think it corresponds to an option that was not working anymore, while the corresponding input variable had left there. I agree with Paolo that what you have in mind is not easily achievable and requires a theory beyond standard DFT (I think Vignale and Rasolt did something in that direction, and probably also other people: you may want to check what's in the literature before trying such kind of calculation). You you may do with the present QE implementation is to constrain the total magnetization of the system (to a value not necessarily corresponding to the ground state) and compute the total energy as a function of that. It still may give useful hints on the properties of your material. HTH GS > > Best > > 2010/5/31 Paolo Giannozzi > Arles V. Gil Rebaza wrote: > > > Hi QE user's, I would like calculate magnetic properties of Fe > alloys > > with a magnetic field applied... I can do this using QE..?? > > no, and I don't think it is easy > > 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 > > > > -- > ###---------> Arles V. <---------### > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/0e8f2be0/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100601/0e8f2be0/attachment.bin From archygu at gmail.com Tue Jun 1 08:08:58 2010 From: archygu at gmail.com (chenjie gu) Date: Tue, 1 Jun 2010 14:08:58 +0800 Subject: [Pw_forum] quenching input file example In-Reply-To: References: Message-ID: Hi Haldar, thank you so much, I will try. 2010/5/31 soumyajyoti haldar > Hi, > > you have to set ion_temperature = 'reduce-T' > it reduce the ionic temperature every "nraise" steps by the (negative) > value "delta_t" > so you need to set those also. > > For more details on the parameter pls refer to you directory>/Doc/INPUT_PW.txt , Name List IONS. > > Reagards, > > > > -- > Soumyajyoti Haldar > > Junior Research Fellow > Advance Computing Laboratory > Department of Physics, University of Pune > Ganeshkhind, Pune - 411007; INDIA > > Tel : (+91 20) 25692678; Extn # 408 > ~~~***~~~***~~~***~~~***~~~***~~~***~~~***~~~ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/c89ed34b/attachment.htm From baroni at sissa.it Tue Jun 1 08:08:56 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 1 Jun 2010 08:08:56 +0200 Subject: [Pw_forum] Is it possible to calculate the phonon dos for each branch? In-Reply-To: <904455.56019.qm@web65709.mail.ac4.yahoo.com> References: <904455.56019.qm@web65709.mail.ac4.yahoo.com> Message-ID: ando also (forgive my ignorance): what's the use of "branch resolved phonon DOS"'s? Stefano B On May 31, 2010, at 6:13 PM, Eyvaz Isaev wrote: > Hi Paolo, > > Sorry for the confusing note I have written. You are right, now QHA in QE v.4.2. > In fact, I was talking about the possibility for branch-resolved phonon DOS, that is not included in the current version of QHA. But you know I am going top upgrade it (QHA), so i will include it, too. One reason for not including of this option was that I had no data (and do not have) to compare. > > Bests, > Eyvaz. > > --- On Mon, 5/31/10, Paolo Giannozzi wrote: > >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] Is it possible to calculate the phonon dos for each branch? >> To: "PWSCF Forum" >> Date: Monday, May 31, 2010, 6:26 PM >> Eyvaz Isaev wrote: >> >>> No. But, in fact, it can be done using QHA, though it >> is not included >>> in its current version. >> >> v.4.2 of QE includes QHA, as far as I know >> >> P. >> -- >> Paolo Giannozzi, Democritos and University of Udine, Italy >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20100601/2560a3b7/attachment-0001.htm From baroni at sissa.it Tue Jun 1 08:11:21 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 1 Jun 2010 08:11:21 +0200 Subject: [Pw_forum] Computing Second order response In-Reply-To: <894050.23278.qm@web38803.mail.mud.yahoo.com> References: <894050.23278.qm@web38803.mail.mud.yahoo.com> Message-ID: what's the gap of the unperturbed system? SB On May 31, 2010, at 6:10 PM, loc duong ding wrote: > Dear all, > > I want calculated IR and Raman of nanoribbon. The problem is when the code calcualtion second order response, it is not convergence. > > This is the output: > > > Calling punch_plot_e > Writing on file drho > > Computing Pc [DH,Drho] |psi> > > Derivative coefficient: 0.001000 Threshold: 1.00E-12 > Non-scf u_k: avg # of iterations = 23.5 > Non-scf Du_k: avg # of iterations = 37.6 > > Dielectric constant from finite-differences > > ( 1.626169126 -0.012354543 0.000000672 ) > ( -0.012354543 1.773889718 -0.001492007 ) > ( 0.000000672 -0.001492007 1.106263603 ) > > Computing Second order response > > > iter # 1 av.it.: 10.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.194E+04 > > > iter # 2 av.it.: 15.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.509E+09 > > > iter # 3 av.it.: 15.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.134E+07 > > > iter # 4 av.it.: 12.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.986E+03 > > > iter # 5 av.it.: 11.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.693E+01 > > > iter # 6 av.it.: 14.3 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.269E+04 > > > iter # 7 av.it.: 13.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.154E+02 > > > iter # 8 av.it.: 12.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.631E+01 > > > iter # 9 av.it.: 11.5 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.136E+00 > > > iter # 10 av.it.: 10.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.116E+02 > > > iter # 11 av.it.: 10.0 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.598E+00 > > > iter # 12 av.it.: 9.3 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.220E+00 > > > iter # 13 av.it.: 10.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.416E+01 > > > iter # 14 av.it.: 10.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.340E+00 > > > iter # 15 av.it.: 10.0 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.648E+01 > > > iter # 16 av.it.: 11.0 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.214E+02 > > > iter # 17 av.it.: 12.3 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.152E+03 > > > iter # 18 av.it.: 12.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.314E-01 > > > iter # 19 av.it.: 12.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.538E+02 > > > iter # 20 av.it.: 11.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.744E+01 > > > iter # 21 av.it.: 13.0 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.150E+04 > > > iter # 22 av.it.: 13.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.426E+03 > > > iter # 23 av.it.: 12.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.238E+03 > > > iter # 24 av.it.: 17.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.143E+07 > > > iter # 25 av.it.: 15.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.118E+06 > > > iter # 26 av.it.: 18.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.122E+08 > > > iter # 27 av.it.: 19.3 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.361E+07 > > > iter # 28 av.it.: 19.5 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.447E+08 > > > iter # 29 av.it.: 22.5 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.186E+11 > > > iter # 30 av.it.: 23.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.390E+10 > > > iter # 31 av.it.: 25.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.538E+12 > > > iter # 32 av.it.: 25.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.231E+12 > > > iter # 33 av.it.: 27.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.105E+14 > > > iter # 34 av.it.: 30.5 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.700E+15 > > > iter # 35 av.it.: 31.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.228E+15 > > > iter # 36 av.it.: 31.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.362E+17 > > > iter # 37 av.it.: 34.0 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.201E+17 > > > iter # 38 av.it.: 35.8 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.245E+19 > > > iter # 39 av.it.: 38.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.370E+20 > > > iter # 40 av.it.: 37.7 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.172E+20 > > > iter # 41 av.it.: 41.2 > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.300E+22 > > Could you give me some instructions to overcome this problem? > > I appreciate to all your helps. > > sincerely, > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > _______________________________________________ > 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/20100601/1c234aa5/attachment.htm From hqzhou at nju.edu.cn Tue Jun 1 09:05:04 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 1 Jun 2010 15:05:04 +0800 Subject: [Pw_forum] My installation of Espresso 4.1/4.2 is not passingbenchmarks References: <18A04F42-0B07-4089-BEEA-DA28A53A992C@ncsu.edu> Message-ID: <21CF29A240904853BD0D889BE8B34C4E@solarflare> If I were you, I'll ignore such minor differences in calculated pressure. In fact, you should feel lucky that you got less number of SCF iterations (^o^) Zhou Huiqun @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Christopher O'Brien" To: Sent: Tuesday, June 01, 2010 8:05 AM Subject: [Pw_forum] My installation of Espresso 4.1/4.2 is not passingbenchmarks > To all: > I have successfully compiled Quantum Espresso 4.2 with the GCC v4.5 (April > 2010) on Mac 10.6.3 (64-bit kernel enabled). I have also installed 4.1 > with ifort 9.0 on a red-had linux cluster. After completing the > installation, I ran the benchmarks included in the 'test' folder of the > distributions but saw many discrepancies. Perhaps the most disturbing were > those involving simple SCF calculations such as: >> Checking atom-pbe...discrepancy in pressure detected >> Reference: -14.44, You got: -14.43 > and >> Checking atom-sigmapbe...discrepancy in pressure detected >> Reference: -15.02, You got: -15.03 > Also, large errors were reported for >> Checking lda+U_gamma...discrepancy in number of scf iterations detected >> Reference: 46, You got: 40 >> discrepancy in force detected >> Reference: 0.4682, You got: 0.4690 >> discrepancy in pressure detected >> Reference: 549.51, You got: 551.15 > > It seems that these discrepancies are due to more than numerical error. Is > this a common problem? Is this related to the fact that the reference > values are from v4.1a? > > Detailed error reports and my configuration file can be found at: > https://sites.google.com/a/ncsu.edu/cjobrien/tutorials-and-guides/quantum-espresso-install-errors > > Thanks in advance. > =================================================================== > Christopher J. O'Brien > Ph.D. Candidate > Computational Materials Group > Department of Materials Science & Engineering > North Carolina State University > ___________________________________________________________________ > Please send all documents in PDF, HTML, RTF, DVI, PS or plain text. > For Word documents: Please use the 'Save as PDF' option before sending. > =================================================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mambom1902 at yahoo.com Tue Jun 1 09:32:32 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 1 Jun 2010 00:32:32 -0700 (PDT) Subject: [Pw_forum] Raman intensities Message-ID: <121035.22899.qm@web38805.mail.mud.yahoo.com> Dear all, I get the result of cross section of Raman and IR. The results is: mode [cm-1] [THz] IR Raman depol 1 -49.14 -1.4731 0.0052 28548.6002 0.3331 2 -1.11 -0.0334 0.0047 27.1463 0.3346 3 -0.96 -0.0287 0.0000 96.7501 0.3334 4 -0.15 -0.0044 0.0000 225.2733 0.3332 5 40.15 1.2036 0.0000 121.0591 0.4037 6 112.68 3.3779 0.0000 185.3034 0.3349 7 128.41 3.8497 0.0000 4.7151 0.3694 8 142.59 4.2746 0.0000 10709.2105 0.7499 9 181.32 5.4357 0.0000 243179.7169 0.7500 10 246.83 7.3996 0.0000 210.2380 0.3358 11 248.15 7.4393 0.0000 946.7975 0.3334 12 257.43 7.7176 0.0006 134557.9663 0.7305 13 277.21 8.3106 181.7555 35.8045 0.5489 14 296.65 8.8934 0.0123 212096.8703 0.7500 15 316.99 9.5031 0.0000 3319515.9438 0.3347 16 322.75 9.6759 0.0002 392852053.6176 0.3331 17 346.79 10.3965 0.0000 9223.9833 0.3332 18 399.65 11.9812 0.0007 57428.3543 0.3331 19 433.43 12.9938 223.9962 31.6281 0.3367 20 459.73 13.7823 0.0000 408.3847 0.3335 21 493.49 14.7944 0.0008 7524.6853 0.3331 22 494.82 14.8344 0.0000 4.6699 0.3366 23 552.96 16.5773 0.0019 4612.5049 0.7498 24 601.32 18.0269 0.0178 100.2209 0.3333 25 657.09 19.6990 0.0005 13086.6164 0.7182 26 691.87 20.7417 0.0221 147783.1907 0.7500 27 712.36 21.3559 316.9795 20.0803 0.4981 28 757.22 22.7009 0.0000 3.7927 0.3535 29 810.51 24.2982 0.0002 49601.6103 0.6321 30 829.99 24.8823 0.0001 378123798.5341 0.3331 31 889.73 26.6732 0.0040 261989.5029 0.7500 32 900.13 26.9851 72.6389 226.1128 0.3424 33 960.43 28.7928 0.2552 163055.4564 0.3333 34 1058.56 31.7346 1.4990 2339.9652 0.3335 35 1094.46 32.8109 0.0003 43125138.6735 0.3333 36 1176.60 35.2734 1.0137 3874332.1531 0.7500 37 1204.18 36.1002 0.1132 71069.5276 0.3333 38 1211.41 36.3170 6485.3035 217.2241 0.6163 39 1264.93 37.9215 79.8659 277323.1409 0.3342 40 1267.13 37.9874 0.00405894499335.7395 0.3333 41 1304.63 39.1116 0.0243 6531558.0536 0.7500 42 1315.15 39.4271 0.0000*************** 0.3334 43 1320.93 39.6002 0.0155 56014.3750 0.7489 44 1340.74 40.1941 173.8033 2011.1932 0.4036 45 1377.51 41.2964 0.0000*************** 0.3333 46 1425.62 42.7388 0.4155 2966610.7786 0.3333 47 1444.87 43.3159 641.8946 1306.3132 0.6139 48 1463.04 43.8606 0.3417 2346744.2359 0.7500 49 1470.38 44.0805 0.0072 1649073.1055 0.3333 50 1673.43 50.1678 0.00053292427777.4092 0.3332 51 1710.56 51.2809 0.6754 361223.8840 0.3333 52 1770.87 53.0891 0.0002*************** 0.3333 53 1902.37 57.0314 0.6005 525782.3731 0.3333 54 2057.64 61.6862 0.0000*************** 0.3333 The result of raman is strange with *******? Is it because the value of raman intensities too large? How can I solve this problem? I wonder another thing is that the raman intensities is strongly dependent on laser direction. What is the meaning of cross section in this calculation? I appreciate to all your instructions. Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From nkxirainbow at gmail.com Tue Jun 1 10:03:08 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 1 Jun 2010 16:03:08 +0800 Subject: [Pw_forum] Raman intensities In-Reply-To: <121035.22899.qm@web38805.mail.mud.yahoo.com> References: <121035.22899.qm@web38805.mail.mud.yahoo.com> Message-ID: Dear Loc Duong Dinh: First of all, there are four modes which are below zero:-49, -1,-0.9, -0.15 cm^-1 Are you sure it is right? The raman intensities is realy dependent on geometry configuration. The cross section is base on PRB 54, 7830 (1996) and refs quoted therein. Searching in the maillist, you can get more information. -- ____________________________________ 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/20100601/ea4d507e/attachment.htm From fwshuchao111 at gmail.com Tue Jun 1 11:14:26 2010 From: fwshuchao111 at gmail.com (Weyl Fang) Date: Tue, 1 Jun 2010 17:14:26 +0800 Subject: [Pw_forum] Phonon frequency calculation Message-ID: <4C04CF72.00001A.02028@FANGWEI-PC> Dear all, When I used the QE 4.1.2 to calculate the phonon frequency of the CO adsorbed on the TiO2 surface, I came with some problem. When I finished the self-consistent calculation, I continued to run the ph.x. But there is some problem with the calculation, the program stopped. The error message is "third order derivatives not implemented with GGA". Does this message mean I can't use GGA to calculate the phonon frequency or others meaning? Can anyone point me into the right direction? Best wishes Wei FANG Graduate student in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ******************************************************* Email: fwshuchao111 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/20100601/9f373587/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 46417 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100601/9f373587/attachment-0001.gif From nnlinh at sissa.it Tue Jun 1 11:39:01 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Tue, 01 Jun 2010 11:39:01 +0200 Subject: [Pw_forum] Phonon frequency calculation In-Reply-To: <4C04CF72.00001A.02028@FANGWEI-PC> References: <4C04CF72.00001A.02028@FANGWEI-PC> Message-ID: <4C04D535.50904@sissa.it> Weyl Fang wrote: > Dear all, > > When I used the QE 4.1.2 to calculate the phonon frequency of the CO > adsorbed on the TiO2 surface, I came with some problem. When I > finished the self-consistent calculation, I continued to run the ph.x. > But there is some problem with the calculation, the program stopped. > The error message is "third order derivatives not implemented with > GGA". Does this message mean I can't use GGA to calculate the phonon > frequency or others meaning? > No, ph.x works well with GGA. You should drop out two input parameters : "elop" and "lraman" or put them = .false. Hope this help, Linh > Can anyone point me into the right direction? > > Best wishes > > > Wei FANG > Graduate student in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ******************************************************* > > Email: fwshuchao111@ gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > > ********************************************************************* > > > > > FREE Animations for your email - by IncrediMail! Click Here! > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From amit99266 at rediffmail.com Tue Jun 1 13:13:37 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 1 Jun 2010 11:13:37 -0000 Subject: [Pw_forum] =?utf-8?q?Is_it_possible_to_calculate_the_phonon_dos_f?= =?utf-8?q?or_each_branch=3F?= In-Reply-To: Message-ID: <1275372418.S.14979.40096.H.WVN0ZWZhbm8gQmFyb25pAFJlOiBbUHdfZm9ydW1dIElzIGl0IHBvc3NpYmxlIHRvIGNhbGN1bGF0ZSB0aGU_.f4-234-227.1275390816.910@webmail.rediffmail.com> "branch resolved phonon DOS" can help to study the contribution of particular mode to (phonon derived) materials properties (e.g. vibration energy, internal energy, etc. ). Regards, Amit N. Harode On Tue, 01 Jun 2010 11:36:58 +0530 wrote >ando also (forgive my ignorance): what's the use of "branch resolved phonon DOS"'s?Stefano B On May 31, 2010, at 6:13 PM, Eyvaz Isaev wrote:Hi Paolo, Sorry for the confusing note I have written. You are right, now QHA in QE v.4.2. In fact, I was talking about the possibility for branch-resolved phonon DOS, that is not included in the current version of QHA. But you know I am going top upgrade it (QHA), so i will include it, too. One reason for not including of this option was that I had no data (and do not have) to compare. Bests, Eyvaz. --- On Mon, 5/31/10, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] Is it possible to calculate the phonon dos for each branch? To: "PWSCF Forum" Date: Monday, May 31, 2010, 6:26 PM Eyvaz Isaev wrote: No. But, in fact, it can be done using QHA, though it is not included in its current version. v.4.2 of QE includes QHA, as far as I know P. -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ---Stefano Baroni - SISSA&DEMOCRITOS National Simulation Center - Triestehttp://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'tsend me MS Word or PowerPoint attachmentsWhy? 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/d62b42fa/attachment.htm From vv0210 at gmail.com Tue Jun 1 16:21:19 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Tue, 1 Jun 2010 10:21:19 -0400 Subject: [Pw_forum] Query regarding Al2O3 system slab calculation Message-ID: Dear All, My final motivation is to simulate adsorption of several small molecules on Al2O3 slab. The strategy I am undertaking (and hence I have few questions) is below. Please correct me if I am wrong at any stage of my calculation. I want to get the ground state of the Al2O3 slab. In this regard, I got the unit cell of Al2O3 which is trigonal ( Space group R-3c, point group D3d, 30 atoms) . This is not the primitive unit cell (which is rhombhohedral and contain 10 atoms). The reason is to eventually simulate 0 0 1 surface. It seems that the structure consist of 2 basis atoms. The rest are defined by different symmetry operations for the point group of Al2O3. Is is possible to make use of symmetry operations and run the calculation on unit cell of Al2O3 by specifying only two basis atoms and then run slab calculation with 30 atoms? Or should I just create a 30 atom unit cell with vacuum along Z direction in a slab geometry and relax it? Best Regards, Vikas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/cb2e45e5/attachment.htm From baroni at sissa.it Tue Jun 1 16:33:28 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 1 Jun 2010 16:33:28 +0200 Subject: [Pw_forum] Is it possible to calculate the phonon dos for each branch? In-Reply-To: <1275372418.S.14979.40096.H.WVN0ZWZhbm8gQmFyb25pAFJlOiBbUHdfZm9ydW1dIElzIGl0IHBvc3NpYmxlIHRvIGNhbGN1bGF0ZSB0aGU_.f4-234-227.1275390816.910@webmail.rediffmail.com> References: <1275372418.S.14979.40096.H.WVN0ZWZhbm8gQmFyb25pAFJlOiBbUHdfZm9ydW1dIElzIGl0IHBvc3NpYmxlIHRvIGNhbGN1bGF0ZSB0aGU_.f4-234-227.1275390816.910@webmail.rediffmail.com> Message-ID: hmmmhh! On Jun 1, 2010, at 1:13 PM, Yamit wrote: > "branch resolved phonon DOS" can help to study the contribution of particular mode to (phonon derived) materials properties (e.g. vibration energy, internal energy, etc. ). > Regards, > Amit N. Harode > > On Tue, 01 Jun 2010 11:36:58 +0530 wrote > >ando also (forgive my ignorance): what's the use of "branch resolved phonon DOS"'s?Stefano B > On May 31, 2010, at 6:13 PM, Eyvaz Isaev wrote:Hi Paolo, > > Sorry for the confusing note I have written. You are right, now QHA in QE v.4.2. > In fact, I was talking about the possibility for branch-resolved phonon DOS, that is not included in the current version of QHA. But you know I am going top upgrade it (QHA), so i will include it, too. One reason for not including of this option was that I had no data (and do not have) to compare. > > Bests, > Eyvaz. > > --- On Mon, 5/31/10, Paolo Giannozzi wrote: > > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Is it possible to calculate the phonon dos for each branch? > To: "PWSCF Forum" > Date: Monday, May 31, 2010, 6:26 PM > Eyvaz Isaev wrote: > > No. But, in fact, it can be done using QHA, though it > is not included > in its current version. > > v.4.2 of QE includes QHA, as far as I know > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ---Stefano Baroni - SISSA&DEMOCRITOS National Simulation Center - Triestehttp://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'tsend me MS Word or PowerPoint attachmentsWhy? 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 --- 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/20100601/d7bb9592/attachment.htm From elie.moujaes at hotmail.co.uk Tue Jun 1 22:47:30 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 1 Jun 2010 21:47:30 +0100 Subject: [Pw_forum] start_q, last_q, start_irr, last_irr Message-ID: Dear all, I am trying to get the phonon dispersion of graphene by taking each q on its own and performing the necessary operations (i.e using start_q, last_q, start_irr, last_irr) then merging the points all together . Can anyone please explain to me more about these parameters. I read the INPUT_PH and the examples in GRID but did not actually understand what these mean..I got that irr is irreducible representation but how can one set these each time one runs the calculation for a q. Thanks ina dvance Elie Moujaes University of nottingham NG7 2RD Nottingham _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/f2adf684/attachment-0001.htm From eyvaz_isaev at yahoo.com Wed Jun 2 00:39:07 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 1 Jun 2010 15:39:07 -0700 (PDT) Subject: [Pw_forum] start_q, last_q, start_irr, last_irr Message-ID: <818298.75527.qm@web65716.mail.ac4.yahoo.com> Dear Elie, --- On Wed, 6/2/10, Elie Moujaes wrote: >I am trying to get the phonon dispersion of graphene by taking each q on >its own and performing the necessary operations (i.e using start_q, >last_q, start_irr, last_irr) then merging the points all together . Can >anyone please explain to me more about these parameters. I never used? start_irr, last_irr, but I use actively start_q and last_q parameters. After you get all dynX (including dyn0) files, just collect them in a directory and run q2r.x. start_q - q-point from which ph.x starts, last_q - up to this q-point from the list of q-points written in dyn0-file. I.e. if you have 12 q-points according to dyn0-file, then you can choose any combination, start_q=1, last_q=1 (usually this one is the Gamma point), or start_q=9, last_q=12 (calculate phonons for q-points from 9th to 12th), or any other combination you like (sure, last_q >= start_q). The same meaning for start_irr and last_irr, but for irreducible representations. >I read the INPUT_PH and the examples in GRID but did not actually >understand what these mean..I got that irr is irreducible representation >but how can one set these each time one runs the calculation for a q. Specify in ph.in files the next lines: ***** start_q=M last_q=N start_irr=I1 last_irr=I2 If M=N, only irreducible representations (IrRep) in the range I1 - I2 will be calculated for a given (defined by M) q-point. By default, all IrRep will be calculated. So easy! Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From jtmullen at ncsu.edu Wed Jun 2 00:51:49 2010 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Tue, 01 Jun 2010 18:51:49 -0400 Subject: [Pw_forum] start_q, last_q, start_irr, last_irr In-Reply-To: References: Message-ID: <4C058F05.9020005@ncsu.edu> Dear Elie, If I understand you correctly, you want to run a series of separate calculations, one for each q in which you are interested. You can perform the calculations for one phonon per input file by setting ldisp=.false. and defining the q you need at the bottom of the file. For example title line &inputph tr2_ph=1.0d-12, prefix='gr', amass(1)=12.01070, . . . ldisp=.false. / 0.0000000 0.0000000 0.0000000 <---- q_x q_y q_z Here I have left out any other variable definitions like thresholds etc. You can then run 10, 20, 30 or however many phonons you need to make your dispersion curve. In this way, you should not need start_q, etc. Cheers Jeff Mullen North Carolina State University On 6/1/10 4:47 PM, Elie Moujaes wrote: > Dear all, > > I am trying to get the phonon dispersion of graphene by taking each q > on its own and performing the necessary operations (i.e using start_q, > last_q, start_irr, last_irr) then merging the points all together . > Can anyone please explain to me more about these parameters. I read > the INPUT_PH and the examples in GRID but did not actually understand > what these mean..I got that irr is irreducible representation but how > can one set these each time one runs the calculation for a q. > > Thanks ina dvance > > Elie Moujaes > University of nottingham > NG7 2RD > Nottingham > > ------------------------------------------------------------------------ > Get a new e-mail account with Hotmail - Free. Sign-up now. > > > > _______________________________________________ > 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/20100601/d85df8b8/attachment.htm From huazhorg at 163.com Wed Jun 2 03:31:18 2010 From: huazhorg at 163.com (=?gbk?B?wfW7qtbS?=) Date: Wed, 2 Jun 2010 09:31:18 +0800 (CST) Subject: [Pw_forum] about the parameter of "nat_todo" Message-ID: <186b744.bbe2.128f648afdb.Coremail.huazhorg@163.com> Dear all, I want to do phonon calculation on an adsorption system with symmetry. So Idid some test calculations. I did a test calculation on a system, say an molecule is adsorbed on a surface. I just want to calculate the vibrational frequencies of the molecule. I set "nat_todo" in the input file of ph.x, and set the list of indices of atoms of the molecule. But in the result file there is not phonons. I don't know what's wrong with it, and how to parameter in the input file of ph.x. Please help me! Thank you! Regards Huazhorg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/ea6745ca/attachment.htm From nnlinh at sissa.it Wed Jun 2 11:07:16 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 02 Jun 2010 11:07:16 +0200 Subject: [Pw_forum] Query regarding Al2O3 system slab calculation In-Reply-To: References: Message-ID: <4C061F44.7010000@sissa.it> Vikas Varshney wrote: > Dear All, > > My final motivation is to simulate adsorption of several small > molecules on Al2O3 slab. The strategy I am undertaking (and hence I > have few questions) is below. Please correct me if I am wrong at any > stage of my calculation. > > I want to get the ground state of the Al2O3 slab. In this regard, I > got the unit cell of Al2O3 which is trigonal ( Space group R-3c, point > group D3d, 30 atoms) . This is not the primitive unit cell (which is > rhombhohedral and contain 10 atoms). The reason is to eventually > simulate 0 0 1 surface. It seems that the structure consist of 2 basis > atoms. The rest are defined by different symmetry operations for the > point group of Al2O3. > > Is is possible to make use of symmetry operations and run the > calculation on unit cell of Al2O3 by specifying only two basis atoms > and then run slab calculation with 30 atoms? Or should I just create > a 30 atom unit cell with vacuum along Z direction in a slab geometry > and relax it? I am not clear about your question much. Anyway, I do the simulation of adsorption on the slab by form a supercell that stores the substrate + vacuum + adsorbate atoms. You can see in previous archives to understand how to form a supercell. Best, Linh > Best Regards, > Vikas > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From 1009ukumar at gmail.com Wed Jun 2 11:08:07 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Wed, 2 Jun 2010 14:38:07 +0530 Subject: [Pw_forum] Error in reading the Pseudopotentials taken from QE site? Message-ID: Dear QE users, I have problem with running of programs with pseudopotentials taken from QE site. error is : %%%%%%%%% task # 0 from readpp : error # 29 file ./Si.pbe-rrkj.UPF not found %%%%%%%%%%% However, when i use the PP of the pseudo directory, the program runs with no error. e.g. I did scf calculations of Si system., with PP Si.pbe-rrkj.UPF taken from QE site,http://www.quantum-espresso.org/pseudo/1.3/html/Si.html Input file is: &control calculation='scf', restart_mode='from_scratch', prefix='Si' pseudo_dir = './', outdir='./' / &system ibrav = 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc = 18.0 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.pbe-rrkj.UPF #[ Si.pz-vbc.UPF- works fine (present in "Pseudo")] ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 I don't know what could be the problem? Can it be a problem with compilation of QE package? I did the tests in "tests" to check the results with references therein, and they were ok with the references. With Regards, Sonu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/e55b0fec/attachment.htm From nnlinh at sissa.it Wed Jun 2 11:13:03 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 02 Jun 2010 11:13:03 +0200 Subject: [Pw_forum] Error in reading the Pseudopotentials taken from QE site? In-Reply-To: References: Message-ID: <4C06209F.1030909@sissa.it> sonu kumar wrote: > Dear QE users, > > I have problem with running of programs with pseudopotentials taken > from QE site. > error is : > %%%%%%%%% > task # 0 > from readpp : error # 29 > file ./Si.pbe-rrkj.UPF not found > %%%%%%%%%%% > > However, when i use the PP of the pseudo directory, the program runs > with no error. Are you sure that the pseudo_dir = './' is specified correctly... Seem to be the error comes from that QE does not find out the file of Si.pbe-rrkj.UPF Best Linh -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From vv0210 at gmail.com Wed Jun 2 15:14:31 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 2 Jun 2010 09:14:31 -0400 Subject: [Pw_forum] Query regarding Al2O3 system slab calculation In-Reply-To: <4C061F44.7010000@sissa.it> References: <4C061F44.7010000@sissa.it> Message-ID: Dear Lin, Thank you very much for your answer. I will definitely go through the archives now you have mentioned supercell approach. Best Regards, Vikas On Wed, Jun 2, 2010 at 5:07 AM, Ngoc Linh Nguyen wrote: > Vikas Varshney wrote: > > Dear All, > > > > My final motivation is to simulate adsorption of several small > > molecules on Al2O3 slab. The strategy I am undertaking (and hence I > > have few questions) is below. Please correct me if I am wrong at any > > stage of my calculation. > > > > I want to get the ground state of the Al2O3 slab. In this regard, I > > got the unit cell of Al2O3 which is trigonal ( Space group R-3c, point > > group D3d, 30 atoms) . This is not the primitive unit cell (which is > > rhombhohedral and contain 10 atoms). The reason is to eventually > > simulate 0 0 1 surface. It seems that the structure consist of 2 basis > > atoms. The rest are defined by different symmetry operations for the > > point group of Al2O3. > > > > Is is possible to make use of symmetry operations and run the > > calculation on unit cell of Al2O3 by specifying only two basis atoms > > and then run slab calculation with 30 atoms? Or should I just create > > a 30 atom unit cell with vacuum along Z direction in a slab geometry > > and relax it? > I am not clear about your question much. > Anyway, I do the simulation of adsorption on the slab by form a > supercell that stores the substrate + vacuum + adsorbate atoms. > You can see in previous archives to understand how to form a supercell. > > Best, > > Linh > > > > > > > > > > Best Regards, > > Vikas > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ----------------------------------------------------- > Nguyen Ngoc Linh, PhD Student > c/o: SISSA & CNR-INFM Democritos, > via Beirut 2-4, 34014 Trieste (Italy) > email: nnlinh at sissa.it > phone: +39 04 03787 319 > skype: ngoclinh84phys > ----------------------------------------------------- > "The physics is theoretical but the fun is real" > > > _______________________________________________ > 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/20100602/d6354d6c/attachment.htm From elie.moujaes at hotmail.co.uk Wed Jun 2 15:30:53 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 2 Jun 2010 14:30:53 +0100 Subject: [Pw_forum] start_q, last_q, start_irr, last_irr In-Reply-To: <818298.75527.qm@web65716.mail.ac4.yahoo.com> References: <818298.75527.qm@web65716.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz and Jeff, Thank you very much for your help. The reason I am doing this is that I am still trying to get the phonon dispersion but using other this new technique implemented in version 4.2 of QE. Everything is going well except that for q-0 (the Gamma point), I am getting an error from davcio : error # 20 error while reading from file The strange thing is that only for this point, I obtain such an error...I guess another guy posted that error earlier with the title Phonon calculations on the Grid. His name is shining star. Jeff, thanks for your suggestion as well. Actually i am still looking at the phono dispersion as a whole but found this technqieu which merges all files at the end and takes less time (I hope!). Regards Elie Moujaes University of Nottingham NG7 2RD UK > Date: Tue, 1 Jun 2010 15:39:07 -0700 > From: eyvaz_isaev at yahoo.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr > > Dear Elie, > > --- On Wed, 6/2/10, Elie Moujaes wrote: > >I am trying to get the phonon dispersion of graphene by taking each q on >its own and performing the necessary operations (i.e using start_q, >last_q, start_irr, last_irr) then merging the points all together . Can >anyone please explain to me more about these parameters. > > I never used start_irr, last_irr, but I use actively start_q and last_q parameters. After you get all dynX (including dyn0) files, just collect them in a directory and run q2r.x. > > start_q - q-point from which ph.x starts, last_q - up to this q-point from the list of q-points written in dyn0-file. I.e. if you have 12 q-points according to dyn0-file, then you can choose any combination, start_q=1, last_q=1 (usually this one is the Gamma point), or start_q=9, last_q=12 (calculate phonons for q-points from 9th to 12th), or any other combination you like (sure, last_q >= start_q). > > The same meaning for start_irr and last_irr, but for irreducible representations. > > >I read the INPUT_PH and the examples in GRID but did not actually >understand what these mean..I got that irr is irreducible representation >but how can one set these each time one runs the calculation for a q. > > Specify in ph.in files the next lines: > > ***** > start_q=M > last_q=N > start_irr=I1 > last_irr=I2 > > If M=N, only irreducible representations (IrRep) in the range I1 - I2 will be calculated for a given (defined by M) q-point. By default, all IrRep will be calculated. > > So easy! > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/bc22e50f/attachment-0001.htm From eyvaz_isaev at yahoo.com Wed Jun 2 16:25:20 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 2 Jun 2010 07:25:20 -0700 (PDT) Subject: [Pw_forum] start_q, last_q, start_irr, last_irr In-Reply-To: Message-ID: <750199.90898.qm@web65715.mail.ac4.yahoo.com> Dear Elie, This error is very famous one. Please read user_guide,pdf, page 56. Again, I have to note Subject is quite different? from the content. Bests, Eyvaz --- On Wed, 6/2/10, Elie Moujaes wrote: From: Elie Moujaes Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr To: pw_forum at pwscf.org Date: Wednesday, June 2, 2010, 5:30 PM Dear Eyvaz and Jeff, ? Thank you very much for your help.?The reason I am doing this is that I am still trying to get the phonon dispersion but using other this new technique implemented in version 4.2 of QE. Everything is going well except that for q-0 (the Gamma point), I am getting an error ? ???? from davcio : error #??????? 20 ???? error while reading from file ? The strange thing is that only for this point, I obtain such an error...I guess another guy posted that error earlier with the title Phonon calculations on the Grid. His?name is shining star.?? ? Jeff, thanks for your suggestion as well. Actually i am still looking at the phono dispersion as a whole but found this technqieu which merges all files at the end and takes less time (I hope!). ? ? Regards ? Elie Moujaes University of Nottingham NG7 2RD UK ? > Date: Tue, 1 Jun 2010 15:39:07 -0700 > From: eyvaz_isaev at yahoo.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr > > Dear Elie, > > --- On Wed, 6/2/10, Elie Moujaes wrote: > >I am trying to get the phonon dispersion of graphene by taking each q on >its own and performing the necessary operations (i.e using start_q, >last_q, start_irr, last_irr) then merging the points all together . Can >anyone please explain to me more about these parameters. > > I never used? start_irr, last_irr, but I use actively start_q and last_q parameters. After you get all dynX (including dyn0) files, just collect them in a directory and run q2r.x. > > start_q - q-point from which ph.x starts, last_q - up to this q-point from the list of q-points written in dyn0-file. I.e. if you have 12 q-points according to dyn0-file, then you can choose any combination, start_q=1, last_q=1 (usually this one is the Gamma point), or start_q=9, last_q=12 (calculate phonons for q-points from 9th to 12th), or any other combination you like (sure, last_q >= start_q). > > The same meaning for start_irr and last_irr, but for irreducible representations. > > >I read the INPUT_PH and the examples in GRID but did not actually >understand what these mean..I got that irr is irreducible representation >but how can one set these each time one runs the calculation for a q. > > Specify in ph.in files the next lines: > > ***** > start_q=M > last_q=N > start_irr=I1 > last_irr=I2 > > If M=N, only irreducible representations (IrRep) in the range I1 - I2 will be calculated for a given (defined by M) q-point. By default, all IrRep will be calculated. > > So easy! > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum Get a free e-mail account with Hotmail. Sign-up now. -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/95c2c4f2/attachment.htm From 1009ukumar at gmail.com Wed Jun 2 16:28:23 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Wed, 2 Jun 2010 19:58:23 +0530 Subject: [Pw_forum] solved:Error in reading the Pseudopotentials taken from QE site? Message-ID: Hi Dear all QE users, Problem is solved now. Thank you for your help! >sonu kumar wrote: > Dear QE users, > > I have problem with running of programs with pseudopotentials taken > from QE site. > error is : > %%%%%%%%% > task # 0 > from readpp : error # 29 > file ./Si.pbe-rrkj.UPF not found > %%%%%%%%%%% > > However, when i use the PP of the pseudo directory, the program runs > with no error. Are you sure that the pseudo_dir = './' is specified correctly... Seem to be the error comes from that QE does not find out the file of Si.pbe-rrkj.UPF Best Linh >> > -- Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/3f0a2024/attachment.htm From eyvaz_isaev at yahoo.com Wed Jun 2 16:28:52 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 2 Jun 2010 07:28:52 -0700 (PDT) Subject: [Pw_forum] davcio error In-Reply-To: <750199.90898.qm@web65715.mail.ac4.yahoo.com> Message-ID: <979885.93960.qm@web65715.mail.ac4.yahoo.com> Ooops, sorry I did not change the Subject in my previous mail. Now I did it. Bests, Eyvaz. --- On Wed, 6/2/10, Eyvaz Isaev wrote: From: Eyvaz Isaev Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr To: "PWSCF Forum" Date: Wednesday, June 2, 2010, 6:25 PM Dear Elie, This error is very famous one. Please read user_guide,pdf, page 56. Again, I have to note Subject is quite different? from the content. Bests, Eyvaz --- On Wed, 6/2/10, Elie Moujaes wrote: From: Elie Moujaes Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr To: pw_forum at pwscf.org Date: Wednesday, June 2, 2010, 5:30 PM Dear Eyvaz and Jeff, ? Thank you very much for your help.?The reason I am doing this is that I am still trying to get the phonon dispersion but using other this new technique implemented in version 4.2 of QE. Everything is going well except that for q-0 (the Gamma point), I am getting an error ? ???? from davcio : error #??????? 20 ???? error while reading from file ? The strange thing is that only for this point, I obtain such an error...I guess another guy posted that error earlier with the title Phonon calculations on the Grid. His?name is shining star.?? ? Jeff, thanks for your suggestion as well. Actually i am still looking at the phono dispersion as a whole but found this technqieu which merges all files at the end and takes less time (I hope!). ? ? Regards ? Elie Moujaes University of Nottingham NG7 2RD UK ? > Date: Tue, 1 Jun 2010 15:39:07 -0700 > From: eyvaz_isaev at yahoo.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr > > Dear Elie, > > --- On Wed, 6/2/10, Elie Moujaes wrote: > >I am trying to get the phonon dispersion of graphene by taking each q on >its own and performing the necessary operations (i.e using start_q, >last_q, start_irr, last_irr) then merging the points all together . Can >anyone please explain to me more about these parameters. > > I never used? start_irr, last_irr, but I use actively start_q and last_q parameters. After you get all dynX (including dyn0) files, just collect them in a directory and run q2r.x. > > start_q - q-point from which ph.x starts, last_q - up to this q-point from the list of q-points written in dyn0-file. I.e. if you have 12 q-points according to dyn0-file, then you can choose any combination, start_q=1, last_q=1 (usually this one is the Gamma point), or start_q=9, last_q=12 (calculate phonons for q-points from 9th to 12th), or any other combination you like (sure, last_q >= start_q). > > The same meaning for start_irr and last_irr, but for irreducible representations. > > >I read the INPUT_PH and the examples in GRID but did not actually >understand what these mean..I got that irr is irreducible representation >but how can one set these each time one runs the calculation for a q. > > Specify in ph.in files the next lines: > > ***** > start_q=M > last_q=N > start_irr=I1 > last_irr=I2 > > If M=N, only irreducible representations (IrRep) in the range I1 - I2 will be calculated for a given (defined by M) q-point. By default, all IrRep will be calculated. > > So easy! > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum Get a free e-mail account with Hotmail. Sign-up now. -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/f3c4017f/attachment.htm From paulatto at sissa.it Wed Jun 2 16:47:57 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 02 Jun 2010 16:47:57 +0200 Subject: [Pw_forum] My installation of Espresso 4.1/4.2 is not passing benchmarks In-Reply-To: <18A04F42-0B07-4089-BEEA-DA28A53A992C@ncsu.edu> References: <18A04F42-0B07-4089-BEEA-DA28A53A992C@ncsu.edu> Message-ID: On Tue, 01 Jun 2010 02:05:35 +0200, Christopher O'Brien wrote: > Perhaps the most disturbing were those involving simple SCF calculations > such as: >> Checking atom-pbe...discrepancy in pressure detected >> Reference: -14.44, You got: -14.43 >> Checking atom-sigmapbe...discrepancy in pressure detected >> Reference: -15.02, You got: -15.03 Dear Christopher, I wouldn't worry about such a discrepancy. Those test involve isolated atoms, where pressure is not really meaningful. In general, different optimized algebraic libraries (ATLAS, MKL, ACML...) use different tricks to increase performance but, as a trade-off, they are not alway consistent. This introduces some noise in the parts of the code that are more sensible to it, especially pressure. regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From modaresi.mohsen at gmail.com Wed Jun 2 19:34:48 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 2 Jun 2010 22:04:48 +0430 Subject: [Pw_forum] Unit cell problem Message-ID: Dear users, I work on ZnS, I faced with a problem. When i use a unit cell with 2 atom every things is OK and the bandstructure has a very good agreement with previous calculation but when i use bigger unit cell every things go wrong, Where is the problem of my calculation? I set my input files for a unit cell with 2 & 16 atoms at below. &SYSTEM ibrav = 2, celldm(1) =10.221527872, nbnd = 50, nat = 2, ntyp = 2, ecutwfc = 40 , ecutrho = 160 , occupations = 'fixed' , / &ELECTRONS conv_thr = 0.0000001 , diago_full_acc = .TRUE., / ATOMIC_SPECIES Zn 65.409 zn_pz.upf S 32.066 s_pz.upf ATOMIC_POSITIONS {angstrom} Zn 0.0 0.0 0.0 S 1.352 1.352 1.352 K_POINTS {automatic} 6 6 6 0 0 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% &SYSTEM ibrav = 2, celldm(1) =20.446835196 , nbnd = 90, nat = 16, ntyp = 2, ecutwfc = 40 , ecutrho = 160 , occupations = 'fixed' , / &ELECTRONS conv_thr = 0.0000001 , diago_full_acc = .TRUE., / ATOMIC_SPECIES Zn 65.409 zn_pz.upf S 32.066 s_pz.upf ATOMIC_POSITIONS {angstrom} Zn 0.0 0.0 0.0 Zn 2.705 2.705 0.0 Zn 2.705 0.0 2.705 Zn 5.409 2.705 2.705 Zn 0.0 2.705 2.705 Zn 2.705 5.409 2.705 Zn 2.705 2.705 5.409 Zn 5.409 5.409 5.409 S 1.352 1.352 1.352 S 4.057 4.057 1.352 S 4.057 1.352 4.057 S 6.762 4.057 4.057 S 1.352 4.057 4.057 S 4.057 6.762 4.057 S 4.057 4.057 6.762 S 6.762 6.762 6.762 K_POINTS {automatic} 5 5 5 0 0 0 Thanks for your answers Mohsen Modarsei Ferdowsi University, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/2c97eb5d/attachment.htm From eyvaz_isaev at yahoo.com Wed Jun 2 23:15:14 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 2 Jun 2010 14:15:14 -0700 (PDT) Subject: [Pw_forum] Unit cell problem Message-ID: <124046.72506.qm@web65709.mail.ac4.yahoo.com> Dear Mohsen, --- On Wed, 6/2/10, mohsen modaresi wrote: >I work on ZnS, I faced with a problem. When i use a unit cell with 2 atom >every things is OK and the bandstructure has a very good agreement with >previous calculation but when i use bigger unit cell every things go >wrong, Where is the problem of my calculation Unclear, what is wrong. If you mean you have different band structure for 2-atomic and 16-atomic unit cells, there is nothing wrong. As you used 2x2x2 supercell, your band structure is downfolded (now you have a BZ which is 8 times smaller that the original BZ). Instead, you can compare DOS, they should be the same for the formula unit. Bests, Eyvaz. ------------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From modaresi.mohsen at gmail.com Thu Jun 3 09:06:16 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 3 Jun 2010 03:06:16 -0400 Subject: [Pw_forum] Unit cell problem In-Reply-To: <124046.72506.qm@web65709.mail.ac4.yahoo.com> References: <124046.72506.qm@web65709.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz, Thanks for your reply. The DOS for a unit cell with 2 atoms has a good (NOT excelent agreement) with reported one but DOS for calculation with 2*2*2 unit cell has'nt ant resembelence to reported one. Mohsen Modaresi From giuseppe.mattioli at mlib.ism.cnr.it Thu Jun 3 12:23:17 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 3 Jun 2010 12:23:17 +0200 Subject: [Pw_forum] mkl problem Message-ID: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> Dear all I'm facing some problems with mkl & QE 4.2 on a linux cluster. In the case of 4.1, the configure script found (and still find...) the installed mkl 10.0.4.023 version and the make.sys looked like BLAS_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t LAPACK_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t QE 4.1 has been succesfully compiled and works fine. In the case of 4.2 the configure script does not find any external lapack or blas lib. I've tryed to use the './configure LIBDIRS=...' command but it still does not find any lapack or blas lib. I would like to manually link the libs (./configure LAPACK_LIBS=... BLAS_LIBS=...) , but I do not know what exactly I'm supposed to link... /opt/intel/mkl/10.0.4.023/lib/64 libguide.a libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.a libmkl_intel_sp2dp.so libmkl_sequential.so libguide.so libmkl_blacs_openmpi_lp64.a libmkl_gf_lp64.so libmkl_intel_thread.a libmkl.so libiomp5.a libmkl_blacs_sgimpt_ilp64.a libmkl_gnu_thread.a libmkl_intel_thread.so libmkl_solver.a libiomp5.so libmkl_blacs_sgimpt_lp64.a libmkl_gnu_thread.so libmkl_ipf.a libmkl_solver_ilp64.a libmkl_blacs_ilp64.a libmkl_cdft.a libmkl_i2p.so libmkl_lapack.a libmkl_solver_ilp64_sequential.a libmkl_blacs_intelmpi20_ilp64.a libmkl_cdft_core.a libmkl_intel_ilp64.a libmkl_lapack.so libmkl_solver_lp64.a libmkl_blacs_intelmpi20_lp64.a libmkl_core.a libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_solver_lp64_sequential.a libmkl_blacs_intelmpi_ilp64.a libmkl_core.so libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_i2p.so libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.a libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_blacs_lp64.a libmkl_gf_ilp64.so libmkl_intel_sp2dp.a libmkl_sequential.a or /opt/intel/mkl/10.0.4.023/lib/em64t libguide.a libmkl_blacs_openmpi_lp64.a libmkl_gnu_thread.a libmkl_lapack.so libmkl_solver_ilp64_sequential.a libguide.so libmkl_cdft.a libmkl_gnu_thread.so libmkl_mc.so libmkl_solver_lp64.a libiomp5.a libmkl_cdft_core.a libmkl_intel_ilp64.a libmkl_p4n.so libmkl_solver_lp64_sequential.a libiomp5.so libmkl_core.a libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_vml_def.so libmkl_blacs_ilp64.a libmkl_core.so libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_mc2.so libmkl_blacs_intelmpi20_ilp64.a libmkl_def.so libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_vml_mc.so libmkl_blacs_intelmpi20_lp64.a libmkl_em64t.a libmkl_intel_sp2dp.a libmkl_sequential.a libmkl_vml_p4n.so libmkl_blacs_intelmpi_ilp64.a libmkl_gf_ilp64.a libmkl_intel_sp2dp.so libmkl_sequential.so libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.so libmkl_intel_thread.a libmkl.so libmkl_blacs_lp64.a libmkl_gf_lp64.a libmkl_intel_thread.so libmkl_solver.a libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.so libmkl_lapack.a libmkl_solver_ilp64.a However, if I link the /acml/ifort64/lib/libacml.a libs (and it does not sound reasonable on a xeon cluster...), everything works fine... Any suggestion? Giuseppe -- ******************************************************** - 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: From rfaccio at fq.edu.uy Thu Jun 3 11:48:56 2010 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Thu, 3 Jun 2010 06:48:56 -0300 (UYT) Subject: [Pw_forum] mkl problem In-Reply-To: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <935c498c8614075c6676841aef519d79.squirrel@webmail.fq.edu.uy> Hi I faced almost the same problem but in a single QuadCore PC, I edited the make.sys file by hand and then it looks like as following. And it works! Regards Ricardo ------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__INTEL -D__FFTW FDFLAGS = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS = -I../include # MOD_FLAGS = flag used by f90 compiler to locate modules # Each Makefile defines the list of needed modules in MODFLAGS MOD_FLAG = -I # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = ifort #F90 = ifort CC = gcc F77 = ifort # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD = ifort LDFLAGS = LD_LIBS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a # BLAS_LIBS_SWITCH = internal BLAS_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_em64t BLAS_LIBS_SWITCH = internal # If you have nothing better, use the local copy : # LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a # LAPACK_LIBS_SWITCH = internal # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack -lmkl_sequential -lmkl_core -lmkl_intel_lp64 LAPACK_LIBS_SWITCH = internal SCALAPACK_LIBS = # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW in DFLAGS) FFT_LIBS = # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = # pgplot libraries (used by some post-processing tools) PGPLOT_LIBS = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv AR = ar ARFLAGS = ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify FLIB_TARGETS = all LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a ../Multigrid/mglib.a LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) # topdir for linking espresso libs with plugins TOPDIR = /home/rfaccio/espresso-4.2 > > Dear all > I'm facing some problems with mkl & QE 4.2 on a linux cluster. In the case > of > 4.1, the configure script found (and still find...) the installed mkl > 10.0.4.023 version and the make.sys looked like > > BLAS_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t > LAPACK_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t > > QE 4.1 has been succesfully compiled and works fine. > > In the case of 4.2 the configure script does not find any external lapack > or > blas lib. I've tryed to use the './configure LIBDIRS=...' command but it > still does not find any lapack or blas lib. I would like to manually link > the > libs (./configure LAPACK_LIBS=... BLAS_LIBS=...) , but I do not know what > exactly I'm supposed to link... > > /opt/intel/mkl/10.0.4.023/lib/64 > > libguide.a libmkl_blacs_openmpi_ilp64.a > libmkl_gf_lp64.a libmkl_intel_sp2dp.so libmkl_sequential.so > libguide.so libmkl_blacs_openmpi_lp64.a > libmkl_gf_lp64.so libmkl_intel_thread.a libmkl.so > libiomp5.a libmkl_blacs_sgimpt_ilp64.a > libmkl_gnu_thread.a libmkl_intel_thread.so libmkl_solver.a > libiomp5.so libmkl_blacs_sgimpt_lp64.a > libmkl_gnu_thread.so libmkl_ipf.a libmkl_solver_ilp64.a > libmkl_blacs_ilp64.a libmkl_cdft.a > libmkl_i2p.so > libmkl_lapack.a libmkl_solver_ilp64_sequential.a > libmkl_blacs_intelmpi20_ilp64.a libmkl_cdft_core.a > libmkl_intel_ilp64.a libmkl_lapack.so libmkl_solver_lp64.a > libmkl_blacs_intelmpi20_lp64.a libmkl_core.a > libmkl_intel_ilp64.so libmkl_scalapack.a > libmkl_solver_lp64_sequential.a > libmkl_blacs_intelmpi_ilp64.a libmkl_core.so > libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_i2p.so > libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.a > libmkl_intel_lp64.so libmkl_scalapack_lp64.a > libmkl_blacs_lp64.a libmkl_gf_ilp64.so > libmkl_intel_sp2dp.a libmkl_sequential.a > > or > > /opt/intel/mkl/10.0.4.023/lib/em64t > > libguide.a libmkl_blacs_openmpi_lp64.a > libmkl_gnu_thread.a libmkl_lapack.so > libmkl_solver_ilp64_sequential.a > libguide.so libmkl_cdft.a > libmkl_gnu_thread.so libmkl_mc.so libmkl_solver_lp64.a > libiomp5.a libmkl_cdft_core.a > libmkl_intel_ilp64.a libmkl_p4n.so > libmkl_solver_lp64_sequential.a > libiomp5.so libmkl_core.a > libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_vml_def.so > libmkl_blacs_ilp64.a libmkl_core.so > libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_mc2.so > libmkl_blacs_intelmpi20_ilp64.a libmkl_def.so > libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_vml_mc.so > libmkl_blacs_intelmpi20_lp64.a libmkl_em64t.a > libmkl_intel_sp2dp.a libmkl_sequential.a libmkl_vml_p4n.so > libmkl_blacs_intelmpi_ilp64.a libmkl_gf_ilp64.a > libmkl_intel_sp2dp.so libmkl_sequential.so > libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.so > libmkl_intel_thread.a libmkl.so > libmkl_blacs_lp64.a libmkl_gf_lp64.a > libmkl_intel_thread.so libmkl_solver.a > libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.so > libmkl_lapack.a > libmkl_solver_ilp64.a > > However, if I link the /acml/ifort64/lib/libacml.a libs (and it does not > sound > reasonable on a xeon cluster...), everything works fine... > > Any suggestion? > > Giuseppe > > -- > ******************************************************** > - 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: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Thu Jun 3 18:53:58 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 3 Jun 2010 09:53:58 -0700 (PDT) Subject: [Pw_forum] Unit cell problem In-Reply-To: Message-ID: <85070.17885.qm@web65708.mail.ac4.yahoo.com> Dear Mohsen, --- On Thu, 6/3/10, mohsen modaresi wrote: > The DOS for a unit cell with 2 atoms has a good (NOT > excelent agreement) with reported one but DOS for calculation with > 2*2*2 unit cell has'nt ant resembelence to reported one. This might mean that you have something different structures. Ideal 2-atomic and 32-atomic supercell should have the same DOS per formula unit, the same shape. Check your supercell construction. Bests, Eyvaz. IFM, Linkoping University, Sweden From modaresi.mohsen at gmail.com Thu Jun 3 22:26:01 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 4 Jun 2010 00:56:01 +0430 Subject: [Pw_forum] Unit cell problem In-Reply-To: <85070.17885.qm@web65708.mail.ac4.yahoo.com> References: <85070.17885.qm@web65708.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz, After increase of K-points, Ecut and nbnd for a unit cell with 16 atoms, DOS problem solved and i get the same DOS for two structure. Is there any relation between the bandstructure for these two situations? Sincerely yours, Mohsen Modaresi Ferdowsi University of Mashhad, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/58668e33/attachment.htm From payam.norouzzadeh at gmail.com Fri Jun 4 06:07:39 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Fri, 4 Jun 2010 08:37:39 +0430 Subject: [Pw_forum] overlap of atoms Message-ID: Hello all I am working on a Clathrate type VIII with group space 217. I calculated the atom coordinates based on the relevant Wyckoff positions and my results are in accordance to reported values in literature but the I have been met with error messages about overlap of atoms while I tried to relax the system. How can I fix the problem? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/3447eef8/attachment.htm From 1009ukumar at gmail.com Fri Jun 4 07:38:09 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Fri, 4 Jun 2010 11:08:09 +0530 Subject: [Pw_forum] Phonons with non-collinear magnetism ? Message-ID: Dear all QE users, Is it possible to do phonon calculations including the non-collinear magnetism using Quantum Espresso code ? Any suggestion would be helpful. With Regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/cbcfeb61/attachment.htm From gianluca.giovannetti at gmail.com Fri Jun 4 07:43:06 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Fri, 4 Jun 2010 07:43:06 +0200 Subject: [Pw_forum] occupancies of density matrix in LDA+U Message-ID: Dear All, i write you as i need to know the occupancies of d states in my calculations and i would like to do it by looking at the occupation matrix. i have made a self-consistent calculation with the following input file: FeSe &control calculation = 'scf' restart_mode = 'from_scratch' prefix = 'fese' tprnfor = .true. pseudo_dir = './' outdir = './' iprint = 2 / &system ibrav = 8 celldm(1) = 10.0852834932257 celldm(2) = 1.00000000000000 celldm(3) = 1.03521095322306 nat = 8 ntyp = 5 ecutwfc = 35.0 ecutrho = 350.0 nbnd = 120 occupations = 'smearing' smearing = 'methfessel-paxton' degauss = 0.01 nspin = 2 starting_magnetization(1) = -1.0 starting_magnetization(2) = 1.0 starting_magnetization(3) = -1.0 starting_magnetization(4) = 1.0 starting_magnetization(5) = 0.0 lda_plus_u =.true. lda_plus_u =.true. Hubbard_U(1) = 1.d-8 Hubbard_U(2) = 1.d-8 Hubbard_U(3) = 1.d-8 Hubbard_U(4) = 1.d-8 Hubbard_alpha(1) = 1.d-8 Hubbard_alpha(2) = 1.d-8 Hubbard_alpha(3) = 1.d-8 Hubbard_alpha(4) = 1.d-8 / &electrons conv_thr = 1.0d-8 diagonalization = 'cg' / ATOMIC_SPECIES Fe1 55.845 Fe.pbe-sp-van.UPF Fe2 55.845 Fe.pbe-sp-van.UPF Fe3 55.845 Fe.pbe-sp-van.UPF Fe4 55.845 Fe.pbe-sp-van.UPF Se 78.96 Se.pbe-van.UPF ATOMIC_POSITIONS { crystal } Fe1 0.00000000 0.50000000 0.00000000 Fe2 1.00000000 0.00000000 0.00000000 Fe3 0.50000000 0.50000000 0.00000000 Fe4 0.50000000 0.00000000 0.00000000 Se 0.24999979 0.74999981 0.73480000 Se 0.75000021 0.74999981 0.26520000 Se 0.75000021 0.25000019 0.73480000 Se 0.24999979 0.25000019 0.26520000 K_POINTS {automatic} 10 10 8 0 0 0 Calculations are fine. As you can see: (i) Fe-Fe bonds are along x and y axes so i`m in the correct framework for calling d states as they are, (ii) i used U=0 to have printed the occupation matrix calculated in LDA+U scheme. In the output file of QE i can read: ------------------------------------------------------------------------------------------------------------- atom 4 spin 1 eigenvalues: 0.9283366 0.9383877 0.9483978 0.9712519 0.9740784 eigenvectors 1 -0.1720270 0.0000000 0.0000000 -0.9850922 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 -1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 0.0000000 -1.0000000 5 -0.9850922 0.0000000 0.0000000 0.1720270 0.0000000 occupations 0.973 0.000 0.000 -0.008 0.000 0.000 0.938 0.000 0.000 0.000 0.000 0.000 0.948 0.000 0.000 -0.008 0.000 0.000 0.930 0.000 0.000 0.000 0.000 0.000 0.971 atom 4 spin 2 eigenvalues: 0.3553238 0.3753074 0.4625234 0.5670451 0.6892263 eigenvectors 1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 2 0.0000000 -1.0000000 0.0000000 0.0000000 0.0000000 3 0.7516066 0.0000000 0.0000000 0.6596117 0.0000000 4 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 5 0.6596117 0.0000000 0.0000000 -0.7516066 0.0000000 occupations 0.561 0.000 0.000 -0.112 0.000 0.000 0.375 0.000 0.000 0.000 0.000 0.000 0.567 0.000 0.000 -0.112 0.000 0.000 0.591 0.000 0.000 0.000 0.000 0.000 0.355 ------------------------------------------------------------------------------------------------------------- what are these quantities? How can i extract the occupancies of d states for this data? What is the order (the relation between label of d state and its occupancy)? I want to make a table having how many electrons i have in z2, xz, yz, x2-y2, xy for up and down components. thank you in advance. ciao Gianluca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/a5160a1e/attachment.htm From dalcorso at sissa.it Fri Jun 4 09:35:06 2010 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 04 Jun 2010 09:35:06 +0200 Subject: [Pw_forum] Phonons with non-collinear magnetism ? In-Reply-To: References: Message-ID: <1275636906.3230.7.camel@dhcp-098.cm.sissa.it> On Fri, 2010-06-04 at 11:08 +0530, sonu kumar wrote: > Dear all QE users, > > Is it possible to do phonon calculations including the non-collinear > magnetism using Quantum Espresso code ? > What is implemented in PH is written at the beginning of the PH/phonon.f90 routine and will be updated when new features will be implemented. ! ... Presently implemented: ! ... dynamical matrix (q/=0) NC [4], US [4], PAW [4] ! ... dynamical matrix (q=0) NC [5], US [5], PAW [4] ! ... dielectric constant NC [5], US [5], PAW [4] ! ... born effective charges NC [5], US [5], PAW [4] ! ... polarizability (iu) NC [2], US [2] ! ... elctron-phonon NC [3], US [3] ! ... electro-optic NC [1] ! ... raman tensor NC [1] ! ! NC = norm conserving pseudopotentials ! US = ultrasoft pseudopotentials ! PAW = projector augmented-wave ! [1] LDA, [2] [1]+GGA, [3] [2]+LSDA/sGGA, [4] [3]+Spin-orbit/nonmagnetic, ! [5] [4]+Spin-orbit/magnetic Noncollinear at gamma point should work. Spin/orbit nonmagnetic should work at gamma and finite q. Noncollinear magnetic at finite q is still experimental and there might be cases in which it is not working. The phonon interpolation (matdyn in particular) is not yet implemented in this case. HTH Andrea > Any suggestion would be helpful. > > > With Regards, > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > _______________________________________________ > 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 giuseppe.mattioli at mlib.ism.cnr.it Fri Jun 4 11:28:23 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 4 Jun 2010 11:28:23 +0200 Subject: [Pw_forum] mkl problem In-Reply-To: <935c498c8614075c6676841aef519d79.squirrel@webmail.fq.edu.uy> References: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> <935c498c8614075c6676841aef519d79.squirrel@webmail.fq.edu.uy> Message-ID: <201006041128.23658.giuseppe.mattioli@mlib.ism.cnr.it> Dear Ricardo It seems to work... But I would ask the developers why does the configure script not found any mkl even if they are in the path... Thank you very much Giuseppe On Thursday 03 June 2010 11:48:56 Ricardo Faccio wrote: > Hi > I faced almost the same problem but in a single QuadCore PC, I edited the > make.sys file by hand and then it looks like as following. > And it works! > Regards > Ricardo > ------------------------------------------------- > Dr. Ricardo Faccio > Prof. Adjunto de F?sica > Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA > Facultad de Qu?mica, Universidad de la Rep?blica > Av. Gral. Flores 2124, C.C. 1157 > C.P. 11800, Montevideo, Uruguay. > E-mail: rfaccio at fq.edu.uy > Phone: 598 2 924 98 59 > 598 2 929 06 48 > Fax: 598 2 9241906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > > # make.sys. Generated from make.sys.in by configure. > > # compilation rules > > .SUFFIXES : > .SUFFIXES : .o .c .f .f90 > > # most fortran compilers can directly preprocess c-like directives: use > # $(MPIF90) $(F90FLAGS) -c $< > # if explicit preprocessing by the C preprocessor is needed, use: > # $(CPP) $(CPPFLAGS) $< -o $*.F90 > # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o > # remember the tabulator in the first column !!! > > .f90.o: > $(MPIF90) $(F90FLAGS) -c $< > > # .f.o and .c.o: do not modify > > .f.o: > $(F77) $(FFLAGS) -c $< > > .c.o: > $(CC) $(CFLAGS) -c $< > > > # DFLAGS = precompilation options (possible arguments to -D and -U) > # used by the C compiler and preprocessor > # FDFLAGS = as DFLAGS, for the f90 compiler > # See include/defs.h.README for a list of options and their meaning > # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) > # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas > > DFLAGS = -D__INTEL -D__FFTW > FDFLAGS = $(DFLAGS) > > # IFLAGS = how to locate directories where files to be included are > # In most cases, IFLAGS = -I../include > > IFLAGS = -I../include > > # MOD_FLAGS = flag used by f90 compiler to locate modules > # Each Makefile defines the list of needed modules in MODFLAGS > > MOD_FLAG = -I > > # Compilers: fortran-90, fortran-77, C > # If a parallel compilation is desired, MPIF90 should be a fortran-90 > # compiler that produces executables for parallel execution using MPI > # (such as for instance mpif90, mpf90, mpxlf90,...); > # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) > # If you have a parallel machine but no suitable candidate for MPIF90, > # try to specify the directory containing "mpif.h" in IFLAGS > # and to specify the location of MPI libraries in MPI_LIBS > > MPIF90 = ifort > #F90 = ifort > CC = gcc > F77 = ifort > > # C preprocessor and preprocessing flags - for explicit preprocessing, > # if needed (see the compilation rules above) > # preprocessing flags must include DFLAGS and IFLAGS > > CPP = cpp > CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) > > # compiler flags: C, F90, F77 > # C flags must include DFLAGS and IFLAGS > # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate > syntax > > CFLAGS = -O3 $(DFLAGS) $(IFLAGS) > F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) > FFLAGS = -O2 -assume byterecl -g -traceback > > # compiler flags without optimization for fortran-77 > # the latter is NEEDED to properly compile dlamch.f, used by lapack > > FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback > > # Linker, linker-specific flags (if any) > # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty > > LD = ifort > LDFLAGS = > LD_LIBS = > > # External Libraries (if any) : blas, lapack, fft, MPI > > # If you have nothing better, use the local copy : > # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a > # BLAS_LIBS_SWITCH = internal > > BLAS_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_em64t > BLAS_LIBS_SWITCH = internal > > # If you have nothing better, use the local copy : > # LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a > # LAPACK_LIBS_SWITCH = internal > > # The following lapack libraries will be available in flib/ : > # ../flib/lapack.a : contains all needed routines > # ../flib/lapack_atlas.a: only routines not present in the Atlas library > # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! > # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order > > LAPACK_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack > -lmkl_sequential -lmkl_core -lmkl_intel_lp64 > LAPACK_LIBS_SWITCH = internal > > SCALAPACK_LIBS = > > # nothing needed here if the the internal copy of FFTW is compiled > # (needs -D__FFTW in DFLAGS) > > FFT_LIBS = > > # For parallel execution, the correct path to MPI libraries must > # be specified in MPI_LIBS (except for IBM if you use mpxlf) > > MPI_LIBS = > > # IBM-specific: MASS libraries, if available and if -D__MASS is defined in > FDFLAGS > > MASS_LIBS = > > # pgplot libraries (used by some post-processing tools) > > PGPLOT_LIBS = > > # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv > > AR = ar > ARFLAGS = ruv > > # ranlib command. If ranlib is not needed (it isn't in most cases) use > # RANLIB = echo > > RANLIB = ranlib > > # all internal and external libraries - do not modify > > FLIB_TARGETS = all > > LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a > ../iotk/src/libiotk.a ../Multigrid/mglib.a > LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) > $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) > > # topdir for linking espresso libs with plugins > TOPDIR = /home/rfaccio/espresso-4.2 > > > Dear all > > I'm facing some problems with mkl & QE 4.2 on a linux cluster. In the > > case of > > 4.1, the configure script found (and still find...) the installed mkl > > 10.0.4.023 version and the make.sys looked like > > > > BLAS_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t > > LAPACK_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t > > > > QE 4.1 has been succesfully compiled and works fine. > > > > In the case of 4.2 the configure script does not find any external lapack > > or > > blas lib. I've tryed to use the './configure LIBDIRS=...' command but it > > still does not find any lapack or blas lib. I would like to manually link > > the > > libs (./configure LAPACK_LIBS=... BLAS_LIBS=...) , but I do not know what > > exactly I'm supposed to link... > > > > /opt/intel/mkl/10.0.4.023/lib/64 > > > > libguide.a libmkl_blacs_openmpi_ilp64.a > > libmkl_gf_lp64.a libmkl_intel_sp2dp.so libmkl_sequential.so > > libguide.so libmkl_blacs_openmpi_lp64.a > > libmkl_gf_lp64.so libmkl_intel_thread.a libmkl.so > > libiomp5.a libmkl_blacs_sgimpt_ilp64.a > > libmkl_gnu_thread.a libmkl_intel_thread.so libmkl_solver.a > > libiomp5.so libmkl_blacs_sgimpt_lp64.a > > libmkl_gnu_thread.so libmkl_ipf.a libmkl_solver_ilp64.a > > libmkl_blacs_ilp64.a libmkl_cdft.a > > libmkl_i2p.so > > libmkl_lapack.a libmkl_solver_ilp64_sequential.a > > libmkl_blacs_intelmpi20_ilp64.a libmkl_cdft_core.a > > libmkl_intel_ilp64.a libmkl_lapack.so libmkl_solver_lp64.a > > libmkl_blacs_intelmpi20_lp64.a libmkl_core.a > > libmkl_intel_ilp64.so libmkl_scalapack.a > > libmkl_solver_lp64_sequential.a > > libmkl_blacs_intelmpi_ilp64.a libmkl_core.so > > libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_i2p.so > > libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.a > > libmkl_intel_lp64.so libmkl_scalapack_lp64.a > > libmkl_blacs_lp64.a libmkl_gf_ilp64.so > > libmkl_intel_sp2dp.a libmkl_sequential.a > > > > or > > > > /opt/intel/mkl/10.0.4.023/lib/em64t > > > > libguide.a libmkl_blacs_openmpi_lp64.a > > libmkl_gnu_thread.a libmkl_lapack.so > > libmkl_solver_ilp64_sequential.a > > libguide.so libmkl_cdft.a > > libmkl_gnu_thread.so libmkl_mc.so libmkl_solver_lp64.a > > libiomp5.a libmkl_cdft_core.a > > libmkl_intel_ilp64.a libmkl_p4n.so > > libmkl_solver_lp64_sequential.a > > libiomp5.so libmkl_core.a > > libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_vml_def.so > > libmkl_blacs_ilp64.a libmkl_core.so > > libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_mc2.so > > libmkl_blacs_intelmpi20_ilp64.a libmkl_def.so > > libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_vml_mc.so > > libmkl_blacs_intelmpi20_lp64.a libmkl_em64t.a > > libmkl_intel_sp2dp.a libmkl_sequential.a libmkl_vml_p4n.so > > libmkl_blacs_intelmpi_ilp64.a libmkl_gf_ilp64.a > > libmkl_intel_sp2dp.so libmkl_sequential.so > > libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.so > > libmkl_intel_thread.a libmkl.so > > libmkl_blacs_lp64.a libmkl_gf_lp64.a > > libmkl_intel_thread.so libmkl_solver.a > > libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.so > > libmkl_lapack.a > > libmkl_solver_ilp64.a > > > > However, if I link the /acml/ifort64/lib/libacml.a libs (and it does not > > sound > > reasonable on a xeon cluster...), everything works fine... > > > > Any suggestion? > > > > Giuseppe > > > > -- > > ******************************************************** > > - 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: > > _______________________________________________ > > 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 -- ******************************************************** - 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: From baroni at sissa.it Fri Jun 4 10:48:06 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 4 Jun 2010 10:48:06 +0200 Subject: [Pw_forum] Unit cell problem In-Reply-To: References: <85070.17885.qm@web65708.mail.ac4.yahoo.com> Message-ID: <7F5606AA-1015-468F-B72B-C8767053A150@sissa.it> On Jun 3, 2010, at 10:26 PM, mohsen modaresi wrote: > Dear Eyvaz, > After increase of K-points, Ecut and nbnd for a unit cell with 16 atoms, DOS problem solved and i get the same DOS for two structure. > Is there any relation between the bandstructure for these two situations? yes: they are the same (if wattched the right way: the Brillouin zones are different) S. > Sincerely yours, > Mohsen Modaresi > Ferdowsi University of Mashhad, Iran. > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/1aa1a905/attachment.htm From baroni at sissa.it Fri Jun 4 10:49:55 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 4 Jun 2010 10:49:55 +0200 Subject: [Pw_forum] overlap of atoms In-Reply-To: References: Message-ID: probably, the atoms do overlap and the structure that you have found is not as good as you think try to examine the structure with xcrysden (say), before feeding it into any actual calculation ... SB On Jun 4, 2010, at 6:07 AM, Payam Norouzzadeh wrote: > Hello all > > I am working on a Clathrate type VIII with group space 217. I calculated the atom coordinates based on the relevant Wyckoff positions and my results are in accordance to reported values in literature but the I have been met with error messages about overlap of atoms while I tried to relax the system. > How can I fix the problem? > > Best regards,Payam Norouzzadeh > > _______________________________________________ > 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/20100604/0c2f6ee6/attachment.htm From archygu at gmail.com Fri Jun 4 11:37:53 2010 From: archygu at gmail.com (chenjie gu) Date: Fri, 4 Jun 2010 17:37:53 +0800 Subject: [Pw_forum] Unit cell problem In-Reply-To: References: <85070.17885.qm@web65708.mail.ac4.yahoo.com> Message-ID: 2010/6/4 mohsen modaresi > Dear Eyvaz, > After increase of K-points, Ecut and nbnd for a unit cell with 16 atoms, > DOS problem solved and i get the same DOS for two structure. > Is there any relation between the bandstructure for these two situations? > Sincerely yours, > Mohsen Modaresi > Ferdowsi University of Mashhad, Iran. > > hi, Mohsen. Just an example for you. If you set the Si Unit Cell as SC > Structure, you will get a bandstructure. > Then set it as fcc, you may get other band structure. the coordinates are as follows: ibrav= 2, celldm(1)= 10.2, ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 ------------------------------------------------- ibrav = 1, celldm(1) =10.21, ATOMIC_POSITIONS Si 0.000 0.000 0.000 Si 0.500 0.500 0.000 Si 0.500 0.000 0.500 Si 0.000 0.500 0.500 Si 0.250 0.250 0.250 Si 0.750 0.750 0.250 Si 0.750 0.250 0.750 Si 0.250 0.750 0.750 > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/8c577ad5/attachment.htm From archygu at gmail.com Fri Jun 4 11:43:50 2010 From: archygu at gmail.com (chenjie gu) Date: Fri, 4 Jun 2010 17:43:50 +0800 Subject: [Pw_forum] some input parameter Message-ID: Hi Pwscf User, when reading the input parameter,I am not very clear, here as follows, can you give me some explaination: nraise: how do we define a nraise step? for ion_temperature=andersen: the collision frequency parameter is given as nu=1/tau defined above, so nu*dt=1/nraise:here what is nu, tau? thank you so much, -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/87036462/attachment-0001.htm From amit99266 at rediffmail.com Fri Jun 4 15:14:51 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 4 Jun 2010 13:14:51 -0000 Subject: [Pw_forum] =?utf-8?q?How_to_calcualte_anharmonic_phonon_lifetimes?= =?utf-8?q?=3F?= Message-ID: <20100604131451.49817.qmail@f4mail-235-230.rediffmail.com> Dear All Can anyone tell me about how to calculate the anharmonic phonon lifetimes using QE? (Please forgive me for my ignorance.) Warm Regards Amit N. Harode CRL INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/1ee0d079/attachment.htm From elie.moujaes at hotmail.co.uk Fri Jun 4 15:25:21 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 4 Jun 2010 14:25:21 +0100 Subject: [Pw_forum] error 208, reading namelist cell Message-ID: Dear All, I am trying to relax a system using vc-relax and I am getting the following error: From payam.norouzzadeh at gmail.com Fri Jun 4 15:25:32 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Fri, 4 Jun 2010 17:55:32 +0430 Subject: [Pw_forum] overlap of atoms Message-ID: Thank you Prof.Baroni for your reply. Actually I used both Xcrysden and Jmol to visualize the structure. The result was good and also I compared the result with available pictures of that structure in literature.One problem is that the positions like 0 0 0 and 0.5 0.5 0.5 are considered overlapped in this structure by QE probably because of symmetry. Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/45f658bb/attachment.htm From baroni at sissa.it Fri Jun 4 15:29:12 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 4 Jun 2010 15:29:12 +0200 Subject: [Pw_forum] overlap of atoms In-Reply-To: References: Message-ID: what is the basis of the Bravais lattive of your crystal? S. On Jun 4, 2010, at 3:25 PM, Payam Norouzzadeh wrote: > Thank you Prof.Baroni for your reply. > > Actually I used both Xcrysden and Jmol to visualize the structure. The result was good and also I compared the result with > available pictures of that structure in literature.One problem is that the positions like 0 0 0 and 0.5 0.5 0.5 are considered overlapped > in this structure by QE probably because of symmetry. > > Best regards,Payam Norouzzadeh > _______________________________________________ > 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/20100604/1b92ed2b/attachment.htm From sclauzer at sissa.it Fri Jun 4 15:34:45 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 4 Jun 2010 15:34:45 +0200 Subject: [Pw_forum] error 208, reading namelist cell In-Reply-To: References: Message-ID: <04F6D367-0034-4C0D-A230-2F39C0274567@sissa.it> Dear Elie, the / should go at the end of each namelist, not at the beginning. The F90 standard prescribes that a namelist named, for instance, TEST, can be accessed with &TEST ... / or &TEST ... &END The namelist "cell" has not been closed in your example. HTH GS Il giorno 04/giu/10, alle ore 15:25, Elie Moujaes ha scritto: > Dear All, > > I am trying to relax a system using vc-relax and I am getting the > following error: > > From read_namelists : error # 1 > reading namelist cell.... > > I have checked that the input is missing and that &ions precedes > &cell in the input. Part of the input is below..Thanks > > / > &system > ibrav= 0, celldm(1) =1.88972, nat=60, ntyp= 1, ecutwfc = > 110D0 ,occupations='smearing', smearing='methfessel-paxton', > degauss=0.01 > / > &electrons > conv_thr=1.D-8, > mixing_beta=0.05D0, > mixing_mode='local-TF', > diagonalization='david' > / > &ions > ion_dynamics = 'bfgs', > pot_extrapolation = 'second-order', > wfc_extrapolation = 'second-order' > / > &cell > cell_dynamics = 'bfgs', > press_conv_thr = 0.1 > > CELL_PARAMETERS hexagonal > > 24.527679 0.000000 0.000000 > 0.000003 6.614491 0.000000 > 0.000000 0.000000 10.000000 > > ATOMIC_SPECIES > C 12.0107 C.pz-vbc.UPF > ATOMIC_POSITIONS angstrom > C -11.737980 -3.561278 0.000000 > C -11.057718 -1.211571 0.000000 > ....... > .............. > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > > Get a new e-mail account with Hotmail - Free. Sign-up now. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/06f6447a/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100604/06f6447a/attachment-0001.bin From elie.moujaes at hotmail.co.uk Fri Jun 4 15:44:41 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 4 Jun 2010 14:44:41 +0100 Subject: [Pw_forum] error 208, reading namelist cell In-Reply-To: <04F6D367-0034-4C0D-A230-2F39C0274567@sissa.it> References: , <04F6D367-0034-4C0D-A230-2F39C0274567@sissa.it> Message-ID: Thanks very much..That was a stupid mistake to do. Regards Elie From: sclauzer at sissa.it To: pw_forum at pwscf.org Date: Fri, 4 Jun 2010 15:34:45 +0200 Subject: Re: [Pw_forum] error 208, reading namelist cell Dear Elie, the / should go at the end of each namelist, not at the beginning. The F90 standard prescribes that a namelist named, for instance, TEST, can be accessed with &TEST ... / or &TEST ... &END The namelist "cell" has not been closed in your example. HTH GS Il giorno 04/giu/10, alle ore 15:25, Elie Moujaes ha scritto: Dear All, I am trying to relax a system using vc-relax and I am getting the following error: From ceresoli at MIT.EDU Fri Jun 4 17:51:22 2010 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Fri, 04 Jun 2010 11:51:22 -0400 Subject: [Pw_forum] how to do fixed volume optimization In-Reply-To: <201005312028518289019@gmail.com> References: <201005302041597969466@gmail.com>, <201005302109318285369@gmail.com>, <201005311614027962613@gmail.com> <201005312028518289019@gmail.com> Message-ID: <4C0920FA.8040502@mit.edu> On 05/31/2010 08:28 AM, Kun Yin wrote: > I see. Thanks for giving the answer, Paolo. I hope this easy-to-implement functionality, doing 'vc-relax' at constant volume, will be done by some enthusiastic guy, since it is very useful in some research such as the study of high-pressure materials. > Dear Kun Yin, I implemented the constant volume/variable shape some time ago. It's in the CVS version now. To use it, simply set cell_dofree = 'shape' in the &cell namelist. Please let me know if it is working properly. 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 (US), +39-347-1001570 (IT) Skype: dceresoli +----------------------------------------------------------+ From elie.moujaes at hotmail.co.uk Fri Jun 4 20:00:11 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 4 Jun 2010 19:00:11 +0100 Subject: [Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique Message-ID: Dear all, I am still using the start_q, last_q, start_irr and last_irr technique (from GRID example) to calculate the phonon dispersion in graphene. Everything is ok until I run ph.x for the first q (q=1 the Gamma point). The input is: Phonon dispersion for monolayer graphene &inputph tr2_ph=1.0d-13, prefix='phmonog', ldisp=.true., nq1=8, nq2=8, nq3=1 start_q=1, last_q=1, start_irr=1, last_irr=4, recover=.true., amass(1)=12.0107, outdir='/tmp/results_MOUJAES/q1', fildyn='mgraph881.dyn', / No errors in running ph.x but teh output is a bit strange like : Program PHONON v.4.2 starts on 4Jun2010 at 14:35:33 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Ultrasoft (Vanderbilt) Pseudopotentials Starting q 2 larger than total number of q points 10 or of last q 1 PHONON : 7.10s CPU time, 7.91s WALL time INITIALIZATION: init_vloc : 0.01s CPU 0.02s WALL ( 1 calls) init_us_1 : 0.02s CPU 0.02s WALL ( 1 calls) DYNAMICAL MATRIX: General routines cft3 : 0.02s CPU 0.02s WALL ( 3 calls) when I run q=2 (next point with 6 irr representations) with input: Phonon dispersion for monolayer graphene &inputph tr2_ph=1.0d-13, prefix='phmonog', ldisp=.true., nq1=8, nq2=8, nq3=1 start_q=2, last_q=2, start_irr=1, last_irr=6, recover=.true., amass(1)=12.0107, outdir='/tmp/results_MOUJAES/q2', fildyn='mgraph881.dyn', / I get a strange error on the screen (not output file which contains no results): WARNING : THERE ARE PENDING ERRORS PENDING ERROR (ierr=1) ERROR IN: iotk_open_read (iotk_files.spp:487) PENDING ERROR (ierr =2) UNRECOVERABLE........ Not sure what all this means. Thanks in adavance for any suffestion... _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/771c296d/attachment-0001.htm From dalcorso at sissa.it Fri Jun 4 21:15:04 2010 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Fri, 04 Jun 2010 21:15:04 +0200 Subject: [Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique Message-ID: <20100604211504.jcc80cx1wow0oo4w@webmail.sissa.it> I am still using the start_q, last_q, start_irr and last_irr technique (from GRID example) to calculate the phonon dispersion in graphene. Everything is ok until I run ph.x for the first q (q=1 the Gamma point). The input is: Phonon dispersion for monolayer graphene &inputph tr2_ph=1.0d-13, prefix='phmonog', ldisp=.true., nq1=8, nq2=8, nq3=1 start_q=1, last_q=1, start_irr=1, last_irr=4, recover=.true., amass(1)=12.0107, outdir='/tmp/results_MOUJAES/q1', fildyn='mgraph881.dyn', / No errors in running ph.x but teh output is a bit strange like : Program PHONON v.4.2 starts on 4Jun2010 at 14:35:33 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Ultrasoft (Vanderbilt) Pseudopotentials Starting q 2 larger than total number of q points 10 or of last q 1 This error depends on the fact that the recover procedure is confused because the code was doing the second q point when it was interrupted and now you are trying to recover (you have recover=.true.) but ask to calculate only q point 1. You are not allowed to change start_q and last_q before finishing a calculation. Probably this part should be more robust for these kind of problems, but at the moment it is not, sorry. When you try again and change q point to 2, the recover files are now a mess and you get an error from the library routine that reads the recovering files. At this point the only solution is to remove the outdir/_ph* files and start again. If you have already the dynamical matrices of all q points but the first you can simply calculate the gamma point starting from scratch. If the problem is still present after cleaning the outdir directory, and it is reproducible, please post also the input of pw.x. HTH Andrea ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From baris.malcioglu at gmail.com Fri Jun 4 21:35:00 2010 From: baris.malcioglu at gmail.com (Osman Baris Malcioglu) Date: Fri, 4 Jun 2010 22:35:00 +0300 Subject: [Pw_forum] mkl problem In-Reply-To: <201006041128.23658.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> <935c498c8614075c6676841aef519d79.squirrel@webmail.fq.edu.uy> <201006041128.23658.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <79B17CA7-2FAC-49C4-B33E-BBF995A7965D@gmail.com> Dear Giuseppe, Please notice that you are using an older (obsolete? eh, Intel certainly thinks so) version of MKL, the new standard INTEL has for MKL compile line is different (http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/) Newer versions of the espresso configure script look for the latter one. If there is significant demand for the older version, the configure script can be modified, with a sacrifice in performance in the configuration step of some select cases. Please let us know, Baris On 04.Haz.2010, at 12:28, Giuseppe Mattioli wrote: > Dear Ricardo > It seems to work... But I would ask the developers why does the configure > script not found any mkl even if they are in the path... > Thank you very much > Giuseppe > > On Thursday 03 June 2010 11:48:56 Ricardo Faccio wrote: >> Hi >> I faced almost the same problem but in a single QuadCore PC, I edited the >> make.sys file by hand and then it looks like as following. >> And it works! >> Regards >> Ricardo >> ------------------------------------------------- >> Dr. Ricardo Faccio >> Prof. Adjunto de F?sica >> Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA >> Facultad de Qu?mica, Universidad de la Rep?blica >> Av. Gral. Flores 2124, C.C. 1157 >> C.P. 11800, Montevideo, Uruguay. >> E-mail: rfaccio at fq.edu.uy >> Phone: 598 2 924 98 59 >> 598 2 929 06 48 >> Fax: 598 2 9241906 >> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm >> >> # make.sys. Generated from make.sys.in by configure. >> >> # compilation rules >> >> .SUFFIXES : >> .SUFFIXES : .o .c .f .f90 >> >> # most fortran compilers can directly preprocess c-like directives: use >> # $(MPIF90) $(F90FLAGS) -c $< >> # if explicit preprocessing by the C preprocessor is needed, use: >> # $(CPP) $(CPPFLAGS) $< -o $*.F90 >> # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o >> # remember the tabulator in the first column !!! >> >> .f90.o: >> $(MPIF90) $(F90FLAGS) -c $< >> >> # .f.o and .c.o: do not modify >> >> .f.o: >> $(F77) $(FFLAGS) -c $< >> >> .c.o: >> $(CC) $(CFLAGS) -c $< >> >> >> # DFLAGS = precompilation options (possible arguments to -D and -U) >> # used by the C compiler and preprocessor >> # FDFLAGS = as DFLAGS, for the f90 compiler >> # See include/defs.h.README for a list of options and their meaning >> # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) >> # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas >> >> DFLAGS = -D__INTEL -D__FFTW >> FDFLAGS = $(DFLAGS) >> >> # IFLAGS = how to locate directories where files to be included are >> # In most cases, IFLAGS = -I../include >> >> IFLAGS = -I../include >> >> # MOD_FLAGS = flag used by f90 compiler to locate modules >> # Each Makefile defines the list of needed modules in MODFLAGS >> >> MOD_FLAG = -I >> >> # Compilers: fortran-90, fortran-77, C >> # If a parallel compilation is desired, MPIF90 should be a fortran-90 >> # compiler that produces executables for parallel execution using MPI >> # (such as for instance mpif90, mpf90, mpxlf90,...); >> # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) >> # If you have a parallel machine but no suitable candidate for MPIF90, >> # try to specify the directory containing "mpif.h" in IFLAGS >> # and to specify the location of MPI libraries in MPI_LIBS >> >> MPIF90 = ifort >> #F90 = ifort >> CC = gcc >> F77 = ifort >> >> # C preprocessor and preprocessing flags - for explicit preprocessing, >> # if needed (see the compilation rules above) >> # preprocessing flags must include DFLAGS and IFLAGS >> >> CPP = cpp >> CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) >> >> # compiler flags: C, F90, F77 >> # C flags must include DFLAGS and IFLAGS >> # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate >> syntax >> >> CFLAGS = -O3 $(DFLAGS) $(IFLAGS) >> F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) >> FFLAGS = -O2 -assume byterecl -g -traceback >> >> # compiler flags without optimization for fortran-77 >> # the latter is NEEDED to properly compile dlamch.f, used by lapack >> >> FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback >> >> # Linker, linker-specific flags (if any) >> # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty >> >> LD = ifort >> LDFLAGS = >> LD_LIBS = >> >> # External Libraries (if any) : blas, lapack, fft, MPI >> >> # If you have nothing better, use the local copy : >> # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a >> # BLAS_LIBS_SWITCH = internal >> >> BLAS_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_em64t >> BLAS_LIBS_SWITCH = internal >> >> # If you have nothing better, use the local copy : >> # LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a >> # LAPACK_LIBS_SWITCH = internal >> >> # The following lapack libraries will be available in flib/ : >> # ../flib/lapack.a : contains all needed routines >> # ../flib/lapack_atlas.a: only routines not present in the Atlas library >> # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! >> # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order >> >> LAPACK_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack >> -lmkl_sequential -lmkl_core -lmkl_intel_lp64 >> LAPACK_LIBS_SWITCH = internal >> >> SCALAPACK_LIBS = >> >> # nothing needed here if the the internal copy of FFTW is compiled >> # (needs -D__FFTW in DFLAGS) >> >> FFT_LIBS = >> >> # For parallel execution, the correct path to MPI libraries must >> # be specified in MPI_LIBS (except for IBM if you use mpxlf) >> >> MPI_LIBS = >> >> # IBM-specific: MASS libraries, if available and if -D__MASS is defined in >> FDFLAGS >> >> MASS_LIBS = >> >> # pgplot libraries (used by some post-processing tools) >> >> PGPLOT_LIBS = >> >> # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv >> >> AR = ar >> ARFLAGS = ruv >> >> # ranlib command. If ranlib is not needed (it isn't in most cases) use >> # RANLIB = echo >> >> RANLIB = ranlib >> >> # all internal and external libraries - do not modify >> >> FLIB_TARGETS = all >> >> LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a >> ../iotk/src/libiotk.a ../Multigrid/mglib.a >> LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) >> $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) >> >> # topdir for linking espresso libs with plugins >> TOPDIR = /home/rfaccio/espresso-4.2 >> >>> Dear all >>> I'm facing some problems with mkl & QE 4.2 on a linux cluster. In the >>> case of >>> 4.1, the configure script found (and still find...) the installed mkl >>> 10.0.4.023 version and the make.sys looked like >>> >>> BLAS_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t >>> LAPACK_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t >>> >>> QE 4.1 has been succesfully compiled and works fine. >>> >>> In the case of 4.2 the configure script does not find any external lapack >>> or >>> blas lib. I've tryed to use the './configure LIBDIRS=...' command but it >>> still does not find any lapack or blas lib. I would like to manually link >>> the >>> libs (./configure LAPACK_LIBS=... BLAS_LIBS=...) , but I do not know what >>> exactly I'm supposed to link... >>> >>> /opt/intel/mkl/10.0.4.023/lib/64 >>> >>> libguide.a libmkl_blacs_openmpi_ilp64.a >>> libmkl_gf_lp64.a libmkl_intel_sp2dp.so libmkl_sequential.so >>> libguide.so libmkl_blacs_openmpi_lp64.a >>> libmkl_gf_lp64.so libmkl_intel_thread.a libmkl.so >>> libiomp5.a libmkl_blacs_sgimpt_ilp64.a >>> libmkl_gnu_thread.a libmkl_intel_thread.so libmkl_solver.a >>> libiomp5.so libmkl_blacs_sgimpt_lp64.a >>> libmkl_gnu_thread.so libmkl_ipf.a libmkl_solver_ilp64.a >>> libmkl_blacs_ilp64.a libmkl_cdft.a >>> libmkl_i2p.so >>> libmkl_lapack.a libmkl_solver_ilp64_sequential.a >>> libmkl_blacs_intelmpi20_ilp64.a libmkl_cdft_core.a >>> libmkl_intel_ilp64.a libmkl_lapack.so libmkl_solver_lp64.a >>> libmkl_blacs_intelmpi20_lp64.a libmkl_core.a >>> libmkl_intel_ilp64.so libmkl_scalapack.a >>> libmkl_solver_lp64_sequential.a >>> libmkl_blacs_intelmpi_ilp64.a libmkl_core.so >>> libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_i2p.so >>> libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.a >>> libmkl_intel_lp64.so libmkl_scalapack_lp64.a >>> libmkl_blacs_lp64.a libmkl_gf_ilp64.so >>> libmkl_intel_sp2dp.a libmkl_sequential.a >>> >>> or >>> >>> /opt/intel/mkl/10.0.4.023/lib/em64t >>> >>> libguide.a libmkl_blacs_openmpi_lp64.a >>> libmkl_gnu_thread.a libmkl_lapack.so >>> libmkl_solver_ilp64_sequential.a >>> libguide.so libmkl_cdft.a >>> libmkl_gnu_thread.so libmkl_mc.so libmkl_solver_lp64.a >>> libiomp5.a libmkl_cdft_core.a >>> libmkl_intel_ilp64.a libmkl_p4n.so >>> libmkl_solver_lp64_sequential.a >>> libiomp5.so libmkl_core.a >>> libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_vml_def.so >>> libmkl_blacs_ilp64.a libmkl_core.so >>> libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_mc2.so >>> libmkl_blacs_intelmpi20_ilp64.a libmkl_def.so >>> libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_vml_mc.so >>> libmkl_blacs_intelmpi20_lp64.a libmkl_em64t.a >>> libmkl_intel_sp2dp.a libmkl_sequential.a libmkl_vml_p4n.so >>> libmkl_blacs_intelmpi_ilp64.a libmkl_gf_ilp64.a >>> libmkl_intel_sp2dp.so libmkl_sequential.so >>> libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.so >>> libmkl_intel_thread.a libmkl.so >>> libmkl_blacs_lp64.a libmkl_gf_lp64.a >>> libmkl_intel_thread.so libmkl_solver.a >>> libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.so >>> libmkl_lapack.a >>> libmkl_solver_ilp64.a >>> >>> However, if I link the /acml/ifort64/lib/libacml.a libs (and it does not >>> sound >>> reasonable on a xeon cluster...), everything works fine... >>> >>> Any suggestion? >>> >>> Giuseppe >>> >>> -- >>> ******************************************************** >>> - 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: >>> _______________________________________________ >>> 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 > > > > -- > ******************************************************** > - 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: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From dhruv.singh at gmail.com Fri Jun 4 21:57:30 2010 From: dhruv.singh at gmail.com (DHRUV SINGH) Date: Fri, 4 Jun 2010 15:57:30 -0400 Subject: [Pw_forum] Problem with ibrav=0 in supercell calculations Message-ID: <195FF159-BE62-4070-9112-0C857192117F@gmail.com> Hi everyone, I am trying to do a supercell calculation of InAs (zinc blende structure) using the following input file(ibrav=0 and specifying cell parameters with cubic symmetry) &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='inas', pseudo_dir = '/home/ba01/u110/singh36/espresso-4.1.3/pseudo/', outdir='./tmp' / &system ibrav=0, celldm(1)=11.05, nat= 8, ntyp= 2, ecutwfc =25.0 ecutrho=250.0 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES In 114.818 In.pz-bhs.UPF As 74.921 As.pz-bhs.UPF CELL PARAMETERS{cubic} 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 ATOMIC_POSITIONS {crystal} In 0.00 0.00 0.00 As 0.25 0.25 0.25 In 0.50 0.50 0.00 As 0.75 0.75 0.25 In 0.00 0.50 0.50 As 0.25 0.75 0.75 In 0.50 0.00 0.50 As 0.75 0.25 0.75 K_POINTS {automatic} 4 4 4 0 0 0 Strangely enough an scf run does not read the cell parameters card and I get an error Waiting for input... Warning: card CELL PARAMETERS{CUBIC} ignored Warning: card 1.0 0.0 0.0 ignored Warning: card 0.0 1.0 0.0 ignored Warning: card 0.0 0.0 1.0 ignored %%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 1 ibrav=0: must read cell parameters %%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------- I have run a few calculations in the past with the cubic supercell specifying different values of cell parameters and they work fine. Also the calculation runs fine with ibrav=1 (and not specifying the cell parameters). However, I am not able to pin down the mistake I am making here (Are we not allowed to specify a free lattice if it has equal cell parameters?). Thanks, Dhruv Singh School of Mechanical Engineering, Purdue University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/d2c5dddb/attachment.htm From mazar83 at gmail.com Fri Jun 4 22:49:11 2010 From: mazar83 at gmail.com (Mark Mazar) Date: Fri, 4 Jun 2010 15:49:11 -0500 Subject: [Pw_forum] Problem with ibrav=0 in supercell calculations In-Reply-To: <195FF159-BE62-4070-9112-0C857192117F@gmail.com> References: <195FF159-BE62-4070-9112-0C857192117F@gmail.com> Message-ID: Your CELL PARAMETERS flag is missing its underscore. On Fri, Jun 4, 2010 at 2:57 PM, DHRUV SINGH wrote: > Hi everyone, > I am trying to do a supercell calculation of InAs (zinc blende structure) > using the following input file(ibrav=0 and specifying cell parameters with > cubic symmetry) > ?&control > ?? ?calculation='scf' > ?? ?restart_mode='from_scratch', > ?? ?tstress = .true. > ?? ?tprnfor = .true. > ?? ?prefix='inas', > ?? ?pseudo_dir = '/home/ba01/u110/singh36/espresso-4.1.3/pseudo/', > ?? ?outdir='./tmp' > ?/ > ?&system > ?? ?ibrav=0, > ?? ?celldm(1)=11.05, > ?? ?nat= ?8, > ?? ?ntyp= 2, > ?? ?ecutwfc =25.0 > ?? ?ecutrho=250.0 > ?/ > ?&electrons > ?? ?conv_thr = ?1.0d-8 > ?? ?mixing_beta = 0.7 > ?/ > ATOMIC_SPECIES > ?In ?114.818 ?In.pz-bhs.UPF > ?As ?74.921 ?As.pz-bhs.UPF > CELL PARAMETERS{cubic} > ?1.0 0.0 0.0 > ?0.0 1.0 0.0 > ?0.0 0.0 1.0 > ATOMIC_POSITIONS {crystal} > ?In 0.00 0.00 0.00 > ?As 0.25 0.25 0.25 > ?In 0.50 0.50 0.00 > ?As 0.75 0.75 0.25 > ?In 0.00 0.50 0.50 > ?As 0.25 0.75 0.75 > ?In 0.50 0.00 0.50 > ?As 0.75 0.25 0.75 > K_POINTS {automatic} > ?4 4 4 0 0 0 > Strangely enough an scf run does not read the cell parameters card and I get > an error > ?Waiting for input... > Warning: card CELL PARAMETERS{CUBIC} ignored > Warning: card ?1.0 0.0 0.0 ignored > Warning: card ?0.0 1.0 0.0 ignored > Warning: card ?0.0 0.0 1.0 ignored > ?%%%%%%%%%%%%%%%%%%%%%%%%% > ?? ? from read_cards : error # ? ? ? ? 1 > ?? ? ibrav=0: must read cell parameters > ?%%%%%%%%%%%%%%%%%%%%%%%%% > ?? ? stopping ... > -------- > I have run a few calculations in the past with the cubic supercell > specifying different values of cell parameters and they work fine. Also the > calculation runs fine with ibrav=1 (and not specifying the cell parameters). > However, I am not able to pin down the mistake I am making here (Are we not > allowed to specify a free lattice if it has equal cell parameters?). > Thanks, > Dhruv Singh > School of Mechanical Engineering, Purdue University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From elie.moujaes at hotmail.co.uk Sat Jun 5 00:06:46 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 4 Jun 2010 23:06:46 +0100 Subject: [Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique In-Reply-To: <20100604211504.jcc80cx1wow0oo4w@webmail.sissa.it> References: <20100604211504.jcc80cx1wow0oo4w@webmail.sissa.it> Message-ID: Dear Andrea, Thanks very much for the information. In fact, when I am running the ph2.in file (for q=2), it runs normally and doesnt give any error except that the output does not have a dynamical matrix i.e. the output looks like: Program PHONON v.4.2 starts on 2Jun2010 at 17:44:23 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Ultrasoft (Vanderbilt) Pseudopotentials Starting q 2 larger than total number of q points 10 or of last q 1 PHONON : 7.04s CPU time, 7.83s WALL time INITIALIZATION: init_vloc : 0.02s CPU 0.02s WALL ( 1 calls) init_us_1 : 0.02s CPU 0.02s WALL ( 1 calls) DYNAMICAL MATRIX: General routines cft3 : 0.03s CPU 0.03s WALL ( 3 calls) so it is empty underneath DYNAMICAL MATRIX. The only way i was able to get rid of the recover error is to omit recover=.true. in the ph.in program but I guess this is essential. I will also post the scf calculation below: &control prefix='phmonog', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' verbosity='high' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.0, nat=2, ntyp= 1, ecutwfc = 110.D0,occupations='smearing', smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-10, diagonalization='david', mixing_mode='plain' / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 C 0.333333 -0.33333 0.000000 K_POINTS automatic 26 26 1 0 0 0 ANY SUGGESTIONS? Thank you Elie Moujaes University fo Nootingham NG7 2RD UK > Date: Fri, 4 Jun 2010 21:15:04 +0200 > From: dalcorso at sissa.it > To: pw_forum at pwscf.org > CC: dalcorso at sissa.it > Subject: [Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique > > I am still using the start_q, last_q, start_irr and last_irr technique > (from GRID example) to calculate the phonon dispersion in graphene. > Everything is ok until I run ph.x for the first q (q=1 the Gamma > point). The input is: > > > > Phonon dispersion for monolayer graphene > > &inputph > > tr2_ph=1.0d-13, > > prefix='phmonog', > > ldisp=.true., > > nq1=8, nq2=8, nq3=1 > > start_q=1, > > last_q=1, > > start_irr=1, > > last_irr=4, > > recover=.true., > > amass(1)=12.0107, > > outdir='/tmp/results_MOUJAES/q1', > > fildyn='mgraph881.dyn', > > / > > No errors in running ph.x but teh output is a bit strange like : > > > > > Program PHONON v.4.2 starts on 4Jun2010 at 14:35:33 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please acknowledge > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > Ultrasoft (Vanderbilt) Pseudopotentials > Starting q 2 larger than total number of q points 10 or of last q 1 > > This error depends on the fact that the recover procedure is confused > because the code was doing the second q point when it was interrupted > and > now you are trying to recover (you have recover=.true.) but ask to calculate > only q point 1. You are not allowed to change start_q and last_q > before finishing a calculation. Probably this part should be more > robust for these kind of problems, but at the moment it is not, sorry. > > When you try again and change q point to 2, the recover files are now > a mess and you get an error from the library routine that reads > the recovering files. > > At this point the only solution is to remove the outdir/_ph* files and > start again. If you have already the dynamical matrices of all q points > but the first you can simply calculate the gamma point starting from scratch. > > If the problem is still present after cleaning the outdir directory, > and it is reproducible, please post also the input of pw.x. > > HTH > > Andrea > > ---------------------------------------------------------------- > 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 _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/23e5f466/attachment-0001.htm From suza.rri at gmail.com Sun Jun 6 11:41:42 2010 From: suza.rri at gmail.com (Suza W) Date: Sun, 6 Jun 2010 05:41:42 -0400 Subject: [Pw_forum] Pseudo Sr Message-ID: > Dear all, > On PWSCF website, only following GGA pseudos are available for Strontium: Sr.pw91-nsp-van.UPF Sr.pbe-nsp-van.UPF Sr.pbe-sp-van.UPF > > Does anyone have a PZ LDA ultrasoft pseudo potential for Sr ? > > Thanking you all, > > Suza W > PhD > RRI, Bangalore > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100606/69369b41/attachment.htm From kazempoor at ph.iut.ac.ir Sun Jun 6 15:14:51 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Sun, 6 Jun 2010 17:44:51 +0430 (IRDT) Subject: [Pw_forum] HSE error In-Reply-To: <41656085.71273.1275829929896.JavaMail.root@mta.iut.ac.ir> Message-ID: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> Dear all I used HSE functional for a single charged supercell and at the begining I got this error, but the calculation for doubly charged suercell is safe. Why does this happen? -------------------------------------------- from read_namelists : error # 88 reading namelist system --------------------------------------------- my input is in following: &control calculation = 'relax' restart_mode='from_scratch' prefix='hseo+' verbosity='high' pseudo_dir = './' outdir='/ptmp/kazempou/scratch/' / &system ibrav= 6 , celldm(1) =17.34,celldm(3)=0.965, nat= 71, ntyp= 2,tot_charge=1,nelec=569, ecutwfc =45.0,ecutrho=180,occupations='fixed', degauss=0.0,nspin=2,nelup=285,neldw=284,input_dft='hse', nqx1 =1, nqx2 =1 , nqx3 = 1,nbnd=320, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-3 / &ions / ATOMIC_SPECIES Ti 43.0 ti.optgga2.fhi.UPF O 16.0 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal Ti -0.023349669 -0.023349669 0.000000000 Ti 0.499349747 0.001769391 0.000000000 Ti 0.001769391 0.499349747 0.000000000 Ti 0.498876973 0.498876973 0.000000000 Ti 0.002405588 0.002405588 0.329360580 Ti 0.499568846 -0.000974012 0.333568764 Ti -0.000974012 0.499568846 0.333568764 Ti 0.507399533 0.507399533 0.336748419 Ti 0.002405588 0.002405588 0.670639450 Ti 0.499568846 -0.000974012 0.666431266 Ti -0.000974012 0.499568846 0.666431266 Ti 0.507399533 0.507399533 0.663251611 Ti 0.269267824 0.269267824 0.186220951 Ti 0.749311691 0.251786232 0.166341491 Ti 0.251786232 0.749311691 0.166341491 Ti 0.741569474 0.741569474 0.170772085 Ti 0.237657593 0.237657593 0.500000000 Ti 0.751221208 0.246208753 0.500000000 Ti 0.246208753 0.751221208 0.500000000 Ti 0.763075374 0.763075374 0.500000000 Ti 0.269267824 0.269267824 0.813779029 Ti 0.749311691 0.251786232 0.833658489 Ti 0.251786232 0.749311691 0.833658489 Ti 0.741569474 0.741569474 0.829227895 O 0.652332320 0.149871487 0.000000000 O 0.149871487 0.652332320 0.000000000 O 0.648713680 0.648713680 0.000000000 O 0.155238060 0.155238060 0.326384494 O 0.652290092 0.150787458 0.333038822 O 0.150787458 0.652290092 0.333038822 O 0.653798667 0.653798667 0.336935635 O 0.155238060 0.155238060 0.673615536 O 0.652290092 0.150787458 0.666961208 O 0.150787458 0.652290092 0.666961208 O 0.653798667 0.653798667 0.663064395 O 0.340201024 0.340201024 0.000000000 O 0.844284770 0.348460645 0.000000000 O 0.348460645 0.844284770 0.000000000 O 0.841167231 0.841167231 0.000000000 O 0.350847343 0.350847343 0.343732671 O 0.846562364 0.346794842 0.332680914 O 0.346794842 0.846562364 0.332680914 O 0.849375587 0.849375587 0.329278748 O 0.350847343 0.350847343 0.656267359 O 0.846562364 0.346794842 0.667319116 O 0.346794842 0.846562364 0.667319116 O 0.849375587 0.849375587 0.670721282 O 0.396954319 0.099266404 0.164239842 O 0.908323382 0.100237125 0.161621944 O 0.400136271 0.594239940 0.166856966 O 0.900420254 0.595644595 0.167042102 O 0.398819672 0.095650761 0.500000000 O 0.905834151 0.099259720 0.500000000 O 0.404318666 0.599248899 0.500000000 O 0.903265490 0.598692666 0.500000000 O 0.396954319 0.099266404 0.835760138 O 0.908323382 0.100237125 0.838378036 O 0.400136271 0.594239940 0.833143014 O 0.900420254 0.595644595 0.832957878 O 0.099266404 0.396954319 0.164239842 O 0.594239940 0.400136271 0.166856966 O 0.100237125 0.908323382 0.161621944 O 0.595644595 0.900420254 0.167042102 O 0.095650761 0.398819672 0.500000000 O 0.599248899 0.404318666 0.500000000 O 0.099259720 0.905834151 0.500000000 O 0.598692666 0.903265490 0.500000000 O 0.099266404 0.396954319 0.835760138 O 0.594239940 0.400136271 0.833143014 O 0.100237125 0.908323382 0.838378036 O 0.595644595 0.900420254 0.832957878 K_POINTS automatic 2 2 2 1 1 1 Thanks a lot Ali Kazempour Physics Department, Isfahn University of Technology From giuseppe.mattioli at mlib.ism.cnr.it Sun Jun 6 18:04:15 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Sun, 6 Jun 2010 18:04:15 +0200 Subject: [Pw_forum] mkl problem In-Reply-To: <79B17CA7-2FAC-49C4-B33E-BBF995A7965D@gmail.com> References: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> <201006041128.23658.giuseppe.mattioli@mlib.ism.cnr.it> <79B17CA7-2FAC-49C4-B33E-BBF995A7965D@gmail.com> Message-ID: <201006061804.16068.giuseppe.mattioli@mlib.ism.cnr.it> Dear Baris Thank you for the explanation. MKL are installed and managed on such cluster by our system administrators, so I may only ask for an update... However, I've compiled QE 4.2 by following Ricardo's advice, and it seems to work fine... Yours Giuseppe On Friday 04 June 2010 21:35:00 Osman Baris Malcioglu wrote: > Dear Giuseppe, > Please notice that you are using an older (obsolete? eh, Intel certainly > thinks so) version of MKL, the new standard INTEL has for MKL compile line > is different > (http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/) > Newer versions of the espresso configure script look for the latter one. If > there is significant demand for the older version, the configure script can > be modified, with a sacrifice in performance in the configuration step of > some select cases. Please let us know, > Baris > > On 04.Haz.2010, at 12:28, Giuseppe Mattioli wrote: > > Dear Ricardo > > It seems to work... But I would ask the developers why does the configure > > script not found any mkl even if they are in the path... > > Thank you very much > > Giuseppe > > > > On Thursday 03 June 2010 11:48:56 Ricardo Faccio wrote: > >> Hi > >> I faced almost the same problem but in a single QuadCore PC, I edited > >> the make.sys file by hand and then it looks like as following. > >> And it works! > >> Regards > >> Ricardo > >> ------------------------------------------------- > >> Dr. Ricardo Faccio > >> Prof. Adjunto de F?sica > >> Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA > >> Facultad de Qu?mica, Universidad de la Rep?blica > >> Av. Gral. Flores 2124, C.C. 1157 > >> C.P. 11800, Montevideo, Uruguay. > >> E-mail: rfaccio at fq.edu.uy > >> Phone: 598 2 924 98 59 > >> 598 2 929 06 48 > >> Fax: 598 2 9241906 > >> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > >> > >> # make.sys. Generated from make.sys.in by configure. > >> > >> # compilation rules > >> > >> .SUFFIXES : > >> .SUFFIXES : .o .c .f .f90 > >> > >> # most fortran compilers can directly preprocess c-like directives: use > >> # $(MPIF90) $(F90FLAGS) -c $< > >> # if explicit preprocessing by the C preprocessor is needed, use: > >> # $(CPP) $(CPPFLAGS) $< -o $*.F90 > >> # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o > >> # remember the tabulator in the first column !!! > >> > >> .f90.o: > >> $(MPIF90) $(F90FLAGS) -c $< > >> > >> # .f.o and .c.o: do not modify > >> > >> .f.o: > >> $(F77) $(FFLAGS) -c $< > >> > >> .c.o: > >> $(CC) $(CFLAGS) -c $< > >> > >> > >> # DFLAGS = precompilation options (possible arguments to -D and -U) > >> # used by the C compiler and preprocessor > >> # FDFLAGS = as DFLAGS, for the f90 compiler > >> # See include/defs.h.README for a list of options and their meaning > >> # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) > >> # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas > >> > >> DFLAGS = -D__INTEL -D__FFTW > >> FDFLAGS = $(DFLAGS) > >> > >> # IFLAGS = how to locate directories where files to be included are > >> # In most cases, IFLAGS = -I../include > >> > >> IFLAGS = -I../include > >> > >> # MOD_FLAGS = flag used by f90 compiler to locate modules > >> # Each Makefile defines the list of needed modules in MODFLAGS > >> > >> MOD_FLAG = -I > >> > >> # Compilers: fortran-90, fortran-77, C > >> # If a parallel compilation is desired, MPIF90 should be a fortran-90 > >> # compiler that produces executables for parallel execution using MPI > >> # (such as for instance mpif90, mpf90, mpxlf90,...); > >> # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, > >> ifort,...) # If you have a parallel machine but no suitable candidate > >> for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS > >> # and to specify the location of MPI libraries in MPI_LIBS > >> > >> MPIF90 = ifort > >> #F90 = ifort > >> CC = gcc > >> F77 = ifort > >> > >> # C preprocessor and preprocessing flags - for explicit preprocessing, > >> # if needed (see the compilation rules above) > >> # preprocessing flags must include DFLAGS and IFLAGS > >> > >> CPP = cpp > >> CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) > >> > >> # compiler flags: C, F90, F77 > >> # C flags must include DFLAGS and IFLAGS > >> # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate > >> syntax > >> > >> CFLAGS = -O3 $(DFLAGS) $(IFLAGS) > >> F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) > >> $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback > >> > >> # compiler flags without optimization for fortran-77 > >> # the latter is NEEDED to properly compile dlamch.f, used by lapack > >> > >> FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback > >> > >> # Linker, linker-specific flags (if any) > >> # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty > >> > >> LD = ifort > >> LDFLAGS = > >> LD_LIBS = > >> > >> # External Libraries (if any) : blas, lapack, fft, MPI > >> > >> # If you have nothing better, use the local copy : > >> # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a > >> # BLAS_LIBS_SWITCH = internal > >> > >> BLAS_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_em64t > >> BLAS_LIBS_SWITCH = internal > >> > >> # If you have nothing better, use the local copy : > >> # LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a > >> # LAPACK_LIBS_SWITCH = internal > >> > >> # The following lapack libraries will be available in flib/ : > >> # ../flib/lapack.a : contains all needed routines > >> # ../flib/lapack_atlas.a: only routines not present in the Atlas library > >> # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! > >> # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order > >> > >> LAPACK_LIBS = -L/opt/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack > >> -lmkl_sequential -lmkl_core -lmkl_intel_lp64 > >> LAPACK_LIBS_SWITCH = internal > >> > >> SCALAPACK_LIBS = > >> > >> # nothing needed here if the the internal copy of FFTW is compiled > >> # (needs -D__FFTW in DFLAGS) > >> > >> FFT_LIBS = > >> > >> # For parallel execution, the correct path to MPI libraries must > >> # be specified in MPI_LIBS (except for IBM if you use mpxlf) > >> > >> MPI_LIBS = > >> > >> # IBM-specific: MASS libraries, if available and if -D__MASS is defined > >> in FDFLAGS > >> > >> MASS_LIBS = > >> > >> # pgplot libraries (used by some post-processing tools) > >> > >> PGPLOT_LIBS = > >> > >> # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv > >> > >> AR = ar > >> ARFLAGS = ruv > >> > >> # ranlib command. If ranlib is not needed (it isn't in most cases) use > >> # RANLIB = echo > >> > >> RANLIB = ranlib > >> > >> # all internal and external libraries - do not modify > >> > >> FLIB_TARGETS = all > >> > >> LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a > >> ../iotk/src/libiotk.a ../Multigrid/mglib.a > >> LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) > >> $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) > >> > >> # topdir for linking espresso libs with plugins > >> TOPDIR = /home/rfaccio/espresso-4.2 > >> > >>> Dear all > >>> I'm facing some problems with mkl & QE 4.2 on a linux cluster. In the > >>> case of > >>> 4.1, the configure script found (and still find...) the installed mkl > >>> 10.0.4.023 version and the make.sys looked like > >>> > >>> BLAS_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t > >>> LAPACK_LIBS = -L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_em64t > >>> > >>> QE 4.1 has been succesfully compiled and works fine. > >>> > >>> In the case of 4.2 the configure script does not find any external > >>> lapack or > >>> blas lib. I've tryed to use the './configure LIBDIRS=...' command but > >>> it still does not find any lapack or blas lib. I would like to manually > >>> link the > >>> libs (./configure LAPACK_LIBS=... BLAS_LIBS=...) , but I do not know > >>> what exactly I'm supposed to link... > >>> > >>> /opt/intel/mkl/10.0.4.023/lib/64 > >>> > >>> libguide.a libmkl_blacs_openmpi_ilp64.a > >>> libmkl_gf_lp64.a libmkl_intel_sp2dp.so libmkl_sequential.so > >>> libguide.so libmkl_blacs_openmpi_lp64.a > >>> libmkl_gf_lp64.so libmkl_intel_thread.a libmkl.so > >>> libiomp5.a libmkl_blacs_sgimpt_ilp64.a > >>> libmkl_gnu_thread.a libmkl_intel_thread.so libmkl_solver.a > >>> libiomp5.so libmkl_blacs_sgimpt_lp64.a > >>> libmkl_gnu_thread.so libmkl_ipf.a libmkl_solver_ilp64.a > >>> libmkl_blacs_ilp64.a libmkl_cdft.a > >>> libmkl_i2p.so > >>> libmkl_lapack.a libmkl_solver_ilp64_sequential.a > >>> libmkl_blacs_intelmpi20_ilp64.a libmkl_cdft_core.a > >>> libmkl_intel_ilp64.a libmkl_lapack.so libmkl_solver_lp64.a > >>> libmkl_blacs_intelmpi20_lp64.a libmkl_core.a > >>> libmkl_intel_ilp64.so libmkl_scalapack.a > >>> libmkl_solver_lp64_sequential.a > >>> libmkl_blacs_intelmpi_ilp64.a libmkl_core.so > >>> libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_i2p.so > >>> libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.a > >>> libmkl_intel_lp64.so libmkl_scalapack_lp64.a > >>> libmkl_blacs_lp64.a libmkl_gf_ilp64.so > >>> libmkl_intel_sp2dp.a libmkl_sequential.a > >>> > >>> or > >>> > >>> /opt/intel/mkl/10.0.4.023/lib/em64t > >>> > >>> libguide.a libmkl_blacs_openmpi_lp64.a > >>> libmkl_gnu_thread.a libmkl_lapack.so > >>> libmkl_solver_ilp64_sequential.a > >>> libguide.so libmkl_cdft.a > >>> libmkl_gnu_thread.so libmkl_mc.so libmkl_solver_lp64.a > >>> libiomp5.a libmkl_cdft_core.a > >>> libmkl_intel_ilp64.a libmkl_p4n.so > >>> libmkl_solver_lp64_sequential.a > >>> libiomp5.so libmkl_core.a > >>> libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_vml_def.so > >>> libmkl_blacs_ilp64.a libmkl_core.so > >>> libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_mc2.so > >>> libmkl_blacs_intelmpi20_ilp64.a libmkl_def.so > >>> libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_vml_mc.so > >>> libmkl_blacs_intelmpi20_lp64.a libmkl_em64t.a > >>> libmkl_intel_sp2dp.a libmkl_sequential.a libmkl_vml_p4n.so > >>> libmkl_blacs_intelmpi_ilp64.a libmkl_gf_ilp64.a > >>> libmkl_intel_sp2dp.so libmkl_sequential.so > >>> libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.so > >>> libmkl_intel_thread.a libmkl.so > >>> libmkl_blacs_lp64.a libmkl_gf_lp64.a > >>> libmkl_intel_thread.so libmkl_solver.a > >>> libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.so > >>> libmkl_lapack.a > >>> libmkl_solver_ilp64.a > >>> > >>> However, if I link the /acml/ifort64/lib/libacml.a libs (and it does > >>> not sound > >>> reasonable on a xeon cluster...), everything works fine... > >>> > >>> Any suggestion? > >>> > >>> Giuseppe > >>> > >>> -- > >>> ******************************************************** > >>> - 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: > >>> _______________________________________________ > >>> 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 > > > > -- > > ******************************************************** > > - 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: > > _______________________________________________ > > 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 -- ******************************************************** - 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: From m.abbasnejad at gmail.com Mon Jun 7 07:23:56 2010 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 7 Jun 2010 09:53:56 +0430 Subject: [Pw_forum] KZK method Message-ID: Dear all, Would you please let me know if KZK method (Kwee, Zhang, and Krakauer) has been implemented in PWscf code? If so, how should I use it? Thanks in advance. Yours, --------------------------------------------------------- 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/20100607/7bf30b7c/attachment.htm From marsamos at democritos.it Mon Jun 7 09:09:52 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Mon, 07 Jun 2010 09:09:52 +0200 Subject: [Pw_forum] HSE error In-Reply-To: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> References: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> Message-ID: <20100607090952.8oca7d1kgockwcww@mail.democritos.it> Dear Ali, did you compile with the flag -DEXX? (you have to add it to make.sys at the DFLAGS level). bests Layla Quoting kazempoor at ph.iut.ac.ir: > > Dear all > I used HSE functional for a single charged supercell and at the > begining I got this error, but the calculation for doubly charged > suercell is safe. Why does this happen? > -------------------------------------------- > > from read_namelists : error # 88 > reading namelist system > --------------------------------------------- > > my input is in following: > > > &control > calculation = 'relax' > restart_mode='from_scratch' > prefix='hseo+' > verbosity='high' > pseudo_dir = './' > outdir='/ptmp/kazempou/scratch/' > / > &system > ibrav= 6 , celldm(1) =17.34,celldm(3)=0.965, nat= 71, ntyp= > 2,tot_charge=1,nelec=569, > ecutwfc =45.0,ecutrho=180,occupations='fixed', > degauss=0.0,nspin=2,nelup=285,neldw=284,input_dft='hse', nqx1 =1, > nqx2 =1 , nqx3 = 1,nbnd=320, > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-3 > / > &ions > / > ATOMIC_SPECIES > Ti 43.0 ti.optgga2.fhi.UPF > O 16.0 o.optgga1.fhi.UPF > ATOMIC_POSITIONS crystal > Ti -0.023349669 -0.023349669 0.000000000 > Ti 0.499349747 0.001769391 0.000000000 > Ti 0.001769391 0.499349747 0.000000000 > Ti 0.498876973 0.498876973 0.000000000 > Ti 0.002405588 0.002405588 0.329360580 > Ti 0.499568846 -0.000974012 0.333568764 > Ti -0.000974012 0.499568846 0.333568764 > Ti 0.507399533 0.507399533 0.336748419 > Ti 0.002405588 0.002405588 0.670639450 > Ti 0.499568846 -0.000974012 0.666431266 > Ti -0.000974012 0.499568846 0.666431266 > Ti 0.507399533 0.507399533 0.663251611 > Ti 0.269267824 0.269267824 0.186220951 > Ti 0.749311691 0.251786232 0.166341491 > Ti 0.251786232 0.749311691 0.166341491 > Ti 0.741569474 0.741569474 0.170772085 > Ti 0.237657593 0.237657593 0.500000000 > Ti 0.751221208 0.246208753 0.500000000 > Ti 0.246208753 0.751221208 0.500000000 > Ti 0.763075374 0.763075374 0.500000000 > Ti 0.269267824 0.269267824 0.813779029 > Ti 0.749311691 0.251786232 0.833658489 > Ti 0.251786232 0.749311691 0.833658489 > Ti 0.741569474 0.741569474 0.829227895 > O 0.652332320 0.149871487 0.000000000 > O 0.149871487 0.652332320 0.000000000 > O 0.648713680 0.648713680 0.000000000 > O 0.155238060 0.155238060 0.326384494 > O 0.652290092 0.150787458 0.333038822 > O 0.150787458 0.652290092 0.333038822 > O 0.653798667 0.653798667 0.336935635 > O 0.155238060 0.155238060 0.673615536 > O 0.652290092 0.150787458 0.666961208 > O 0.150787458 0.652290092 0.666961208 > O 0.653798667 0.653798667 0.663064395 > O 0.340201024 0.340201024 0.000000000 > O 0.844284770 0.348460645 0.000000000 > O 0.348460645 0.844284770 0.000000000 > O 0.841167231 0.841167231 0.000000000 > O 0.350847343 0.350847343 0.343732671 > O 0.846562364 0.346794842 0.332680914 > O 0.346794842 0.846562364 0.332680914 > O 0.849375587 0.849375587 0.329278748 > O 0.350847343 0.350847343 0.656267359 > O 0.846562364 0.346794842 0.667319116 > O 0.346794842 0.846562364 0.667319116 > O 0.849375587 0.849375587 0.670721282 > O 0.396954319 0.099266404 0.164239842 > O 0.908323382 0.100237125 0.161621944 > O 0.400136271 0.594239940 0.166856966 > O 0.900420254 0.595644595 0.167042102 > O 0.398819672 0.095650761 0.500000000 > O 0.905834151 0.099259720 0.500000000 > O 0.404318666 0.599248899 0.500000000 > O 0.903265490 0.598692666 0.500000000 > O 0.396954319 0.099266404 0.835760138 > O 0.908323382 0.100237125 0.838378036 > O 0.400136271 0.594239940 0.833143014 > O 0.900420254 0.595644595 0.832957878 > O 0.099266404 0.396954319 0.164239842 > O 0.594239940 0.400136271 0.166856966 > O 0.100237125 0.908323382 0.161621944 > O 0.595644595 0.900420254 0.167042102 > O 0.095650761 0.398819672 0.500000000 > O 0.599248899 0.404318666 0.500000000 > O 0.099259720 0.905834151 0.500000000 > O 0.598692666 0.903265490 0.500000000 > O 0.099266404 0.396954319 0.835760138 > O 0.594239940 0.400136271 0.833143014 > O 0.100237125 0.908323382 0.838378036 > O 0.595644595 0.900420254 0.832957878 > K_POINTS automatic > 2 2 2 1 1 1 > > Thanks a lot > Ali Kazempour > Physics Department, Isfahn University of Technology > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From marsamos at democritos.it Mon Jun 7 09:12:23 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Mon, 07 Jun 2010 09:12:23 +0200 Subject: [Pw_forum] HSE error In-Reply-To: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> References: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> Message-ID: <20100607091223.jms4anoxa8cs04g4@mail.democritos.it> Sorry I did not noticed that you said it already works for doubly charged. Quoting kazempoor at ph.iut.ac.ir: > > Dear all > I used HSE functional for a single charged supercell and at the > begining I got this error, but the calculation for doubly charged > suercell is safe. Why does this happen? > -------------------------------------------- > > from read_namelists : error # 88 > reading namelist system > --------------------------------------------- > > my input is in following: > > > &control > calculation = 'relax' > restart_mode='from_scratch' > prefix='hseo+' > verbosity='high' > pseudo_dir = './' > outdir='/ptmp/kazempou/scratch/' > / > &system > ibrav= 6 , celldm(1) =17.34,celldm(3)=0.965, nat= 71, ntyp= > 2,tot_charge=1,nelec=569, > ecutwfc =45.0,ecutrho=180,occupations='fixed', > degauss=0.0,nspin=2,nelup=285,neldw=284,input_dft='hse', nqx1 =1, > nqx2 =1 , nqx3 = 1,nbnd=320, > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-3 > / > &ions > / > ATOMIC_SPECIES > Ti 43.0 ti.optgga2.fhi.UPF > O 16.0 o.optgga1.fhi.UPF > ATOMIC_POSITIONS crystal > Ti -0.023349669 -0.023349669 0.000000000 > Ti 0.499349747 0.001769391 0.000000000 > Ti 0.001769391 0.499349747 0.000000000 > Ti 0.498876973 0.498876973 0.000000000 > Ti 0.002405588 0.002405588 0.329360580 > Ti 0.499568846 -0.000974012 0.333568764 > Ti -0.000974012 0.499568846 0.333568764 > Ti 0.507399533 0.507399533 0.336748419 > Ti 0.002405588 0.002405588 0.670639450 > Ti 0.499568846 -0.000974012 0.666431266 > Ti -0.000974012 0.499568846 0.666431266 > Ti 0.507399533 0.507399533 0.663251611 > Ti 0.269267824 0.269267824 0.186220951 > Ti 0.749311691 0.251786232 0.166341491 > Ti 0.251786232 0.749311691 0.166341491 > Ti 0.741569474 0.741569474 0.170772085 > Ti 0.237657593 0.237657593 0.500000000 > Ti 0.751221208 0.246208753 0.500000000 > Ti 0.246208753 0.751221208 0.500000000 > Ti 0.763075374 0.763075374 0.500000000 > Ti 0.269267824 0.269267824 0.813779029 > Ti 0.749311691 0.251786232 0.833658489 > Ti 0.251786232 0.749311691 0.833658489 > Ti 0.741569474 0.741569474 0.829227895 > O 0.652332320 0.149871487 0.000000000 > O 0.149871487 0.652332320 0.000000000 > O 0.648713680 0.648713680 0.000000000 > O 0.155238060 0.155238060 0.326384494 > O 0.652290092 0.150787458 0.333038822 > O 0.150787458 0.652290092 0.333038822 > O 0.653798667 0.653798667 0.336935635 > O 0.155238060 0.155238060 0.673615536 > O 0.652290092 0.150787458 0.666961208 > O 0.150787458 0.652290092 0.666961208 > O 0.653798667 0.653798667 0.663064395 > O 0.340201024 0.340201024 0.000000000 > O 0.844284770 0.348460645 0.000000000 > O 0.348460645 0.844284770 0.000000000 > O 0.841167231 0.841167231 0.000000000 > O 0.350847343 0.350847343 0.343732671 > O 0.846562364 0.346794842 0.332680914 > O 0.346794842 0.846562364 0.332680914 > O 0.849375587 0.849375587 0.329278748 > O 0.350847343 0.350847343 0.656267359 > O 0.846562364 0.346794842 0.667319116 > O 0.346794842 0.846562364 0.667319116 > O 0.849375587 0.849375587 0.670721282 > O 0.396954319 0.099266404 0.164239842 > O 0.908323382 0.100237125 0.161621944 > O 0.400136271 0.594239940 0.166856966 > O 0.900420254 0.595644595 0.167042102 > O 0.398819672 0.095650761 0.500000000 > O 0.905834151 0.099259720 0.500000000 > O 0.404318666 0.599248899 0.500000000 > O 0.903265490 0.598692666 0.500000000 > O 0.396954319 0.099266404 0.835760138 > O 0.908323382 0.100237125 0.838378036 > O 0.400136271 0.594239940 0.833143014 > O 0.900420254 0.595644595 0.832957878 > O 0.099266404 0.396954319 0.164239842 > O 0.594239940 0.400136271 0.166856966 > O 0.100237125 0.908323382 0.161621944 > O 0.595644595 0.900420254 0.167042102 > O 0.095650761 0.398819672 0.500000000 > O 0.599248899 0.404318666 0.500000000 > O 0.099259720 0.905834151 0.500000000 > O 0.598692666 0.903265490 0.500000000 > O 0.099266404 0.396954319 0.835760138 > O 0.594239940 0.400136271 0.833143014 > O 0.100237125 0.908323382 0.838378036 > O 0.595644595 0.900420254 0.832957878 > K_POINTS automatic > 2 2 2 1 1 1 > > Thanks a lot > Ali Kazempour > Physics Department, Isfahn University of Technology > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From sclauzer at sissa.it Mon Jun 7 09:27:16 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 7 Jun 2010 09:27:16 +0200 Subject: [Pw_forum] HSE error In-Reply-To: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> References: <1831344285.71277.1275830091441.JavaMail.root@mta.iut.ac.ir> Message-ID: Dear Ali, which version of QE are you using? You should always specify it when posting this kind of problems. Il giorno 06/giu/10, alle ore 15:14, kazempoor at ph.iut.ac.ir ha scritto: > > Dear all > I used HSE functional for a single charged supercell and at the > begining I got this error, but the calculation for doubly charged > suercell is safe. Why does this happen? > -------------------------------------------- > > from read_namelists : error # 88 > reading namelist system > --------------------------------------------- > > my input is in following: > > > &control > calculation = 'relax' > restart_mode='from_scratch' > prefix='hseo+' > verbosity='high' > pseudo_dir = './' > outdir='/ptmp/kazempou/scratch/' > / > &system > ibrav= 6 , celldm(1) =17.34,celldm(3)=0.965, nat= 71, ntyp= > 2,tot_charge=1,nelec=569, > ecutwfc =45.0,ecutrho=180,occupations='fixed', > degauss=0.0,nspin=2,nelup=285,neldw=284,input_dft='hse', nqx1 =1, > nqx2 =1 , nqx3 = 1,nbnd=320, I know that in version 4.2 the nelec flag has been disabled, since it was redundant (you only need the pseudopotentials, which define the total number of valence electrons, and the total charge, as given in tot_charge). Please pay also attention at the nelup and neldw flags, I think they are also obsolete in v4.2. You should use tot_magnetization or multiplicity instead. BTW, how was the input for the doubly charged cell? Assuming that you are using QE-4.2, if you have specified nelec or nelup or neldw, the program should have stopped with the same error message. As a general remark, when you see such kind of errors (error while reading namelist) it means (with 99.9% probability) that there is a mistake in your input file, so you should check it again and have a look at the input file descriptions in the Doc/ folder. Regards, GS ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100607/9e4ee1de/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100607/9e4ee1de/attachment.bin From dalcorso at sissa.it Mon Jun 7 09:33:54 2010 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Mon, 07 Jun 2010 09:33:54 +0200 Subject: [Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique In-Reply-To: References: <20100604211504.jcc80cx1wow0oo4w@webmail.sissa.it> Message-ID: <1275896034.3250.9.camel@dhcp-098.cm.sissa.it> On Fri, 2010-06-04 at 23:06 +0100, Elie Moujaes wrote: > Dear Andrea, > > Thanks very much for the information. In fact, when I am running the > ph2.in file (for q=2), it runs normally and doesnt give any error > except that the output does not have a dynamical matrix i.e. the > output looks like: > > > > > Program PHONON v.4.2 starts on 2Jun2010 at 17:44:23 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please acknowledge > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 > (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More > details at > > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > Ultrasoft (Vanderbilt) Pseudopotentials > Starting q 2 larger than total number of q points 10 or of > last q You still have some file in the outdir directory that is confusing the recover procedure. I tried your input and it runs smoothly. Gamma point is calculated correctly and the grid example seems to work. Please check that your outdir directory is clean before starting the ph.x GRID run. Andrea > > PHONON : 7.04s CPU time, 7.83s WALL time > > INITIALIZATION: > > init_vloc : 0.02s CPU 0.02s WALL ( 1 calls) > init_us_1 : 0.02s CPU 0.02s WALL ( 1 calls) > > DYNAMICAL MATRIX: > > > > > > > > > > > > > > > > General routines > cft3 : 0.03s CPU 0.03s WALL ( 3 calls) > > > > > so it is empty underneath DYNAMICAL MATRIX. The only way i was able to > get rid of the recover error is to omit recover=.true. in the ph.in > program but I guess this is essential. I will also post the scf > calculation below: > > > > > > &control > > prefix='phmonog', > > calculation='scf', > > restart_mode='from_scratch', > > pseudo_dir = '/espresso-4.2/pseudo/', > > outdir='/tmp/results_MOUJAES/' > > verbosity='high' > > > > / > > &system > > ibrav= 4, celldm(1) =4.608737, celldm(3)=5.0, nat=2, ntyp= 1, > > ecutwfc = 110.D0,occupations='smearing', > smearing='methfessel-paxton', degauss=0.01 > > / > > &electrons > > conv_thr=1.D-10, > > diagonalization='david', > > mixing_mode='plain' > > / > > ATOMIC_SPECIES > > C 12.0107 C.pz-vbc.UPF > > ATOMIC_POSITIONS crystal > > C 0.000000 0.000000 0.000000 > > C 0.333333 -0.33333 0.000000 > > K_POINTS automatic > > 26 26 1 0 0 0 > > > > ANY SUGGESTIONS? > > > > Thank you > > > > Elie Moujaes > > University fo Nootingham > > NG7 2RD > > UK > > > > > > > > Date: Fri, 4 Jun 2010 21:15:04 +0200 > > From: dalcorso at sissa.it > > To: pw_forum at pwscf.org > > CC: dalcorso at sissa.it > > Subject: [Pw_forum] error while compiling the start_q, last_q, > start_irr and last_irr technique > > > > I am still using the start_q, last_q, start_irr and last_irr > technique > > (from GRID example) to calculate the phonon dispersion in graphene. > > Everything is ok until I run ph.x for the first q (q=1 the Gamma > > point). The input is: > > > > > > > > Phonon dispersion for monolayer graphene > > > > &inputph > > > > tr2_ph=1.0d-13, > > > > prefix='phmonog', > > > > ldisp=.true., > > > > nq1=8, nq2=8, nq3=1 > > > > start_q=1, > > > > last_q=1, > > > > start_irr=1, > > > > last_irr=4, > > > > recover=.true., > > > > amass(1)=12.0107, > > > > outdir='/tmp/results_MOUJAES/q1', > > > > fildyn='mgraph881.dyn', > > > > / > > > > No errors in running ph.x but teh output is a bit strange like : > > > > > > > > > > Program PHONON v.4.2 starts on 4Jun2010 at 14:35:33 > > > > This program is part of the open-source Quantum ESPRESSO suite > > for quantum simulation of materials; please acknowledge > > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > > URL http://www.quantum-espresso.org", > > in publications or presentations arising from this work. More > details at > > > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > > > Ultrasoft (Vanderbilt) Pseudopotentials > > Starting q 2 larger than total number of q points 10 or of last q 1 > > > > This error depends on the fact that the recover procedure is > confused > > because the code was doing the second q point when it was > interrupted > > and > > now you are trying to recover (you have recover=.true.) but ask to > calculate > > only q point 1. You are not allowed to change start_q and last_q > > before finishing a calculation. Probably this part should be more > > robust for these kind of problems, but at the moment it is not, > sorry. > > > > When you try again and change q point to 2, the recover files are > now > > a mess and you get an error from the library routine that reads > > the recovering files. > > > > At this point the only solution is to remove the outdir/_ph* files > and > > start again. If you have already the dynamical matrices of all q > points > > but the first you can simply calculate the gamma point starting from > scratch. > > > > If the problem is still present after cleaning the outdir > directory, > > and it is reproducible, please post also the input of pw.x. > > > > HTH > > > > Andrea > > > > ---------------------------------------------------------------- > > 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 > > > ______________________________________________________________________ > Get a free e-mail account with Hotmail. Sign-up now. > _______________________________________________ > 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 giacsport at libero.it Mon Jun 7 09:39:07 2010 From: giacsport at libero.it (giacsport at libero.it) Date: Mon, 7 Jun 2010 09:39:07 +0200 (CEST) Subject: [Pw_forum] checkallsym : error Message-ID: <8591360.306061275896347448.JavaMail.defaultUser@defaultHost> Dear All, I am performing a geometry relaxation of alpha-N2 system After 3 scf cycles I got this message task # 0 from checkallsym : error # 1 some of the original symmetry operations not satisfied Could anybody kindly help me? Moreover, is there a way to search in the forum directly specifying some Keywords Here I also report my input &control calculation='relax', pseudo_dir='/home/giacomo/src/pseudo/' prefix='N2' wf_collect=.true. outdir='/scr/giacomo/PWSCF_test/GaN/Nitrogen/ecutwfc_30/' / &system ntyp=1, nat=8, ibrav=1, a= 5.644, ecutwfc= 30., nosym=.false. / &ELECTRONS conv_thr= 1.d-10, mixing_beta = 0.7 diago_thr_init = 1.0e-6 diago_full_acc = .true. / &IONS bfgs_ndim = 3, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES N 1. N.pz-vbc.UPF ATOMIC_POSITIONS crystal N 0.054 0.054 0.054 N 0.946 0.946 0.946 N 0.446 0.946 0.554 N 0.554 0.054 0.446 N 0.446 0.554 0.054 N 0.554 0.446 0.946 N 0.054 0.446 0.554 N 0.946 0.554 0.446 K_POINTS (automatic) 8 8 8 1 1 1 Very best, Giacomo Giacomo Giorgi, PhD Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656 From sclauzer at sissa.it Mon Jun 7 12:03:04 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 7 Jun 2010 12:03:04 +0200 Subject: [Pw_forum] occupancies of density matrix in LDA+U In-Reply-To: References: Message-ID: Dear Gianluca, Il giorno 04/giu/10, alle ore 07:43, Gianluca Giovannetti ha scritto: > Dear All, > > i write you as i need to know the occupancies of d states in my > calculations and i would like to do it by looking at the occupation > matrix. > > i have made a self-consistent calculation with the following input > file: > > FeSe > &control > calculation = 'scf' > restart_mode = 'from_scratch' > prefix = 'fese' > tprnfor = .true. > pseudo_dir = './' > outdir = './' > iprint = 2 > / > &system > ibrav = 8 > celldm(1) = 10.0852834932257 > celldm(2) = 1.00000000000000 > celldm(3) = 1.03521095322306 > nat = 8 > ntyp = 5 > ecutwfc = 35.0 > ecutrho = 350.0 > nbnd = 120 > occupations = 'smearing' > smearing = 'methfessel-paxton' > degauss = 0.01 > nspin = 2 > starting_magnetization(1) = -1.0 > starting_magnetization(2) = 1.0 > starting_magnetization(3) = -1.0 > starting_magnetization(4) = 1.0 > starting_magnetization(5) = 0.0 > lda_plus_u =.true. > lda_plus_u =.true. > Hubbard_U(1) = 1.d-8 > Hubbard_U(2) = 1.d-8 > Hubbard_U(3) = 1.d-8 > Hubbard_U(4) = 1.d-8 > Hubbard_alpha(1) = 1.d-8 > Hubbard_alpha(2) = 1.d-8 > Hubbard_alpha(3) = 1.d-8 > Hubbard_alpha(4) = 1.d-8 > / > &electrons > conv_thr = 1.0d-8 > diagonalization = 'cg' > / > ATOMIC_SPECIES > Fe1 55.845 Fe.pbe-sp-van.UPF > Fe2 55.845 Fe.pbe-sp-van.UPF > Fe3 55.845 Fe.pbe-sp-van.UPF > Fe4 55.845 Fe.pbe-sp-van.UPF > Se 78.96 Se.pbe-van.UPF > ATOMIC_POSITIONS { crystal } > Fe1 0.00000000 0.50000000 0.00000000 > Fe2 1.00000000 0.00000000 0.00000000 > Fe3 0.50000000 0.50000000 0.00000000 > Fe4 0.50000000 0.00000000 0.00000000 > Se 0.24999979 0.74999981 0.73480000 > Se 0.75000021 0.74999981 0.26520000 > Se 0.75000021 0.25000019 0.73480000 > Se 0.24999979 0.25000019 0.26520000 > K_POINTS {automatic} > 10 10 8 0 0 0 > > Calculations are fine. > As you can see: > (i) Fe-Fe bonds are along x and y axes so i`m in the correct > framework for calling d states as they are, What does this mean? In my understanding, as soon as you break spherical simmetry, d states can mix among themselves and they can also hybridize with states with different angular momentum. > (ii) i used U=0 to have printed the occupation matrix calculated in > LDA+U scheme. > > In the output file of QE i can read: > ------------------------------------------------------------------------------------------------------------- > atom 4 spin 1 > eigenvalues: 0.9283366 0.9383877 0.9483978 0.9712519 0.9740784 > eigenvectors > 1 -0.1720270 0.0000000 0.0000000 -0.9850922 0.0000000 > 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 > 3 0.0000000 0.0000000 -1.0000000 0.0000000 0.0000000 > 4 0.0000000 0.0000000 0.0000000 0.0000000 -1.0000000 > 5 -0.9850922 0.0000000 0.0000000 0.1720270 0.0000000 > occupations > 0.973 0.000 0.000 -0.008 0.000 > 0.000 0.938 0.000 0.000 0.000 > 0.000 0.000 0.948 0.000 0.000 > -0.008 0.000 0.000 0.930 0.000 > 0.000 0.000 0.000 0.000 0.971 > atom 4 spin 2 > eigenvalues: 0.3553238 0.3753074 0.4625234 0.5670451 0.6892263 > eigenvectors > 1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 > 2 0.0000000 -1.0000000 0.0000000 0.0000000 0.0000000 > 3 0.7516066 0.0000000 0.0000000 0.6596117 0.0000000 > 4 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 > 5 0.6596117 0.0000000 0.0000000 -0.7516066 0.0000000 > occupations > 0.561 0.000 0.000 -0.112 0.000 > 0.000 0.375 0.000 0.000 0.000 > 0.000 0.000 0.567 0.000 0.000 > -0.112 0.000 0.000 0.591 0.000 > 0.000 0.000 0.000 0.000 0.355 > ------------------------------------------------------------------------------------------------------------- > > what are these quantities? The eigenvalues and eigenvectors of the occupation matrix built by project KS eigenstates onto the d atomic orbitals (as defined, for instace, in PP/projwfc.f90) and summing over the BZ. > How can i extract the occupancies of d states for this data? You can get the occupancies by "grepping" the lines which start with "eigenvalues". The eigenvectors tell you which of the original d states take part in each eigenstate and their weight. > What is the order (the relation between label of d state and its > occupancy)? > I want to make a table having how many electrons i have in z2, xz, > yz, x2-y2, xy for up and down components. The "occupations" matrix should be what you want. It is the n_{I,m,m', \sigma} matrix before the diagonalization procedure of above, hence it contains the occupations on the orginal atomic orbitals (not mixed). Please have a look at the PRB of Cococcioni & de Gironcoli (2005) and at subroutines write_ns.f90 and new_ns.f90 in the PW/ folder. HTH GS > > > thank you in advance. > > ciao > > Gianluca > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100607/30627c04/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100607/30627c04/attachment-0001.bin From paulatto at sissa.it Mon Jun 7 12:27:58 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 07 Jun 2010 12:27:58 +0200 Subject: [Pw_forum] overlap of atoms In-Reply-To: References: Message-ID: On Fri, 04 Jun 2010 15:25:32 +0200, Payam Norouzzadeh wrote: > Actually I used both Xcrysden and Jmol to visualize the structure. The > result was good If I remember correctly, XCrysDen automatically removes overlapping atoms, it will just print a warning to the terminal, which may pass unnoticed. regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From gianluca.giovannetti at gmail.com Mon Jun 7 12:44:39 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Mon, 7 Jun 2010 12:44:39 +0200 Subject: [Pw_forum] occupancies of density matrix in LDA+U In-Reply-To: References: Message-ID: Dear Gabriele, thank you for your reply. i think i get what i wanted from your explanation. ciao Gianluca On Mon, Jun 7, 2010 at 12:03 PM, Gabriele Sclauzero wrote: > Dear Gianluca, > > Il giorno 04/giu/10, alle ore 07:43, Gianluca Giovannetti ha scritto: > > Dear All, > > i write you as i need to know the occupancies of d states in my > calculations and i would like to do it by looking at the occupation matrix. > > i have made a self-consistent calculation with the following input file: > > FeSe > &control > calculation = 'scf' > restart_mode = 'from_scratch' > prefix = 'fese' > tprnfor = .true. > pseudo_dir = './' > outdir = './' > iprint = 2 > / > &system > ibrav = 8 > celldm(1) = 10.0852834932257 > celldm(2) = 1.00000000000000 > celldm(3) = 1.03521095322306 > nat = 8 > ntyp = 5 > ecutwfc = 35.0 > ecutrho = 350.0 > nbnd = 120 > occupations = 'smearing' > smearing = 'methfessel-paxton' > degauss = 0.01 > nspin = 2 > starting_magnetization(1) = -1.0 > starting_magnetization(2) = 1.0 > starting_magnetization(3) = -1.0 > starting_magnetization(4) = 1.0 > starting_magnetization(5) = 0.0 > lda_plus_u =.true. > lda_plus_u =.true. > Hubbard_U(1) = 1.d-8 > Hubbard_U(2) = 1.d-8 > Hubbard_U(3) = 1.d-8 > Hubbard_U(4) = 1.d-8 > Hubbard_alpha(1) = 1.d-8 > Hubbard_alpha(2) = 1.d-8 > Hubbard_alpha(3) = 1.d-8 > Hubbard_alpha(4) = 1.d-8 > / > &electrons > conv_thr = 1.0d-8 > diagonalization = 'cg' > / > ATOMIC_SPECIES > Fe1 55.845 Fe.pbe-sp-van.UPF > Fe2 55.845 Fe.pbe-sp-van.UPF > Fe3 55.845 Fe.pbe-sp-van.UPF > Fe4 55.845 Fe.pbe-sp-van.UPF > Se 78.96 Se.pbe-van.UPF > ATOMIC_POSITIONS { crystal } > Fe1 0.00000000 0.50000000 0.00000000 > Fe2 1.00000000 0.00000000 0.00000000 > Fe3 0.50000000 0.50000000 0.00000000 > Fe4 0.50000000 0.00000000 0.00000000 > Se 0.24999979 0.74999981 0.73480000 > Se 0.75000021 0.74999981 0.26520000 > Se 0.75000021 0.25000019 0.73480000 > Se 0.24999979 0.25000019 0.26520000 > K_POINTS {automatic} > 10 10 8 0 0 0 > > Calculations are fine. > As you can see: > (i) Fe-Fe bonds are along x and y axes so i`m in the correct framework for > calling d states as they are, > > > What does this mean? > In my understanding, as soon as you break spherical simmetry, d states can > mix among themselves and they can also hybridize with states with different > angular momentum. > > (ii) i used U=0 to have printed the occupation matrix calculated in LDA+U > scheme. > > In the output file of QE i can read: > > ------------------------------------------------------------------------------------------------------------- > atom 4 spin 1 > eigenvalues: 0.9283366 0.9383877 0.9483978 0.9712519 0.9740784 > eigenvectors > 1 -0.1720270 0.0000000 0.0000000 -0.9850922 0.0000000 > 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 > 3 0.0000000 0.0000000 -1.0000000 0.0000000 0.0000000 > 4 0.0000000 0.0000000 0.0000000 0.0000000 -1.0000000 > 5 -0.9850922 0.0000000 0.0000000 0.1720270 0.0000000 > occupations > 0.973 0.000 0.000 -0.008 0.000 > 0.000 0.938 0.000 0.000 0.000 > 0.000 0.000 0.948 0.000 0.000 > -0.008 0.000 0.000 0.930 0.000 > 0.000 0.000 0.000 0.000 0.971 > atom 4 spin 2 > eigenvalues: 0.3553238 0.3753074 0.4625234 0.5670451 0.6892263 > eigenvectors > 1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 > 2 0.0000000 -1.0000000 0.0000000 0.0000000 0.0000000 > 3 0.7516066 0.0000000 0.0000000 0.6596117 0.0000000 > 4 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 > 5 0.6596117 0.0000000 0.0000000 -0.7516066 0.0000000 > occupations > 0.561 0.000 0.000 -0.112 0.000 > 0.000 0.375 0.000 0.000 0.000 > 0.000 0.000 0.567 0.000 0.000 > -0.112 0.000 0.000 0.591 0.000 > 0.000 0.000 0.000 0.000 0.355 > > ------------------------------------------------------------------------------------------------------------- > > what are these quantities? > > > The eigenvalues and eigenvectors of the occupation matrix built by project > KS eigenstates onto the d atomic orbitals (as defined, for instace, in > PP/projwfc.f90) and summing over the BZ. > > > How can i extract the occupancies of d states for this data? > > > You can get the occupancies by "grepping" the lines which start with > "eigenvalues". The eigenvectors tell you which of the original d states take > part in each eigenstate and their weight. > > What is the order (the relation between label of d state and its > occupancy)? > I want to make a table having how many electrons i have in z2, xz, yz, > x2-y2, xy for up and down components. > > > The "occupations" matrix should be what you want. It is the > n_{I,m,m',\sigma} matrix before the diagonalization procedure of above, > hence it contains the occupations on the orginal atomic orbitals (not > mixed). > > Please have a look at the PRB of Cococcioni & de Gironcoli (2005) and at > subroutines write_ns.f90 and new_ns.f90 in the PW/ folder. > > > HTH > > > GS > > > > > thank you in advance. > > ciao > > Gianluca > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > _______________________________________________ > 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/20100607/4dfd4f37/attachment.htm From niuli1978 at yahoo.com.cn Mon Jun 7 15:09:59 2010 From: niuli1978 at yahoo.com.cn (li niu) Date: Mon, 7 Jun 2010 21:09:59 +0800 (CST) Subject: [Pw_forum] LDA norm-conserving pseudopotentials of Zn, Ga or In atoms Message-ID: <122419.15446.qm@web15006.mail.cnb.yahoo.com> Dear users and developers, I want to calculate Raman spectrum of InGaO3(ZnO)n compounds. USPP can not be used to calculate Raman intensity, and there is not NCPP in the official website for Zn, In and Ga atoms. I?m now looking for suitable pseudopotentials. Does anyone have a PZ LDA norm-conserving pseudopotentials for Zn, In or Ga atoms ? Thanks in advance and kind regards. ? Li Niu School of Physics and Electronic Engineering, Harbin Normal University , Harbin 150025, China ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100607/52425153/attachment.htm From giannozz at democritos.it Mon Jun 7 15:36:53 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Jun 2010 15:36:53 +0200 Subject: [Pw_forum] checkallsym : error In-Reply-To: <8591360.306061275896347448.JavaMail.defaultUser@defaultHost> References: <8591360.306061275896347448.JavaMail.defaultUser@defaultHost> Message-ID: <8646EB81-B476-4B8C-B92B-80A08AF8C05A@democritos.it> On Jun 7, 2010, at 9:39 , giacsport at libero.it wrote: > from checkallsym : error # 1 > some of the original symmetry operations not satisfied your input works for me in serial execution, with the current (CVS) version. If you do not specify the version you are using and how you are using it, it is hard to see if a problem is real or not. > Moreover, is there a way to search in the forum > directly specifying some Keywords there are two search links here: http://www.quantum-espresso.org/contacts.php 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 Mon Jun 7 17:39:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Jun 2010 17:39:02 +0200 Subject: [Pw_forum] mkl problem In-Reply-To: <79B17CA7-2FAC-49C4-B33E-BBF995A7965D@gmail.com> References: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> <935c498c8614075c6676841aef519d79.squirrel@webmail.fq.edu.uy> <201006041128.23658.giuseppe.mattioli@mlib.ism.cnr.it> <79B17CA7-2FAC-49C4-B33E-BBF995A7965D@gmail.com> Message-ID: <5D5D789D-A19B-4F61-9D36-DC3DB181A632@democritos.it> On Jun 4, 2010, at 21:35 , Osman Baris Malcioglu wrote: > If there is significant demand for the older version, the configure > script > can be modified, with a sacrifice in performance in the configuration > step of some select cases. the problem is not just performance, but having a readable configure.ac file (or at least, a non-unreadable one). The MKL libraries are a major contributor to entropy. I took the point of view that from now on, only "recent" versions of MKL are supported, and only if they are properly installed (i.e. with environment variables LD_LIBRARY_PATH and LIBRARY_PATH pointing to them), are supported. "Recent" in the above sentence means "later than those installed on my work PC 2.5 years ago", so not exactly "the latest and the greatest". Of course there can be mistakes in the configure.ac file, which are revealed by a careful inspection of the config.log file (admittedly, not a fun reading). 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 wparker at mps.ohio-state.edu Mon Jun 7 17:21:03 2010 From: wparker at mps.ohio-state.edu (William Parker) Date: Mon, 7 Jun 2010 11:21:03 -0400 (EDT) Subject: [Pw_forum] KZK method In-Reply-To: References: Message-ID: Hi Mohaddeseh, KZK is in QE. Just use input_dft='kzk', and QE will use the volume of your cell to calculate the finite-size correction. Compare that to the value using PZ-LDA to get your correction for QMC. --William ====================================================================== William Parker Tel : +1 (614) 292-2887 Graduate Research Associate Fax : +1 (614) 292-7557 Ohio State University Department of Physics 191 West Woodruff Avenue email: wparker at mps.ohio-state.edu Columbus, OH 43210-1117 http://www.physics.ohio-state.edu/~wparker U.S.A. Office: 2025 Physics Research Building ====================================================================== On Mon, 7 Jun 2010, mohaddeseh abbasnejad wrote: > Dear all, > > Would you please let me know if KZK method (Kwee, Zhang, and Krakauer) has > been implemented in PWscf code? If so, how should I use it? > Thanks in advance. > > Yours, > --------------------------------------------------------- > > 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 > > --------------------------------------------------------- > From giannozz at democritos.it Mon Jun 7 18:21:33 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Jun 2010 18:21:33 +0200 Subject: [Pw_forum] checkallsym : error In-Reply-To: <8591360.306061275896347448.JavaMail.defaultUser@defaultHost> References: <8591360.306061275896347448.JavaMail.defaultUser@defaultHost> Message-ID: <3970CD2A-B6EE-4A06-8FF8-A13FE65CF2E3@democritos.it> On Jun 7, 2010, at 9:39 , giacsport at libero.it wrote: > bfgs_ndim = 3 use the default. For some reason this little-tested (amd little-used) option has some numerical instability in this specific case when run on parallel machines 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 quantumdft at gmail.com Mon Jun 7 19:29:32 2010 From: quantumdft at gmail.com (vega lew) Date: Tue, 8 Jun 2010 01:29:32 +0800 Subject: [Pw_forum] a question about plotrho.x Message-ID: Dear all, Just now, I wanted to 2D map of charge density difference. When everything was done, I tried to use plotrho.x of QE 4.1.2 to plot the 2D map. I found the "Logarithmic scale (y/n)? >" option is missing, which was indicated clearly in the hands on QE tutorial.(#17 Page of tutorial_postproc.pdf) I wonder how could I plot the 2D charge density (difference) map using Logarithmic scale? thank you for reading 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/20100608/47c79a95/attachment.htm From giannozz at democritos.it Mon Jun 7 19:47:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Jun 2010 19:47:10 +0200 Subject: [Pw_forum] a question about plotrho.x In-Reply-To: References: Message-ID: <6D8A8F6C-5215-4806-B21F-95CC3C0F7FB8@democritos.it> On Jun 7, 2010, at 19:29 , vega lew wrote: > I wonder how could I plot the 2D charge density (difference) > map using Logarithmic scale? charge density differences can be positive or negative. Can you see why the logarithmic scale is disabled? 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 elie.moujaes at hotmail.co.uk Mon Jun 7 22:19:33 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 7 Jun 2010 21:19:33 +0100 Subject: [Pw_forum] vc-relax of a 60 atom supercell Message-ID: Dear all, I am trying to relax a 60 atom supercell of graphene using vc-relax. (1) I want the relaxation to be with respect to both atomic coordinates and supercell vectors, Is vc-relax the correct calculation to use. (2) I used a vc relax to my superstructure but the programm stopped at the 9th iteration (well it did not stop literally but the calculations ended with no 9th iterations and no converged results along with errors related to the c_bands): Initial potential from superposition of free atoms Check: negative starting charge= -1.223428 starting charge 239.99756, renormalised to 240.00000 negative rho (up, down): 0.122E+01 0.000E+00 Starting wfc are 240 atomic wfcs total cpu time spent up to now is 11871.45 secs per-process dynamical memory: 384.3 Mb Self-consistent Calculation iteration # 1 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 6.7 negative rho (up, down): 0.117E+01 0.000E+00 total cpu time spent up to now is 47489.34 secs total energy = -643.54940490 Ry Harris-Foulkes estimate = -643.62010992 Ry estimated scf accuracy < 4.23960826 Ry iteration # 2 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.77E-03, avg # of iterations = 2.2 negative rho (up, down): 0.109E+00 0.000E+00 total cpu time spent up to now is 64468.90 secs total energy = -642.58636317 Ry Harris-Foulkes estimate = -643.55371202 Ry estimated scf accuracy < 3.93330724 Ry iteration # 3 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.64E-03, avg # of iterations = 2.0 negative rho (up, down): 0.148E+00 0.000E+00 total cpu time spent up to now is 85947.86 secs total energy = -642.70459925 Ry Harris-Foulkes estimate = -642.70343771 Ry estimated scf accuracy < 0.07850650 Ry iteration # 4 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 3.27E-05, avg # of iterations = 12.4 negative rho (up, down): 0.151E+00 0.000E+00 total cpu time spent up to now is 112929.09 secs total energy = -642.71219905 Ry Harris-Foulkes estimate = -642.71283310 Ry estimated scf accuracy < 0.06999785 Ry iteration # 5 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 2.92E-05, avg # of iterations = 1.1 negative rho (up, down): 0.349E+00 0.000E+00 total cpu time spent up to now is 135493.02 secs total energy = -642.68724348 Ry Harris-Foulkes estimate = -642.71241729 Ry estimated scf accuracy < 0.06752485 Ry iteration # 6 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 2.81E-05, avg # of iterations = 8.8 negative rho (up, down): 0.397E+00 0.000E+00 total cpu time spent up to now is 167131.43 secs total energy = -642.68305797 Ry Harris-Foulkes estimate = -642.69027767 Ry estimated scf accuracy < 0.02138677 Ry iteration # 7 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 8.91E-06, avg # of iterations = 9.6 negative rho (up, down): 0.375E+00 0.000E+00 total cpu time spent up to now is 195521.38 secs total energy = -642.68507799 Ry Harris-Foulkes estimate = -642.68373726 Ry estimated scf accuracy < 0.01412971 Ry iteration # 8 ecut= 10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 5.89E-06, avg # of iterations = 1.2 negative rho (up, down): 0.241E+00 0.000E+00 total cpu time spent up to now is 217886.22 secs total energy = -642.68307655 Ry Harris-Foulkes estimate = -642.68513864 Ry estimated scf accuracy < 0.01367803 Ry iteration # 9 ecut= 10.00 Ry beta=0.05 The input file is: &control prefix='GB mgraphene', calculation='vc-relax', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/Moujaes-Results/', tstress = .true., tprnfor = .true., disk_io = 'low' / &system ibrav= 0, celldm(1) =1.88972, nat=60, ntyp= 1, ecutwfc = 110D0 ,occupations='smearing', smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-8, mixing_beta=0.05D0, mixing_mode='local-TF', diagonalization='david' / & ions ion_dynamics = 'bfgs', pot_extrapolation = 'second-order', wfc_extrapolation = 'second-order' / & cell cell_dynamics = 'bfgs', press_conv_thr = 0.1 ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C -11.737980 -3.561278 0.000000 C -11.057718 -1.211571 0.000000 C -12.450000 -7.189838 0.000000 C -12.450000 -5.773759 0.000000 ..................... (up to the remainder of the 60 atoms) K_POINTS automatic 26 26 1 0 0 0 CELL_PARAMETERS hexagonal 24.527679 0.000000 0.000000 0.000003 6.614491 0.000000 0.000000 0.000000 10.000000 _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100607/441d3de5/attachment-0001.htm From tkaloni at gmail.com Tue Jun 8 06:17:49 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Tue, 8 Jun 2010 10:02:49 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 21 In-Reply-To: References: Message-ID: Dear all How one can calculate the cell parameter in hexagonal lattice and is there any relation between ecutwfc and lattice parameter. On Tue, Jun 8, 2010 at 2:04 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: KZK method (William Parker) > 2. Re: checkallsym : error (Paolo Giannozzi) > 3. a question about plotrho.x (vega lew) > 4. Re: a question about plotrho.x (Paolo Giannozzi) > 5. vc-relax of a 60 atom supercell (Elie Moujaes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Jun 2010 11:21:03 -0400 (EDT) > From: William Parker > Subject: Re: [Pw_forum] KZK method > To: PWSCF Forum > Message-ID: > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Mohaddeseh, > > KZK is in QE. Just use input_dft='kzk', and QE will use the volume of > your cell to calculate the finite-size correction. Compare that to the > value using PZ-LDA to get your correction for QMC. > > --William > > ====================================================================== > William Parker Tel : +1 (614) 292-2887 > Graduate Research Associate Fax : +1 (614) 292-7557 > Ohio State University > Department of Physics > 191 West Woodruff Avenue email: wparker at mps.ohio-state.edu > Columbus, OH 43210-1117 http://www.physics.ohio-state.edu/~wparker > U.S.A. > > Office: 2025 Physics Research Building > ====================================================================== > > On Mon, 7 Jun 2010, mohaddeseh abbasnejad wrote: > > > Dear all, > > > > Would you please let me know if KZK method (Kwee, Zhang, and Krakauer) > has > > been implemented in PWscf code? If so, how should I use it? > > Thanks in advance. > > > > Yours, > > --------------------------------------------------------- > > > > 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 > > > > --------------------------------------------------------- > > > > > ------------------------------ > > Message: 2 > Date: Mon, 7 Jun 2010 18:21:33 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] checkallsym : error > To: "giacsport at libero.it" , PWSCF Forum > > Message-ID: <3970CD2A-B6EE-4A06-8FF8-A13FE65CF2E3 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Jun 7, 2010, at 9:39 , giacsport at libero.it wrote: > > > bfgs_ndim = 3 > > use the default. For some reason this little-tested (amd little-used) > option has some numerical instability in this specific case when run > on parallel machines > > 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: 3 > Date: Tue, 8 Jun 2010 01:29:32 +0800 > From: vega lew > Subject: [Pw_forum] a question about plotrho.x > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > Just now, I wanted to 2D map of charge density difference. When everything > was done, I tried to use plotrho.x of QE 4.1.2 to plot the 2D map. > > I found the "Logarithmic scale (y/n)? >" option is missing, which was > indicated clearly in the hands on QE tutorial.(#17 Page of > tutorial_postproc.pdf) > > I wonder how could I plot the 2D charge density (difference) map using > Logarithmic scale? > > thank you for reading > > 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/20100608/47c79a95/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Mon, 7 Jun 2010 19:47:10 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] a question about plotrho.x > To: PWSCF Forum > Message-ID: <6D8A8F6C-5215-4806-B21F-95CC3C0F7FB8 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Jun 7, 2010, at 19:29 , vega lew wrote: > > > I wonder how could I plot the 2D charge density (difference) > > map using Logarithmic scale? > > charge density differences can be positive or negative. > Can you see why the logarithmic scale is disabled? > > 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: 5 > Date: Mon, 7 Jun 2010 21:19:33 +0100 > From: Elie Moujaes > Subject: [Pw_forum] vc-relax of a 60 atom supercell > To: > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Dear all, I am trying to relax a 60 atom supercell of graphene using > vc-relax. > > > > (1) I want the relaxation to be with respect to both atomic coordinates and > supercell vectors, Is vc-relax the correct calculation to use. > > > > (2) I used a vc relax to my superstructure but the programm stopped at the > 9th iteration (well it did not stop literally but the calculations ended > with no 9th iterations and no converged results along with errors related to > the c_bands): > > > > Initial potential from superposition of free atoms > Check: negative starting charge= -1.223428 > > starting charge 239.99756, renormalised to 240.00000 > > negative rho (up, down): 0.122E+01 0.000E+00 > Starting wfc are 240 atomic wfcs > > total cpu time spent up to now is 11871.45 secs > > per-process dynamical memory: 384.3 Mb > > Self-consistent Calculation > > iteration # 1 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 6.7 > > negative rho (up, down): 0.117E+01 0.000E+00 > > total cpu time spent up to now is 47489.34 secs > > total energy = -643.54940490 Ry > Harris-Foulkes estimate = -643.62010992 Ry > estimated scf accuracy < 4.23960826 Ry > > iteration # 2 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > ethr = 1.77E-03, avg # of iterations = 2.2 > > negative rho (up, down): 0.109E+00 0.000E+00 > > total cpu time spent up to now is 64468.90 secs > > total energy = -642.58636317 Ry > Harris-Foulkes estimate = -643.55371202 Ry > estimated scf accuracy < 3.93330724 Ry > > iteration # 3 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > ethr = 1.64E-03, avg # of iterations = 2.0 > > negative rho (up, down): 0.148E+00 0.000E+00 > > total cpu time spent up to now is 85947.86 secs > > total energy = -642.70459925 Ry > Harris-Foulkes estimate = -642.70343771 Ry > estimated scf accuracy < 0.07850650 Ry > > iteration # 4 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > ethr = 3.27E-05, avg # of iterations = 12.4 > > negative rho (up, down): 0.151E+00 0.000E+00 > > total cpu time spent up to now is 112929.09 secs > > total energy = -642.71219905 Ry > Harris-Foulkes estimate = -642.71283310 Ry > estimated scf accuracy < 0.06999785 Ry > > iteration # 5 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > ethr = 2.92E-05, avg # of iterations = 1.1 > > negative rho (up, down): 0.349E+00 0.000E+00 > > total cpu time spent up to now is 135493.02 secs > > total energy = -642.68724348 Ry > Harris-Foulkes estimate = -642.71241729 Ry > estimated scf accuracy < 0.06752485 Ry > > iteration # 6 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > ethr = 2.81E-05, avg # of iterations = 8.8 > > negative rho (up, down): 0.397E+00 0.000E+00 > > total cpu time spent up to now is 167131.43 secs > > total energy = -642.68305797 Ry > Harris-Foulkes estimate = -642.69027767 Ry > estimated scf accuracy < 0.02138677 Ry > > iteration # 7 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > ethr = 8.91E-06, avg # of iterations = 9.6 > > negative rho (up, down): 0.375E+00 0.000E+00 > > total cpu time spent up to now is 195521.38 secs > > total energy = -642.68507799 Ry > Harris-Foulkes estimate = -642.68373726 Ry > estimated scf accuracy < 0.01412971 Ry > > iteration # 8 ecut= 10.00 Ry beta=0.05 > Davidson diagonalization with overlap > ethr = 5.89E-06, avg # of iterations = 1.2 > > negative rho (up, down): 0.241E+00 0.000E+00 > > total cpu time spent up to now is 217886.22 secs > > total energy = -642.68307655 Ry > Harris-Foulkes estimate = -642.68513864 Ry > estimated scf accuracy < 0.01367803 Ry > > iteration # 9 ecut= 10.00 Ry beta=0.05 > > The input file is: > > > > > > &control > prefix='GB mgraphene', > calculation='vc-relax', > restart_mode='from_scratch', > pseudo_dir = > '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', > outdir='/exp/home/caiapo/emoujaes/Moujaes-Results/', > tstress = .true., > tprnfor = .true., > disk_io = 'low' > > / > &system > ibrav= 0, celldm(1) =1.88972, nat=60, ntyp= 1, ecutwfc = 110D0 > ,occupations='smearing', smearing='methfessel-paxton', degauss=0.01 > / > &electrons > conv_thr=1.D-8, > mixing_beta=0.05D0, > mixing_mode='local-TF', > diagonalization='david' > / > & ions > ion_dynamics = 'bfgs', > pot_extrapolation = 'second-order', > wfc_extrapolation = 'second-order' > / > & cell > cell_dynamics = 'bfgs', > press_conv_thr = 0.1 > > ATOMIC_SPECIES > C 12.0107 C.pz-vbc.UPF > ATOMIC_POSITIONS angstrom > C -11.737980 -3.561278 0.000000 > C -11.057718 -1.211571 0.000000 > C -12.450000 -7.189838 0.000000 > C -12.450000 -5.773759 0.000000 > > ..................... > > (up to the remainder of the 60 atoms) > > > > K_POINTS automatic > 26 26 1 0 0 0 > > CELL_PARAMETERS hexagonal > > 24.527679 0.000000 0.000000 > 0.000003 6.614491 0.000000 > 0.000000 0.000000 10.000000 > > > _________________________________________________________________ > http://clk.atdmt.com/UKM/go/197222280/direct/01/ > Do you have a story that started on Hotmail? Tell us now > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100607/441d3de5/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 36, Issue 21 > **************************************** > -- ################################### ****************************************** Thaneshwor Prashad Kaloni TWAS-BOSE FELLOW /JRF S N Bose national Centre for Basic Sciences Kolkata 700098, INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100608/359be55d/attachment-0001.htm From baroni at sissa.it Tue Jun 8 07:50:16 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 8 Jun 2010 07:50:16 +0200 Subject: [Pw_forum] PLEASE, USE MESSAGE-SPECIFIC "subject" HEADERS - Re: Pw_forum Digest, Vol 36, Issue 21 In-Reply-To: References: Message-ID: <449B84B2-02A7-41BA-93B5-4D2D9C51A065@sissa.it> As a matter of courtesy to other members of the forum, please take the time to write a regular post (specifying a meaningful "subject" field), rather than hitting hurriedly "reply" to a blulky digest mailing. On Jun 8, 2010, at 6:17 AM, Thaneshwor Kaloni wrote: > > Dear all > How one can calculate the cell parameter in hexagonal lattice as with any other lattice. you have to minimize the crystal energy as a function of the crystal volume and of all the internal degrees of freedom of the unit cell (positions of the atoms in the lattice basis) > and is there any relation between ecutwfc and lattice parameter. NO - ecutwfc is a property of the PW basis set, which only depends on the type of pseudopotential(s) in use. Best wishes, Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100608/20692189/attachment.htm From quantumdft at gmail.com Tue Jun 8 08:17:24 2010 From: quantumdft at gmail.com (vega lew) Date: Tue, 8 Jun 2010 14:17:24 +0800 Subject: [Pw_forum] a question about plotrho.x In-Reply-To: <6D8A8F6C-5215-4806-B21F-95CC3C0F7FB8@democritos.it> References: <6D8A8F6C-5215-4806-B21F-95CC3C0F7FB8@democritos.it> Message-ID: Dear sir Thank you for you reply. I see. best, vega On Tue, Jun 8, 2010 at 1:47 AM, Paolo Giannozzi wrote: > > On Jun 7, 2010, at 19:29 , vega lew wrote: > > > I wonder how could I plot the 2D charge density (difference) > > map using Logarithmic scale? > > charge density differences can be positive or negative. > Can you see why the logarithmic scale is disabled? > > 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 > -- ================================================================================== 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/20100608/38ff512e/attachment.htm From tkaloni at gmail.com Tue Jun 8 09:32:36 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Tue, 8 Jun 2010 13:17:36 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 23 In-Reply-To: References: Message-ID: Dear all, I am calculating the band structure of graphene but ,unable to get it. My input is as... # self-consistent calculation cat > c.scf.in << EOF &control calculation='scf' restart_mode='from_scratch', prefix='c' pseudo_dir = '/home/kaloni/hpc/espresso-4.1.2/pseudo', outdir='./' / &system ibrav = 0, celldm(1) = 1.8897261249935, nat = 2, ntyp = 1, ecutwfc =40.0 occupations='smearing', smearing='cold', degauss=0.02 / &electrons startingwfc='random' diagonalization='cg' conv_thr = 1.0e-8 / CELL_PARAMETERS cubic 2.1304215583 -1.2299994602 0.0000000000 0.0000000000 2.4599989204 0.0000000000 0.0000000000 0.0000000000 7.0000000000 / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS C 0.0000000000 0.0000000000 0.0000000000 C 0.3333333333 0.6666666667 0.0000000000 K_POINTS (AUTOMATIC) 9 9 9 1 1 1 EOF $ECHO " running the scf calculation...\c" $PW_COMMAND < c.scf.in > c.scf.out check_failure $? $ECHO " done" # post-processing for charge density cat > c.pp_rho.in << EOF &inputpp prefix = 'c' outdir = './' filplot = 'ccharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'ccharge' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'c.rho.dat' e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, nx=56, ny=40 / EOF $ECHO " running pp.x to do a 2-d plot of the charge density...\c" $PP_COMMAND < c.pp_rho.in > c.pp_rho.out check_failure $? $ECHO " done" # plotrho cat > c.plotrho.in << EOF c.rho.dat c.rho.ps n 0 0.09 6 EOF $ECHO " running plotrho.x to generate rho.ps...\c" $PLOTRHO_COMMAND < c.plotrho.in > c.plotrho.out $ECHO " done" # band structure calculation along high-symmetry lines cat > c.band.in << EOF &control calculation='bands' pseudo_dir = '/home/kaloni/hpc/espresso-4.1.2/pseudo/', outdir='./', prefix='c' / &system ibrav = 0, celldm(1) = 1.8897261249935, nat = 2, ntyp = 1, ecutwfc =40.0 occupations='smearing', smearing='cold', degauss=0.02 / &electrons startingwfc='random' diagonalization='cg' conv_thr = 1.0e-8 / CELL_PARAMETERS cubic 2.1304215583 -1.2299994602 0.0000000000 0.0000000000 2.4599989204 0.0000000000 0.0000000000 0.0000000000 7.0000000000 / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS C 0.0000000000 0.0000000000 0.0000000000 C 0.3333333333 0.6666666667 0.0000000000 K_POINTS 61 0.000000000 0.000000000 0.000000000 1.0 0.016666666 0.026838318 0.000000000 1.0 0.033333333 0.053676635 0.000000000 1.0 0.049999999 0.080514952 0.000000000 1.0 0.066666666 0.107353270 0.000000000 1.0 0.083333332 0.134191587 0.000000000 1.0 0.099999999 0.161029905 0.000000000 1.0 0.116666665 0.187868222 0.000000000 1.0 0.133333332 0.214706540 0.000000000 1.0 0.149999999 0.241544857 0.000000000 1.0 0.166666665 0.268383175 0.000000000 1.0 0.183333332 0.295221493 0.000000000 1.0 0.199999998 0.322059810 0.000000000 1.0 0.216666664 0.348898127 0.000000000 1.0 0.233333331 0.375736445 0.000000000 1.0 0.249999997 0.402574762 0.000000000 1.0 0.266666664 0.429413080 0.000000000 1.0 0.283333330 0.456251397 0.000000000 1.0 0.299999997 0.483089715 0.000000000 1.0 0.316666663 0.509928032 0.000000000 1.0 0.333333330 0.536766350 0.000000000 1.0 0.341666663 0.524315857 0.000000000 1.0 0.349999997 0.511865365 0.000000000 1.0 0.358333330 0.499414872 0.000000000 1.0 0.366666664 0.486964380 0.000000000 1.0 0.374999998 0.474513887 0.000000000 1.0 0.383333331 0.462063395 0.000000000 1.0 0.391666664 0.449612902 0.000000000 1.0 0.399999998 0.437162410 0.000000000 1.0 0.408333332 0.424711917 0.000000000 1.0 0.416666665 0.412261425 0.000000000 1.0 0.424999999 0.399810932 0.000000000 1.0 0.433333332 0.387360440 0.000000000 1.0 0.441666665 0.374909948 0.000000000 1.0 0.449999999 0.362459455 0.000000000 1.0 0.458333332 0.350008963 0.000000000 1.0 0.466666666 0.337558470 0.000000000 1.0 0.474999999 0.325107977 0.000000000 1.0 0.483333333 0.312657485 0.000000000 1.0 0.491666667 0.300206993 0.000000000 1.0 0.500000000 0.287756500 0.000000000 1.0 0.475000000 0.273368675 0.000000000 1.0 0.450000000 0.258980850 0.000000000 1.0 0.425000000 0.244593025 0.000000000 1.0 0.400000000 0.230205200 0.000000000 1.0 0.375000000 0.215817375 0.000000000 1.0 0.350000000 0.201429550 0.000000000 1.0 0.325000000 0.187041725 0.000000000 1.0 0.300000000 0.172653900 0.000000000 1.0 0.275000000 0.158266075 0.000000000 1.0 0.250000000 0.143878250 0.000000000 1.0 0.225000000 0.129490425 0.000000000 1.0 0.200000000 0.115102600 0.000000000 1.0 0.175000000 0.100714775 0.000000000 1.0 0.150000000 0.086326950 0.000000000 1.0 0.125000000 0.071939125 0.000000000 1.0 0.100000000 0.057551300 0.000000000 1.0 0.075000000 0.043163475 0.000000000 1.0 0.050000000 0.028775650 0.000000000 1.0 0.025000000 0.014387825 0.000000000 1.0 0.000000000 0.000000000 0.000000000 1.0 EOF $ECHO " running the band-structure calculation for C...\c" $PW_COMMAND < c.band.in > c.band.out check_failure $? $ECHO " done" # post-processing for band structure cat > c.bands.in << EOF &inputpp prefix = 'c' outdir = './' filband = 'cbands.dat' / EOF $ECHO " running the post-processing for band structure...\c" $BANDS_COMMAND < c.bands.in > c.bands.out check_failure $? $ECHO " done" # plotband.x cat > c.plotband.in << EOF cbands.dat -10.0 10 cbands.xmgr cbands.ps -3.14 1.0 3.14 EOF $ECHO " running plotband.x to generate cbands.ps...\c" $PLOTBAND_COMMAND < c.plotband.in > c.plotband.out check_failure $? $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100608/773505ba/attachment.htm From degironc at sissa.it Tue Jun 8 10:38:14 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 08 Jun 2010 10:38:14 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 23 In-Reply-To: References: Message-ID: <4C0E0176.50409@sissa.it> Dear Thaneshwor Kaloni, it works for me, however the structure does not look like graphene to me. have you tried to visualize your structure by xcrysden or some other software ? it seams to me that some of your C-C bonds are VERY short (0.7 A) and some VERY long (1.9 A). stefano Thaneshwor Kaloni wrote: > Dear all, > I am calculating the band structure of graphene but ,unable to get it. > My input is as... > # self-consistent calculation > cat > c.scf.in << EOF > &control > calculation='scf' > restart_mode='from_scratch', > prefix='c' > pseudo_dir = '/home/kaloni/hpc/espresso-4.1.2/pseudo', > outdir='./' > / > &system > ibrav = 0, > celldm(1) = 1.8897261249935, > nat = 2, > ntyp = 1, > ecutwfc =40.0 > occupations='smearing', smearing='cold', degauss=0.02 > / > &electrons > startingwfc='random' > diagonalization='cg' > conv_thr = 1.0e-8 > / > CELL_PARAMETERS cubic > 2.1304215583 -1.2299994602 0.0000000000 > 0.0000000000 2.4599989204 0.0000000000 > 0.0000000000 0.0000000000 7.0000000000 > > / > ATOMIC_SPECIES > C 12.0107 C.pz-vbc.UPF > ATOMIC_POSITIONS > C 0.0000000000 0.0000000000 0.0000000000 > C 0.3333333333 0.6666666667 0.0000000000 > K_POINTS (AUTOMATIC) > 9 9 9 1 1 1 > EOF > $ECHO " running the scf calculation...\c" > $PW_COMMAND < c.scf.in > c.scf.out > check_failure $? > $ECHO " done" > > # post-processing for charge density > cat > c.pp_rho.in << EOF > &inputpp > prefix = 'c' > outdir = './' > filplot = 'ccharge' > plot_num= 0 > / > &plot > nfile = 1 > filepp(1) = 'ccharge' > weight(1) = 1.0 > iflag = 2 > output_format = 2 > fileout = 'c.rho.dat' > e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > nx=56, ny=40 > / > EOF > $ECHO " running pp.x to do a 2-d plot of the charge density...\c" > $PP_COMMAND < c.pp_rho.in > c.pp_rho.out > check_failure $? > $ECHO " done" > > # plotrho > cat > c.plotrho.in << EOF > c.rho.dat > c.rho.ps > n > 0 0.09 6 > EOF > $ECHO " running plotrho.x to generate rho.ps...\c" > $PLOTRHO_COMMAND < c.plotrho.in > c.plotrho.out > $ECHO " done" > > # band structure calculation along high-symmetry lines > cat > c.band.in << EOF > &control > calculation='bands' > pseudo_dir = '/home/kaloni/hpc/espresso-4.1.2/pseudo/', > outdir='./', > prefix='c' > / > &system > ibrav = 0, > celldm(1) = 1.8897261249935, > nat = 2, > ntyp = 1, > ecutwfc =40.0 > occupations='smearing', smearing='cold', degauss=0.02 > / > &electrons > startingwfc='random' > diagonalization='cg' > conv_thr = 1.0e-8 > / > CELL_PARAMETERS cubic > 2.1304215583 -1.2299994602 0.0000000000 > 0.0000000000 2.4599989204 0.0000000000 > 0.0000000000 0.0000000000 7.0000000000 > / > ATOMIC_SPECIES > C 12.0107 C.pz-vbc.UPF > ATOMIC_POSITIONS > C 0.0000000000 0.0000000000 0.0000000000 > C 0.3333333333 0.6666666667 0.0000000000 > K_POINTS > 61 > 0.000000000 0.000000000 0.000000000 1.0 > 0.016666666 0.026838318 0.000000000 1.0 > 0.033333333 0.053676635 0.000000000 1.0 > 0.049999999 0.080514952 0.000000000 1.0 > 0.066666666 0.107353270 0.000000000 1.0 > 0.083333332 0.134191587 0.000000000 1.0 > 0.099999999 0.161029905 0.000000000 1.0 > 0.116666665 0.187868222 0.000000000 1.0 > 0.133333332 0.214706540 0.000000000 1.0 > 0.149999999 0.241544857 0.000000000 1.0 > 0.166666665 0.268383175 0.000000000 1.0 > 0.183333332 0.295221493 0.000000000 1.0 > 0.199999998 0.322059810 0.000000000 1.0 > 0.216666664 0.348898127 0.000000000 1.0 > 0.233333331 0.375736445 0.000000000 1.0 > 0.249999997 0.402574762 0.000000000 1.0 > 0.266666664 0.429413080 0.000000000 1.0 > 0.283333330 0.456251397 0.000000000 1.0 > 0.299999997 0.483089715 0.000000000 1.0 > 0.316666663 0.509928032 0.000000000 1.0 > 0.333333330 0.536766350 0.000000000 1.0 > 0.341666663 0.524315857 0.000000000 1.0 > 0.349999997 0.511865365 0.000000000 1.0 > 0.358333330 0.499414872 0.000000000 1.0 > 0.366666664 0.486964380 0.000000000 1.0 > 0.374999998 0.474513887 0.000000000 1.0 > 0.383333331 0.462063395 0.000000000 1.0 > 0.391666664 0.449612902 0.000000000 1.0 > 0.399999998 0.437162410 0.000000000 1.0 > 0.408333332 0.424711917 0.000000000 1.0 > 0.416666665 0.412261425 0.000000000 1.0 > 0.424999999 0.399810932 0.000000000 1.0 > 0.433333332 0.387360440 0.000000000 1.0 > 0.441666665 0.374909948 0.000000000 1.0 > 0.449999999 0.362459455 0.000000000 1.0 > 0.458333332 0.350008963 0.000000000 1.0 > 0.466666666 0.337558470 0.000000000 1.0 > 0.474999999 0.325107977 0.000000000 1.0 > 0.483333333 0.312657485 0.000000000 1.0 > 0.491666667 0.300206993 0.000000000 1.0 > 0.500000000 0.287756500 0.000000000 1.0 > 0.475000000 0.273368675 0.000000000 1.0 > 0.450000000 0.258980850 0.000000000 1.0 > 0.425000000 0.244593025 0.000000000 1.0 > 0.400000000 0.230205200 0.000000000 1.0 > 0.375000000 0.215817375 0.000000000 1.0 > 0.350000000 0.201429550 0.000000000 1.0 > 0.325000000 0.187041725 0.000000000 1.0 > 0.300000000 0.172653900 0.000000000 1.0 > 0.275000000 0.158266075 0.000000000 1.0 > 0.250000000 0.143878250 0.000000000 1.0 > 0.225000000 0.129490425 0.000000000 1.0 > 0.200000000 0.115102600 0.000000000 1.0 > 0.175000000 0.100714775 0.000000000 1.0 > 0.150000000 0.086326950 0.000000000 1.0 > 0.125000000 0.071939125 0.000000000 1.0 > 0.100000000 0.057551300 0.000000000 1.0 > 0.075000000 0.043163475 0.000000000 1.0 > 0.050000000 0.028775650 0.000000000 1.0 > 0.025000000 0.014387825 0.000000000 1.0 > 0.000000000 0.000000000 0.000000000 1.0 > > EOF > $ECHO " running the band-structure calculation for C...\c" > $PW_COMMAND < c.band.in > c.band.out > check_failure $? > $ECHO " done" > > # post-processing for band structure > cat > c.bands.in << EOF > &inputpp > prefix = 'c' > outdir = './' > filband = 'cbands.dat' > / > EOF > $ECHO " running the post-processing for band structure...\c" > $BANDS_COMMAND < c.bands.in > c.bands.out > check_failure $? > $ECHO " done" > > # plotband.x > cat > c.plotband.in << EOF > cbands.dat > -10.0 10 > cbands.xmgr > cbands.ps > -3.14 > 1.0 3.14 > EOF > $ECHO " running plotband.x to generate cbands.ps...\c" > $PLOTBAND_COMMAND < c.plotband.in > c.plotband.out > check_failure $? > $ECHO " done" > > $ECHO > $ECHO "$EXAMPLE_DIR: done" > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From fwshuchao111 at gmail.com Tue Jun 8 12:48:10 2010 From: fwshuchao111 at gmail.com (Weyl Fang) Date: Tue, 8 Jun 2010 18:48:10 +0800 Subject: [Pw_forum] Rs: the charge of the individual atom Message-ID: Dear all, I am working on TiO2 with the QE-4.1.2. I am a beginner to use QE. Recently I want to know the charge of the individual atom in the system. Can I get the charge value like mulliken charge? If I can, How can i get the value? Any suggestion would be helpful. Thanks! With regards Weyl FANG Graduate student in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China Email: weylfang 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/20100608/085fecf7/attachment-0001.htm From lfhuang at theory.issp.ac.cn Tue Jun 8 13:29:19 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 08 Jun 2010 19:29:19 +0800 Subject: [Pw_forum] =?utf-8?q?the_charge_of_the_individual_atom?= Message-ID: <20100608112919.9766.qmail@ms.hfcas.ac.cn> Dear W. Fang: You can run the excutable "projwfc.x" to get the charge of an individual atom. Note: it is not the Mulliken population analysis, but the Lowdin population analysis. The former takes accounts the overlaps between orbitals, while the latter not and a spilling factor is used to judge the contribution of the omitting term. Despite this difference, these two population analyses can both precisely tell the physics behind in vast cases. You can read the INPUT file for the "projwfc.x" and the text on the head of projwfc.f90 for details. Best Wishes! Yours Sincerely L. F. Huang > Weyl Fang wrote: > I want to know the charge of the individual atom in the system. Can I get the charge value like mulliken charge? >If I can, How can i get the value? ------ ====================================================================== L.F.Huang(???) 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/20100608/ffb954d1/attachment.htm From giannozz at democritos.it Tue Jun 8 18:02:45 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Jun 2010 18:02:45 +0200 Subject: [Pw_forum] mkl problem In-Reply-To: <5D5D789D-A19B-4F61-9D36-DC3DB181A632@democritos.it> References: <201006031223.17527.giuseppe.mattioli@mlib.ism.cnr.it> <935c498c8614075c6676841aef519d79.squirrel@webmail.fq.edu.uy> <201006041128.23658.giuseppe.mattioli@mlib.ism.cnr.it> <79B17CA7-2FAC-49C4-B33E-BBF995A7965D@gmail.com> <5D5D789D-A19B-4F61-9D36-DC3DB181A632@democritos.it> Message-ID: <739658EC-AA8D-4FBE-8ADF-7E28C2B6989D@democritos.it> On Jun 7, 2010, at 17:39 , Paolo Giannozzi wrote: > Of course there can be mistakes in the configure.ac file ..or in some other place. It turns out that the downloaded packages do not contain some text files that are needed in order to link MKL libraries (a glitch in the packaging script: they are present in the original version). Fix (no warranty): - download and unpack the attached "missing-mkl.tar.gz" file, containing the missing files; OR - download and unpack the attached "newconf.tar.gz" file, containing the development version of "configure" (it doesn't need those files any longer) and some other modified install/ files. Thanks to all people reporting problems with MKL and to Baris and Martin who reported the solution. Paolo -------------- next part -------------- A non-text attachment was scrubbed... Name: missing-mkl.tar.gz Type: application/x-gzip Size: 314 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100608/50a35dac/attachment-0002.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: newconf.tar.gz Type: application/x-gzip Size: 68605 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100608/50a35dac/attachment-0003.bin -------------- 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 giannozz at democritos.it Tue Jun 8 22:36:14 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Jun 2010 22:36:14 +0200 Subject: [Pw_forum] vc-relax of a 60 atom supercell In-Reply-To: References: Message-ID: <59E60839-235B-4956-893F-4EC2E930717F@democritos.it> On Jun 7, 2010, at 22:19 , Elie Moujaes wrote: > I used a vc relax to my superstructure but the programm stopped at > the 9th iteration see here: http://www.quantum-espresso.org/user_guide/ node50.html#SECTION000111080000000000000 > (well it did not stop literally but the calculations ended with no > 9th iterations and no converged results along with errors related > to the c_bands): there are no errors. > iteration # 1 ecut= 10.00 Ry beta=0.05 > ecutwfc = 110D0 they don't look the same to me > ibrav= 0, celldm(1) =1.88972, > CELL_PARAMETERS hexagonal > 24.527679 0.000000 0.000000 > 0.000003 6.614491 0.000000 > 0.000000 0.000000 10.000000 why you all take pride in finding the most absurd way to specify > lattice parameters? 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 fwshuchao111 at gmail.com Wed Jun 9 02:51:13 2010 From: fwshuchao111 at gmail.com (Weyl Fang) Date: Wed, 9 Jun 2010 08:51:13 +0800 Subject: [Pw_forum] the charge of the individual atom References: Message-ID: Dear L. F. Huang, Thank you for your reply. I will follow your instruction to execute projwfc.x and see the result. Best wishes! Weyl Fang, fwshuchao111 at gmail.com 2010-06-09 Message: 1 Date: Tue, 08 Jun 2010 19:29:19 +0800 From: " lfhuang " Subject: Re: [Pw_forum] the charge of the individual atom To: " pw_forum " Message-ID: <20100608112919.9766.qmail at ms.hfcas.ac.cn> Content-Type: text/plain; charset="utf-8" Dear W. Fang: You can run the excutable "projwfc.x" to get the charge of an individual atom. Note: it is not the Mulliken population analysis, but the Lowdin population analysis. The former takes accounts the overlaps between orbitals, while the latter not and a spilling factor is used to judge the contribution of the omitting term. Despite this difference, these two population analyses can both precisely tell the physics behind in vast cases. You can read the INPUT file for the "projwfc.x" and the text on the head of projwfc.f90 for details. Best Wishes! Yours Sincerely L. F. Huang > Weyl Fang wrote: > I want to know the charge of the individual atom in the system. Can I get the charge value like mulliken charge? >If I can, How can i get the value? ------ ====================================================================== L.F.Huang(???) 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/20100609/07519a28/attachment.htm From hrhee at ucdavis.edu Wed Jun 9 02:56:43 2010 From: hrhee at ucdavis.edu (Hahnbidt Rhee) Date: Tue, 8 Jun 2010 17:56:43 -0700 Subject: [Pw_forum] Calculating multiple el-ph matrices simultaneously Message-ID: Hello, all. I am doing electron-phonon calculations, and my question pertains specifically to getting the el-ph matrices for each q-point. I have noticed that, although calculating a matrix of one q-point is independent of that of another q-point, the code calculates one q-point at a time--ie, one after the other--which makes for an inefficient and very time-consuming run. This is based on the elph.in input file (for ph.x), given in Example07 of the examples given by PWSCF, in which there is a line to specify the q-pt grid, nq1=4, nq2=4, nq3=4 > but not individual q-pts. So one run takes care of all the q-points. Is there an option (that I don't know of) to create separate jobs for each q-point so that I can calculate el-ph matrices of multiple inequivalent q-pts SIMULTANEOUSLY? I am using the parallel version of the latest code (v4.2), so it seems reasonable for there to be this option. Thank you! HB Rhee UC Davis -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100608/5094de50/attachment.htm From mohnish.iitk at gmail.com Wed Jun 9 05:46:53 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 9 Jun 2010 09:16:53 +0530 Subject: [Pw_forum] Rs: the charge of the individual atom In-Reply-To: References: Message-ID: Dear Fang ! Browse the link below. http://www.democritos.it/pipermail/pw_forum/2010-May/016847.html 2010/6/8 Weyl Fang > Dear all, > > I am working on TiO2 with the QE-4.1.2. I am a beginner to use QE. Recently > I want to know the charge of the individual atom in the system. Can I get > the charge value like mulliken charge? If I can, How can i get the value? > > Any suggestion would be helpful. Thanks! > > With regards > > Weyl FANG > Graduate student in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > Email: weylfang at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100609/45f8505e/attachment.htm From hqzhou at nju.edu.cn Wed Jun 9 07:17:36 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 9 Jun 2010 13:17:36 +0800 Subject: [Pw_forum] Calculating multiple el-ph matrices simultaneously References: Message-ID: Carefully read the "Additional information" of INPUT_PH.html, then you can do easilly what you want. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: Hahnbidt Rhee To: pw_forum at pwscf.org Sent: Wednesday, June 09, 2010 8:56 AM Subject: [Pw_forum] Calculating multiple el-ph matrices simultaneously Hello, all. I am doing electron-phonon calculations, and my question pertains specifically to getting the el-ph matrices for each q-point. I have noticed that, although calculating a matrix of one q-point is independent of that of another q-point, the code calculates one q-point at a time--ie, one after the other--which makes for an inefficient and very time-consuming run. This is based on the elph.in input file (for ph.x), given in Example07 of the examples given by PWSCF, in which there is a line to specify the q-pt grid, nq1=4, nq2=4, nq3=4 but not individual q-pts. So one run takes care of all the q-points. Is there an option (that I don't know of) to create separate jobs for each q-point so that I can calculate el-ph matrices of multiple inequivalent q-pts SIMULTANEOUSLY? I am using the parallel version of the latest code (v4.2), so it seems reasonable for there to be this option. Thank you! HB Rhee UC Davis ------------------------------------------------------------------------------ _______________________________________________ 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/20100609/f3f3a047/attachment.htm From amiri_physics at yahoo.com Wed Jun 9 09:35:29 2010 From: amiri_physics at yahoo.com (peyman amiri) Date: Wed, 9 Jun 2010 00:35:29 -0700 (PDT) Subject: [Pw_forum] MnSe-passivation Message-ID: <786829.76361.qm@web58008.mail.re3.yahoo.com> I am working on?a?(100) free surfaces of NaCl type MnSe structures with?(1 1 1) AF order, after passivation of Mn?& Se surface atroms?by Hydrogen atoms?the band gap reduces a little?(in compare of free surface without passivation)?and?from the results of cohesive energy we saw that the free surface MnSe is more stable than the free surface?after passivation. Now i am sure that passivation is not needed?in my work. How can i show?and prove this matter? May these results be due to?a computational errors? In principle when does we need to passive the?semiconductor surfaces? ? Any suggestions will be appreciated. Thanks Peiman ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ From degironc at sissa.it Wed Jun 9 10:27:06 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 09 Jun 2010 10:27:06 +0200 Subject: [Pw_forum] MnSe-passivation In-Reply-To: <786829.76361.qm@web58008.mail.re3.yahoo.com> References: <786829.76361.qm@web58008.mail.re3.yahoo.com> Message-ID: <4C0F505A.7030800@sissa.it> pristine semiconductor surfaces may show dangling bonds which correspond to partially filled electronic surface states in the gap. Nature dislikes this situation and semiconductor surfaces reconstruct , even in rather complicated ways, in order to eliminate these partially filled surface states. Passivating with hydrogen is a computationally easy way to saturate these dangling bonds without inducing large reconstructions/relaxations. If your surface does not show dangling bonds you do not need to passivate them. best, stefano peyman amiri wrote: > I am working on a (100) free surfaces of NaCl type MnSe structures with (1 1 1) AF order, after passivation of Mn & Se surface atroms by Hydrogen atoms the band gap reduces a little (in compare of free surface without passivation) and from the results of cohesive energy we saw that the free surface MnSe is more stable than the free surface after passivation. Now i am sure that passivation is not needed in my work. > > How can i show and prove this matter? > > May these results be due to a computational errors? > > In principle when does we need to passive the semiconductor surfaces? > > Any suggestions will be appreciated. > Thanks > Peiman > ====================================== > Peiman Amiri > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology, Iran > > Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 > ------------------------------ > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From kazempoor at ph.iut.ac.ir Wed Jun 9 11:45:33 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Wed, 9 Jun 2010 14:15:33 +0430 (IRDT) Subject: [Pw_forum] error in gamma In-Reply-To: <2038905288.86440.1276076547822.JavaMail.root@mta.iut.ac.ir> Message-ID: <275812171.86469.1276076733897.JavaMail.root@mta.iut.ac.ir> Dear all I used input file for supercell with gamma and gamma-shifted k-point for using in sax. I used 32 node each contain 32 core . The number of bands is set to 1024 . The problem is espresso can safely run pw1.in with shifetd 1 1 1 0.5 kpoint , but fails with error for run of pw2.in with 0 0 0 0.5 kpoint. The only difference in pw1.in and pw2.in is in thier k-points. the error is known is mailing-list : task # 952 from pzpotrf : error # 47 problems computing cholesky decomposition This is very strange because when I set nbnd=512 the pw1.in and pw2.in run without any problem . Can any one help me what can I do to remove the error ? PW1.IN &CONTROL title="tio2-gga" calculation='scf', restart_mode = 'from_scratch', outdir='/ptmp/kazempou/scratch/' tprnfor=.t., PSEUDO_DIR='./', verbosity='high', prefix='tio2-72-o-u', / &SYSTEM ibrav = 6, celldm(1) = 17.58, celldm(3) = 0.963 nat =71 ntyp = 2,occupations='smearing', smearing='gauss', degauss=0.001, ecutwfc = 70.0 , ecutrho = 400 nosym=.true., nbnd = 1024,lda_plus_u=.true. Hubbard_U(1)=1, / &ELECTRONS / ATOMIC_SPECIES Ti 47.86700 22-Ti.GGA.fhi.UPF O 15.99940 08-O.GGA.fhi.UPF ATOMIC_POSITIONS crystal Ti -0.022948970 -0.022948970 0.000000000 Ti 0.499127385 0.000981412 0.000000000 Ti 0.000981412 0.499127385 0.000000000 Ti 0.498277051 0.498277051 0.000000000 Ti 0.003537803 0.003537803 0.330828725 Ti 0.499009731 -0.001419922 0.333393463 Ti -0.001419922 0.499009731 0.333393463 Ti 0.506189041 0.506189041 0.336127942 Ti 0.003537803 0.003537803 0.669171305 Ti 0.499009731 -0.001419922 0.666606567 Ti -0.001419922 0.499009731 0.666606567 Ti 0.506189041 0.506189041 0.663872088 Ti 0.268917923 0.268917923 0.187187053 Ti 0.749579785 0.250958403 0.166291832 Ti 0.250958403 0.749579785 0.166291832 Ti 0.742203458 0.742203458 0.171302797 Ti 0.239402619 0.239402619 0.500000000 Ti 0.750089537 0.246842167 0.500000000 Ti 0.246842167 0.750089537 0.500000000 Ti 0.761637928 0.761637928 0.500000000 Ti 0.268917923 0.268917923 0.812812927 Ti 0.749579785 0.250958403 0.833708148 Ti 0.250958403 0.749579785 0.833708148 Ti 0.742203458 0.742203458 0.828697183 O 0.652474561 0.150441528 0.000000000 O 0.150441528 0.652474561 0.000000000 O 0.648560860 0.648560860 0.000000000 O 0.153969233 0.153969233 0.324248834 O 0.652414270 0.150940518 0.332607420 O 0.150940518 0.652414270 0.332607420 O 0.653738367 0.653738367 0.337187919 O 0.153969233 0.153969233 0.675751196 O 0.652414270 0.150940518 0.667392610 O 0.150940518 0.652414270 0.667392610 O 0.653738367 0.653738367 0.662812111 O 0.339454502 0.339454502 0.000000000 O 0.844778622 0.348893728 0.000000000 O 0.348893728 0.844778622 0.000000000 O 0.840933832 0.840933832 0.000000000 O 0.352032505 0.352032505 0.345820835 O 0.846957421 0.346857919 0.332674461 O 0.346857919 0.846957421 0.332674461 O 0.849410420 0.849410420 0.328573169 O 0.352032505 0.352032505 0.654179195 O 0.846957421 0.346857919 0.667325569 O 0.346857919 0.846957421 0.667325569 O 0.849410420 0.849410420 0.671426861 O 0.397198927 0.098954078 0.164473604 O 0.908215879 0.100420838 0.160976065 O 0.400213963 0.594460776 0.167107125 O 0.900868739 0.595756588 0.166898617 O 0.399551464 0.095780996 0.500000000 O 0.904680377 0.098999545 0.500000000 O 0.404692654 0.600239187 0.500000000 O 0.903193826 0.598576177 0.500000000 O 0.397198927 0.098954078 0.835526376 O 0.908215879 0.100420838 0.839023915 O 0.400213963 0.594460776 0.832892855 O 0.900868739 0.595756588 0.833101363 O 0.098954078 0.397198927 0.164473604 O 0.594460776 0.400213963 0.167107125 O 0.100420838 0.908215879 0.160976065 O 0.595756588 0.900868739 0.166898617 O 0.095780996 0.399551464 0.500000000 O 0.600239187 0.404692654 0.500000000 O 0.098999545 0.904680377 0.500000000 O 0.598576177 0.903193826 0.500000000 O 0.098954078 0.397198927 0.835526376 O 0.594460776 0.400213963 0.832892855 O 0.100420838 0.908215879 0.839023915 O 0.595756588 0.900868739 0.833101363 K_POINTS crystal 1 1.000000000 1.000000000 1.000000000 0.500000000 and PW2.in &CONTROL title="tio2-gga" calculation='scf', restart_mode = 'from_scratch', outdir='/ptmp/kazempou/scratch/' tprnfor=.t., PSEUDO_DIR='./', prefix='tio2-72-o-u', / &SYSTEM ibrav = 6, celldm(1) = 17.58, celldm(3) = 0.963 nat = 71, ntyp = 2, ecutwfc = 70.0 ,occupations='smearing', smearing='gauss', degauss=0.001, ecutrho = 400, nosym = .true. , nbnd = 1024,lda_plus_u=.true. Hubbard_U(1)=1, / &ELECTRONS / ATOMIC_SPECIES Ti 47.86700 22-Ti.GGA.fhi.UPF O 15.99940 08-O.GGA.fhi.UPF ATOMIC_POSITIONS crystal Ti -0.022948970 -0.022948970 0.000000000 Ti 0.499127385 0.000981412 0.000000000 Ti 0.000981412 0.499127385 0.000000000 Ti 0.498277051 0.498277051 0.000000000 Ti 0.003537803 0.003537803 0.330828725 Ti 0.499009731 -0.001419922 0.333393463 Ti -0.001419922 0.499009731 0.333393463 Ti 0.506189041 0.506189041 0.336127942 Ti 0.003537803 0.003537803 0.669171305 Ti 0.499009731 -0.001419922 0.666606567 Ti -0.001419922 0.499009731 0.666606567 Ti 0.506189041 0.506189041 0.663872088 Ti 0.268917923 0.268917923 0.187187053 Ti 0.749579785 0.250958403 0.166291832 Ti 0.250958403 0.749579785 0.166291832 Ti 0.742203458 0.742203458 0.171302797 Ti 0.239402619 0.239402619 0.500000000 Ti 0.750089537 0.246842167 0.500000000 Ti 0.246842167 0.750089537 0.500000000 Ti 0.761637928 0.761637928 0.500000000 Ti 0.268917923 0.268917923 0.812812927 Ti 0.749579785 0.250958403 0.833708148 Ti 0.250958403 0.749579785 0.833708148 Ti 0.742203458 0.742203458 0.828697183 O 0.652474561 0.150441528 0.000000000 O 0.150441528 0.652474561 0.000000000 O 0.648560860 0.648560860 0.000000000 O 0.153969233 0.153969233 0.324248834 O 0.652414270 0.150940518 0.332607420 O 0.150940518 0.652414270 0.332607420 O 0.653738367 0.653738367 0.337187919 O 0.153969233 0.153969233 0.675751196 O 0.652414270 0.150940518 0.667392610 O 0.150940518 0.652414270 0.667392610 O 0.653738367 0.653738367 0.662812111 O 0.339454502 0.339454502 0.000000000 O 0.844778622 0.348893728 0.000000000 O 0.348893728 0.844778622 0.000000000 O 0.840933832 0.840933832 0.000000000 O 0.352032505 0.352032505 0.345820835 O 0.846957421 0.346857919 0.332674461 O 0.346857919 0.846957421 0.332674461 O 0.849410420 0.849410420 0.328573169 O 0.352032505 0.352032505 0.654179195 O 0.846957421 0.346857919 0.667325569 O 0.346857919 0.846957421 0.667325569 O 0.849410420 0.849410420 0.671426861 O 0.397198927 0.098954078 0.164473604 O 0.908215879 0.100420838 0.160976065 O 0.400213963 0.594460776 0.167107125 O 0.900868739 0.595756588 0.166898617 O 0.399551464 0.095780996 0.500000000 O 0.904680377 0.098999545 0.500000000 O 0.404692654 0.600239187 0.500000000 O 0.903193826 0.598576177 0.500000000 O 0.397198927 0.098954078 0.835526376 O 0.908215879 0.100420838 0.839023915 O 0.400213963 0.594460776 0.832892855 O 0.900868739 0.595756588 0.833101363 O 0.098954078 0.397198927 0.164473604 O 0.594460776 0.400213963 0.167107125 O 0.100420838 0.908215879 0.160976065 O 0.595756588 0.900868739 0.166898617 O 0.095780996 0.399551464 0.500000000 O 0.600239187 0.404692654 0.500000000 O 0.098999545 0.904680377 0.500000000 O 0.598576177 0.903193826 0.500000000 O 0.098954078 0.397198927 0.835526376 O 0.594460776 0.400213963 0.832892855 O 0.100420838 0.908215879 0.839023915 O 0.595756588 0.900868739 0.833101363 K_POINTS crystal 1 0.000000000 0.000000000 0.000000000 0.500000000 Thanks a lot Ali Kazempour Physics Department, Isfahn University of Technology From giuseppe.mattioli at mlib.ism.cnr.it Wed Jun 9 13:01:54 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Wed, 9 Jun 2010 13:01:54 +0200 Subject: [Pw_forum] strange behaviour in LDA+U calculations Message-ID: <201006091301.54756.giuseppe.mattioli@mlib.ism.cnr.it> Dear all I'm facing strange problems while attempting to perform LDA+U calculations on Co-O clusters. PBE calculations work fine, both with PW and CP, both in closed shell and LSDA framework. In particular, ferromagnetic or antiferromagnetic initial guesses lead to closed shell electronic structures, i.e., total and absolute magnetization equal (or very close) to zero, and a safe insulating system. In order to improve the p-d hybridization between O 2p and Co 3d orbitals (their contributions to the DOS are quite separated in PBE calculations, and they are expected to be strongly mixed near to the valence band maximum) I've performed some PBE+U calculations by using reasonable values for the Co 3d and O 2p channels. In the case of closed shell calculations I obtain quite reasonable results, i.e., equilibrium geometries nicely similar to PBE ones, and an improved DOS in a better agreement with the available experimental data. I've tried to perform open shell calculations since January, I've tried to apply all of the standard and less standard tricks, but I have never (!) been able to converge a single calculation. There are no errors, they simply does not converge, with the system magnetization dancing around some selected values, depending on the initial guess (fm or afm). Notice that the system is still insulating (at a PBE+U closed shell level) and I've tried everything from fixed occupations to quite high smearing (gaussian, cold, ...) values. I thought that the CP code could help me, but I'm facing an even more strange problem... The very robust CP minimization of electronic dof successfully reach some ground state at the PBE+U level, the only (minor) problem being that you must put into the inpfile the final magnetization of the system. Then, I've tried to perform both damped and NVT (with Nose thermostats) MD simulations, trying several different open shell (nspin=2) configurations, ranging from tot_magnetization=0 to tot_magnetization=20. In the case of damped MD, the system temperature was kept very low, but my Co-O clusters tried to split into pieces (they are quite stable in both PBE and PBE+U PW calculations) while the total energy lowers. In the case of NVT MD thermostats went bananas and my clusters melt. You can scrub away Co and O scattered atoms from the supercell walls...:-) In the case of PBE calculations (both damped and NVT MD) everything went fine (no explosions, reasonably fast thermalization of the investigated systems, averaged bond distances similar to PW ones...) I can provide input files, but I suspect that this is not a matter of input failures... Is it LDA+U variational? I suspect it isn't... Is it foolish to perform MD calculation in such framework? Could you lend me a heavy hammer to persuade PW open shell calculations into convergence...? Thank you in advance for suggestions Giuseppe -- ******************************************************** - 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: From huazhorg at 163.com Wed Jun 9 13:09:48 2010 From: huazhorg at 163.com (=?gbk?B?wfW7qtbS?=) Date: Wed, 9 Jun 2010 19:09:48 +0800 (CST) Subject: [Pw_forum] "nat_todo",could anyone help me? Message-ID: Dear all, I want to do phonon calculation on an adsorption system with symmetry. So Idid some test calculations. I did a test calculation on a system, say an molecule is adsorbed on a surface. I just want to calculate the vibrational frequencies of the molecule. I set "nat_todo" in the input file of ph.x, and set the list of indices of atoms of the molecule. But in the result file there is not phonons. I don't know what's wrong with it, and how to set parameter in the input file of ph.x. Could anyone help me? Thank you! Regards Huazhong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100609/49039d1b/attachment.htm From nnlinh at sissa.it Wed Jun 9 14:29:51 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 09 Jun 2010 14:29:51 +0200 Subject: [Pw_forum] "nat_todo",could anyone help me? In-Reply-To: References: Message-ID: <4C0F893F.7030403@sissa.it> ??? wrote: > Dear all, > I want to do phonon calculation on an adsorption system with symmetry. > So Idid some test calculations. > I did a test calculation on a system, say an molecule is adsorbed on a > surface. I just want to calculate the vibrational frequencies of the > molecule. I set "nat_todo" in the input file of ph.x, and set the list > of indices of atoms of the molecule. But in the result file there is > not phonons. I don't know what's wrong with it, and how to set > parameter in the input file of ph.x. Could anyone help me? Can you be more specific? Is the outcome an error? or don't you understand the outcome? Please attach the output files, and we can consider that Also, Please enclose your affiliate when you post the question and discussion on forum. Best regards, Linh > Thank you! > > Regards > Huazhong > > > ------------------------------------------------------------------------ > ???????????????(????) > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From giannozz at democritos.it Wed Jun 9 16:51:59 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 09 Jun 2010 16:51:59 +0200 Subject: [Pw_forum] Calculating multiple el-ph matrices simultaneously In-Reply-To: References: Message-ID: <4C0FAA8F.6070402@democritos.it> Hahnbidt Rhee wrote: > Is there an option (that I don't know of) to create separate jobs for each > q-point so that I can calculate el-ph matrices of multiple inequivalent > q-pts SIMULTANEOUSLY? for sure there is the possibility to run each q-point separately: see examples/GRID_example. In principle it should work for el-ph matrices as well, but it is safe to try it for a simple system first just to be sure that it works Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From matteo at umn.edu Wed Jun 9 16:40:23 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Wed, 09 Jun 2010 09:40:23 -0500 Subject: [Pw_forum] strange behaviour in LDA+U calculations In-Reply-To: <201006091301.54756.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006091301.54756.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <4C0FA7D7.1080909@umn.edu> Dear Giuseppe, first of all: LDA+U is variational and the energy should be minimized during the electronic convergence independently from the algorithm you use. the answer/solution to your problem, however, is probably not easy. Of course it depends on many details (which are not in your email) about the oxidation state of Co, the splitting between d orbitals, the magnetic state. To me, from what you describe, it looks like it could be a case where a multi-reference wavefunction is needed to describe the ground state as it happens to be the case (I believe) for some TMOs when they become paramegnetic still preserving their Mott insulating character (LDA or GGA would predict a metal) This paper mentions this problem for some of the high pressure of MnO arXiv:1006.0565v1 [cond-mat.str-el] 3 Jun 2010 LDA+U works when you have a single determinant or when you break the symmetry to precipitate the system in one of those solutions. This is good when these solutions are degenerate, a bit worse when they are not.... so, at first I would try to understand what is the degeneracy situation in your system and how the different solutions between which your system oscillates differ from each other in terms of occupation of d and p orbitals. hope this helps. Matteo Giuseppe Mattioli wrote: > Dear all > I'm facing strange problems while attempting to perform LDA+U calculations on > Co-O clusters. PBE calculations work fine, both with PW and CP, both in > closed shell and LSDA framework. In particular, ferromagnetic or > antiferromagnetic initial guesses lead to closed shell electronic structures, > i.e., total and absolute magnetization equal (or very close) to zero, and a > safe insulating system. > In order to improve the p-d hybridization between O 2p and Co 3d orbitals > (their contributions to the DOS are quite separated in PBE calculations, and > they are expected to be strongly mixed near to the valence band maximum) > I've performed some PBE+U calculations by using reasonable values for the Co > 3d and O 2p channels. In the case of closed shell calculations I obtain quite > reasonable results, i.e., equilibrium geometries nicely similar to PBE ones, > and an improved DOS in a better agreement with the available experimental > data. I've tried to perform open shell calculations since January, I've tried > to apply all of the standard and less standard tricks, but I have never (!) > been able to converge a single calculation. There are no errors, they simply > does not converge, with the system magnetization dancing around some selected > values, depending on the initial guess (fm or afm). Notice that the system is > still insulating (at a PBE+U closed shell level) and I've tried everything > from fixed occupations to quite high smearing (gaussian, cold, ...) values. > > I thought that the CP code could help me, but I'm facing an even more strange > problem... The very robust CP minimization of electronic dof successfully > reach some ground state at the PBE+U level, the only (minor) problem being > that you must put into the inpfile the final magnetization of the system. > Then, I've tried to perform both damped and NVT (with Nose thermostats) MD > simulations, trying several different open shell (nspin=2) configurations, > ranging from tot_magnetization=0 to tot_magnetization=20. In the case of > damped MD, the system temperature was kept very low, but my Co-O clusters > tried to split into pieces (they are quite stable in both PBE and PBE+U PW > calculations) while the total energy lowers. In the case of NVT MD > thermostats went bananas and my clusters melt. You can scrub away Co and O > scattered atoms from the supercell walls...:-) > In the case of PBE calculations (both damped and NVT MD) everything went fine > (no explosions, reasonably fast thermalization of the investigated systems, > averaged bond distances similar to PW ones...) > I can provide input files, but I suspect that this is not a matter of input > failures... Is it LDA+U variational? I suspect it isn't... Is it foolish to > perform MD calculation in such framework? Could you lend me a heavy hammer to > persuade PW open shell calculations into convergence...? > > Thank you in advance for suggestions > > Giuseppe > > From marzari at MIT.EDU Wed Jun 9 21:32:35 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 09 Jun 2010 20:32:35 +0100 Subject: [Pw_forum] strange behaviour in LDA+U calculations In-Reply-To: <201006091301.54756.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006091301.54756.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <4C0FEC53.5010905@mit.edu> Dear Giuseppe, it looks like 1) PW does not converge PBE+U. Only things to try are really large smearings, and very small mixing factors. If the smearings are large, and the mixing is small, it should ultimately converge, and then you can reduce the smearing. For this purpose, fermi-dirac is probably the best choice, with its long tails occupying empty states. 2) glad that CP converged. the PBE+U solution, be it better or worse than PBE, leads to dissociation of the cluster - that's why damped dynamics leads to the cluster fragmenting, and canonical md shows it exploding. Nothing too unconventional - but the truth might be that these are very difficult systems to describe accurately in DFT - and PBE+U seems, for better or for worse, lead to dissociation. What is the right solution ? Impossible to say. If the clusters are stable experimentally, at one of the magnetizations you tried, than a dissociated solution is certainly wrong, and one that is not is only probably wrong. Start from something really simple (maybe one Co at most), and compare there PBE, PBE+U, and quantum chemsitry (ideally MRCI) solutions. Does anything work ? These are incredibly difficult systems to study - have also a look at e.g. Kulik et al JCP 2008. nicola Giuseppe Mattioli wrote: > Dear all > I'm facing strange problems while attempting to perform LDA+U calculations on > Co-O clusters. PBE calculations work fine, both with PW and CP, both in > closed shell and LSDA framework. In particular, ferromagnetic or > antiferromagnetic initial guesses lead to closed shell electronic structures, > i.e., total and absolute magnetization equal (or very close) to zero, and a > safe insulating system. > In order to improve the p-d hybridization between O 2p and Co 3d orbitals > (their contributions to the DOS are quite separated in PBE calculations, and > they are expected to be strongly mixed near to the valence band maximum) > I've performed some PBE+U calculations by using reasonable values for the Co > 3d and O 2p channels. In the case of closed shell calculations I obtain quite > reasonable results, i.e., equilibrium geometries nicely similar to PBE ones, > and an improved DOS in a better agreement with the available experimental > data. I've tried to perform open shell calculations since January, I've tried > to apply all of the standard and less standard tricks, but I have never (!) > been able to converge a single calculation. There are no errors, they simply > does not converge, with the system magnetization dancing around some selected > values, depending on the initial guess (fm or afm). Notice that the system is > still insulating (at a PBE+U closed shell level) and I've tried everything > from fixed occupations to quite high smearing (gaussian, cold, ...) values. > > I thought that the CP code could help me, but I'm facing an even more strange > problem... The very robust CP minimization of electronic dof successfully > reach some ground state at the PBE+U level, the only (minor) problem being > that you must put into the inpfile the final magnetization of the system. > Then, I've tried to perform both damped and NVT (with Nose thermostats) MD > simulations, trying several different open shell (nspin=2) configurations, > ranging from tot_magnetization=0 to tot_magnetization=20. In the case of > damped MD, the system temperature was kept very low, but my Co-O clusters > tried to split into pieces (they are quite stable in both PBE and PBE+U PW > calculations) while the total energy lowers. In the case of NVT MD > thermostats went bananas and my clusters melt. You can scrub away Co and O > scattered atoms from the supercell walls...:-) > In the case of PBE calculations (both damped and NVT MD) everything went fine > (no explosions, reasonably fast thermalization of the investigated systems, > averaged bond distances similar to PW ones...) > I can provide input files, but I suspect that this is not a matter of input > failures... Is it LDA+U variational? I suspect it isn't... Is it foolish to > perform MD calculation in such framework? Could you lend me a heavy hammer to > persuade PW open shell calculations into convergence...? > > Thank you in advance for suggestions > > Giuseppe > > -- --------------------------------------------------------------------- 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 huazhorg at 163.com Thu Jun 10 05:04:04 2010 From: huazhorg at 163.com (=?gbk?B?wfW7qtbS?=) Date: Thu, 10 Jun 2010 11:04:04 +0800 (CST) Subject: [Pw_forum] "nat_todo",could anyone help me? Message-ID: Dear all, I want to do phonon calculation on an adsorption system with symmetry. So Idid some test calculations. I did a test calculation on a system, say an molecule is adsorbed on a surface. I just want to calculate the vibrational frequencies of the molecule. I set "nat_todo" in the input file of ph.x, and set the list of indices of atoms of the molecule. But in the result file there is not phonons. I don't know what's wrong with it, and how to set parameter in the input file of ph.x. Please help me! Thank you! This is the output that I have set "nat_todo" in the input file,from output file we can't find the phonon data at the end of file: Representation # 12 mode # 12 Self-consistent Calculation iter # 1 total cpu time : 77.3 secs av.it.: 4.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.128E-07 iter # 2 total cpu time : 78.3 secs av.it.: 9.0 thresh= 0.113E-04 alpha_mix = 0.700 |ddv_scf|^2 = 0.274E-08 iter # 3 total cpu time : 79.5 secs av.it.: 9.0 thresh= 0.524E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.182E-10 iter # 4 total cpu time : 80.6 secs av.it.: 9.0 thresh= 0.426E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.678E-11 iter # 5 total cpu time : 81.6 secs av.it.: 8.0 thresh= 0.260E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.270E-13 iter # 6 total cpu time : 82.7 secs av.it.: 9.0 thresh= 0.164E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.140E-14 iter # 7 total cpu time : 83.7 secs av.it.: 8.0 thresh= 0.374E-08 alpha_mix = 0.700 |ddv_scf|^2 = 0.344E-16 End of self-consistent calculation Convergence has been achieved Stopping because representation 3 is not done PHONON : 1m12.13s CPU time, 1m24.02s WALL time INITIALIZATION: phq_setup : 0.04s CPU 0.04s WALL ( 1 calls) phq_init : 4.69s CPU 5.19s WALL ( 1 calls) phq_init : 4.69s CPU 5.19s WALL ( 1 calls) init_vloc : 0.02s CPU 0.02s WALL ( 1 calls) init_us_1 : 0.15s CPU 0.17s WALL ( 1 calls) newd : 0.11s CPU 0.13s WALL ( 1 calls) dvanqq : 1.90s CPU 2.11s WALL ( 1 calls) drho : 1.59s CPU 1.82s WALL ( 1 calls) DYNAMICAL MATRIX: dynmat0 : 0.17s CPU 0.18s WALL ( 1 calls) ?????????? and below is the normal output that I have not set "nat_todo" in the inputfile, from which we can see the phonon data at the end of file: Representation # 12 mode # 12 Self-consistent Calculation iter # 1 total cpu time : 1155.5 secs av.it.: 5.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.319E-07 iter # 2 total cpu time : 1164.9 secs av.it.: 12.0 thresh= 0.179E-04 alpha_mix = 0.700 |ddv_scf|^2 = 0.161E-08 iter # 3 total cpu time : 1174.6 secs av.it.: 12.0 thresh= 0.401E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.157E-09 iter # 4 total cpu time : 1184.7 secs av.it.: 13.0 thresh= 0.125E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.126E-10 iter # 5 total cpu time : 1194.7 secs av.it.: 13.0 thresh= 0.355E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.184E-11 iter # 6 total cpu time : 1204.7 secs av.it.: 13.0 thresh= 0.136E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.701E-12 iter # 7 total cpu time : 1214.2 secs av.it.: 12.0 thresh= 0.837E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.131E-12 iter # 8 total cpu time : 1223.8 secs av.it.: 12.0 thresh= 0.361E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.149E-15 iter # 9 total cpu time : 1233.4 secs av.it.: 13.0 thresh= 0.122E-08 alpha_mix = 0.700 |ddv_scf|^2 = 0.157E-16 End of self-consistent calculation Convergence has been achieved Number of q in the star = 1 List of q in the star: 1 0.000000000 0.000000000 0.000000000 Dielectric constant in cartesian axis ( 1.031610391 -0.000228657 -0.003149580 ) ( -0.000228341 1.027755025 -0.000009279 ) ( -0.003149520 -0.000009203 1.019026580 ) Polarizability (a.u.)^3 Polarizability (A^3) 23.14 -0.17 -2.33 3.4285 -0.0250 -0.3452 -0.17 20.34 -0.01 -0.0251 3.0141 -0.0010 -2.33 -0.01 13.98 -0.3452 -0.0010 2.0722 Effective charges (d Force / dE) in cartesian axis atom 1 C Ex ( 1.02010 -0.00463 -0.20246 ) Ey ( 0.00824 0.87800 -0.00178 ) Ez ( -0.20024 -0.00018 0.24077 ) atom 2 O Ex ( -0.71604 0.00033 0.12390 ) Ey ( -0.00376 -0.27604 0.00052 ) Ez ( 0.12315 -0.00045 -0.22813 ) atom 3 H Ex ( -0.03234 -0.13357 0.03345 ) Ey ( -0.09805 -0.18872 0.02571 ) Ez ( 0.03330 0.03431 0.09234 ) atom 4 H Ex ( -0.03402 0.13935 0.03451 ) Ey ( 0.09420 -0.17340 -0.02427 ) Ez ( 0.03316 -0.03389 0.09281 ) Effective charges (d P / du) in cartesian axis atom 1 C Px ( 0.78251 0.00752 -0.18968 ) Py ( -0.00610 0.63820 0.00003 ) Pz ( -0.19199 -0.00193 0.04292 ) atom 2 O Px ( -0.71616 -0.00367 0.12322 ) Py ( 0.00032 -0.27610 -0.00045 ) Pz ( 0.12395 0.00050 -0.22806 ) atom 3 H Px ( -0.03233 -0.09805 0.03330 ) Py ( -0.13358 -0.18873 0.03431 ) Pz ( 0.03349 0.02571 0.09233 ) atom 4 H Px ( -0.03402 0.09420 0.03316 ) Py ( 0.13936 -0.17336 -0.03389 ) Pz ( 0.03455 -0.02427 0.09280 ) Diagonalizing the dynamical matrix q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -4.939872 [THz] = -164.777486 [cm-1] omega( 2) = -0.211017 [THz] = -7.038823 [cm-1] omega( 3) = -0.078881 [THz] = -2.631210 [cm-1] omega( 4) = -0.004765 [THz] = -0.158929 [cm-1] omega( 5) = 3.572645 [THz] = 119.171410 [cm-1] omega( 6) = 4.364949 [THz] = 145.600002 [cm-1] omega( 7) = 33.896117 [THz] = 1130.660267 [cm-1] omega( 8) = 35.856463 [THz] = 1196.050798 [cm-1] omega( 9) = 43.444675 [THz] = 1449.167993 [cm-1] omega(10) = 51.275820 [THz] = 1710.388618 [cm-1] omega(11) = 84.045119 [THz] = 2803.462049 [cm-1] omega(12) = 85.673216 [THz] = 2857.769859 [cm-1] ************************************************************************** Mode symmetry, C_1 (1) point group: omega( 7 - 7) = 1130.7 [cm-1] --> A I+R omega( 8 - 8) = 1196.1 [cm-1] --> A I+R omega( 9 - 9) = 1449.2 [cm-1] --> A I+R omega( 10 - 10) = 1710.4 [cm-1] --> A I+R omega( 11 - 11) = 2803.5 [cm-1] --> A I+R omega( 12 - 12) = 2857.8 [cm-1] --> A I+R ************************************************************************** PHONON : 19m24.01s CPU time, 20m34.88s WALL time INITIALIZATION: phq_setup : 0.36s CPU 0.39s WALL ( 1 calls) phq_init : 95.50s CPU 97.48s WALL ( 1 calls) phq_init : 95.50s CPU 97.48s WALL ( 1 calls) init_vloc : 12.90s CPU 12.95s WALL ( 1 calls) init_us_1 : 1.16s CPU 1.21s WALL ( 1 calls) newd : 2.21s CPU 2.45s WALL ( 1 calls) dvanqq : 38.14s CPU 38.66s WALL ( 1 calls) drho : 28.73s CPU 30.10s WALL ( 1 calls) cmpt_qdipol : 0.00s CPU 0.00s WALL ( 1 calls) DIELECTRIC CONSTANT AND EFFECTIVE CHARGES: solve_e : 269.98s CPU 302.42s WALL ( 1 calls) dielec : 0.01s CPU 0.05s WALL ( 1 calls) zstar_eu : 13.30s CPU 16.84s WALL ( 1 calls) DYNAMICAL MATRIX: dynmat0 : 1.56s CPU 1.57s WALL ( 1 calls) The attachment is the output file of input that I have set "nat_todo=2", the molecule is HCHO, just for test. Here is the input file: vibrations of hcho &inputph nat_todo=2, tr2_ph=4.0d-17, prefix='HCHO', outdir='/home/jerry/tmp', amass(1)=12.d0, amass(2)=16.d0, amass(3)=1.d0, fildyn='hcho.dyn', iverbosity=1, trans=.true., nogg=.true. / 0.0 0.0 0.0 1 3 But in the result file there is not any vibration modes data. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100610/c0e85a1e/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: hcho.ph.out Type: application/octet-stream Size: 33828 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100610/c0e85a1e/attachment-0001.obj From luotengf at msu.edu Thu Jun 10 05:01:33 2010 From: luotengf at msu.edu (Tengfei Luo) Date: Wed, 9 Jun 2010 23:01:33 -0400 Subject: [Pw_forum] LDA psudopotential for La Message-ID: <15106E87B14B40B6A548C9D5C523E825@mit.edu> Dear all: Does anyone happen to have an LDA psudopotential for La? I want to use LDA to calculate the band structure as the input to the DMFT calculation. I found that there is no LDA psudo for La on the QE psudo website. Thank you very much! Tengfei 35-312 MIT Cambridge, MA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100609/5123898c/attachment.htm From m.abbasnejad at gmail.com Thu Jun 10 09:39:55 2010 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 10 Jun 2010 12:09:55 +0430 Subject: [Pw_forum] KZK method In-Reply-To: References: Message-ID: Dear all, In order to perform KZK correction, I wonder if it is needed to relax the L*L*L structure? Thanks in advance. Yours, Mohaddeseh On Mon, Jun 7, 2010 at 7:51 PM, William Parker wrote: > Hi Mohaddeseh, > > KZK is in QE. Just use input_dft='kzk', and QE will use the volume of > your cell to calculate the finite-size correction. Compare that to the > value using PZ-LDA to get your correction for QMC. > > --William > > ====================================================================== > William Parker Tel : +1 (614) 292-2887 > Graduate Research Associate Fax : +1 (614) 292-7557 > Ohio State University > Department of Physics > 191 West Woodruff Avenue email: wparker at mps.ohio-state.edu > Columbus, OH 43210-1117 http://www.physics.ohio-state.edu/~wparker > U.S.A. > > Office: 2025 Physics Research Building > ====================================================================== > > On Mon, 7 Jun 2010, mohaddeseh abbasnejad wrote: > > > Dear all, > > > > Would you please let me know if KZK method (Kwee, Zhang, and Krakauer) > has > > been implemented in PWscf code? If so, how should I use it? > > Thanks in advance. > > > > Yours, > > --------------------------------------------------------- > > > > 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 > -- --------------------------------------------------------- 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/20100610/0424af51/attachment.htm From giannozz at democritos.it Thu Jun 10 13:01:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Jun 2010 13:01:00 +0200 Subject: [Pw_forum] some input parameter In-Reply-To: References: Message-ID: <4C10C5EC.1050000@democritos.it> chenjie gu wrote: > for ion_temperature=andersen: the collision frequency parameter is given > as nu=1/tau defined above "above", in the documentation, you find the following definition: tau = nraise*dt. "nraise" is an integer of your choice; dt is the time step. So the collision frequency parameter nu of the Andersen thermostat is nu=1/(nraise*dt), or, in a more transparent way, nu*dt = 1/nraise, that is, every nraise time steps there is a "collision", i.e. the velocity of one randomly selected particle gets a random value, distributed according to the maxwellian distribution for temperature T (I hope I remember correctly how the Andersen thermostat works). The way the various thermostats in pw.x are introduced is a confusing because the same parameter "nraise" has different meanings for different thermostats. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Jun 10 13:44:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Jun 2010 13:44:20 +0200 Subject: [Pw_forum] error in gamma In-Reply-To: <275812171.86469.1276076733897.JavaMail.root@mta.iut.ac.ir> References: <275812171.86469.1276076733897.JavaMail.root@mta.iut.ac.ir> Message-ID: <4C10D014.40802@democritos.it> kazempoor at ph.iut.ac.ir wrote: > from pzpotrf : error # 47 > problems computing cholesky decomposition > > This is very strange because when I set nbnd=512 > the pw1.in and pw2.in run without any problem . it is not strange. The diagonalization algorithm in PWscf is expected to work for a number of bands that is much smaller than the dimension of the basis set. It usually works great if you calculate occupied bands and a few unoccupied bands. The more bands you add, the more you are likely to run into numerical trouble. The error here occurs in a Scalapack routine (pzpotrf). Finding out why and how is a highly nontrivial task Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giuseppe.mattioli at mlib.ism.cnr.it Thu Jun 10 15:28:26 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 10 Jun 2010 15:28:26 +0200 Subject: [Pw_forum] strange behaviour in LDA+U calculations In-Reply-To: <4C0FEC53.5010905@mit.edu> References: <201006091301.54756.giuseppe.mattioli@mlib.ism.cnr.it> <4C0FEC53.5010905@mit.edu> Message-ID: <201006101528.26737.giuseppe.mattioli@mlib.ism.cnr.it> Dear Matteo and Nicola Thank you for your comments and suggestions I'll try to work out something and, possibly, to report the results. Giuseppe On Wednesday 09 June 2010 21:32:35 Nicola Marzari wrote: > Dear Giuseppe, > > it looks like > > 1) PW does not converge PBE+U. Only things to try are really large > smearings, and > very small mixing factors. If the smearings are large, and the mixing is > small, it should ultimately > converge, and then you can reduce the smearing. For this purpose, > fermi-dirac is probably the best > choice, with its long tails occupying empty states. > > 2) glad that CP converged. the PBE+U solution, be it better or worse > than PBE, leads to > dissociation of the cluster - that's why damped dynamics leads to the > cluster fragmenting, and > canonical md shows it exploding. > > Nothing too unconventional - but the truth might be that these are very > difficult systems > to describe accurately in DFT - and PBE+U seems, for better or for > worse, lead to dissociation. > > What is the right solution ? Impossible to say. If the clusters are > stable experimentally, at one of > the magnetizations you tried, than a dissociated solution is certainly > wrong, and one that is not > is only probably wrong. > > Start from something really simple (maybe one Co at most), and compare > there PBE, PBE+U, > and quantum chemsitry (ideally MRCI) solutions. Does anything work ? > > These are incredibly difficult systems to study - have also a look at > e.g. Kulik et al JCP 2008. > > nicola > > Giuseppe Mattioli wrote: > > Dear all > > I'm facing strange problems while attempting to perform LDA+U > > calculations on Co-O clusters. PBE calculations work fine, both with PW > > and CP, both in closed shell and LSDA framework. In particular, > > ferromagnetic or antiferromagnetic initial guesses lead to closed shell > > electronic structures, i.e., total and absolute magnetization equal (or > > very close) to zero, and a safe insulating system. > > In order to improve the p-d hybridization between O 2p and Co 3d orbitals > > (their contributions to the DOS are quite separated in PBE calculations, > > and they are expected to be strongly mixed near to the valence band > > maximum) I've performed some PBE+U calculations by using reasonable > > values for the Co 3d and O 2p channels. In the case of closed shell > > calculations I obtain quite reasonable results, i.e., equilibrium > > geometries nicely similar to PBE ones, and an improved DOS in a better > > agreement with the available experimental data. I've tried to perform > > open shell calculations since January, I've tried to apply all of the > > standard and less standard tricks, but I have never (!) been able to > > converge a single calculation. There are no errors, they simply does not > > converge, with the system magnetization dancing around some selected > > values, depending on the initial guess (fm or afm). Notice that the > > system is still insulating (at a PBE+U closed shell level) and I've tried > > everything from fixed occupations to quite high smearing (gaussian, cold, > > ...) values. > > > > I thought that the CP code could help me, but I'm facing an even more > > strange problem... The very robust CP minimization of electronic dof > > successfully reach some ground state at the PBE+U level, the only (minor) > > problem being that you must put into the inpfile the final magnetization > > of the system. Then, I've tried to perform both damped and NVT (with Nose > > thermostats) MD simulations, trying several different open shell > > (nspin=2) configurations, ranging from tot_magnetization=0 to > > tot_magnetization=20. In the case of damped MD, the system temperature > > was kept very low, but my Co-O clusters tried to split into pieces (they > > are quite stable in both PBE and PBE+U PW calculations) while the total > > energy lowers. In the case of NVT MD thermostats went bananas and my > > clusters melt. You can scrub away Co and O scattered atoms from the > > supercell walls...:-) > > In the case of PBE calculations (both damped and NVT MD) everything went > > fine (no explosions, reasonably fast thermalization of the investigated > > systems, averaged bond distances similar to PW ones...) > > I can provide input files, but I suspect that this is not a matter of > > input failures... Is it LDA+U variational? I suspect it isn't... Is it > > foolish to perform MD calculation in such framework? Could you lend me a > > heavy hammer to persuade PW open shell calculations into convergence...? > > > > Thank you in advance for suggestions > > > > Giuseppe -- ******************************************************** - 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: From kazempoor2000 at yahoo.com Thu Jun 10 16:20:06 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 10 Jun 2010 07:20:06 -0700 (PDT) Subject: [Pw_forum] error in gamma In-Reply-To: <4C10D014.40802@democritos.it> Message-ID: <205053.10501.qm@web114408.mail.gq1.yahoo.com> Dear Paolo Thank you for reply. I didn't say that when I use 1 node each have 32 cores , I don't have any problem with run of pw1.in and pw2.in wiith nbnd=1024. But once I increase? the number of proccessors to 32 node each have 32 core this error happen. Best regards 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 --- On Thu, 6/10/10, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] error in gamma To: "PWSCF Forum" Date: Thursday, June 10, 2010, 4:44 AM kazempoor at ph.iut.ac.ir wrote: >? ? ? from? pzpotrf? : error #? ? ? ? 47 >? ? ???problems computing cholesky decomposition > > This is very strange because when I set nbnd=512 > the pw1.in and pw2.in run without any problem . it is not strange. The diagonalization algorithm in PWscf is expected to work for a number of bands that is much smaller than the dimension of the basis set. It usually works great if you calculate occupied bands and a few unoccupied bands. The more bands you add, the more you are likely to run into numerical trouble. The error here occurs in a Scalapack routine (pzpotrf). Finding out why and how is a highly nontrivial task Paolo -- 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/20100610/7e4f37cf/attachment.htm From giannozz at democritos.it Thu Jun 10 17:50:41 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Jun 2010 17:50:41 +0200 Subject: [Pw_forum] error in gamma In-Reply-To: <205053.10501.qm@web114408.mail.gq1.yahoo.com> References: <205053.10501.qm@web114408.mail.gq1.yahoo.com> Message-ID: <4C1109D1.6010808@democritos.it> ali kazempour wrote: > I didn't say that when I use 1 node each have 32 cores , > I don't have any problem with run of pw1.in and pw2.in with > nbnd=1024. But once I increase the number of proccessors to > 32 node each have 32 core this error happen. ...and what should one deduce from such obscure statements? The important pieces of information here are: - total number of MPI processes - number of processors in the "linear-algebra" group, as specified by the -ndiag or -northo keyword. This is a square integer, and should be set to whatever gives the fastest diagonalization time, not to the maximum number P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Thu Jun 10 18:07:23 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 10 Jun 2010 18:07:23 +0200 Subject: [Pw_forum] "nat_todo",could anyone help me? In-Reply-To: References: Message-ID: On Thu, 10 Jun 2010 05:04:04 +0200, ??? wrote: > This is the output that I have set "nat_todo" in the input file,from > output file we can't find the phonon data at the end of file: Dear ???, first of all you need to have really clear that what you are trying to do is in general meaningless and wrong. The vibrational mode of the molecule is coupled will all the other modes in the system. I repeat: computing only one mode has no meaning. However, if you really know what you are doing, you can open the file PH/dynmatrix.f90 around line 120 you'll find the following block of code: DO irr=0,nirr IF (done_irr(irr)==0.and..not.ldisp) THEN WRITE(stdout,& '(/,5x,"Stopping because representation", i5, " is not done")') irr CALL close_phq(.TRUE.) CALL stop_ph(.TRUE.) ENDIF IF (done_irr(irr)==0.and.ldisp) THEN WRITE(stdout, '(/5x,"Not diagonalizing because representation", & & i5, " is not done")') irr RETURN ENDIF ENDDO remove it from the code and the partial dynamical matrix will be printed to the fildyn file. if you also want a printout of the (mostly wrong!) frequencies, you have to further go down to line ~200: ! ! Diagonalizes the dynamical matrix at q ! IF (all_comp) THEN call dyndia (xq, nmodes, nat, ntyp, ityp, pmass, iudyn, dyn, w2) IF (search_sym) CALL find_mode_sym (dyn, w2, at, bg, nat, nsymq, sr, & irt, xq, rtau, pmass, ntyp, ityp, 1) END IF remove the IF condition, so that the code looks like this: call dyndia (xq, nmodes, nat, ntyp, ityp, pmass, iudyn, dyn, w2) IF (search_sym) CALL find_mode_sym (dyn, w2, at, bg, nat, nsymq, sr, & irt, xq, rtau, pmass, ntyp, ityp, 1) then recompile phonon. In doing so you take full responsibility, keep in mind that the frequencies you did not compute will most likely be TOTALLY WRONG, the ones you did compute may or may NOT be relatively close to the "real" ones. regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From lshulenburger at gmail.com Thu Jun 10 18:44:17 2010 From: lshulenburger at gmail.com (Luke Shulenburger) Date: Thu, 10 Jun 2010 12:44:17 -0400 Subject: [Pw_forum] KZK method In-Reply-To: References: Message-ID: Are you meaning that you would like to use a nonuniform mesh of kpoints to generate a supercell from your DFT calculation? If so, I have some code that I have been using that computes the volume for KZK from cell volume * number of k_points enumerated. Luke Shulenburger Geophysical Laboratory Carnegie Institution of Washignton On Thu, Jun 10, 2010 at 3:39 AM, mohaddeseh abbasnejad wrote: > > Dear all, > > In order to perform KZK correction, I wonder if it is needed to relax the > L*L*L structure? > > Thanks in advance. > > Yours, > Mohaddeseh > > > > On Mon, Jun 7, 2010 at 7:51 PM, William Parker > wrote: >> >> Hi Mohaddeseh, >> >> KZK is in QE. ?Just use input_dft='kzk', and QE will use the volume of >> your cell to calculate the finite-size correction. ?Compare that to the >> value using PZ-LDA to get your correction for QMC. >> >> --William >> >> ====================================================================== >> William Parker ? ? ? ? ? ? ?Tel : ?+1 (614) 292-2887 >> Graduate Research Associate Fax : ?+1 (614) 292-7557 >> Ohio State University >> Department of Physics >> 191 West Woodruff Avenue ? ?email: wparker at mps.ohio-state.edu >> Columbus, OH ?43210-1117 ? ?http://www.physics.ohio-state.edu/~wparker >> U.S.A. >> >> Office: 2025 Physics Research Building >> ====================================================================== >> >> On Mon, 7 Jun 2010, mohaddeseh abbasnejad wrote: >> >> > Dear all, >> > >> > Would you please let me know if KZK method (Kwee, Zhang, and Krakauer) >> > has >> > been implemented in PWscf code? If so, how should I use it? >> > Thanks in advance. >> > >> > Yours, >> > --------------------------------------------------------- >> > >> > 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 > > > > -- > --------------------------------------------------------- > > 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 > > From m.abbasnejad at gmail.com Thu Jun 10 20:27:11 2010 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 10 Jun 2010 22:57:11 +0430 Subject: [Pw_forum] KZK method In-Reply-To: References: Message-ID: Dear Luke, Thanks for your reply. I meant that if I want to calculate the LDA energy with a L*L*L mesh using KZK functional ( for correction of QMC L*L*L supercell calculation): E=Edmc(L*L*L)+Elda-converged-Elda-kzk(L*L*L) Do i have to relax structure, because for example the stresses on the structure with KZK correction and L*L*L mesh are not small at all? Thanks in advance. Yours, Mohaddeseh On Thu, Jun 10, 2010 at 9:14 PM, Luke Shulenburger wrote: > Are you meaning that you would like to use a nonuniform mesh of > kpoints to generate a supercell from your DFT calculation? If so, I > have some code that I have been using that computes the volume for KZK > from cell volume * number of k_points enumerated. > > Luke Shulenburger > Geophysical Laboratory > Carnegie Institution of Washignton > > On Thu, Jun 10, 2010 at 3:39 AM, mohaddeseh abbasnejad > wrote: > > > > Dear all, > > > > In order to perform KZK correction, I wonder if it is needed to relax the > > L*L*L structure? > > > > Thanks in advance. > > > > Yours, > > Mohaddeseh > > > > > > > > On Mon, Jun 7, 2010 at 7:51 PM, William Parker < > wparker at mps.ohio-state.edu> > > wrote: > >> > >> Hi Mohaddeseh, > >> > >> KZK is in QE. Just use input_dft='kzk', and QE will use the volume of > >> your cell to calculate the finite-size correction. Compare that to the > >> value using PZ-LDA to get your correction for QMC. > >> > >> --William > >> > >> ====================================================================== > >> William Parker Tel : +1 (614) 292-2887 > >> Graduate Research Associate Fax : +1 (614) 292-7557 > >> Ohio State University > >> Department of Physics > >> 191 West Woodruff Avenue email: wparker at mps.ohio-state.edu > >> Columbus, OH 43210-1117 http://www.physics.ohio-state.edu/~wparker > >> U.S.A. > >> > >> Office: 2025 Physics Research Building > >> ====================================================================== > >> > >> On Mon, 7 Jun 2010, mohaddeseh abbasnejad wrote: > >> > >> > Dear all, > >> > > >> > Would you please let me know if KZK method (Kwee, Zhang, and Krakauer) > >> > has > >> > been implemented in PWscf code? If so, how should I use it? > >> > Thanks in advance. > >> > > >> > Yours, > >> > --------------------------------------------------------- > >> > > >> > 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 > > > > > > > > -- > > --------------------------------------------------------- > > > > 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 > > > > > _______________________________________________ > 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/20100610/1b6a1791/attachment.htm From lshulenburger at gmail.com Thu Jun 10 20:50:33 2010 From: lshulenburger at gmail.com (Luke Shulenburger) Date: Thu, 10 Jun 2010 14:50:33 -0400 Subject: [Pw_forum] KZK method In-Reply-To: References: Message-ID: My understanding is that the correction should apply regardless of the stress on the structure. Certainly the correction would not be right if the KZK structure was different from the one used for QMC and LDA. At the end of the day though, the only way to be 100% sure this is working correctly is to try a couple of supercell sizes and see two things. The first is that the corrected energy agrees for larger supercell sizes and the second is that extrapolations of the uncorrected energy to the infinite supercell limit agree with the finite size corrected result. Figure 3 of the original KZK paper (Phys. Rev. Lett. 100, 126404 (2008)) should illustrate how this works for Si. You might also want to compare the results to those obtained using the MPC+Chiesa correction (Phys. Rev. Lett. 97, 076404 (2006)) if your QMC code supports it. Luke Geophysical Laboratory Carnegie Institution of Washington On Thu, Jun 10, 2010 at 2:27 PM, mohaddeseh abbasnejad wrote: > Dear Luke, > > Thanks for your reply. > I meant that if I want to calculate the LDA energy with a L*L*L mesh using > KZK functional > ( for correction of QMC L*L*L supercell calculation): > ?E=Edmc(L*L*L)+Elda-converged-Elda-kzk(L*L*L) > Do i have to relax structure, because for example the stresses on the > structure with KZK correction and L*L*L mesh are not small at all? > Thanks in advance. > > Yours, > Mohaddeseh > > > On Thu, Jun 10, 2010 at 9:14 PM, Luke Shulenburger > wrote: >> >> Are you meaning that you would like to use a nonuniform mesh of >> kpoints to generate a supercell from your DFT calculation? ?If so, I >> have some code that I have been using that computes the volume for KZK >> from cell volume * number of k_points enumerated. >> >> Luke Shulenburger >> Geophysical Laboratory >> Carnegie Institution of Washignton >> >> On Thu, Jun 10, 2010 at 3:39 AM, mohaddeseh abbasnejad >> wrote: >> > >> > Dear all, >> > >> > In order to perform KZK correction, I wonder if it is needed to relax >> > the >> > L*L*L structure? >> > >> > Thanks in advance. >> > >> > Yours, >> > Mohaddeseh >> > >> > >> > >> > On Mon, Jun 7, 2010 at 7:51 PM, William Parker >> > >> > wrote: >> >> >> >> Hi Mohaddeseh, >> >> >> >> KZK is in QE. ?Just use input_dft='kzk', and QE will use the volume of >> >> your cell to calculate the finite-size correction. ?Compare that to the >> >> value using PZ-LDA to get your correction for QMC. >> >> >> >> --William >> >> >> >> ====================================================================== >> >> William Parker ? ? ? ? ? ? ?Tel : ?+1 (614) 292-2887 >> >> Graduate Research Associate Fax : ?+1 (614) 292-7557 >> >> Ohio State University >> >> Department of Physics >> >> 191 West Woodruff Avenue ? ?email: wparker at mps.ohio-state.edu >> >> Columbus, OH ?43210-1117 ? ?http://www.physics.ohio-state.edu/~wparker >> >> U.S.A. >> >> >> >> Office: 2025 Physics Research Building >> >> ====================================================================== >> >> >> >> On Mon, 7 Jun 2010, mohaddeseh abbasnejad wrote: >> >> >> >> > Dear all, >> >> > >> >> > Would you please let me know if KZK method (Kwee, Zhang, and >> >> > Krakauer) >> >> > has >> >> > been implemented in PWscf code? If so, how should I use it? >> >> > Thanks in advance. >> >> > >> >> > Yours, >> >> > --------------------------------------------------------- >> >> > >> >> > 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 >> > >> > >> > >> > -- >> > --------------------------------------------------------- >> > >> > 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 >> > >> > >> _______________________________________________ >> 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 > > From vovi47 at yahoo.com Thu Jun 10 21:47:31 2010 From: vovi47 at yahoo.com (Vi Vo) Date: Thu, 10 Jun 2010 12:47:31 -0700 (PDT) Subject: [Pw_forum] DFT+U Message-ID: <151723.38876.qm@web114519.mail.gq1.yahoo.com> Dear PWSCF users, In the PW_INPUT, I see there is an option for using LDA+U. Is it true that only LDA can be used with QE. How about GGA+U and PBE+U? Are they implemented? Thank you very much, Vi Vo Chemical Engineering Department University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100610/61fe7519/attachment.htm From rfaccio at fq.edu.uy Thu Jun 10 21:50:26 2010 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Thu, 10 Jun 2010 16:50:26 -0300 Subject: [Pw_forum] DFT+U References: <151723.38876.qm@web114519.mail.gq1.yahoo.com> Message-ID: <013701cb08d6$2c84df00$0e02a8c0@ricardof> Hi If you use GGA pseudos, then you will get GGA+U results. Regards Ricardo ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm --------------------------------------------------------------------------------- ----- Original Message ----- From: Vi Vo To: pw_forum at pwscf.org Sent: Thursday, June 10, 2010 4:47 PM Subject: [Pw_forum] DFT+U Dear PWSCF users, In the PW_INPUT, I see there is an option for using LDA+U. Is it true that only LDA can be used with QE. How about GGA+U and PBE+U? Are they implemented? Thank you very much, Vi Vo Chemical Engineering Department University of Houston ------------------------------------------------------------------------------ _______________________________________________ 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/20100610/6c45c766/attachment-0001.htm From vovi47 at yahoo.com Thu Jun 10 21:54:41 2010 From: vovi47 at yahoo.com (Vi Vo) Date: Thu, 10 Jun 2010 12:54:41 -0700 (PDT) Subject: [Pw_forum] DFT+U In-Reply-To: <013701cb08d6$2c84df00$0e02a8c0@ricardof> References: <151723.38876.qm@web114519.mail.gq1.yahoo.com> <013701cb08d6$2c84df00$0e02a8c0@ricardof> Message-ID: <219729.50466.qm@web114508.mail.gq1.yahoo.com> Dear Prof. Faccio, Thank you! Vi ________________________________ From: Ricardo Faccio To: PWSCF Forum Sent: Thu, June 10, 2010 12:50:26 PM Subject: Re: [Pw_forum] DFT+U Hi If you use GGA pseudos, then you will get GGA+U results. Regards Ricardo ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm --------------------------------------------------------------------------------- ----- Original Message ----- >From: Vi Vo >To: pw_forum at pwscf.org >Sent: Thursday, June 10, 2010 4:47 > PM >Subject: [Pw_forum] DFT+U > > >Dear PWSCF users, > >In the PW_INPUT, I see there is an option for > using LDA+U. Is it true that only LDA can be used with QE. How > about GGA+U and PBE+U? Are they implemented? > >Thank you very > much, > >Vi Vo >Chemical > Engineering Department >University > of Houston > ________________________________ > _______________________________________________ >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/20100610/ee53fa6e/attachment.htm From mambom1902 at yahoo.com Fri Jun 11 09:07:45 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Fri, 11 Jun 2010 00:07:45 -0700 (PDT) Subject: [Pw_forum] Phonon restart error Message-ID: <252171.16892.qm@web38805.mail.mud.yahoo.com> Dear all, I try to restart the phonon calculation and I get the error: cannot open xml_recover file for writing I see there was a topic in PWscf, but I can not solve this problem. Could you give me some instructions? I appreciate to all your help. Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100611/f057b680/attachment.htm From ma at nano.ku.dk Fri Jun 11 09:43:53 2010 From: ma at nano.ku.dk (Martin Andersson) Date: Fri, 11 Jun 2010 09:43:53 +0200 (CEST) Subject: [Pw_forum] "nat_todo",could anyone help me? In-Reply-To: References: Message-ID: <929b4714a6bec0f0a1a647d61b0de94f.squirrel@hermes.fys.ku.dk> Hi all, It is certainly not meaningless to calculate only adsrobate modes for a molecule adsorbed on a surface. I have in fact tried the same thing with QE and failed in te same way that the phonons are not computed. Most vibrational modes in a molecule adsorbed on a surface have a much higher frequency than the lattice vibrations of the substrate and are thus essentially decoupled. If one performs frequency calculations for a molecule adsorbed on a metal cluster with another program, the internal modes of the molecule are almost converged as soon as the local adsorbation geometry is correct. I have also tried other plane wave programs where this is possible, and the difference between including the surface in the hessian is only marginal. The frustrated translational and rotational modes are also only slightly shifted. It is an approximation, as so many other things we do, and convergence can be checked by successfully including more and more atoms in the hessian. I would also very much like to be able to limit the hessian in a phonon calculation (This is a not so subtle hint for the developers...:) ) Cheers, Martin Andersson, NanoGeoScience, University of Copenhagen > On Thu, 10 Jun 2010 05:04:04 +0200, ????????? wrote: >> This is the output that I have set "nat_todo" in the input file,from >> output file we can't find the phonon data at the end of file: > > Dear ?????????, > first of all you need to have really clear that what you are trying to do > is in general meaningless and wrong. The vibrational mode of the molecule > is coupled will all the other modes in the system. I repeat: computing > only one mode has no meaning. > > > > > > > > However, if you really know what you are doing, you can open the file > PH/dynmatrix.f90 around line 120 you'll find the following block of code: > > > DO irr=0,nirr > IF (done_irr(irr)==0.and..not.ldisp) THEN > WRITE(stdout,& > '(/,5x,"Stopping because representation", i5, " is not done")') > irr > CALL close_phq(.TRUE.) > CALL stop_ph(.TRUE.) > ENDIF > IF (done_irr(irr)==0.and.ldisp) THEN > WRITE(stdout, '(/5x,"Not diagonalizing because representation", & > & i5, " is not done")') irr > RETURN > ENDIF > ENDDO > > remove it from the code and the partial dynamical matrix will be printed > to the fildyn file. > > if you also want a printout of the (mostly wrong!) frequencies, you have > to further go down to line ~200: > > ! > ! Diagonalizes the dynamical matrix at q > ! > IF (all_comp) THEN > call dyndia (xq, nmodes, nat, ntyp, ityp, pmass, iudyn, dyn, w2) > IF (search_sym) CALL find_mode_sym (dyn, w2, at, bg, nat, nsymq, sr, > & > irt, xq, rtau, pmass, ntyp, ityp, 1) > END IF > > remove the IF condition, so that the code looks like this: > > call dyndia (xq, nmodes, nat, ntyp, ityp, pmass, iudyn, dyn, w2) > IF (search_sym) CALL find_mode_sym (dyn, w2, at, bg, nat, nsymq, sr, > & > irt, xq, rtau, pmass, ntyp, ityp, 1) > > then recompile phonon. In doing so you take full responsibility, keep in > mind that the frequencies you did not compute will most likely be TOTALLY > WRONG, the ones you did compute may or may NOT be relatively close to the > "real" ones. > > regards > > -- > Lorenzo Paulatto > > *** Note: my affiliation has changed! please send future > correspondence to: *** > > post-doc @ IMPMC/UPMC - Universit?? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously: > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From asafis at yahoo.com.br Fri Jun 11 17:14:03 2010 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Fri, 11 Jun 2010 08:14:03 -0700 (PDT) Subject: [Pw_forum] pseudopotntial for K Message-ID: <537408.99412.qm@web52304.mail.re2.yahoo.com> Hello users PWscf, someone can provide a PBE GGA pseudopotential for potassium? Sincerely, ?lvaro Alves Univesidade Federal Fluminense Niter?i-Rio de Janeiro-Brasil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100611/79d6ba6a/attachment.htm From stewart at cnf.cornell.edu Fri Jun 11 17:30:49 2010 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Fri, 11 Jun 2010 11:30:49 -0400 Subject: [Pw_forum] pseudopotntial for K In-Reply-To: <537408.99412.qm@web52304.mail.re2.yahoo.com> References: <537408.99412.qm@web52304.mail.re2.yahoo.com> Message-ID: <4C1256A9.4070201@cnf.cornell.edu> Dear Alvaro, If there isn't one available already for QE, there is a Troullier-Martins PBE GGA pseudopotential for Postassium available in the fhi format: http://charter.cnf.cornell.edu/psp_files/19-K.GGA.fhi You should be able to convert it to UPF format using fhi2upf in the upftools directory of the QE distribution. Best regards, 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 On 6/11/2010 11:14 AM, ?lvaro Alves wrote: > Hello users PWscf, someone can provide a PBE GGA pseudopotential for > potassium? > > Sincerely, > > ?lvaro Alves > Univesidade Federal Fluminense > Niter?i-Rio de Janeiro-Brasil > > > > _______________________________________________ > 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/20100611/fbf84a4c/attachment.htm From rana_nand at yahoo.com Fri Jun 11 19:58:53 2010 From: rana_nand at yahoo.com (nand) Date: Fri, 11 Jun 2010 10:58:53 -0700 (PDT) Subject: [Pw_forum] On line DFT calculations In-Reply-To: Message-ID: <987693.72006.qm@web65811.mail.ac4.yahoo.com> Hi, I am trying to do some supercell calculations for Mn Doped GaAs. How ever my RAM is not sufficient?and the time taken by these calculations too long for my PC. I would like to know if there is any online facility where i can?do these large supercell calculations. Also can any one tell?how much RAM is required for a 64 atom supercell calculations.?Any other suugestion that can help. Thanking you in advance. ? Nand Kumar Rana Ranchi University India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100611/287ac43e/attachment.htm From paulatto at sissa.it Fri Jun 11 20:13:41 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 11 Jun 2010 20:13:41 +0200 Subject: [Pw_forum] On line DFT calculations In-Reply-To: <987693.72006.qm@web65811.mail.ac4.yahoo.com> References: <987693.72006.qm@web65811.mail.ac4.yahoo.com> Message-ID: Replying to message "[Pw_forum] On line DFT calculations" from nand (11/06/10): > I am trying to do some supercell calculations for Mn Doped GaAs. How > ever my RAM is not sufficient and the time taken by these calculations > too long for my PC. I would like to know if there is any online facility > where i can do these large supercell calculations. None that I know: disk space is cheap, but computational time is expensive. However, your university or institution may provide some computing facility. You can also apply for interantional grants of computing time, of course the scale of times in this case is long. > Also can any one tell how much RAM is required for a 64 atom supercell > calculations. Any other suugestion that can help. It is written during the run, e.g. per-process dynamical memory: 52.3 Mb if you have it for a smaller supercell you can consider that it scales more or less with the cube of the unit cell -- 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 snd2mra at yahoo.com Fri Jun 11 21:44:33 2010 From: snd2mra at yahoo.com (Madan Mithra. L. M) Date: Fri, 11 Jun 2010 12:44:33 -0700 (PDT) Subject: [Pw_forum] About 'qcutz', 'q2sigma' and 'ecfixed' in 'vc-relax' Message-ID: <421112.65758.qm@web53302.mail.re2.yahoo.com> Dear All, I have some doubts regarding setting the parameter values of 'qcutz', 'q2sigma' and 'ecfixed' in 'vc-relax'. I went through the original paper of M. Bernasconi et al, J. Phys. Chem. Solids 56, 501 (1995) and arrived at these conclusions : To mimic a constant cut-off run at 40Ry, they used the following settings for the vc-relax : A = 70Ry , sigma = 8Ry and E_0 = 35 Ry ecfixed = 2*E_0 = 70 Ry (ie, 1.75 times Ecut(constant) = 40Ry) q2sigma = 2*sigma = 16 Ry (ie, 0.4 times Ecut(constant) = 40Ry) qcutz = A = 70Ry (ie, 1.75 times Ecut(constant) = 40Ry) ecutwfc = 35 Ry (0.875 times Ecut(constant) = 40Ry) Can we generalize these findings and arrive at a conclusion that for an arbitrary value of Ecut(constant), one has to set : ecfixed (and qcutz) at 1.75*Ecut(constant) q2sigma at 0.4*Ecut(constant) ecutwfc at 0.875*Ecut(constant) I would also like to know whether these is any systematic way of improving the quality of vc-relax calculations by varying the three parameters (qcutz, ecfixed and ecutwfc). Thank you - Madan ---------------------------------------- Madan Mithra .L.M Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) FAX : (080) 360 2602 ----------------------------------------- From chenhanghuipwscf at gmail.com Fri Jun 11 23:01:01 2010 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Fri, 11 Jun 2010 17:01:01 -0400 Subject: [Pw_forum] tot_magnetization Message-ID: Dear QE developers, In the latest version (4.2), the 'tot_magnetization' becomes real (in the earlier version, it is an integer). However, since both tot_charge and tot_magnetization are now real number, then why in the code it requires: ! odd tot_magnetization requires an odd number of electrons ! even tot_magnetization requires an even number of electrons For alloys (using virtual crystal approximation), the number of electrons depends on the percentage of mixing and is usually fractional. Why do you set such a requirement? I am also confused that since both nelup and neldw are real numbers, why do you define them by: nelup_loc = ( INT(nelec_) + tot_magnetization_ ) / 2 neldw_loc = ( INT(nelec_) - tot_magnetization_ ) / 2 instead of the more native way: nelup_loc = ( nelec_ + tot_magnetization_ ) / 2 neldw_loc = ( nelec_ - tot_magnetization_ ) / 2 Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100611/fcc4959a/attachment.htm From mahkameh_va at yahoo.com Sun Jun 13 12:22:56 2010 From: mahkameh_va at yahoo.com (raheleh vaziri) Date: Sun, 13 Jun 2010 03:22:56 -0700 (PDT) Subject: [Pw_forum] k_points Message-ID: <953932.29965.qm@web32906.mail.mud.yahoo.com> Dear all, I have some questions about the relation between grid (nk1, nk2, nk3) and (k1, k2, k3) offset. I am wondering if determination of offset depends on the grid or not? Also, when the grid is even, is the offset certainly odd? For example, I calculated energy for a system with two kinds of k_points (2 2 5 0 0 0 and 2 2 5 1 1 1) and I observed different energy for each of them. thanks for any help. Mahkameh Vaziri PhD student of physical chemistry K. N. Toosi university of Technology, Tehran, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100613/1f41fe62/attachment.htm From nkxirainbow at gmail.com Sun Jun 13 15:48:29 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 13 Jun 2010 21:48:29 +0800 Subject: [Pw_forum] k_points In-Reply-To: <953932.29965.qm@web32906.mail.mud.yahoo.com> References: <953932.29965.qm@web32906.mail.mud.yahoo.com> Message-ID: Dear Mahkameh Vaziri: The energy difference between (2 2 5 0 0 0) and (2 2 5 1 1 1) indicates that you did not get convergence about k mesh. On Sun, Jun 13, 2010 at 6:22 PM, raheleh vaziri wrote: > Dear all, > > > I have some questions about the relation between grid (nk1, nk2, nk3) and > (k1, k2, k3) offset. I am wondering if determination of offset depends on > the grid or not? > > Also, when the grid is even, is the offset certainly odd? > For example, I calculated energy for a system with two kinds of k_points > (2 2 5 0 0 0 and 2 2 5 1 1 1) and I observed different energy for each of > them. > thanks for any help. > > Mahkameh Vaziri > *PhD student of physical chemistry** > K. N. Toosi university of Technology, Tehran, Iran* > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100613/16c8eae8/attachment.htm From kirtinandan07 at gmail.com Mon Jun 14 07:52:14 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 14 Jun 2010 11:22:14 +0530 Subject: [Pw_forum] not able to install espresso Message-ID: hi i am trying to install espresso-4.2 . i could do ./configure succesfully but when i type make all i get the following error print_out.f90: In function 'printout_new_x': print_out.f90:77: internal compiler error: Segmentation fault Please submit a full bug report, with preprocessed source if appropriate. See for instructions. make[1]: *** [print_out.o] Error 1 make[1]: Leaving directory `/home//Software/espresso-4.2/CPV' make: *** [cp] Error 2 then i tried all version from espresso-4.1 onwards i get same error. can somebody help what is the problem. regards vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/7df4f1e6/attachment.htm From kirtinandan07 at gmail.com Mon Jun 14 08:24:44 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 14 Jun 2010 11:54:44 +0530 Subject: [Pw_forum] PP for Rhenium Message-ID: Hi I am performing pw.x on Nickel system with *Ni.pbe-nd-rrkjus.UPF P**P*. I want to study effect of Rhenium as an alloying element in Nickel so i used the only available PP *Re.pw91-n-van.UPF*. but it is giving me the error. most probably the exchangr correlation function are not of same type for Ni and Re. can any body suggest me what is the problem and if PP is a problem how to get *pbe PP* for Re Re.pw91-n-van.UPF Program PWSCF v.4.0.4 starts ... Today is 14Jun2010 at 12: 2:24 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readpp : error # 3 inconsistent DFT read %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... regards vickysingh Research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/dba268b8/attachment.htm From giannozz at democritos.it Mon Jun 14 08:50:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Jun 2010 08:50:30 +0200 Subject: [Pw_forum] not able to install espresso In-Reply-To: References: Message-ID: <4A16A274-E1B8-442D-9F09-B7BEF2A39F74@democritos.it> On Jun 14, 2010, at 7:52 , vicky singh wrote: > print_out.f90:77: internal compiler error: Segmentation fault from the user guide: "If you get Compiler Internal Error' or similar messages: your compiler version is buggy. Try to lower the optimization level, or to remove optimization just for the routine that has problems. If it doesn't work, or if you experience weird problems at run time, try to install patches for your version of the compiler (most vendors release at least a few patches for free), or to upgrade to a more recent compiler version." 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 Mon Jun 14 08:53:21 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Jun 2010 08:53:21 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: References: Message-ID: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> On Jun 14, 2010, at 8:24 , vicky singh wrote: > > from readpp : error # 3 > inconsistent DFT read From the user guie: "10.1.0.6 .x stops with inconsistent DFT error As a rule, the flavor of DFT used in the calculation should be the same as the one used in the generation of pseudopotentials, which should all be generated using the same flavor of DFT. This is actually enforced: the type of DFT is read from pseudopotential files and it is checked that the same DFT is read from all PPs. If this does not hold, the code stops with the above error message. Use - at your own risk - input variable input_dft to force the usage of the DFT you like." > Research student ...and searching the documentation in case of errors is not part of research, is that true? --- 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 Mon Jun 14 09:06:49 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Jun 2010 09:06:49 +0200 Subject: [Pw_forum] k_points In-Reply-To: <953932.29965.qm@web32906.mail.mud.yahoo.com> References: <953932.29965.qm@web32906.mail.mud.yahoo.com> Message-ID: <0B377588-A8B7-426F-9D98-E89F6FDB4ACF@democritos.it> On Jun 13, 2010, at 12:22 , raheleh vaziri wrote: > I am wondering if determination of offset depends on the grid or > not? Also, when the grid is even, is the offset certainly odd? > see here: http://media.quantum-espresso.org/santa_barbara_2009_07/ index.php in particular http://www.quantum-espresso.org/wiki/images/9/97/ Ucsb_sn_lec1.pdf pag. 26 and following 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 nnlinh at sissa.it Mon Jun 14 10:39:46 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 14 Jun 2010 10:39:46 +0200 Subject: [Pw_forum] Phonon restart error In-Reply-To: <252171.16892.qm@web38805.mail.mud.yahoo.com> References: <252171.16892.qm@web38805.mail.mud.yahoo.com> Message-ID: <4C15EAD2.7000909@sissa.it> loc duong ding wrote: > Dear all, > I try to restart the phonon calculation and I get the error: > > cannot open xml_recover file for writing > > I see there was a topic in PWscf, but I can not solve this problem. > > Could you give me some instructions? This error has been suggested how to solve by Paolo Giannozzi previously: "Re-opened (it was closed by mistake) although this does not look like a bug of the code" Thus, you can do follow that suggestions to check if it is a mistake of xml_recover file, or rerun the calculation from initial step. Help this hope, Linh > > I appreciate to all your help. > > Sincerely, > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From tkaloni at gmail.com Mon Jun 14 10:48:39 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Mon, 14 Jun 2010 14:33:39 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 34 In-Reply-To: References: Message-ID: Dear All, I want to calculate the cohesive energy of graphite, I have total energy of graphite its around -11.39 Ryd. How can i calculate this. Sincerely Thaneshwor Prashad Kaloni S N Bose National Centre for basic Sciences Kolkata Indai On Mon, Jun 14, 2010 at 12:44 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. k_points (raheleh vaziri) > 2. Re: k_points (xirainbow) > 3. not able to install espresso (vicky singh) > 4. PP for Rhenium (vicky singh) > 5. Re: not able to install espresso (Paolo Giannozzi) > 6. Re: PP for Rhenium (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 13 Jun 2010 03:22:56 -0700 (PDT) > From: raheleh vaziri > Subject: [Pw_forum] k_points > To: pwscf > Message-ID: <953932.29965.qm at web32906.mail.mud.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > > I have some questions > about the relation > between grid (nk1, > nk2, nk3) and (k1, k2, k3) offset. I am wondering > if determination of offset depends on the grid or not? > Also, when the grid is > even, is the offset certainly odd? > For example, > I calculated energy for a system with two kinds of k_points (2 2 5 0 0 0 > and 2 2 5 1 1 1) and I observed different energy for each of them. > thanks for any help. > > Mahkameh Vaziri > PhD student of physical chemistry > K. N. Toosi university of > Technology, Tehran, Iran > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100613/1f41fe62/attachment.html > > ------------------------------ > > Message: 2 > Date: Sun, 13 Jun 2010 21:48:29 +0800 > From: xirainbow > Subject: Re: [Pw_forum] k_points > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Mahkameh Vaziri: > The energy difference between (2 2 5 0 0 0) and (2 2 5 1 1 1) indicates > that you did not get convergence about k mesh. > > > On Sun, Jun 13, 2010 at 6:22 PM, raheleh vaziri >wrote: > > > Dear all, > > > > > > I have some questions about the relation between grid (nk1, nk2, nk3) and > > (k1, k2, k3) offset. I am wondering if determination of offset depends on > > the grid or not? > > > > Also, when the grid is even, is the offset certainly odd? > > For example, I calculated energy for a system with two kinds of k_points > > (2 2 5 0 0 0 and 2 2 5 1 1 1) and I observed different energy for each > of > > them. > > thanks for any help. > > > > Mahkameh Vaziri > > *PhD student of physical chemistry** > > K. N. Toosi university of Technology, Tehran, Iran* > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100613/16c8eae8/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Mon, 14 Jun 2010 11:22:14 +0530 > From: vicky singh > Subject: [Pw_forum] not able to install espresso > To: Pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > hi > i am trying to install espresso-4.2 . i could do ./configure succesfully > but > when i type make all i get the following error > > print_out.f90: In function 'printout_new_x': > print_out.f90:77: internal compiler error: Segmentation fault > Please submit a full bug report, > with preprocessed source if appropriate. > See for instructions. > make[1]: *** [print_out.o] Error 1 > make[1]: Leaving directory `/home//Software/espresso-4.2/CPV' > make: *** [cp] Error 2 > > then i tried all version from espresso-4.1 onwards i get same error. > > can somebody help what is the problem. > > regards > > vicky singh > research student > Bangalore > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/7df4f1e6/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Mon, 14 Jun 2010 11:54:44 +0530 > From: vicky singh > Subject: [Pw_forum] PP for Rhenium > To: Pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi > I am performing pw.x on Nickel system with *Ni.pbe-nd-rrkjus.UPF P**P*. I > want to study effect of Rhenium as an alloying element in Nickel so i used > the only available PP *Re.pw91-n-van.UPF*. but it is giving me the error. > most probably the exchangr correlation function are not of same type for Ni > and Re. > can any body suggest me what is the problem and if PP is a problem how to > get *pbe PP* for Re > > Re.pw91-n-van.UPF > > Program PWSCF v.4.0.4 starts ... > Today is 14Jun2010 at 12: 2:24 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from readpp : error # 3 > inconsistent DFT read > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > regards > > vickysingh > Research student > Bangalore > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/dba268b8/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Mon, 14 Jun 2010 08:50:30 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] not able to install espresso > To: PWSCF Forum > Message-ID: <4A16A274-E1B8-442D-9F09-B7BEF2A39F74 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Jun 14, 2010, at 7:52 , vicky singh wrote: > > > print_out.f90:77: internal compiler error: Segmentation fault > > from the user guide: > "If you get Compiler Internal Error' or similar messages: your > compiler version is buggy. > Try to lower the optimization level, or to remove optimization > just for the routine that > has problems. If it doesn't work, or if you experience weird > problems at run time, try to > install patches for your version of the compiler (most vendors > release at least a few > patches for free), or to upgrade to a more recent compiler version." > > 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: 6 > Date: Mon, 14 Jun 2010 08:53:21 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] PP for Rhenium > To: PWSCF Forum > Message-ID: <94F6595B-D716-4240-A307-BF0F4F21271B at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > > from readpp : error # 3 > > inconsistent DFT read > > From the user guie: > "10.1.0.6 .x stops with inconsistent DFT error > As a rule, the flavor of DFT used in the calculation should be the > same as the one used > in the generation of pseudopotentials, which should all be > generated using the same flavor > of DFT. This is actually enforced: the type of DFT is read from > pseudopotential files and it > is checked that the same DFT is read from all PPs. If this does not > hold, the code stops > with the above error message. Use - at your own risk - input > variable input_dft to force > the usage of the DFT you like." > > > Research student > > ...and searching the documentation in case of errors is not part of > research, is that true? > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 36, Issue 34 > **************************************** > -- ################################### ****************************************** Thaneshwor Prashad Kaloni TWAS-BOSE FELLOW /JRF S N Bose national Centre for Basic Sciences Kolkata 700098, INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/f9f9e836/attachment.htm From mambom1902 at yahoo.com Mon Jun 14 11:03:44 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 14 Jun 2010 02:03:44 -0700 (PDT) Subject: [Pw_forum] Computing Second order response In-Reply-To: References: Message-ID: <890798.87887.qm@web38804.mail.mud.yahoo.com> >what's the gap of the unperturbed > system? >SB Actually, this is the firs time I calculate the Raman spectrum. I don't clear about the gap of the unperturbed system? It means the electronic band gap? I appreciate to your explanation. I am sorry about my late reply. >>On May 31, 2010, at 6:10 PM, loc duong ding >> wrote: > >Dear all, > > > >I want calculated IR and Raman of > >nanoribbon. The problem is when the code calcualtion second order response, it > >is not convergence. >> ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From nnlinh at sissa.it Mon Jun 14 11:05:37 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 14 Jun 2010 11:05:37 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 34 In-Reply-To: References: Message-ID: <4C15F0E1.40107@sissa.it> Thaneshwor Kaloni wrote: > Dear All, > I want to calculate the cohesive energy of graphite, I have total > energy of graphite its around -11.39 Ryd. > How can i calculate this. Firstly, you should understand "what cohesive energy is". Reference in some basic text books, or in previous archives http://www.democritos.it/pipermail/pw_forum/2008-January/008195.html Then do the calculations: such as total energy for the isolated C atom E_{iso C}, and total energy of graphite E_{total}. The cohesive energy = E_{total} - N_C *E_{iso C} Hope this helps, Linh p/s you should not submit the topic of question as a general Pw_forum Digest, and reply with a lot of previous question. That makes the submittion very messy. > Sincerely > Thaneshwor Prashad Kaloni > S N Bose National Centre for basic Sciences > Kolkata Indai > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From baroni at sissa.it Mon Jun 14 12:02:57 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 14 Jun 2010 12:02:57 +0200 Subject: [Pw_forum] Computing Second order response In-Reply-To: <890798.87887.qm@web38804.mail.mud.yahoo.com> References: <890798.87887.qm@web38804.mail.mud.yahoo.com> Message-ID: <27313F28-6102-44D8-AD0E-D90366D2CBA1@sissa.it> yes - SB On Jun 14, 2010, at 11:03 AM, loc duong ding wrote: >> what's the gap of the unperturbed >> system? >> SB > > Actually, this is the firs time I calculate the Raman spectrum. I don't clear about the gap of the unperturbed system? It means the electronic band gap? > > I appreciate to your explanation. I am sorry about my late reply. > > > >>> On May 31, 2010, at 6:10 PM, loc duong ding >>> wrote: > >>> Dear all, >>> >>> I want calculated IR and Raman of >>> nanoribbon. The problem is when the code calcualtion second order response, it >>> is not convergence. >>> > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > _______________________________________________ > 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/20100614/f3204378/attachment.htm From kirtinandan07 at gmail.com Mon Jun 14 12:19:05 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 14 Jun 2010 15:49:05 +0530 Subject: [Pw_forum] PP for Rhenium In-Reply-To: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> Message-ID: Hi Thank you very much. but sorry i could not understand "Use - at your own risk - input variable input_dft to force the usage of the DFT you like. " can you please help. regards vickysingh Research student Bangalore On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi wrote: > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > > from readpp : error # 3 > > inconsistent DFT read > > From the user guie: > "10.1.0.6 .x stops with inconsistent DFT error > As a rule, the flavor of DFT used in the calculation should be the > same as the one used > in the generation of pseudopotentials, which should all be > generated using the same flavor > of DFT. This is actually enforced: the type of DFT is read from > pseudopotential files and it > is checked that the same DFT is read from all PPs. If this does not > hold, the code stops > with the above error message. Use - at your own risk - input > variable input_dft to force > the usage of the DFT you like." > > > Research student > > ...and searching the documentation in case of errors is not part of > research, is that true? > --- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/c5b790ed/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Mon Jun 14 12:58:42 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 14 Jun 2010 12:58:42 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> Message-ID: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> Dear vickysingh It means that you are forcing the code to use a PP generated by using some xc functional as a PP generated by using a different xc functional. You do it at your own risk because it is, in principle, wrong, and can lead to unpredictable (and not acknowledged by the community) results. If you know what are you doing, you can force a given xc functional by means of the input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to gain further insight... Hope this helps Giuseppe On Monday 14 June 2010 12:19:05 vicky singh wrote: > Hi > Thank you very much. but sorry i could not understand > "Use - at your own risk - input variable input_dft to force the usage > of the DFT you like. " > can you please help. > > regards > > vickysingh > Research student > Bangalore > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi wrote: > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > from readpp : error # 3 > > > inconsistent DFT read > > > > From the user guie: > > "10.1.0.6 .x stops with inconsistent DFT error > > As a rule, the flavor of DFT used in the calculation should be the > > same as the one used > > in the generation of pseudopotentials, which should all be > > generated using the same flavor > > of DFT. This is actually enforced: the type of DFT is read from > > pseudopotential files and it > > is checked that the same DFT is read from all PPs. If this does not > > hold, the code stops > > with the above error message. Use - at your own risk - input > > variable input_dft to force > > the usage of the DFT you like." > > > > > Research student > > > > ...and searching the documentation in case of errors is not part of > > research, is that true? > > --- > > 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 -- ******************************************************** - 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: From baroni at sissa.it Mon Jun 14 12:52:43 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 14 Jun 2010 12:52:43 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> Message-ID: <3D5B13B9-8DA9-4584-9EFB-151055A8FE61@sissa.it> you use an xc functional different from the one that used to generate the pseudopotential, hence "us at your own risk". this issue has been dscussed many time on this forum in the past, I believe ... SB On Jun 14, 2010, at 12:19 PM, vicky singh wrote: > Hi > Thank you very much. but sorry i could not understand > "Use - at your own risk - input variable input_dft to force the usage of the DFT you like. " > can you please help. > > regards > > vickysingh > Research student > Bangalore > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi wrote: > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > > from readpp : error # 3 > > inconsistent DFT read > > From the user guie: > "10.1.0.6 .x stops with inconsistent DFT error > As a rule, the flavor of DFT used in the calculation should be the > same as the one used > in the generation of pseudopotentials, which should all be > generated using the same flavor > of DFT. This is actually enforced: the type of DFT is read from > pseudopotential files and it > is checked that the same DFT is read from all PPs. If this does not > hold, the code stops > with the above error message. Use - at your own risk - input > variable input_dft to force > the usage of the DFT you like." > > > Research student > > ...and searching the documentation in case of errors is not part of > research, is that true? > --- > 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 > > _______________________________________________ > 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/20100614/a5f3343a/attachment-0001.htm From giannozz at democritos.it Mon Jun 14 12:53:17 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Jun 2010 12:53:17 +0200 Subject: [Pw_forum] tot_magnetization In-Reply-To: References: Message-ID: <4C160A1D.6010901@democritos.it> hanghui chen wrote: > For alloys (using virtual crystal approximation), the number of > electrons depends on the percentage of mixing and is usually fractional. > Why do you set such a requirement? likely for no other reason than "it used to be there once upon a time". Please remove all checks on integer occupancies and all assumptions that the number of electrons (up, down, total) is integer, verify if things work with fractional occupancy (and if they work the same way with integer occupancies), let us know Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From mahkameh_va at yahoo.com Mon Jun 14 13:33:55 2010 From: mahkameh_va at yahoo.com (raheleh vaziri) Date: Mon, 14 Jun 2010 04:33:55 -0700 (PDT) Subject: [Pw_forum] k_points Message-ID: <413895.6929.qm@web32903.mail.mud.yahoo.com> Dear Paolo ? Thanks very much for your reply. I read the lectures and I understand that offset shift only points and not change the total energy. Am I wrong? I?calculated energy for a system with two kinds of k_points (2 2 5 0 0 0 and 2 2 5 1 1 1) and I observed different energy for each of them. How to determine the offset for any kpoints? Is there need for convergence? Thanks in advance Mahkameh Vaziri ? PhD student of physical chemistry K. N. Toosi university of Technology, Tehran, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/40c69086/attachment.htm From kirtinandan07 at gmail.com Mon Jun 14 14:13:01 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 14 Jun 2010 17:43:01 +0530 Subject: [Pw_forum] PP for Rhenium In-Reply-To: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Thanks Giuseppe. On Mon, Jun 14, 2010 at 4:28 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > Dear vickysingh > It means that you are forcing the code to use a PP generated by using some > xc > functional as a PP generated by using a different xc functional. You do it > at > your own risk because it is, in principle, wrong, and can lead to > unpredictable (and not acknowledged by the community) results. If you know > what are you doing, you can force a given xc functional by means of the > input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to gain > further insight... > Hope this helps > Giuseppe > > On Monday 14 June 2010 12:19:05 vicky singh wrote: > > Hi > > Thank you very much. but sorry i could not understand > > "Use - at your own risk - input variable input_dft to force the > usage > > of the DFT you like. " > > can you please help. > > > > regards > > > > vickysingh > > Research student > > Bangalore > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi > wrote: > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > from readpp : error # 3 > > > > inconsistent DFT read > > > > > > From the user guie: > > > "10.1.0.6 .x stops with inconsistent DFT error > > > As a rule, the flavor of DFT used in the calculation should be the > > > same as the one used > > > in the generation of pseudopotentials, which should all be > > > generated using the same flavor > > > of DFT. This is actually enforced: the type of DFT is read from > > > pseudopotential files and it > > > is checked that the same DFT is read from all PPs. If this does not > > > hold, the code stops > > > with the above error message. Use - at your own risk - input > > > variable input_dft to force > > > the usage of the DFT you like." > > > > > > > Research student > > > > > > ...and searching the documentation in case of errors is not part of > > > research, is that true? > > > --- > > > 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 > > > > -- > ******************************************************** > - 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: > _______________________________________________ > 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/20100614/31438b52/attachment.htm From baroni at sissa.it Mon Jun 14 14:13:18 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 14 Jun 2010 14:13:18 +0200 Subject: [Pw_forum] k_points In-Reply-To: <413895.6929.qm@web32903.mail.mud.yahoo.com> References: <413895.6929.qm@web32903.mail.mud.yahoo.com> Message-ID: On Jun 14, 2010, at 1:33 PM, raheleh vaziri wrote: > Dear Paolo > > Thanks very much for your reply. I read the lectures and I understand that offset shift only points and not change the total energy. Am I wrong? yes > I calculated energy for a system with two kinds of k_points (2 2 5 0 0 0 and 2 2 5 1 1 1) and I observed different energy for each of them. How to determine the offset for any kpoints? I do not quite understand what the question is. whatever it may be, the short answer is: kpoint sets are uniform grids in reciprocal space. for a given density of points (inreciprocal space), you have the freedom to chose the coordinates of one point of the grid (the others are fixed by the periodicity of the grid. the "offset" is simply the position of such point. Usually, it is choosen in such a way that the origing is located in the middle of one elementary paralleliped of the grid (rather than at one corner) SB > Is there need for convergence? > Thanks in advance > > Mahkameh Vaziri > PhD student of physical chemistry > K. N. Toosi university of Technology, Tehran, Iran > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/92b69030/attachment-0001.htm From kirtinandan07 at gmail.com Mon Jun 14 14:14:10 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 14 Jun 2010 17:44:10 +0530 Subject: [Pw_forum] PP for Rhenium In-Reply-To: <3D5B13B9-8DA9-4584-9EFB-151055A8FE61@sissa.it> References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> <3D5B13B9-8DA9-4584-9EFB-151055A8FE61@sissa.it> Message-ID: Thanks a lot. vickysingh On Mon, Jun 14, 2010 at 4:22 PM, Stefano Baroni wrote: > you use an xc functional different from the one that used to generate the > pseudopotential, hence "us at your own risk". this issue has been dscussed > many time on this forum in the past, I believe ... SB > > On Jun 14, 2010, at 12:19 PM, vicky singh wrote: > > Hi > Thank you very much. but sorry i could not understand > "Use - at your own risk - input variable input_dft to force the usage > of the DFT you like. " > can you please help. > > regards > > vickysingh > Research student > Bangalore > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi wrote: > >> >> On Jun 14, 2010, at 8:24 , vicky singh wrote: >> >> > >> > from readpp : error # 3 >> > inconsistent DFT read >> >> From the user guie: >> "10.1.0.6 .x stops with inconsistent DFT error >> As a rule, the flavor of DFT used in the calculation should be the >> same as the one used >> in the generation of pseudopotentials, which should all be >> generated using the same flavor >> of DFT. This is actually enforced: the type of DFT is read from >> pseudopotential files and it >> is checked that the same DFT is read from all PPs. If this does not >> hold, the code stops >> with the above error message. Use - at your own risk - input >> variable input_dft to force >> the usage of the DFT you like." >> >> > Research student >> >> ...and searching the documentation in case of errors is not part of >> research, is that true? >> --- >> 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 >> > > _______________________________________________ > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/059ace46/attachment.htm From kirtinandan07 at gmail.com Mon Jun 14 14:18:34 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 14 Jun 2010 17:48:34 +0530 Subject: [Pw_forum] PP for Rhenium In-Reply-To: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Now what is the right method. how to get the required PP of Rhenium i mean xc functional with pbe approximation. i need the result which has to have the reliability. is there any way out. regards vicky singh On Mon, Jun 14, 2010 at 4:28 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > Dear vickysingh > It means that you are forcing the code to use a PP generated by using some > xc > functional as a PP generated by using a different xc functional. You do it > at > your own risk because it is, in principle, wrong, and can lead to > unpredictable (and not acknowledged by the community) results. If you know > what are you doing, you can force a given xc functional by means of the > input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to gain > further insight... > Hope this helps > Giuseppe > > On Monday 14 June 2010 12:19:05 vicky singh wrote: > > Hi > > Thank you very much. but sorry i could not understand > > "Use - at your own risk - input variable input_dft to force the > usage > > of the DFT you like. " > > can you please help. > > > > regards > > > > vickysingh > > Research student > > Bangalore > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi > wrote: > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > from readpp : error # 3 > > > > inconsistent DFT read > > > > > > From the user guie: > > > "10.1.0.6 .x stops with inconsistent DFT error > > > As a rule, the flavor of DFT used in the calculation should be the > > > same as the one used > > > in the generation of pseudopotentials, which should all be > > > generated using the same flavor > > > of DFT. This is actually enforced: the type of DFT is read from > > > pseudopotential files and it > > > is checked that the same DFT is read from all PPs. If this does not > > > hold, the code stops > > > with the above error message. Use - at your own risk - input > > > variable input_dft to force > > > the usage of the DFT you like." > > > > > > > Research student > > > > > > ...and searching the documentation in case of errors is not part of > > > research, is that true? > > > --- > > > 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 > > > > -- > ******************************************************** > - 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: > _______________________________________________ > 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/20100614/30ff9da0/attachment.htm From baroni at sissa.it Mon Jun 14 15:20:53 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 14 Jun 2010 15:20:53 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: References: <94F6595B-D716-4240-A307-BF0F4F21271B@democritos.it> <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <3A0C1F48-7CC2-4D35-BB0C-4F3EDAF19614@sissa.it> three possibilities: 1) use the XC functional used to generate the PP you have 2) generate a PP with the XC functional you want 3) ask somebody else to do (2) for you SB On Jun 14, 2010, at 2:18 PM, vicky singh wrote: > Now what is the right method. how to get the required PP of Rhenium i mean xc functional with pbe approximation. i need the result which has to have the reliability. is there any way out. > > regards > vicky singh > > On Mon, Jun 14, 2010 at 4:28 PM, Giuseppe Mattioli wrote: > Dear vickysingh > It means that you are forcing the code to use a PP generated by using some xc > functional as a PP generated by using a different xc functional. You do it at > your own risk because it is, in principle, wrong, and can lead to > unpredictable (and not acknowledged by the community) results. If you know > what are you doing, you can force a given xc functional by means of the > input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to gain > further insight... > Hope this helps > Giuseppe > > On Monday 14 June 2010 12:19:05 vicky singh wrote: > > Hi > > Thank you very much. but sorry i could not understand > > "Use - at your own risk - input variable input_dft to force the usage > > of the DFT you like. " > > can you please help. > > > > regards > > > > vickysingh > > Research student > > Bangalore > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi > wrote: > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > from readpp : error # 3 > > > > inconsistent DFT read > > > > > > From the user guie: > > > "10.1.0.6 .x stops with inconsistent DFT error > > > As a rule, the flavor of DFT used in the calculation should be the > > > same as the one used > > > in the generation of pseudopotentials, which should all be > > > generated using the same flavor > > > of DFT. This is actually enforced: the type of DFT is read from > > > pseudopotential files and it > > > is checked that the same DFT is read from all PPs. If this does not > > > hold, the code stops > > > with the above error message. Use - at your own risk - input > > > variable input_dft to force > > > the usage of the DFT you like." > > > > > > > Research student > > > > > > ...and searching the documentation in case of errors is not part of > > > research, is that true? > > > --- > > > 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 > > > > -- > ******************************************************** > - 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: > _______________________________________________ > 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 --- 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/20100614/3db3a1fa/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Mon Jun 14 15:38:31 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 14 Jun 2010 15:38:31 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: References: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> You can find (and download) two PBE Rh PPs in http://www.pwscf.org/pseudo/1.3/html/Rh.html As for the reliability, you should test the pseudopotentials on some well understood system in order to reproduce its known properties... G. On Monday 14 June 2010 14:18:34 vicky singh wrote: > Now what is the right method. how to get the required PP of Rhenium i mean > xc functional with pbe approximation. i need the result which has to have > the reliability. is there any way out. > > regards > vicky singh > > On Mon, Jun 14, 2010 at 4:28 PM, Giuseppe Mattioli < > > giuseppe.mattioli at mlib.ism.cnr.it> wrote: > > Dear vickysingh > > It means that you are forcing the code to use a PP generated by using > > some xc > > functional as a PP generated by using a different xc functional. You do > > it at > > your own risk because it is, in principle, wrong, and can lead to > > unpredictable (and not acknowledged by the community) results. If you > > know what are you doing, you can force a given xc functional by means of > > the input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to > > gain further insight... > > Hope this helps > > Giuseppe > > > > On Monday 14 June 2010 12:19:05 vicky singh wrote: > > > Hi > > > Thank you very much. but sorry i could not understand > > > "Use - at your own risk - input variable input_dft to force the > > > > usage > > > > > of the DFT you like. " > > > can you please help. > > > > > > regards > > > > > > vickysingh > > > Research student > > > Bangalore > > > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi > > > > wrote: > > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > > from readpp : error # 3 > > > > > inconsistent DFT read > > > > > > > > From the user guie: > > > > "10.1.0.6 .x stops with inconsistent DFT error > > > > As a rule, the flavor of DFT used in the calculation should be the > > > > same as the one used > > > > in the generation of pseudopotentials, which should all be > > > > generated using the same flavor > > > > of DFT. This is actually enforced: the type of DFT is read from > > > > pseudopotential files and it > > > > is checked that the same DFT is read from all PPs. If this does not > > > > hold, the code stops > > > > with the above error message. Use - at your own risk - input > > > > variable input_dft to force > > > > the usage of the DFT you like." > > > > > > > > > Research student > > > > > > > > ...and searching the documentation in case of errors is not part of > > > > research, is that true? > > > > --- > > > > 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 > > > > -- > > ******************************************************** > > - 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: > > _______________________________________________ > > 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: From paulatto at sissa.it Mon Jun 14 16:03:31 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Jun 2010 16:03:31 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: On Mon, 14 Jun 2010 15:38:31 +0200, Giuseppe Mattioli wrote: > http://www.pwscf.org/pseudo/1.3/html/Rh.html Rh is Rhodium, not Rhenium (re). Unfortunately, there is not intersection between the ensemble of XC functional we have for Nickel and the ones we have for Rhenium (in the QE pseudopotential library). The wisest solution, in my opinion, would be to take the PW91 pseudopotential for Rhenium and regenerate it for PBE. regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From nazari at iasbs.ac.ir Mon Jun 14 20:39:32 2010 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Mon, 14 Jun 2010 19:39:32 +0100 (BST) Subject: [Pw_forum] SIGSEGV, segmentation fault occurred In-Reply-To: <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <31844.85.185.211.90.1276540772.squirrel@mail.iasbs.ac.ir> Dear All, I wish to run QE on REDHAT OS with: ifort 11.1.072, mkl -- 11.1.07, and Intel MPI 4.0, I faced withe the folloeing error: SIGSEGV, segmentation fault occurred, libmkl_mc.so 00002ADA8953633E Unknown I did search in forum but non of them work . Any suggesion regards Fariba Nazari Iasbs From giuseppe.mattioli at mlib.ism.cnr.it Mon Jun 14 17:22:49 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 14 Jun 2010 17:22:49 +0200 Subject: [Pw_forum] PP for Rhenium In-Reply-To: References: <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201006141722.50148.giuseppe.mattioli@mlib.ism.cnr.it> I'm sorry... G. On Monday 14 June 2010 16:03:31 Lorenzo Paulatto wrote: > On Mon, 14 Jun 2010 15:38:31 +0200, Giuseppe Mattioli > > wrote: > > http://www.pwscf.org/pseudo/1.3/html/Rh.html > > Rh is Rhodium, not Rhenium (re). Unfortunately, there is not intersection > between the ensemble of XC functional we have for Nickel and the ones we > have for Rhenium (in the QE pseudopotential library). The wisest solution, > in my opinion, would be to take the PW91 pseudopotential for Rhenium and > regenerate it for PBE. > > regards -- ******************************************************** - 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: From tkaloni at gmail.com Mon Jun 14 19:27:19 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Mon, 14 Jun 2010 23:12:19 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 38 In-Reply-To: References: Message-ID: Dear All, I have total energy of graphite, I need to calculate the cohesive energy of the system, for that I need to calculate the energy of single carbon atom, so would any one help me? Thaneshwor Kaloni PhD student SNBNCBS kolkata www.bose.res.in On Mon, Jun 14, 2010 at 7:05 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: PP for Rhenium (vicky singh) > 2. Re: PP for Rhenium (vicky singh) > 3. Re: PP for Rhenium (Stefano Baroni) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 14 Jun 2010 17:44:10 +0530 > From: vicky singh > Subject: Re: [Pw_forum] PP for Rhenium > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Thanks a lot. > vickysingh > > On Mon, Jun 14, 2010 at 4:22 PM, Stefano Baroni wrote: > > > you use an xc functional different from the one that used to generate the > > pseudopotential, hence "us at your own risk". this issue has been > dscussed > > many time on this forum in the past, I believe ... SB > > > > On Jun 14, 2010, at 12:19 PM, vicky singh wrote: > > > > Hi > > Thank you very much. but sorry i could not understand > > "Use - at your own risk - input variable input_dft to force the > usage > > of the DFT you like. " > > can you please help. > > > > regards > > > > vickysingh > > Research student > > Bangalore > > > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi < > giannozz at democritos.it>wrote: > > > >> > >> On Jun 14, 2010, at 8:24 , vicky singh wrote: > >> > >> > > >> > from readpp : error # 3 > >> > inconsistent DFT read > >> > >> From the user guie: > >> "10.1.0.6 .x stops with inconsistent DFT error > >> As a rule, the flavor of DFT used in the calculation should be the > >> same as the one used > >> in the generation of pseudopotentials, which should all be > >> generated using the same flavor > >> of DFT. This is actually enforced: the type of DFT is read from > >> pseudopotential files and it > >> is checked that the same DFT is read from all PPs. If this does not > >> hold, the code stops > >> with the above error message. Use - at your own risk - input > >> variable input_dft to force > >> the usage of the DFT you like." > >> > >> > Research student > >> > >> ...and searching the documentation in case of errors is not part of > >> research, is that true? > >> --- > >> 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 > >> > > > > _______________________________________________ > > 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 > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/059ace46/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Mon, 14 Jun 2010 17:48:34 +0530 > From: vicky singh > Subject: Re: [Pw_forum] PP for Rhenium > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Now what is the right method. how to get the required PP of Rhenium i mean > xc functional with pbe approximation. i need the result which has to have > the reliability. is there any way out. > > regards > vicky singh > > On Mon, Jun 14, 2010 at 4:28 PM, Giuseppe Mattioli < > giuseppe.mattioli at mlib.ism.cnr.it> wrote: > > > Dear vickysingh > > It means that you are forcing the code to use a PP generated by using > some > > xc > > functional as a PP generated by using a different xc functional. You do > it > > at > > your own risk because it is, in principle, wrong, and can lead to > > unpredictable (and not acknowledged by the community) results. If you > know > > what are you doing, you can force a given xc functional by means of the > > input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to > gain > > further insight... > > Hope this helps > > Giuseppe > > > > On Monday 14 June 2010 12:19:05 vicky singh wrote: > > > Hi > > > Thank you very much. but sorry i could not understand > > > "Use - at your own risk - input variable input_dft to force the > > usage > > > of the DFT you like. " > > > can you please help. > > > > > > regards > > > > > > vickysingh > > > Research student > > > Bangalore > > > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi > > wrote: > > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > > from readpp : error # 3 > > > > > inconsistent DFT read > > > > > > > > From the user guie: > > > > "10.1.0.6 .x stops with inconsistent DFT error > > > > As a rule, the flavor of DFT used in the calculation should be the > > > > same as the one used > > > > in the generation of pseudopotentials, which should all be > > > > generated using the same flavor > > > > of DFT. This is actually enforced: the type of DFT is read from > > > > pseudopotential files and it > > > > is checked that the same DFT is read from all PPs. If this does not > > > > hold, the code stops > > > > with the above error message. Use - at your own risk - input > > > > variable input_dft to force > > > > the usage of the DFT you like." > > > > > > > > > Research student > > > > > > > > ...and searching the documentation in case of errors is not part of > > > > research, is that true? > > > > --- > > > > 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 > > > > > > > > -- > > ******************************************************** > > - 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: > > _______________________________________________ > > 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/20100614/30ff9da0/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Mon, 14 Jun 2010 15:20:53 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] PP for Rhenium > To: PWSCF Forum > Message-ID: <3A0C1F48-7CC2-4D35-BB0C-4F3EDAF19614 at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > three possibilities: > 1) use the XC functional used to generate the PP you have > 2) generate a PP with the XC functional you want > 3) ask somebody else to do (2) for you > SB > > On Jun 14, 2010, at 2:18 PM, vicky singh wrote: > > > Now what is the right method. how to get the required PP of Rhenium i > mean xc functional with pbe approximation. i need the result which has to > have the reliability. is there any way out. > > > > regards > > vicky singh > > > > On Mon, Jun 14, 2010 at 4:28 PM, Giuseppe Mattioli < > giuseppe.mattioli at mlib.ism.cnr.it> wrote: > > Dear vickysingh > > It means that you are forcing the code to use a PP generated by using > some xc > > functional as a PP generated by using a different xc functional. You do > it at > > your own risk because it is, in principle, wrong, and can lead to > > unpredictable (and not acknowledged by the community) results. If you > know > > what are you doing, you can force a given xc functional by means of the > > input_dft keyword. Look into your myespresso/Doc/INPUT_PW.txt file to > gain > > further insight... > > Hope this helps > > Giuseppe > > > > On Monday 14 June 2010 12:19:05 vicky singh wrote: > > > Hi > > > Thank you very much. but sorry i could not understand > > > "Use - at your own risk - input variable input_dft to force the > usage > > > of the DFT you like. " > > > can you please help. > > > > > > regards > > > > > > vickysingh > > > Research student > > > Bangalore > > > > > > On Mon, Jun 14, 2010 at 12:23 PM, Paolo Giannozzi > > wrote: > > > > On Jun 14, 2010, at 8:24 , vicky singh wrote: > > > > > from readpp : error # 3 > > > > > inconsistent DFT read > > > > > > > > From the user guie: > > > > "10.1.0.6 .x stops with inconsistent DFT error > > > > As a rule, the flavor of DFT used in the calculation should be the > > > > same as the one used > > > > in the generation of pseudopotentials, which should all be > > > > generated using the same flavor > > > > of DFT. This is actually enforced: the type of DFT is read from > > > > pseudopotential files and it > > > > is checked that the same DFT is read from all PPs. If this does not > > > > hold, the code stops > > > > with the above error message. Use - at your own risk - input > > > > variable input_dft to force > > > > the usage of the DFT you like." > > > > > > > > > Research student > > > > > > > > ...and searching the documentation in case of errors is not part of > > > > research, is that true? > > > > --- > > > > 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 > > > > > > > > -- > > ******************************************************** > > - 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: > > _______________________________________________ > > 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 > > --- > 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/20100614/3db3a1fa/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 36, Issue 38 > **************************************** > -- ################################### ****************************************** Thaneshwor Prashad Kaloni TWAS-BOSE FELLOW /JRF S N Bose national Centre for Basic Sciences Kolkata 700098, INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/8b6c146e/attachment-0001.htm From baroni at sissa.it Mon Jun 14 21:46:21 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 14 Jun 2010 21:46:21 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 38 In-Reply-To: References: Message-ID: <00C95B98-1653-45E2-866D-DD6CA6B61BCD@sissa.it> Dear Thaneshwor, The total energy of graphite, as provided by any simple XC functional, is crap 'cause simple XC functionals fail to provide an (even approximate) account of the weak dispersion forces responsible for the inter-plane binding. This being said, the calculation of atomic energies also poses some problems, because isolated atoms 9such as C, have open electron shells, whose multiplet structure is not straightforward to describe using DFT. All this considered, a sensible strategy would be to compare the energy of closed-shell structures, not dramatically affected by dispersion forces, nor generacy effects. You may want, for instance, to compare the energy of a single graphene sheet (plus the appropriate amount of hydrogen molecules) with the energy of the (appropriate amount of) methane molecules (or something of that sort). Hope you see the main point(s) and you can provide by yourself the missing pieces of the argument. SB PS: please, take the time of indicating the actual subject of your post in the "subject field" and remove all the unnecessary attachments from it. On Jun 14, 2010, at 7:27 PM, Thaneshwor Kaloni wrote: > Dear All, > I have total energy of graphite, I need to calculate the cohesive energy of the system, for that I need to calculate the energy of single carbon atom, so would any one help me? > Thaneshwor Kaloni > PhD student > SNBNCBS > kolkata > www.bose.res.in --- 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/20100614/91131d82/attachment.htm From eyvaz_isaev at yahoo.com Mon Jun 14 22:21:25 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 14 Jun 2010 13:21:25 -0700 (PDT) Subject: [Pw_forum] right method In-Reply-To: Message-ID: <399436.78749.qm@web65713.mail.ac4.yahoo.com> Dear Vicky, --- On Mon, 6/14/10, vicky singh wrote: > Now what is the right method. The right method is "Try and Fail". > i need the result which has to have the reliability. is there > any way out. The reliability is your responsibility. You should do many tests, verify and trust your own results. That is the way. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/fc495fe0/attachment.htm From matteo at umn.edu Mon Jun 14 22:50:09 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 14 Jun 2010 15:50:09 -0500 Subject: [Pw_forum] total potential plot Message-ID: <4C169601.8090402@umn.edu> Dear all, I have two technical questions. I'm interested in a (2d or 3d) plot of the total potential the electrons are subjected to (V_ext + V_H + V_xc). 1) If I read Doc/INPUT_PP I find: Variable: plot_num Type: INTEGER Description: selects what to save in filplot: 0 = charge 1 = total potential V_bare+V_H + V_xc 2 = local ionic potential 3 = local density of states at e_fermi 4 = local density of electronic entropy 5 = STM images 6 = spin polarization (rho(up)-rho(down)) 7 = |psi|^2 So, I guess, the total potential is the sum of two files obtained with a pp.x run with plot_num = 1 and a second with plot_num = 2. If I do this the result is reasonable (e.g., the potential is attractive around the ions and positive in other regions where electronic charge mostly concentrates). However I'm not 100% sure this is right. For example, is there any overlap (redundance) between the quantities obtained with plot_num = 1 and plot_num = 2? I have given a look to the routines but doesn't look too easy to understand.... 2) is there any known reason why plotrho fails when trying to make a 2D plot of the potential? following example05 I can obtain 2D plots of the charge density with no problem, but not the potential. The files have the same format except for the fact that the potential can go negative. is this the problem? Thanks, Matteo From mambom1902 at yahoo.com Tue Jun 15 03:50:18 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 14 Jun 2010 18:50:18 -0700 (PDT) Subject: [Pw_forum] Computing Second order response In-Reply-To: References: Message-ID: <34603.31563.qm@web38808.mail.mud.yahoo.com> I calculate zigag nano ribbon with hydrogen terminated at the edge. I checked DOS that showed no gap. > yes - SB On Jun 14, 2010, at >> 11:03 AM, loc duong ding wrote: >> what's the gap of the > unperturbed >> system? >> SB > > Actually, this > is the firs time I calculate the Raman spectrum. I don't clear about the gap of > the unperturbed system? It means the electronic band gap? > > I > appreciate to your explanation. I am sorry about my late reply. > > > > >>> On May 31, 2010, at 6:10 PM, loc duong ding > >>> wrote: > >>> Dear all, >>> > >>> I want calculated IR and Raman of >>> nanoribbon. > The problem is when the code calcualtion second order response, it > >>> is not convergence. ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu ------------------------------ From yukihiro_okuno at fujifilm.co.jp Tue Jun 15 05:06:30 2010 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Tue, 15 Jun 2010 12:06:30 +0900 Subject: [Pw_forum] Can we use "Blue moon sampling" in PWSCF Message-ID: Dear PWSCF users and developmers. We want to calculate the reactive system and in order to calculate such a system, I knew the constrained dynamics is useful like J.Am.Chem.Soc (1998) vol 120 2746 which use "Blue moon sampling" that imposes constrained condition in MD. (Blue moon sampling's paper are Journal of Chemical Physics vol 109 7737 (1998) ) Can we use "Blue moon sampling" in PWSCF ? (I found in CPV, there are "SHAKE" method and can we use it instead of "Blue moon sampling " ? ) Sincerely. Yukihiro Okuno. From rana_nand at yahoo.com Tue Jun 15 07:50:54 2010 From: rana_nand at yahoo.com (nand) Date: Mon, 14 Jun 2010 22:50:54 -0700 (PDT) Subject: [Pw_forum] Wrong Mn Pdos Orbital In-Reply-To: References: Message-ID: <564352.34465.qm@web65810.mail.ac4.yahoo.com> Hi All, When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As atoms in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d when i am expecting wfc to be 3d. How ever it gets corrected automatically for a supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug or i can assume it to be 3d and why we get this error. Thanking in advance Nand Kr Rana Ranchi Univeristy Inadia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/a2b93cc3/attachment.htm From bipulrr at gmail.com Tue Jun 15 07:53:16 2010 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 15 Jun 2010 11:23:16 +0530 Subject: [Pw_forum] Wrong Mn Pdos Orbital In-Reply-To: <564352.34465.qm@web65810.mail.ac4.yahoo.com> References: <564352.34465.qm@web65810.mail.ac4.yahoo.com> Message-ID: the 5d here doesnt mean the principle quantum no.=5 On Tue, Jun 15, 2010 at 11:20 AM, nand wrote: > Hi All, > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As atoms > in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d > when i am expecting wfc to be 3d. How ever it gets corrected automatically > for a supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug or i > can assume it to be 3d and why we get this error. > > Thanking in advance > > Nand Kr Rana > Ranchi Univeristy > Inadia > > > _______________________________________________ > 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/20100615/79863544/attachment-0001.htm From giannozz at democritos.it Tue Jun 15 09:08:23 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Jun 2010 09:08:23 +0200 Subject: [Pw_forum] Wrong Mn Pdos Orbital In-Reply-To: <564352.34465.qm@web65810.mail.ac4.yahoo.com> References: <564352.34465.qm@web65810.mail.ac4.yahoo.com> Message-ID: On Jun 15, 2010, at 7:50 , nand wrote: > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 > As atoms in GaAs structure it generates a file named prefix.pdos_#1 > (Mn)_wfc#5d when i am expecting > wfc to be 3d. wfc#5d does not mean "atomic orbital 5d", but "atomic orbital number 5, l=2" ! projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M (l), ! where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f ! (one file per atomic wavefunction found in the pseudopotential file) 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 Jun 15 09:17:47 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Jun 2010 09:17:47 +0200 Subject: [Pw_forum] total potential plot In-Reply-To: <4C169601.8090402@umn.edu> References: <4C169601.8090402@umn.edu> Message-ID: <6AB6284C-A7F3-494F-8DCC-3F7BA296A356@democritos.it> On Jun 14, 2010, at 22:50 , Matteo Cococcioni wrote: > (V_ext + V_H + V_xc) V_ext = nuclear (pseudo-)potential acting on electrons? > 1 = total potential V_bare+V_H + V_xc then this is what you need. > 2 = local ionic potential The latest QE version is more explicit: > 2 = local ionic potential V_bare > 2) is there any known reason why plotrho fails when trying to make > a 2D > plot of the potential? it doesn't fail. Run it interactively. 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 tkaloni at gmail.com Tue Jun 15 09:45:22 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Tue, 15 Jun 2010 13:30:22 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 40 In-Reply-To: References: Message-ID: Dear All, What is the relation between ibrav , celldm, electron, ecuoff, smearing? I will be really happy, if somebody write me about my question. Sincerely Thaneshwor Kaloni SNBNCBS On Tue, Jun 15, 2010 at 11:38 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Pw_forum Digest, Vol 36, Issue 38 (Stefano Baroni) > 2. Re: right method (Eyvaz Isaev) > 3. total potential plot (Matteo Cococcioni) > 4. Re: Computing Second order response (loc duong ding) > 5. Can we use "Blue moon sampling" in PWSCF > (yukihiro_okuno at fujifilm.co.jp) > 6. Wrong Mn Pdos Orbital (nand) > 7. Re: Wrong Mn Pdos Orbital (Bipul Rakshit) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 14 Jun 2010 21:46:21 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 36, Issue 38 > To: PWSCF Forum > Message-ID: <00C95B98-1653-45E2-866D-DD6CA6B61BCD at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Thaneshwor, > > The total energy of graphite, as provided by any simple XC functional, is > crap 'cause simple XC functionals fail to provide an (even approximate) > account of the weak dispersion forces responsible for the inter-plane > binding. > > This being said, the calculation of atomic energies also poses some > problems, because isolated atoms 9such as C, have open electron shells, > whose multiplet structure is not straightforward to describe using DFT. > > All this considered, a sensible strategy would be to compare the energy of > closed-shell structures, not dramatically affected by dispersion forces, nor > generacy effects. You may want, for instance, to compare the energy of a > single graphene sheet (plus the appropriate amount of hydrogen molecules) > with the energy of the (appropriate amount of) methane molecules (or > something of that sort). > > Hope you see the main point(s) and you can provide by yourself the missing > pieces of the argument. > > SB > > PS: please, take the time of indicating the actual subject of your post in > the "subject field" and remove all the unnecessary attachments from it. > > > On Jun 14, 2010, at 7:27 PM, Thaneshwor Kaloni wrote: > > > Dear All, > > I have total energy of graphite, I need to calculate the cohesive energy > of the system, for that I need to calculate the energy of single carbon > atom, so would any one help me? > > Thaneshwor Kaloni > > PhD student > > SNBNCBS > > kolkata > > www.bose.res.in > > --- > 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/20100614/91131d82/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Mon, 14 Jun 2010 13:21:25 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] right method > To: PWSCF Forum > Message-ID: <399436.78749.qm at web65713.mail.ac4.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > Dear Vicky, > > --- On Mon, 6/14/10, vicky singh wrote: > > > Now what is the right method. > > The right method is "Try and Fail". > > > i need the result which has to have the reliability. is there > > any way out. > > The reliability is your responsibility. You should do many tests, > verify and trust your own results. That is the way. > > Bests, > Eyvaz. > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com? > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/fc495fe0/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Mon, 14 Jun 2010 15:50:09 -0500 > From: Matteo Cococcioni > Subject: [Pw_forum] total potential plot > To: PWSCF Forum > Message-ID: <4C169601.8090402 at umn.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Dear all, > > I have two technical questions. I'm interested in a (2d or 3d) plot of > the total potential the electrons are subjected to > (V_ext + V_H + V_xc). > > 1) If I read Doc/INPUT_PP I find: > > Variable: plot_num > > Type: INTEGER > Description: selects what to save in filplot: > > 0 = charge > > 1 = total potential V_bare+V_H + V_xc > > 2 = local ionic potential > > 3 = local density of states at e_fermi > > 4 = local density of electronic entropy > > 5 = STM images > > 6 = spin polarization (rho(up)-rho(down)) > > 7 = |psi|^2 > > > So, I guess, the total potential is the sum of two files obtained with a > pp.x run with plot_num = 1 and a second with plot_num = 2. > If I do this the result is reasonable (e.g., the potential is attractive > around the ions and positive in other regions where > electronic charge mostly concentrates). However I'm not 100% sure this > is right. For example, is there any overlap (redundance) between > the quantities obtained with plot_num = 1 and plot_num = 2? I have given > a look to the routines but doesn't look too easy to understand.... > > 2) is there any known reason why plotrho fails when trying to make a 2D > plot of the potential? following example05 I can obtain > 2D plots of the charge density with no problem, but not the potential. > The files have the same format except for the fact that the potential > can go negative. is this the problem? > > Thanks, > > Matteo > > > > > ------------------------------ > > Message: 4 > Date: Mon, 14 Jun 2010 18:50:18 -0700 (PDT) > From: loc duong ding > Subject: Re: [Pw_forum] Computing Second order response > To: pw_forum at pwscf.org > Message-ID: <34603.31563.qm at web38808.mail.mud.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > I calculate zigag nano ribbon with hydrogen terminated at the edge. I > checked DOS that showed no gap. > > > yes - SB > > On Jun 14, 2010, at > >> 11:03 AM, loc duong ding wrote: > > >> what's the gap of the > > unperturbed > >> system? > >> SB > > > > Actually, this > > is the firs time I calculate the Raman spectrum. I don't clear about the > gap of > > the unperturbed system? It means the electronic band gap? > > > > I > > appreciate to your explanation. I am sorry about my late reply. > > > > > > > > > >>> On May 31, 2010, at 6:10 PM, loc duong ding > > > >>> wrote: > > > >>> Dear all, > >>> > > > >>> I want calculated IR and Raman of > >>> nanoribbon. > > The problem is when the code calcualtion second order response, it > > > >>> is not convergence. > > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > ------------------------------ > > > > > > ------------------------------ > > Message: 5 > Date: Tue, 15 Jun 2010 12:06:30 +0900 > From: yukihiro_okuno at fujifilm.co.jp > Subject: [Pw_forum] Can we use "Blue moon sampling" in PWSCF > To: pw_forum at pwscf.org > Message-ID: > < > OF6125EE5C.936BE9EA-ON49257743.001053D1-49257743.001111A5 at mta.fujifilm.co.jp > > > > Content-Type: text/plain; charset=US-ASCII > > > Dear PWSCF users and developmers. > > We want to calculate the reactive system and in order to calculate > > such a system, I knew the constrained dynamics is useful like > > J.Am.Chem.Soc (1998) vol 120 2746 > > which use "Blue moon sampling" that imposes constrained condition > in MD. > > (Blue moon sampling's paper are > > Journal of Chemical Physics vol 109 7737 (1998) ) > > Can we use "Blue moon sampling" in PWSCF ? > > (I found in CPV, there are "SHAKE" method and can we use > > it instead of "Blue moon sampling " ? ) > > Sincerely. > > Yukihiro Okuno. > > > > > ------------------------------ > > Message: 6 > Date: Mon, 14 Jun 2010 22:50:54 -0700 (PDT) > From: nand > Subject: [Pw_forum] Wrong Mn Pdos Orbital > To: pw_forum at pwscf.org > Message-ID: <564352.34465.qm at web65810.mail.ac4.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As atoms > in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d when > i am expecting wfc to be 3d. How ever it gets corrected automatically for a > supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug or i can > assume it to be 3d and why we get this error. > > Thanking in advance > > Nand Kr Rana > Ranchi Univeristy > Inadia > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/a2b93cc3/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Tue, 15 Jun 2010 11:23:16 +0530 > From: Bipul Rakshit > Subject: Re: [Pw_forum] Wrong Mn Pdos Orbital > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > the 5d here doesnt mean the principle quantum no.=5 > > > > On Tue, Jun 15, 2010 at 11:20 AM, nand wrote: > > > Hi All, > > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As > atoms > > in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d > > when i am expecting wfc to be 3d. How ever it gets corrected > automatically > > for a supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug > or i > > can assume it to be 3d and why we get this error. > > > > Thanking in advance > > > > Nand Kr Rana > > Ranchi Univeristy > > Inadia > > > > > > _______________________________________________ > > 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/20100615/79863544/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 36, Issue 40 > **************************************** > -- ################################### ****************************************** Thaneshwor Prashad Kaloni TWAS-BOSE FELLOW /JRF S N Bose national Centre for Basic Sciences Kolkata 700098, INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100615/5ca9cc20/attachment-0001.htm From giannozz at democritos.it Tue Jun 15 09:47:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Jun 2010 09:47:30 +0200 Subject: [Pw_forum] SIGSEGV, segmentation fault occurred In-Reply-To: <31844.85.185.211.90.1276540772.squirrel@mail.iasbs.ac.ir> References: <201006141258.42802.giuseppe.mattioli@mlib.ism.cnr.it> <201006141538.32226.giuseppe.mattioli@mlib.ism.cnr.it> <31844.85.185.211.90.1276540772.squirrel@mail.iasbs.ac.ir> Message-ID: <4C173012.3070303@democritos.it> nazari at iasbs.ac.ir wrote: > ifort 11.1.072, mkl -- 11.1.07, and Intel MPI 4.0, try OpenMPI P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Tue Jun 15 10:15:52 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 15 Jun 2010 10:15:52 +0200 Subject: [Pw_forum] Computing Second order response In-Reply-To: <34603.31563.qm@web38808.mail.mud.yahoo.com> References: <34603.31563.qm@web38808.mail.mud.yahoo.com> Message-ID: so, the the Raman activity should be zero ... SB On Jun 15, 2010, at 3:50 AM, loc duong ding wrote: > I calculate zigag nano ribbon with hydrogen terminated at the edge. I checked DOS that showed no gap. > >> yes - SB > > On Jun 14, 2010, at >>> 11:03 AM, loc duong ding wrote: > >>> what's the gap of the >> unperturbed >>> system? >>> SB >> >> Actually, this >> is the firs time I calculate the Raman spectrum. I don't clear about the gap of >> the unperturbed system? It means the electronic band gap? >> >> I >> appreciate to your explanation. I am sorry about my late reply. >> >> >> >> >>>> On May 31, 2010, at 6:10 PM, loc duong ding >> >>>> wrote: >> >>>> Dear all, >>>> >> >>>> I want calculated IR and Raman of >>>> nanoribbon. >> The problem is when the code calcualtion second order response, it >> >>>> is not convergence. > > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > ------------------------------ > > > > _______________________________________________ > 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/20100615/04ca845a/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Jun 15 10:28:51 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 15 Jun 2010 10:28:51 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 40 In-Reply-To: References: Message-ID: <201006151028.51953.giuseppe.mattioli@mlib.ism.cnr.it> Dear Thaneshwor Please consider that this forum cannot help people who knows nothing about solid state physics and first principle calculations. Here you can find help on quite specific theoretical and/or computational problems, after you read the QE manuals and forum archives to be sure that your questions does not find an answer there. Yours Giuseppe On Tuesday 15 June 2010 09:45:22 Thaneshwor Kaloni wrote: > Dear All, > What is the relation between ibrav , celldm, electron, ecuoff, smearing? > I will be really happy, if somebody write me about my question. > Sincerely > Thaneshwor Kaloni > SNBNCBS > > On Tue, Jun 15, 2010 at 11:38 AM, wrote: > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. Re: Pw_forum Digest, Vol 36, Issue 38 (Stefano Baroni) > > 2. Re: right method (Eyvaz Isaev) > > 3. total potential plot (Matteo Cococcioni) > > 4. Re: Computing Second order response (loc duong ding) > > 5. Can we use "Blue moon sampling" in PWSCF > > (yukihiro_okuno at fujifilm.co.jp) > > 6. Wrong Mn Pdos Orbital (nand) > > 7. Re: Wrong Mn Pdos Orbital (Bipul Rakshit) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 14 Jun 2010 21:46:21 +0200 > > From: Stefano Baroni > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 36, Issue 38 > > To: PWSCF Forum > > Message-ID: <00C95B98-1653-45E2-866D-DD6CA6B61BCD at sissa.it> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Thaneshwor, > > > > The total energy of graphite, as provided by any simple XC functional, is > > crap 'cause simple XC functionals fail to provide an (even approximate) > > account of the weak dispersion forces responsible for the inter-plane > > binding. > > > > This being said, the calculation of atomic energies also poses some > > problems, because isolated atoms 9such as C, have open electron shells, > > whose multiplet structure is not straightforward to describe using DFT. > > > > All this considered, a sensible strategy would be to compare the energy > > of closed-shell structures, not dramatically affected by dispersion > > forces, nor generacy effects. You may want, for instance, to compare the > > energy of a single graphene sheet (plus the appropriate amount of > > hydrogen molecules) with the energy of the (appropriate amount of) > > methane molecules (or something of that sort). > > > > Hope you see the main point(s) and you can provide by yourself the > > missing pieces of the argument. > > > > SB > > > > PS: please, take the time of indicating the actual subject of your post > > in the "subject field" and remove all the unnecessary attachments from > > it. > > > > On Jun 14, 2010, at 7:27 PM, Thaneshwor Kaloni wrote: > > > Dear All, > > > I have total energy of graphite, I need to calculate the cohesive > > > energy > > > > of the system, for that I need to calculate the energy of single carbon > > atom, so would any one help me? > > > > > Thaneshwor Kaloni > > > PhD student > > > SNBNCBS > > > kolkata > > > www.bose.res.in > > > > --- > > 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/20100614/91131d82 > >/attachment-0001.htm > > > > ------------------------------ > > > > Message: 2 > > Date: Mon, 14 Jun 2010 13:21:25 -0700 (PDT) > > From: Eyvaz Isaev > > Subject: Re: [Pw_forum] right method > > To: PWSCF Forum > > Message-ID: <399436.78749.qm at web65713.mail.ac4.yahoo.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > > > > > > > > > > > Dear Vicky, > > > > --- On Mon, 6/14/10, vicky singh wrote: > > > Now what is the right method. > > > > The right method is "Try and Fail". > > > > > i need the result which has to have the reliability. is there > > > any way out. > > > > The reliability is your responsibility. You should do many tests, > > verify and trust your own results. That is the way. > > > > Bests, > > Eyvaz. > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Department of Physics, Chemistry, and Biology (IFM), Linkoping > > University, Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com? > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/fc495fe0 > >/attachment-0001.htm > > > > ------------------------------ > > > > Message: 3 > > Date: Mon, 14 Jun 2010 15:50:09 -0500 > > From: Matteo Cococcioni > > Subject: [Pw_forum] total potential plot > > To: PWSCF Forum > > Message-ID: <4C169601.8090402 at umn.edu> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > Dear all, > > > > I have two technical questions. I'm interested in a (2d or 3d) plot of > > the total potential the electrons are subjected to > > (V_ext + V_H + V_xc). > > > > 1) If I read Doc/INPUT_PP I find: > > > > Variable: plot_num > > > > Type: INTEGER > > Description: selects what to save in filplot: > > > > 0 = charge > > > > 1 = total potential V_bare+V_H + V_xc > > > > 2 = local ionic potential > > > > 3 = local density of states at e_fermi > > > > 4 = local density of electronic entropy > > > > 5 = STM images > > > > 6 = spin polarization (rho(up)-rho(down)) > > > > 7 = |psi|^2 > > > > > > So, I guess, the total potential is the sum of two files obtained with a > > pp.x run with plot_num = 1 and a second with plot_num = 2. > > If I do this the result is reasonable (e.g., the potential is attractive > > around the ions and positive in other regions where > > electronic charge mostly concentrates). However I'm not 100% sure this > > is right. For example, is there any overlap (redundance) between > > the quantities obtained with plot_num = 1 and plot_num = 2? I have given > > a look to the routines but doesn't look too easy to understand.... > > > > 2) is there any known reason why plotrho fails when trying to make a 2D > > plot of the potential? following example05 I can obtain > > 2D plots of the charge density with no problem, but not the potential. > > The files have the same format except for the fact that the potential > > can go negative. is this the problem? > > > > Thanks, > > > > Matteo > > > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Mon, 14 Jun 2010 18:50:18 -0700 (PDT) > > From: loc duong ding > > Subject: Re: [Pw_forum] Computing Second order response > > To: pw_forum at pwscf.org > > Message-ID: <34603.31563.qm at web38808.mail.mud.yahoo.com> > > Content-Type: text/plain; charset=us-ascii > > > > I calculate zigag nano ribbon with hydrogen terminated at the edge. I > > checked DOS that showed no gap. > > > > > yes - SB > > > > On Jun 14, 2010, at > > > > >> 11:03 AM, loc duong ding wrote: > > >> > > >> what's the gap of the > > > > > > unperturbed > > > > > >> system? > > >> SB > > > > > > Actually, this > > > is the firs time I calculate the Raman spectrum. I don't clear about > > > the > > > > gap of > > > > > the unperturbed system? It means the electronic band gap? > > > > > > I > > > appreciate to your explanation. I am sorry about my late reply. > > > > > >>> On May 31, 2010, at 6:10 PM, loc duong ding > > >>> > > >>> wrote: > > >>> > > >>> Dear all, > > >>> > > >>> > > >>> I want calculated IR and Raman of > > >>> nanoribbon. > > > > > > The problem is when the code calcualtion second order response, it > > > > > >>> is not convergence. > > > > ----------------------------------------------- > > Loc Duong Dinh > > Ms-Ph.D Student > > Sungkyunkwan Advanced Institute of Nanotechnology, > > Sungkyunkwan University, > > Suwon, 440-746, Korea > > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 15 Jun 2010 12:06:30 +0900 > > From: yukihiro_okuno at fujifilm.co.jp > > Subject: [Pw_forum] Can we use "Blue moon sampling" in PWSCF > > To: pw_forum at pwscf.org > > Message-ID: > > < > > OF6125EE5C.936BE9EA-ON49257743.001053D1-49257743.001111A5 at mta.fujifilm.co > >.jp > > > > > > Content-Type: text/plain; charset=US-ASCII > > > > > > Dear PWSCF users and developmers. > > > > We want to calculate the reactive system and in order to calculate > > > > such a system, I knew the constrained dynamics is useful like > > > > J.Am.Chem.Soc (1998) vol 120 2746 > > > > which use "Blue moon sampling" that imposes constrained condition > > in MD. > > > > (Blue moon sampling's paper are > > > > Journal of Chemical Physics vol 109 7737 (1998) ) > > > > Can we use "Blue moon sampling" in PWSCF ? > > > > (I found in CPV, there are "SHAKE" method and can we use > > > > it instead of "Blue moon sampling " ? ) > > > > Sincerely. > > > > Yukihiro Okuno. > > > > > > > > > > ------------------------------ > > > > Message: 6 > > Date: Mon, 14 Jun 2010 22:50:54 -0700 (PDT) > > From: nand > > Subject: [Pw_forum] Wrong Mn Pdos Orbital > > To: pw_forum at pwscf.org > > Message-ID: <564352.34465.qm at web65810.mail.ac4.yahoo.com> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi All, > > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As > > atoms in GaAs structure it generates a file named > > prefix.pdos_#1(Mn)_wfc#5d when i am expecting wfc to be 3d. How ever it > > gets corrected automatically for a supercell of 17 atoms( Mn1As4Ga12). > > Plz tell if its a serious bug or i can assume it to be 3d and why we get > > this error. > > > > Thanking in advance > > > > Nand Kr Rana > > Ranchi Univeristy > > Inadia > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > http://www.democritos.it/pipermail/pw_forum/attachments/20100614/a2b93cc3 > >/attachment-0001.htm > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 15 Jun 2010 11:23:16 +0530 > > From: Bipul Rakshit > > Subject: Re: [Pw_forum] Wrong Mn Pdos Orbital > > To: PWSCF Forum > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > the 5d here doesnt mean the principle quantum no.=5 > > > > On Tue, Jun 15, 2010 at 11:20 AM, nand wrote: > > > Hi All, > > > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As > > > > atoms > > > > > in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d > > > when i am expecting wfc to be 3d. How ever it gets corrected > > > > automatically > > > > > for a supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug > > > > or i > > > > > can assume it to be 3d and why we get this error. > > > > > > Thanking in advance > > > > > > Nand Kr Rana > > > Ranchi Univeristy > > > Inadia > > > > > > > > > _______________________________________________ > > > 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/20100615/79863544 > >/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 36, Issue 40 > > **************************************** -- ******************************************************** - 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: From uccaati at ucl.ac.uk Tue Jun 15 11:41:05 2010 From: uccaati at ucl.ac.uk (Antonio Tilocca) Date: Tue, 15 Jun 2010 10:41:05 +0100 (BST) Subject: [Pw_forum] Can we use "Blue moon sampling" in PWSCF In-Reply-To: References: Message-ID: Dear Yukihiro Okuno, provided that you can identify a geometrical parameter (distance, angle, etc) whose evolution is representative of the progress of the reactive process that you want to model, you can run several constrained MD trajectories using cp.x, where this representative parameter ("reaction coordinate") is constrained to several discrete values, going from the "reactant" to "products" side, see for instance J. Chem. Phys. 2003, 119, 7445. The free energy profile of the reaction is then obtained by integrating the average constraint force of each of these trajectories. (I guess the same can be done using pw.x) Antonio Tilocca UCL > 5. Can we use "Blue moon sampling" in PWSCF > (yukihiro_okuno at fujifilm.co.jp) > > Date: Tue, 15 Jun 2010 12:06:30 +0900 > From: yukihiro_okuno at fujifilm.co.jp > Subject: [Pw_forum] Can we use "Blue moon sampling" in PWSCF > To: pw_forum at pwscf.org > Message-ID: > > > > Dear PWSCF users and developmers. > > We want to calculate the reactive system and in order to calculate > > such a system, I knew the constrained dynamics is useful like > > J.Am.Chem.Soc (1998) vol 120 2746 > > which use "Blue moon sampling" that imposes constrained condition > in MD. > > (Blue moon sampling's paper are > > Journal of Chemical Physics vol 109 7737 (1998) ) > > Can we use "Blue moon sampling" in PWSCF ? > > (I found in CPV, there are "SHAKE" method and can we use > > it instead of "Blue moon sampling " ? ) > > Sincerely. > > Yukihiro Okuno. > From o.sedelnikova at gmail.com Tue Jun 15 11:47:33 2010 From: o.sedelnikova at gmail.com (Olga Sedelnikova) Date: Tue, 15 Jun 2010 16:47:33 +0700 Subject: [Pw_forum] PP for Au Message-ID: Dear All, I'm interesting in calculation of the Au monolayer (111)/graphene slab. What PP for Au do you recommend for my purpose? -- Thanks, Olga Sedelnikova Nikolaev Institute of Inorganic Chemistry of SB RAS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100615/f93a12cd/attachment.htm From baroni at sissa.it Tue Jun 15 12:08:06 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 15 Jun 2010 12:08:06 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 40 In-Reply-To: References: Message-ID: May I suggest that you invest a few weeks studying a textbook in electronic-structure theory? There are a few that you may want to consider. http://books.google.it/books?id=dmRTFLpSGNsC&printsec=frontcover&dq=electronic+structure+kohanoff&source=gbs_similarbooks_s&cad=1#v=onepage&q=electronic%20structure%20kohanoff&f=false http://books.google.it/books?id=v2ElZFCKeBsC&printsec=frontcover&dq=electronic+structure+kohanoff&source=bl&ots=t9ik5Q69eT&sig=ReaoOtMe5vd8XOgROiwHmqfeJP4&hl=it&ei=708XTIPONNmpsQby48XYCQ&sa=X&oi=book_result&ct=result&resnum=1&ved=0CB0Q6AEwAA#v=onepage&q&f=false http://books.google.it/books?id=yZrkcSwlr2YC&printsec=frontcover&dq=electronic+structure+kohanoff&source=gbs_similarbooks_s&cad=1#v=onepage&q&f=false Also, may I implore you *NOT* to hit "reply" to digest mailing to write to this forum, and take the few seconds that are needed to specify an intelligible "subject" in the appropriate e-mail field? Have fun studying and learning! Stefano B On Jun 15, 2010, at 9:45 AM, Thaneshwor Kaloni wrote: > Dear All, > What is the relation between ibrav , celldm, electron, ecuoff, smearing? > I will be really happy, if somebody write me about my question. > Sincerely > Thaneshwor Kaloni > SNBNCBS > > On Tue, Jun 15, 2010 at 11:38 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Pw_forum Digest, Vol 36, Issue 38 (Stefano Baroni) > 2. Re: right method (Eyvaz Isaev) > 3. total potential plot (Matteo Cococcioni) > 4. Re: Computing Second order response (loc duong ding) > 5. Can we use "Blue moon sampling" in PWSCF > (yukihiro_okuno at fujifilm.co.jp) > 6. Wrong Mn Pdos Orbital (nand) > 7. Re: Wrong Mn Pdos Orbital (Bipul Rakshit) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 14 Jun 2010 21:46:21 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 36, Issue 38 > To: PWSCF Forum > Message-ID: <00C95B98-1653-45E2-866D-DD6CA6B61BCD at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Thaneshwor, > > The total energy of graphite, as provided by any simple XC functional, is crap 'cause simple XC functionals fail to provide an (even approximate) account of the weak dispersion forces responsible for the inter-plane binding. > > This being said, the calculation of atomic energies also poses some problems, because isolated atoms 9such as C, have open electron shells, whose multiplet structure is not straightforward to describe using DFT. > > All this considered, a sensible strategy would be to compare the energy of closed-shell structures, not dramatically affected by dispersion forces, nor generacy effects. You may want, for instance, to compare the energy of a single graphene sheet (plus the appropriate amount of hydrogen molecules) with the energy of the (appropriate amount of) methane molecules (or something of that sort). > > Hope you see the main point(s) and you can provide by yourself the missing pieces of the argument. > > SB > > PS: please, take the time of indicating the actual subject of your post in the "subject field" and remove all the unnecessary attachments from it. > > > On Jun 14, 2010, at 7:27 PM, Thaneshwor Kaloni wrote: > > > Dear All, > > I have total energy of graphite, I need to calculate the cohesive energy of the system, for that I need to calculate the energy of single carbon atom, so would any one help me? > > Thaneshwor Kaloni > > PhD student > > SNBNCBS > > kolkata > > www.bose.res.in > > --- > 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/20100614/91131d82/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Mon, 14 Jun 2010 13:21:25 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] right method > To: PWSCF Forum > Message-ID: <399436.78749.qm at web65713.mail.ac4.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > Dear Vicky, > > --- On Mon, 6/14/10, vicky singh wrote: > > > Now what is the right method. > > The right method is "Try and Fail". > > > i need the result which has to have the reliability. is there > > any way out. > > The reliability is your responsibility. You should do many tests, > verify and trust your own results. That is the way. > > Bests, > Eyvaz. > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com? > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/fc495fe0/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Mon, 14 Jun 2010 15:50:09 -0500 > From: Matteo Cococcioni > Subject: [Pw_forum] total potential plot > To: PWSCF Forum > Message-ID: <4C169601.8090402 at umn.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Dear all, > > I have two technical questions. I'm interested in a (2d or 3d) plot of > the total potential the electrons are subjected to > (V_ext + V_H + V_xc). > > 1) If I read Doc/INPUT_PP I find: > > Variable: plot_num > > Type: INTEGER > Description: selects what to save in filplot: > > 0 = charge > > 1 = total potential V_bare+V_H + V_xc > > 2 = local ionic potential > > 3 = local density of states at e_fermi > > 4 = local density of electronic entropy > > 5 = STM images > > 6 = spin polarization (rho(up)-rho(down)) > > 7 = |psi|^2 > > > So, I guess, the total potential is the sum of two files obtained with a > pp.x run with plot_num = 1 and a second with plot_num = 2. > If I do this the result is reasonable (e.g., the potential is attractive > around the ions and positive in other regions where > electronic charge mostly concentrates). However I'm not 100% sure this > is right. For example, is there any overlap (redundance) between > the quantities obtained with plot_num = 1 and plot_num = 2? I have given > a look to the routines but doesn't look too easy to understand.... > > 2) is there any known reason why plotrho fails when trying to make a 2D > plot of the potential? following example05 I can obtain > 2D plots of the charge density with no problem, but not the potential. > The files have the same format except for the fact that the potential > can go negative. is this the problem? > > Thanks, > > Matteo > > > > > ------------------------------ > > Message: 4 > Date: Mon, 14 Jun 2010 18:50:18 -0700 (PDT) > From: loc duong ding > Subject: Re: [Pw_forum] Computing Second order response > To: pw_forum at pwscf.org > Message-ID: <34603.31563.qm at web38808.mail.mud.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > I calculate zigag nano ribbon with hydrogen terminated at the edge. I checked DOS that showed no gap. > > > yes - SB > > On Jun 14, 2010, at > >> 11:03 AM, loc duong ding wrote: > > >> what's the gap of the > > unperturbed > >> system? > >> SB > > > > Actually, this > > is the firs time I calculate the Raman spectrum. I don't clear about the gap of > > the unperturbed system? It means the electronic band gap? > > > > I > > appreciate to your explanation. I am sorry about my late reply. > > > > > > > > > >>> On May 31, 2010, at 6:10 PM, loc duong ding > > > >>> wrote: > > > >>> Dear all, > >>> > > > >>> I want calculated IR and Raman of > >>> nanoribbon. > > The problem is when the code calcualtion second order response, it > > > >>> is not convergence. > > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > ------------------------------ > > > > > > ------------------------------ > > Message: 5 > Date: Tue, 15 Jun 2010 12:06:30 +0900 > From: yukihiro_okuno at fujifilm.co.jp > Subject: [Pw_forum] Can we use "Blue moon sampling" in PWSCF > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset=US-ASCII > > > Dear PWSCF users and developmers. > > We want to calculate the reactive system and in order to calculate > > such a system, I knew the constrained dynamics is useful like > > J.Am.Chem.Soc (1998) vol 120 2746 > > which use "Blue moon sampling" that imposes constrained condition > in MD. > > (Blue moon sampling's paper are > > Journal of Chemical Physics vol 109 7737 (1998) ) > > Can we use "Blue moon sampling" in PWSCF ? > > (I found in CPV, there are "SHAKE" method and can we use > > it instead of "Blue moon sampling " ? ) > > Sincerely. > > Yukihiro Okuno. > > > > > ------------------------------ > > Message: 6 > Date: Mon, 14 Jun 2010 22:50:54 -0700 (PDT) > From: nand > Subject: [Pw_forum] Wrong Mn Pdos Orbital > To: pw_forum at pwscf.org > Message-ID: <564352.34465.qm at web65810.mail.ac4.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As atoms in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d when i am expecting wfc to be 3d. How ever it gets corrected automatically for a supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug or i can assume it to be 3d and why we get this error. > > Thanking in advance > > Nand Kr Rana > Ranchi Univeristy > Inadia > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100614/a2b93cc3/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Tue, 15 Jun 2010 11:23:16 +0530 > From: Bipul Rakshit > Subject: Re: [Pw_forum] Wrong Mn Pdos Orbital > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > the 5d here doesnt mean the principle quantum no.=5 > > > > On Tue, Jun 15, 2010 at 11:20 AM, nand wrote: > > > Hi All, > > When I calculate Mn pdos in a supercell(of 5 atom Mn1 As4) with 4 As atoms > > in GaAs structure it generates a file named prefix.pdos_#1(Mn)_wfc#5d > > when i am expecting wfc to be 3d. How ever it gets corrected automatically > > for a supercell of 17 atoms( Mn1As4Ga12). Plz tell if its a serious bug or i > > can assume it to be 3d and why we get this error. > > > > Thanking in advance > > > > Nand Kr Rana > > Ranchi Univeristy > > Inadia > > > > > > _______________________________________________ > > 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/20100615/79863544/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 36, Issue 40 > **************************************** > > > > -- > ################################### > ****************************************** > Thaneshwor Prashad Kaloni > TWAS-BOSE FELLOW /JRF > S N Bose national Centre for Basic Sciences > Kolkata 700098, > INDIA > _______________________________________________ > 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/20100615/0b77c985/attachment-0001.htm From glaweh at physik.fu-berlin.de Tue Jun 15 12:02:04 2010 From: glaweh at physik.fu-berlin.de (Henning Glawe) Date: Tue, 15 Jun 2010 12:02:04 +0200 Subject: [Pw_forum] BUG: OpenMP in espresso 4.2 Message-ID: <20100615100204.GB28266@ford.simpsons.bogus> Moin, just found a small bug in configure.ac, which prevented the openmp compiler flag to be added. -- c u henning -------------- next part -------------- A non-text attachment was scrubbed... Name: espresso-4.2-omp-configure-fix.diff Type: text/x-diff Size: 539 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100615/2c0e5707/attachment.diff From giannozz at democritos.it Tue Jun 15 12:25:27 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Jun 2010 12:25:27 +0200 Subject: [Pw_forum] BUG: OpenMP in espresso 4.2 In-Reply-To: <20100615100204.GB28266@ford.simpsons.bogus> References: <20100615100204.GB28266@ford.simpsons.bogus> Message-ID: <4C175517.5000002@democritos.it> Henning Glawe wrote: > just found a small bug in configure.ac, which prevented > the openmp compiler flag to be added. thank you! P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From samadpoormahmood at yahoo.com Tue Jun 15 13:42:26 2010 From: samadpoormahmood at yahoo.com (Mahmood Samadpoor) Date: Tue, 15 Jun 2010 04:42:26 -0700 (PDT) Subject: [Pw_forum] plotband.x problem Message-ID: <49103.20224.qm@web120020.mail.ne1.yahoo.com> Dear all Hi I did a scf and nscf calculation for Cdse Zinc Blende structure. i wanted to plot the band structure, so i used bands.x to produce band.dat(band structure data file) and it did not report any error and band structure data were successfully written to the file and i used the plotband.x to plot my data. but when i want to see the final .ps file, i just see a sentence : " Loading . . ." , and it doesn't show any diagram. but i can plot the band structure by Microsoft excel software. I would appreciate if you help me in this regard. M. Samadpour PHD student Sharif university of technology Tehran Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100615/7b68e52e/attachment.htm From psavita at crlindia.com Tue Jun 15 13:53:59 2010 From: psavita at crlindia.com (psavita at crlindia.com) Date: Tue, 15 Jun 2010 17:23:59 +0530 Subject: [Pw_forum] 2. PP for Au In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100615/f7c65bb0/attachment-0001.htm From mambom1902 at yahoo.com Tue Jun 15 14:56:10 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 15 Jun 2010 05:56:10 -0700 (PDT) Subject: [Pw_forum] Computing Second order response In-Reply-To: References: Message-ID: <508640.34950.qm@web38802.mail.mud.yahoo.com> I don't understand why Raman activity in this case is zero. In practical, metallic system also provide Raman peak (ex. Carbon nannotube). I try to calculate graphene (no gap) and I get the proper result. Can you give some more explanation or suggest me some reference about this topic? I appreciate to your instructions. >So, the the Raman activity should be > zero ... >SB On Jun 15, 2010, at 3:50 AM, loc duong ding > wrote: > I calculate zigag nano ribbon with hydrogen terminated at the > edge. I checked DOS that showed no gap. > >> yes - SB > > > On Jun 14, 2010, at >>> 11:03 AM, loc duong ding > wrote: > >>> what's the gap of the >> unperturbed > >>> system? >>> SB >> >> Actually, > this >> is the firs time I calculate the Raman spectrum. I don't clear > about the gap of >> the unperturbed system? It means the electronic > band gap? ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From samolyuk at gmail.com Tue Jun 15 16:27:43 2010 From: samolyuk at gmail.com (German Samolyuk) Date: Tue, 15 Jun 2010 10:27:43 -0400 Subject: [Pw_forum] pseudo-potential for virtual atom Message-ID: Dear all, I need to produce pseudo-potential for virtual atom, something like W_{1-x}Re_x. The pseudo-potentials from the database, W.pw91-nsp-van.UPF and Re.pw91-nsp-van.UPF, have different number of valence electrons states and utility vitual.x does not work for this two ps because of this reason. However, if I make ps for these two elements with the same number of wave functions using ld1.x, virtual.x can not read ps files because UPF format has been changed. I tried versions 4.1, 4.1.1 and 4.2. What should I do to solve this problem? Thank you in advance. German Samolyuk, Oak Ridge National Laboratory, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100615/05a128e2/attachment.htm From matteo at umn.edu Tue Jun 15 17:34:34 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 15 Jun 2010 10:34:34 -0500 Subject: [Pw_forum] total potential plot In-Reply-To: <6AB6284C-A7F3-494F-8DCC-3F7BA296A356@democritos.it> References: <4C169601.8090402@umn.edu> <6AB6284C-A7F3-494F-8DCC-3F7BA296A356@democritos.it> Message-ID: <4C179D8A.6050503@umn.edu> Thanks Paolo. Paolo Giannozzi wrote: > On Jun 14, 2010, at 22:50 , Matteo Cococcioni wrote: > > >> (V_ext + V_H + V_xc) >> > > V_ext = nuclear (pseudo-)potential acting on electrons? > > yes, that's what I meant. In fact I wasn't sure this corresponds to "V_bare" or to "local ionic potential". I will use plot_num = 1. regards, Matteo >> 1 = total potential V_bare+V_H + V_xc >> > > then this is what you need. > > >> 2 = local ionic potential >> > > The latest QE version is more explicit: > > >> 2 = local ionic potential V_bare >> > > > >> 2) is there any known reason why plotrho fails when trying to make >> a 2D >> plot of the potential? >> > > it doesn't fail. Run it interactively. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Tue Jun 15 18:01:36 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 15 Jun 2010 18:01:36 +0200 Subject: [Pw_forum] Computing Second order response In-Reply-To: <508640.34950.qm@web38802.mail.mud.yahoo.com> References: <508640.34950.qm@web38802.mail.mud.yahoo.com> Message-ID: <0953D55F-8EEF-47DA-8FE4-BB8FFF770F1F@sissa.it> well, you probably know more than I do, but the cross section for (off-resonant) Raman scattering is basically the derivative of the dielectric constant with respect to the amplitude of the vibrational distortion. I do not know what exactly is measured (you probably do), but this is what is calculated, and the dielectric tensor of a metal is infinite ... in any case, it is always a good idea to know what is measured (which I don't, in this case), and what is calculated (which you do not seem to do, in this case ...). graphene may be another story, because the density of states at the fermi energy is zero ... Stefano B On Jun 15, 2010, at 2:56 PM, loc duong ding wrote: > I don't understand why Raman activity in this case is zero. In practical, metallic system also provide Raman peak (ex. Carbon nannotube). I try to calculate graphene (no gap) and I get the proper result. Can you give some more explanation or suggest me some reference about this topic? > > I appreciate to your instructions. > >> So, the the Raman activity should be >> zero ... >> SB > > On Jun 15, 2010, at 3:50 AM, loc duong ding >> wrote: > >> I calculate zigag nano ribbon with hydrogen terminated at the >> edge. I checked DOS that showed no gap. >> >>> yes - SB >> >> >> On Jun 14, 2010, at >>>> 11:03 AM, loc duong ding >> wrote: >> >>>> what's the gap of the >>> unperturbed >> >>>> system? >>>> SB >>> >>> Actually, >> this >>> is the firs time I calculate the Raman spectrum. I don't clear >> about the gap of >>> the unperturbed system? It means the electronic >> band gap? > > > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > _______________________________________________ > 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/20100615/c8219b04/attachment.htm From 1009ukumar at gmail.com Tue Jun 15 19:51:56 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Tue, 15 Jun 2010 23:21:56 +0530 Subject: [Pw_forum] Problem in reading PP's taken from QE site? Message-ID: Dear all QE users, I m having problem with reading of pp's taken from QE site http://www.quantum-espresso.org/pseudo.php I did many scf runs e.g. on Al, AlAs, PbTiO3 etc., and found the problem in reading the pp file. Error of not finding the pp file comes( like file ./Al.pz-vbc_s1.UPF not found), while with exactly same pp present in "pseudo", no error comes. e.g with Al, As pp's : Al.pz-vbc.UPF, As.pz-bhs.UPF etc. I, further, checked by reading the first two lines of pp's. PP's present in "pseudo" are read but that taken from site are not read. small trivial program used to read is: program red implicit none character :: char1*10, char2*50 open(unit=1, file="As.pz-bhs.UPF", status="old") read (1,"(A10)") char1 read (1,"(A50)") char2 write(*,"(A10)") char1 write(*,"(A50)") char2 end program red Output of above program: 1)For pp As.pz-bhs.UPF in " pseudo " is : Generated using unknown code 2) For EXACTLY SAME pp As.pz-bhs.UPF from site is: forrtl: No such file or directory forrtl: severe (29): file not found, unit 1, file /home/hcg/Desktop/DESKTOP_sonu/CODES/pwscf/sonu-exercise_QE/AlAs/As.pz-bhs_s1.UPF Image PC Routine Line Source a.out 000000000046E6BD Unknown Unknown Unknown a.out 000000000046D1C5 Unknown Unknown Unknown a.out 0000000000447EE9 Unknown Unknown Unknown a.out 000000000043596F Unknown Unknown Unknown a.out 00000000004351A2 Unknown Unknown Unknown a.out 0000000000408FDD Unknown Unknown Unknown a.out 0000000000402CC4 Unknown Unknown Unknown a.out 0000000000402C2C Unknown Unknown Unknown libc.so.6 00007FDAD9BB6586 Unknown Unknown Unknown a.out 0000000000402B29 Unknown Unknown Unknown I don't know why the pp's are not read by the program? I really need your help !!! Please help me to find the solution. With Kind Regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100615/fd26a9a9/attachment-0001.htm From modaresi.mohsen at gmail.com Tue Jun 15 22:03:46 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 16 Jun 2010 00:33:46 +0430 Subject: [Pw_forum] plotband.x problem In-Reply-To: <49103.20224.qm@web120020.mail.ne1.yahoo.com> References: <49103.20224.qm@web120020.mail.ne1.yahoo.com> Message-ID: Dear Samadpour, You can plot the output of Bands.x with xmgrace (in linux) and orgin (in windows). Hope it helps, Mohsen Modaresi Ferdowsi University of Mashhad, Iran. On Tue, Jun 15, 2010 at 4:12 PM, Mahmood Samadpoor < samadpoormahmood at yahoo.com> wrote: > Dear all > Hi > I did a scf and nscf calculation for Cdse Zinc Blende structure. i wanted > to plot the band structure, so i used bands.x to produce band.dat(band > structure data file) and it did not report any error and band structure data > were successfully written to the file and i used the plotband.x to plot my > data. but when i want to see the final .ps file, i just see a sentence : " > Loading . . ." , and it doesn't show any diagram. but i can plot the band > structure by Microsoft excel software. > I would appreciate if you help me in this regard. > > M. Samadpour > PHD student > Sharif university of technology > Tehran > Iran > > > _______________________________________________ > 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/20100616/f891e51f/attachment.htm From o.sedelnikova at gmail.com Wed Jun 16 05:41:00 2010 From: o.sedelnikova at gmail.com (Olga Sedelnikova) Date: Wed, 16 Jun 2010 10:41:00 +0700 Subject: [Pw_forum] 2. PP for Au (psavita@crlindia.com) Message-ID: Dear Dr. Savita Pundlik, Thank you very much for your response! -- Best wishes, Olga Sedelnikova Nikolaev Institute of Inorganic Chemistry of SB RAS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100616/79bd2bdb/attachment.htm From giacsport at libero.it Wed Jun 16 05:55:37 2010 From: giacsport at libero.it (giacsport at libero.it) Date: Wed, 16 Jun 2010 05:55:37 +0200 (CEST) Subject: [Pw_forum] Zn NCPP pseudopotential Message-ID: <7299167.187121276660537346.JavaMail.defaultUser@defaultHost> Dear All, excuse me if the question maybe can appear as "weird" but I am quite new with PWSCF. I would like to do some calculations on ZnO systems by using NCPP (in principle PBE at this level could be OK) Anyway, I checked the database of pseudopotentials and I noticed that an NCPP for Zn is missing. Reading the suggestions in the Doc I went to the Rappe Group PSP Page for GGA generated Potentials and I found Zn psp in abinit (fhi) format. ( http://www.sas.upenn.edu/rappegroup/htdocs/Research/PSP/zn.optgga1.fhi ) I used the "fhi2upf" tools following the instructions required and thus I generated both a NCPP for both Zn and O. (In details Zn 4S,2 4P,0 3d,10 3f,0 and O 2S,2 2P,4) then I tested it on a "vc-relax' calculation on the WZ-like structure of ZnO this is my input file >&control > calculation='vc-relax', > pseudo_dir='/home/giacomo/src/pseudo/' > prefix='ZnO' > wf_collect=.true. > outdir='/scr/giacomo/PWSCF_test/ZnO/test_pseudo/' > tprnfor=.true. > etot_conv_thr=1.0D-8 > forc_conv_thr=1.0D-4 >/ >&system > ntyp=2, nat=4, ibrav=4, a=3.2417, c= 5.18760, > ecutwfc= 30., force_symmorphic=.true. >/ >&ELECTRONS > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-8 >/ >&IONS > ion_dynamics = 'bfgs', >/ >&cell > cell_dynamics='bfgs' >/ >ATOMIC_SPECIES >Zn 65.39 30-Zn.PBE.fhi.UPF >O 15.9994 08-O.PBE.fhi.UPF >ATOMIC_POSITIONS crystal > Zn 0.33330 0.66670 0.00000 > Zn 0.66660 0.33330 0.50000 > O 0.33330 0.66670 0.38190 > O 0.66660 0.33330 0.88190 >K_POINTS (automatic) > 4 4 4 1 1 1 and this is what I got in the output: ..... > bravais-lattice index = 4 > lattice parameter (a_0) = 6.1259 a.u. > unit-cell volume = 318.5953 (a.u.)^3 > number of atoms/cell = 4 > number of atomic types = 2 > number of electrons = 36.00 > number of Kohn-Sham states= 18 > kinetic-energy cutoff = 30.0000 Ry > charge density cutoff = 120.0000 Ry > convergence threshold = 1.0E-08 > mixing beta = 0.7000 > number of iterations used = 8 plain mixing > Exchange-correlation = SLA PZ NOGX NOGC (1100) > nstep = 50 > > > celldm(1)= 6.125925 celldm(2)= 0.000000 celldm(3)= 1.600271 > 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) = ( -0.500000 0.866025 0.000000 ) > a(3) = ( 0.000000 0.000000 1.600271 ) >.... > Initial potential from superposition of free atoms > Check: negative starting charge= -0.000653 > > starting charge 35.99993, renormalised to 36.00000 >..... and at the end >..... > bfgs converged in 13 scf cycles and 11 bfgs steps > (criteria: energy < 0.10E-07, force < 0.10E-03, cell < 0.50E+00) > > End of BFGS Geometry Optimization > > Final enthalpy = -269.5939008350 Ry > new unit-cell volume = 196.26255 a.u.^3 ( 29.08311 Ang^3 ) > >CELL_PARAMETERS (alat) > 0.850885542 -0.000000001 0.000009624 > -0.425442771 0.736893797 -0.000004810 > 0.000015404 0.000000004 1.361589938 > >ATOMIC_POSITIONS (crystal) >Zn 0.333283929 0.666666020 0.000176085 >Zn 0.666617909 0.333333981 0.500176085 >O 0.333282225 0.666666288 0.381723915 >O 0.666615937 0.333333711 0.881723915 > >...... that makes me very suspicious about a so big reduction of the unit-cell volume. I know that there are a lot of variables that can influence this result (not only the pseudopotential), but since I am a dummy in creating them I wonder if someone can give me few hints in order to improve my ones. or even better if someone could share an already tested NCPP at PBE level I would really appreciate it. Thanks in advance Very best, Giacomo Giacomo Giorgi, Ph. D., Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Japan From tkaloni at gmail.com Wed Jun 16 07:36:59 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Wed, 16 Jun 2010 11:21:59 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 45 In-Reply-To: References: Message-ID: Dear All, I want to calculate the cohesive energy of graphite. I am taking C-pz-vbc.UPF for graphite and C-pz.rrkjus.UPF for isolated carbon atom, is this acceptable? Sincerely, Thanehwor Kaloni SNBNCBS www.bose.res.in On Tue, Jun 15, 2010 at 11:37 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Computing Second order response (loc duong ding) > 2. pseudo-potential for virtual atom (German Samolyuk) > 3. Re: total potential plot (Matteo Cococcioni) > 4. Re: Computing Second order response (Stefano Baroni) > 5. Problem in reading PP's taken from QE site? (sonu kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Jun 2010 05:56:10 -0700 (PDT) > From: loc duong ding > Subject: Re: [Pw_forum] Computing Second order response > To: pw_forum at pwscf.org > Message-ID: <508640.34950.qm at web38802.mail.mud.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > I don't understand why Raman activity in this case is zero. In practical, > metallic system also provide Raman peak (ex. Carbon nannotube). I try to > calculate graphene (no gap) and I get the proper result. Can you give some > more explanation or suggest me some reference about this topic? > > I appreciate to your instructions. > > >So, the the Raman activity should be > > zero ... > >SB > > On Jun 15, 2010, at 3:50 AM, loc duong ding > > wrote: > > > I calculate zigag nano ribbon with hydrogen terminated at the > > edge. I checked DOS that showed no gap. > > > >> yes - SB > > > > > > On Jun 14, 2010, at > >>> 11:03 AM, loc duong ding > > wrote: > > > >>> what's the gap of the > >> unperturbed > > > >>> system? > >>> SB > >> > >> Actually, > > this > >> is the firs time I calculate the Raman spectrum. I don't clear > > about the gap of > >> the unperturbed system? It means the electronic > > band gap? > > > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 15 Jun 2010 10:27:43 -0400 > From: German Samolyuk > Subject: [Pw_forum] pseudo-potential for virtual atom > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I need to produce pseudo-potential for virtual atom, something like > W_{1-x}Re_x. The pseudo-potentials from the database, > > W.pw91-nsp-van.UPF and Re.pw91-nsp-van.UPF, have different number of > valence > electrons states and utility vitual.x does not > work for this two ps because of this reason. However, if I make ps for > these > two elements with the same number of wave functions using ld1.x, > virtual.x can not read ps files because UPF format has been changed. I > tried > versions 4.1, 4.1.1 and 4.2. > What should I do to solve this problem? > Thank you in advance. > > German Samolyuk, > Oak Ridge National Laboratory, USA > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100615/05a128e2/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Tue, 15 Jun 2010 10:34:34 -0500 > From: Matteo Cococcioni > Subject: Re: [Pw_forum] total potential plot > To: PWSCF Forum > Message-ID: <4C179D8A.6050503 at umn.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Thanks Paolo. > > > Paolo Giannozzi wrote: > > On Jun 14, 2010, at 22:50 , Matteo Cococcioni wrote: > > > > > >> (V_ext + V_H + V_xc) > >> > > > > V_ext = nuclear (pseudo-)potential acting on electrons? > > > > > > yes, that's what I meant. In fact I wasn't sure this corresponds to > "V_bare" or to "local ionic potential". > I will use plot_num = 1. > > regards, > > Matteo > > >> 1 = total potential V_bare+V_H + V_xc > >> > > > > then this is what you need. > > > > > >> 2 = local ionic potential > >> > > > > The latest QE version is more explicit: > > > > > >> 2 = local ionic potential V_bare > >> > > > > > > > >> 2) is there any known reason why plotrho fails when trying to make > >> a 2D > >> plot of the potential? > >> > > > > it doesn't fail. Run it interactively. > > > > 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 > > > > > > ------------------------------ > > Message: 4 > Date: Tue, 15 Jun 2010 18:01:36 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] Computing Second order response > To: PWSCF Forum > Message-ID: <0953D55F-8EEF-47DA-8FE4-BB8FFF770F1F at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > well, you probably know more than I do, but the cross section for > (off-resonant) Raman scattering is basically the derivative of the > dielectric constant with respect to the amplitude of the vibrational > distortion. I do not know what exactly is measured (you probably do), but > this is what is calculated, and the dielectric tensor of a metal is infinite > ... in any case, it is always a good idea to know what is measured (which I > don't, in this case), and what is calculated (which you do not seem to do, > in this case ...). > > graphene may be another story, because the density of states at the fermi > energy is zero ... > > Stefano B > > On Jun 15, 2010, at 2:56 PM, loc duong ding wrote: > > > I don't understand why Raman activity in this case is zero. In practical, > metallic system also provide Raman peak (ex. Carbon nannotube). I try to > calculate graphene (no gap) and I get the proper result. Can you give some > more explanation or suggest me some reference about this topic? > > > > I appreciate to your instructions. > > > >> So, the the Raman activity should be > >> zero ... > >> SB > > > > On Jun 15, 2010, at 3:50 AM, loc duong ding > >> wrote: > > > >> I calculate zigag nano ribbon with hydrogen terminated at the > >> edge. I checked DOS that showed no gap. > >> > >>> yes - SB > >> > >> > >> On Jun 14, 2010, at > >>>> 11:03 AM, loc duong ding > >> wrote: > >> > >>>> what's the gap of the > >>> unperturbed > >> > >>>> system? > >>>> SB > >>> > >>> Actually, > >> this > >>> is the firs time I calculate the Raman spectrum. I don't clear > >> about the gap of > >>> the unperturbed system? It means the electronic > >> band gap? > > > > > > ----------------------------------------------- > > Loc Duong Dinh > > Ms-Ph.D Student > > Sungkyunkwan Advanced Institute of Nanotechnology, > > Sungkyunkwan University, > > Suwon, 440-746, Korea > > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > > > _______________________________________________ > > 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/20100615/c8219b04/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Tue, 15 Jun 2010 23:21:56 +0530 > From: sonu kumar <1009ukumar at gmail.com> > Subject: [Pw_forum] Problem in reading PP's taken from QE site? > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all QE users, > > I m having problem with reading of pp's taken from QE site > http://www.quantum-espresso.org/pseudo.php > > I did many scf runs e.g. on Al, AlAs, PbTiO3 etc., and found the problem in > reading the pp file. > > Error of not finding the pp file comes( like file ./Al.pz-vbc_s1.UPF not > found), while with exactly same pp present in "pseudo", no error comes. e.g > with Al, As pp's : Al.pz-vbc.UPF, As.pz-bhs.UPF etc. > > I, further, checked by reading the first two lines of pp's. PP's present > in > "pseudo" are read but that taken from site are not read. > > small trivial program used to read is: > program red > implicit none > character :: char1*10, char2*50 > open(unit=1, file="As.pz-bhs.UPF", status="old") > > read (1,"(A10)") char1 > read (1,"(A50)") char2 > > write(*,"(A10)") char1 > write(*,"(A50)") char2 > end program red > > Output of above program: > > 1)For pp As.pz-bhs.UPF in " pseudo " is : > > > Generated using unknown code > > 2) For EXACTLY SAME pp As.pz-bhs.UPF from site is: > > forrtl: No such file or directory > forrtl: severe (29): file not found, unit 1, file > > /home/hcg/Desktop/DESKTOP_sonu/CODES/pwscf/sonu-exercise_QE/AlAs/As.pz-bhs_s1.UPF > Image PC Routine Line > Source > a.out 000000000046E6BD Unknown Unknown Unknown > a.out 000000000046D1C5 Unknown Unknown Unknown > a.out 0000000000447EE9 Unknown Unknown Unknown > a.out 000000000043596F Unknown Unknown Unknown > a.out 00000000004351A2 Unknown Unknown Unknown > a.out 0000000000408FDD Unknown Unknown Unknown > a.out 0000000000402CC4 Unknown Unknown Unknown > a.out 0000000000402C2C Unknown Unknown Unknown > libc.so.6 00007FDAD9BB6586 Unknown Unknown Unknown > a.out 0000000000402B29 Unknown Unknown Unknown > > > > I don't know why the pp's are not read by the program? > > I really need your help !!! > Please help me to find the solution. > > With Kind Regards, > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100615/fd26a9a9/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 36, Issue 45 > **************************************** > -- ################################### ****************************************** Thaneshwor Prashad Kaloni TWAS-BOSE FELLOW /JRF S N Bose national Centre for Basic Sciences Kolkata 700098, INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100616/dd76c6c0/attachment-0001.htm From paulatto at sissa.it Wed Jun 16 11:00:13 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 16 Jun 2010 11:00:13 +0200 Subject: [Pw_forum] Zn NCPP pseudopotential In-Reply-To: <7299167.187121276660537346.JavaMail.defaultUser@defaultHost> References: <7299167.187121276660537346.JavaMail.defaultUser@defaultHost> Message-ID: Dear Giacomo, >> Exchange-correlation = SLA PZ NOGX NOGC (1100) This line indicates that pw.x thinks the functional of the pseudopotential is plain LDA, not PBE. If I remember correctly fhi2upf asks the user for the functional, are you sure you typed "GGA"? > I know that there are a lot of variables that can influence this result Maybe the ecutwfc you've chosen is too small for norm-conserving pseudopotential (I would expect oxygen to require 50Ry, or even more). Yet, it would not be sufficient to cause such a huge disagreement with experimental data. cheers -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From giannozz at democritos.it Wed Jun 16 13:09:41 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Jun 2010 13:09:41 +0200 Subject: [Pw_forum] Zn NCPP pseudopotential In-Reply-To: <7299167.187121276660537346.JavaMail.defaultUser@defaultHost> References: <7299167.187121276660537346.JavaMail.defaultUser@defaultHost> Message-ID: On Jun 16, 2010, at 5:55 , giacsport at libero.it wrote: > I would like to do some calculations on ZnO systems by using NCPP (in > principle PBE at this level could be OK) I wouldn't be so sure: ZnO is a rather nasty beast. Try first ZnS or ZnSe. >> ecutwfc= 30., force_symmorphic=.true. 30 Ry is not enough for both O and NC Zn and 3d in valence 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 Wed Jun 16 14:52:11 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Jun 2010 14:52:11 +0200 Subject: [Pw_forum] Problem in reading PP's taken from QE site? In-Reply-To: References: Message-ID: On Jun 15, 2010, at 19:51 , sonu kumar wrote: > forrtl: severe (29): file not found, unit 1, file /home/hcg/Desktop/ > DESKTOP_sonu/CODES/pwscf/sonu-exercise_QE/AlAs/As.pz-bhs_s1.UPF What do you get with command ls -l /home/hcg/Desktop/DESKTOP_sonu/CODES/pwscf/sonu-exercise_QE/ AlAs/As.pz-bhs_s1.UPF ? > I don't know why the pp's are not read by the program? because they are not there, or they are not readable (in the unix sense) 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 Jun 16 14:55:58 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Jun 2010 14:55:58 +0200 Subject: [Pw_forum] Cohesive energy (was: annoying irrelevant In-Reply-To: References: Message-ID: <60694123-0BB7-4EBC-A2E3-9D12A99F4053@democritos.it> On Jun 16, 2010, at 7:36 , Thaneshwor Kaloni wrote: > I want to calculate the cohesive energy of graphite. I am taking C- > pz-vbc.UPF for graphite and C-pz.rrkjus.UPF for isolated carbon > atom, is this acceptable? no: you need to calculate all energies with the same pseudopotential. It is also not acceptable that you keep making "Reply" to a digest, without removing irrelevant contents, and without changing the subject to something appropriate --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Wed Jun 16 18:48:10 2010 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 16 Jun 2010 18:48:10 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 45 In-Reply-To: References: Message-ID: <1B263D9C-5C74-4EBF-B91D-72AFBBD8F347@sissa.it> Dear Thaneshwor, do you ever happen to read the answers to your own posts? They may be wrong (or "not even wrong", as some may say), but they do exist, and it is frustrating to see that you keep asking the same question(s) over and over again, ignoring those who have taken the time to try to answer them. For the N-th time, please, refrain to hit "reply" to a digest mailing to post to this forum, and take the time to indicate the actual subject of your post in the "subjet" field of the e-mail. SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100616/184dbca2/attachment.htm From rezaebraahimi at yahoo.com Wed Jun 16 21:20:35 2010 From: rezaebraahimi at yahoo.com (Reza Ebraahimi) Date: Wed, 16 Jun 2010 12:20:35 -0700 (PDT) Subject: [Pw_forum] About the flattening of phonon branches Message-ID: <738680.8091.qm@web59403.mail.ac4.yahoo.com> Hello everyone I have a question, i wonder what is the physics behind the?flatterning?of the acoustic and optical phonon branches in some specific directions of the 1st Brillouin zone of some of the crystals?? Thanks for any comment -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100616/3b2d2eb3/attachment.htm From baroni at sissa.it Wed Jun 16 21:57:10 2010 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 16 Jun 2010 21:57:10 +0200 Subject: [Pw_forum] About the flattening of phonon branches In-Reply-To: <738680.8091.qm@web59403.mail.ac4.yahoo.com> References: <738680.8091.qm@web59403.mail.ac4.yahoo.com> Message-ID: Hi: can you be more specific? Also, would you mind signing your posts? SB On Jun 16, 2010, at 9:20 PM, Reza Ebraahimi wrote: > Hello everyone > I have a question, i wonder what is the physics behind the flatterning of the acoustic and optical phonon branches in some specific directions of the 1st Brillouin zone of some of the crystals? > Thanks for any comment > > _______________________________________________ > 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/20100616/5b15a83d/attachment-0001.htm From payam.norouzzadeh at gmail.com Wed Jun 16 22:29:34 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 17 Jun 2010 00:59:34 +0430 Subject: [Pw_forum] overlap of atoms Message-ID: Hello Espresso users I have checked the structure I want to relax it by Xcrysden and Jmole and there was no overlap between atoms but Espresso leave an error message like : overlap between atoms 1 and 5, 2 and 6 ,.... Could someone please have a look to my input file and let me know how can I fix it? Best regards,Payam Norouzzadeh &CONTROL title = Ba , calculation = 'relax' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = '/lustre/work/pnorouzz/espresso/Ba/relax' , wfcdir = '/lustre/work/pnorouzz/espresso/Ba/relax' , pseudo_dir = '/lustre/work/pnorouzz/espresso/Ba/relax' , dt = 20 , / &SYSTEM ibrav = 3, celldm(1) = 11.6, nat = 54, ntyp = 3, ecutwfc = 50 , ecutrho = 500 , / &ELECTRONS conv_thr = 1.D-8 , mixing_beta = 0.5D0 , / &IONS ion_dynamics = 'damp' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , upscale = 100 , / ATOMIC_SPECIES Ba 137.327 Ba.pw91-nsp-van.UPF Sn 118.710 Sn.pw91-n-van.UPF Ga 71.0843639 Ga.pw91-n-van.UPF ATOMIC_POSITIONS Ba 0.186 0.186 0.186 Ba 0.814 0.814 0.186 Ba 0.814 0.186 0.814 Ba 0.186 0.814 0.814 Ba 0.686 0.686 0.686 Ba 0.314 0.314 0.686 Ba 0.314 0.686 0.314 Ba 0.686 0.314 0.314 Sn 0 0 0 Sn 0.5 0.5 0.5 Sn 0.6348 0.6348 0.3652 Sn 0.3652 0.6348 0.6348 Sn 0.1348 0.1348 0.8652 Sn 0.8652 0.1348 0.1348 Sn 0.41596 0.41596 0.1441 Sn 0.58404 0.58404 0.1441 Sn 0.58404 0.41596 0.8559 Sn 0.41596 0.58404 0.8559 Sn 0.1441 0.41596 0.41596 Sn 0.8559 0.41596 0.58404 Sn 0.41596 0.1441 0.41596 Sn 0.58404 0.1441 0.58404 Sn 0.91596 0.91596 0.6441 Sn 0.08404 0.08404 0.6441 Sn 0.08404 0.91596 0.3559 Sn 0.91596 0.08404 0.3559 Sn 0.6441 0.91596 0.91596 Sn 0.3559 0.91596 0.08404 Sn 0.91596 0.6441 0.91596 Sn 0.08404 0.6441 0.08404 Sn 0.91596 0.3559 0.08404 Sn 0.08404 0.3559 0.91596 Sn 0 0.25 0.5 Sn 0 0.75 0.5 Sn 0.5 0 0.25 Sn 0.5 0 0.75 Sn 0 0.5 0.25 Sn 0 0.5 0.75 Ga 0.3652 0.3652 0.3652 Ga 0.6348 0.3652 0.6348 Ga 0.8652 0.8652 0.8652 Ga 0.1348 0.8652 0.1348 Ga 0.1441 0.58404 0.58404 Ga 0.8559 0.58404 0.41596 Ga 0.41596 0.8559 0.58404 Ga 0.58404 0.8559 0.41596 Ga 0.6441 0.08404 0.08404 Ga 0.3559 0.08404 0.91596 Ga 0.25 0.5 0 Ga 0.75 0.5 0 Ga 0.5 0.25 0 Ga 0.5 0.75 0 Ga 0.25 0 0.5 Ga 0.75 0 0.5 K_POINTS automatic 4 4 4 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/c6bc6ef3/attachment.htm From sclauzer at sissa.it Wed Jun 16 22:50:57 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 16 Jun 2010 22:50:57 +0200 Subject: [Pw_forum] PP for Au In-Reply-To: References: Message-ID: <4C193931.3030904@sissa.it> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100616/5d9fb2db/attachment.htm From elbuesta at icqmail.com Thu Jun 17 00:19:06 2010 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Wed, 16 Jun 2010 18:19:06 -0400 Subject: [Pw_forum] overlap of atoms In-Reply-To: References: Message-ID: <8CCDBB911D96802-1804-255A@webmail-d083.sysops.aol.com> I may be missing something, but when I opened your structure with the XCrysden there were many warning messages, including many messages of atoms overlapped. I don't have Jmole to re-check, but it seems to me that your structure is too much compressed. Fabio Negreiros Ribeiro Laboratorio de Fisica de Superficies da Universidade Federal de Minas Gerais, Brasil -----Original Message----- From: Payam Norouzzadeh To: pw_forum at pwscf.org Sent: Wed, Jun 16, 2010 5:29 pm Subject: [Pw_forum] overlap of atoms Hello Espresso users I have checked the structure I want to relax it by Xcrysden and Jmole and there was no overlap between atoms but Espresso leave an error message like : overlap between atoms 1 and 5, 2 and 6 ,.... Could someone please have a look to my input file and let me know how can I fix it? Best regards,Payam Norouzzadeh &CONTROL title = Ba , calculation = 'relax' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = '/lustre/work/pnorouzz/espresso/Ba/relax' , wfcdir = '/lustre/work/pnorouzz/espresso/Ba/relax' , pseudo_dir = '/lustre/work/pnorouzz/espresso/Ba/relax' , dt = 20 , / &SYSTEM ibrav = 3, celldm(1) = 11.6, nat = 54, ntyp = 3, ecutwfc = 50 , ecutrho = 500 , / &ELECTRONS conv_thr = 1.D-8 , mixing_beta = 0.5D0 , / &IONS ion_dynamics = 'damp' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , upscale = 100 , / ATOMIC_SPECIES Ba 137.327 Ba.pw91-nsp-van.UPF Sn 118.710 Sn.pw91-n-van.UPF Ga 71.0843639 Ga.pw91-n-van.UPF ATOMIC_POSITIONS Ba 0.186 0.186 0.186 Ba 0.814 0.814 0.186 Ba 0.814 0.186 0.814 Ba 0.186 0.814 0.814 Ba 0.686 0.686 0.686 Ba 0.314 0.314 0.686 Ba 0.314 0.686 0.314 Ba 0.686 0.314 0.314 Sn 0 0 0 Sn 0.5 0.5 0.5 Sn 0.6348 0.6348 0.3652 Sn 0.3652 0.6348 0.6348 Sn 0.1348 0.1348 0.8652 Sn 0.8652 0.1348 0.1348 Sn 0.41596 0.41596 0.1441 Sn 0.58404 0.58404 0.1441 Sn 0.58404 0.41596 0.8559 Sn 0.41596 0.58404 0.8559 Sn 0.1441 0.41596 0.41596 Sn 0.8559 0.41596 0.58404 Sn 0.41596 0.1441 0.41596 Sn 0.58404 0.1441 0.58404 Sn 0.91596 0.91596 0.6441 Sn 0.08404 0.08404 0.6441 Sn 0.08404 0.91596 0.3559 Sn 0.91596 0.08404 0.3559 Sn 0.6441 0.91596 0.91596 Sn 0.3559 0.91596 0.08404 Sn 0.91596 0.6441 0.91596 Sn 0.08404 0.6441 0.08404 Sn 0.91596 0.3559 0.08404 Sn 0.08404 0.3559 0.91596 Sn 0 0.25 0.5 Sn 0 0.75 0.5 Sn 0.5 0 0.25 Sn 0.5 0 0.75 Sn 0 0.5 0.25 Sn 0 0.5 0.75 Ga 0.3652 0.3652 0.3652 Ga 0.6348 0.3652 0.6348 Ga 0.8652 0.8652 0.8652 Ga 0.1348 0.8652 0.1348 Ga 0.1441 0.58404 0.58404 Ga 0.8559 0.58404 0.41596 Ga 0.41596 0.8559 0.58404 Ga 0.58404 0.8559 0.41596 Ga 0.6441 0.08404 0.08404 Ga 0.3559 0.08404 0.91596 Ga 0.25 0.5 0 Ga 0.75 0.5 0 Ga 0.5 0.25 0 Ga 0.5 0.75 0 Ga 0.25 0 0.5 Ga 0.75 0 0.5 K_POINTS automatic 4 4 4 0 0 0 _______________________________________________ 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/20100616/663fd49a/attachment-0001.htm From paulatto at sissa.it Thu Jun 17 00:23:13 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 17 Jun 2010 00:23:13 +0200 Subject: [Pw_forum] overlap of atoms In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] overlap of atoms" from Payam Norouzzadeh (16/06/10): > I have checked the structure I want to relax it by Xcrysden and Jmole and > there was no overlap between atoms but Espresso leave > an error message like : overlap between atoms 1 and 5, 2 and 6 ,.... Dear Payam, please check again... > Ba 0.186 0.186 0.186 <-- atom 1 > Ba 0.686 0.686 0.686 <-- atom 5 this two atoms are clearly in the equivalent positions, if you add the basis vector a/2*(1,1,1) of the bcc lattice. (the same is true for atoms 2 and 6 and many others) 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 weylfang at gmail.com Thu Jun 17 04:54:04 2010 From: weylfang at gmail.com (Weyl Fang) Date: Thu, 17 Jun 2010 10:54:04 +0800 Subject: [Pw_forum] spin multiplicity Message-ID: <4C198E4C.30109@gmail.com> Dear all, Recently i am working on a slab with the QE-4.1.2. I use the spin-polarized calculation through setting spin multiplicity. But i can not find the spin multiplicity in QE-4.2. Is this not provided in QE-4.2? If i want to set the spin multiplicity, how can i do it? Any suggestions will be appreciated. Thanks! Weyl FANG ===================================================================== Weyl FANG Graduate student in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ********************************************************************* Email: weylfang at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ********************************************************************* From 1009ukumar at gmail.com Thu Jun 17 06:37:04 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Thu, 17 Jun 2010 10:07:04 +0530 Subject: [Pw_forum] Problem in reading PP's taken from QE site? Message-ID: Dear Sir, Thank you for your reply ! >>What do you get with command >>ls -l /home/hcg/Desktop/DESKTOP_sonu/CODES/pwscf/sonu-exercise_QE/ >>AlAs/As.pz-bhs_s1.UPF ? I Got: > ls -l As.pz-bhs_s1.UPF\ -rw-r--r-- 1 hcg users 78987 2010-06-14 19:29 As.pz-bhs_s1.UPF >>because they are not there, or they are not readable (in the unix sense) They are there, but not readable. Perhaps, the problem is with the fortran compiler (ifort 11.0). i checked above said UPF file on other system 's compiler (ifort 9.0) and it reads perfectly with no error. Could you (or any QE user) please tell me, what could be the problem with compiler or libraries associated with it ? Does other softwares, which use ifort, can change or corrupt the ifort? I am not aware of functioning of ifort, but what should i do now? I am not able to use the PP's ? With Kind Regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/c866d073/attachment.htm From modaresi.mohsen at gmail.com Thu Jun 17 07:30:08 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 17 Jun 2010 10:00:08 +0430 Subject: [Pw_forum] Problem in reading PP's taken from QE site? In-Reply-To: References: Message-ID: Dear sonu,Check permission of pp in your system? (lon in as root or change the permission of your files) Mohsen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/aba88aba/attachment.htm From giacsport at libero.it Thu Jun 17 08:02:50 2010 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 17 Jun 2010 08:02:50 +0200 (CEST) Subject: [Pw_forum] R: Re: Zn NCPP pseudopotential Message-ID: <1725378.386061276754570895.JavaMail.defaultUser@defaultHost> Dear Paolo and Lorenzo, thanks a lot! According to your suggestion the error on the volume of the WZ ZnO has reduced to 0.32% (!!) with respect to the experimental value in the vc-relax calculation. Of course, it is the first step, but at least it is encouraging.... Very best, Giacomo >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 16/06/2010 13.09 >A: "giacsport at libero.it", "PWSCF Forum" >Ogg: Re: [Pw_forum] Zn NCPP pseudopotential > >On Jun 16, 2010, at 5:55 , giacsport at libero.it wrote: > >> I would like to do some calculations on ZnO systems by using NCPP (in >> principle PBE at this level could be OK) > >I wouldn't be so sure: ZnO is a rather nasty beast. Try first ZnS or >ZnSe. > >>> ecutwfc= 30., force_symmorphic=.true. > >30 Ry is not enough for both O and NC Zn and 3d in valence > >Paolo >--- >Paolo Giannozzi, Dept of Physics, University of Udine >via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > Giacomo Giorgi, Ph. D., Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Japan From giannozz at democritos.it Thu Jun 17 08:16:33 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Jun 2010 08:16:33 +0200 Subject: [Pw_forum] spin multiplicity In-Reply-To: <4C198E4C.30109@gmail.com> References: <4C198E4C.30109@gmail.com> Message-ID: <84BE6ABA-FA64-4DB0-96F9-45B2A859015C@democritos.it> On Jun 17, 2010, at 4:54 , Weyl Fang wrote: > i can not find the spin multiplicity in QE-4.2. use "tot_magnetization" - 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 rezaebraahimi at yahoo.com Thu Jun 17 08:52:38 2010 From: rezaebraahimi at yahoo.com (Reza Ebraahimi) Date: Wed, 16 Jun 2010 23:52:38 -0700 (PDT) Subject: [Pw_forum] About the flattening of phonon branches Message-ID: <968409.893.qm@web59403.mail.ac4.yahoo.com> Hello I mean, for example in the case of ALAs?(P. Giannozzi et al PRB 43, 7231 (1991)), the LO mode in the Gamma-X direction is very flat (mentioned by the authors, too). Is it related to the long interaction caused by the band structure (Sokel & Harrison PRL 36, 61)? Sorry about the affiliation Thank You R. Ebraahimi Graduate Student- Tehran University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100616/13b3c9bb/attachment.htm From giannozz at democritos.it Thu Jun 17 09:07:19 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Jun 2010 09:07:19 +0200 Subject: [Pw_forum] Problem in reading PP's taken from QE site? In-Reply-To: References: Message-ID: <4C19C9A7.2010607@democritos.it> sonu kumar wrote: > I Got: > > ls -l As.pz-bhs_s1.UPF\ it looks like there is something at the end of the file name > -rw-r--r-- 1 hcg users 78987 2010-06-14 19:29 As.pz-bhs_s1.UPF you should do "ls -l" followed by THE COMPLETE FILE NAME THAT THE CODE SAY IS NOT FOUND, IN EXACTLY THE SAME FORMAT. Run one case that doesn't work, than get the complete file name from the output, using cut and paste, do "ls -l" of this. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From Michael at ihpc.a-star.edu.sg Thu Jun 17 07:26:09 2010 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Thu, 17 Jun 2010 13:26:09 +0800 Subject: [Pw_forum] Problem in reading PP's taken from QE site? In-Reply-To: References: Message-ID: Sonu Kumar: I'm not having any trouble with Intel 11. I'd double check my pseudo_dir and make sure the file is where you think it is (without any typos anywhere). I usually have a typo or point to the wrong directory. Good luck! Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of sonu kumar Sent: Thursday, June 17, 2010 12:37 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Problem in reading PP's taken from QE site? Dear Sir, Thank you for your reply ! >>What do you get with command >>ls -l /home/hcg/Desktop/DESKTOP_sonu/CODES/pwscf/sonu-exercise_QE/ >>AlAs/As.pz-bhs_s1.UPF ? I Got: > ls -l As.pz-bhs_s1.UPF\ -rw-r--r-- 1 hcg users 78987 2010-06-14 19:29 As.pz-bhs_s1.UPF >>because they are not there, or they are not readable (in the unix sense) They are there, but not readable. Perhaps, the problem is with the fortran compiler (ifort 11.0). i checked above said UPF file on other system 's compiler (ifort 9.0) and it reads perfectly with no error. Could you (or any QE user) please tell me, what could be the problem with compiler or libraries associated with it ? Does other softwares, which use ifort, can change or corrupt the ifort? I am not aware of functioning of ifort, but what should i do now? I am not able to use the PP's ? With Kind Regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ ________________________________ This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/297bc274/attachment.htm From payam.norouzzadeh at gmail.com Thu Jun 17 15:12:04 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 17 Jun 2010 17:42:04 +0430 Subject: [Pw_forum] overlap of atoms Message-ID: Hello Espresso users I want to relax the given structure in below that is a Clathrate with BCC structure and 54 atoms. I am getting errors about overlap of atoms. As Dr.Lorenzo Paulatto mentioned if I apply the basis vector a/2*(1,1,1) of the bcc lattice I notice that some atoms overlap each other (1 and 5,2 and 6 ,....). I am sure that the positions are correct and I used other softwares like ABINIT and VASP and got relaxed structures without trouble. Likely I should stop checking the symmetry of structure.Does any one know how can I do that? This is my input file: &CONTROL title = Ba , calculation = 'relax' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = '/lustre/work/pnorouzz/espresso//Ba/relax' , wfcdir = '/lustre/work/pnorouzz/espresso/Ba/relax' , pseudo_dir = '/lustre/work/pnorouzz/espresso//Ba/relax' , dt = 20 , / &SYSTEM ibrav = 3, celldm(1) = 22, nat = 54, ntyp = 3, ecutwfc = 50 , ecutrho = 500 , / &ELECTRONS conv_thr = 1.D-8 , mixing_beta = 0.5D0 , / &IONS ion_dynamics = 'damp' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , upscale = 100 , / ATOMIC_SPECIES Ba 137.327 Ba.pw91-nsp-van.UPF Sn 118.710 Sn.pw91-n-van.UPF Ga 71.0843639 Ga.pw91-n-van.UPF ATOMIC_POSITIONS Ba 0.186 0.186 0.186 Ba 0.814 0.814 0.186 Ba 0.814 0.186 0.814 Ba 0.186 0.814 0.814 Ba 0.686 0.686 0.686 Ba 0.314 0.314 0.686 Ba 0.314 0.686 0.314 Ba 0.686 0.314 0.314 Sn 0 0 0 Sn 0.5 0.5 0.5 Sn 0.6348 0.6348 0.3652 Sn 0.3652 0.6348 0.6348 Sn 0.1348 0.1348 0.8652 Sn 0.8652 0.1348 0.1348 Sn 0.41596 0.41596 0.1441 Sn 0.58404 0.58404 0.1441 Sn 0.58404 0.41596 0.8559 Sn 0.41596 0.58404 0.8559 Sn 0.1441 0.41596 0.41596 Sn 0.8559 0.41596 0.58404 Sn 0.41596 0.1441 0.41596 Sn 0.58404 0.1441 0.58404 Sn 0.91596 0.91596 0.6441 Sn 0.08404 0.08404 0.6441 Sn 0.08404 0.91596 0.3559 Sn 0.91596 0.08404 0.3559 Sn 0.6441 0.91596 0.91596 Sn 0.3559 0.91596 0.08404 Sn 0.91596 0.6441 0.91596 Sn 0.08404 0.6441 0.08404 Sn 0.91596 0.3559 0.08404 Sn 0.08404 0.3559 0.91596 Sn 0 0.25 0.5 Sn 0 0.75 0.5 Sn 0.5 0 0.25 Sn 0.5 0 0.75 Sn 0 0.5 0.25 Sn 0 0.5 0.75 Ga 0.3652 0.3652 0.3652 Ga 0.6348 0.3652 0.6348 Ga 0.8652 0.8652 0.8652 Ga 0.1348 0.8652 0.1348 Ga 0.1441 0.58404 0.58404 Ga 0.8559 0.58404 0.41596 Ga 0.41596 0.8559 0.58404 Ga 0.58404 0.8559 0.41596 Ga 0.6441 0.08404 0.08404 Ga 0.3559 0.08404 0.91596 Ga 0.25 0.5 0 Ga 0.75 0.5 0 Ga 0.5 0.25 0 Ga 0.5 0.75 0 Ga 0.25 0 0.5 Ga 0.75 0 0.5 K_POINTS automatic 4 4 4 0 0 0 Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/39dc7aba/attachment-0001.htm From paulatto at sissa.it Thu Jun 17 15:23:43 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 17 Jun 2010 15:23:43 +0200 Subject: [Pw_forum] overlap of atoms In-Reply-To: References: Message-ID: On Thu, 17 Jun 2010 15:12:04 +0200, Payam Norouzzadeh wrote: > I am sure that the positions are correct Dear Payam, I'm sure the structure is *wrong*: it is not a matter of symmetry, but of periodicity. If you *think* it is right, maybe you are not using the kind of unit cell you wanted. You have chosen a BCC (*Body* centered cubic, ibrav=3) cell, maybe you wanted an SC (*simple* cubic, ibrav=1) cell. If you have no idea what I'm talking about don't, please see or any solid state book. best regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From 1009ukumar at gmail.com Thu Jun 17 15:33:59 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Thu, 17 Jun 2010 19:03:59 +0530 Subject: [Pw_forum] Problem in reading PP's taken from QE site? Message-ID: Dear Paolo and Michael, > ls -l As.pz-bhs_s1.UPF\ >it looks like there is something at the end of the file name This was the first problem....actually when i was renaming the file, BY DEFAULT "one or two spaces" are added to end of .UPF file. However, in window interface, these spaces can not be detected. So, lesson to me: Use command line interface. Second problem was incomplete .UPF file. >I'm not having any trouble with Intel 11. Now, me too also. Thank You once again ! With Wishes, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/74b3a9ff/attachment.htm From chengyu.young at gmail.com Thu Jun 17 23:26:41 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 17 Jun 2010 17:26:41 -0400 Subject: [Pw_forum] different structure under xyz file and scf file for carbon nanotube In-Reply-To: References: Message-ID: Hi everyone, I have a question. When I put my atom positions unde .xyz file, and input into xcrysden, they will generate a round carbon nanotube . However, when I put the same atomic positions under scf.in file, and then input them into xcrysden, I got departed four parts like four quarters of a nanotube, all outwards. I feel very stange about this. Can anyone tell me is there anything wrong with the scf file? I want a round carbon nanotube because it is more vivid and instinctive. my input files are like this: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/mems/espresso-4.2/tmp/' , pseudo_dir = '/home/mems/espresso-4.2/pseudo/' , prefix = 'cnt' , / &SYSTEM ibrav = 6, celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 24, ntyp = 1, ecutwfc = 75 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 K_POINTS automatic 4 4 4 1 1 1 and my .xyz file are like 24 (6,6) Nanotube -- TubeGen 3.3, J T Frey, University of Delaware C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 ------- Chengyu Yang Graduate student Material Science and Engineering. U of Central Florida Chengyu.young at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/e94cbbef/attachment.htm From chengyu.young at gmail.com Thu Jun 17 23:37:06 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 17 Jun 2010 17:37:06 -0400 Subject: [Pw_forum] Fwd: different structure under xyz file and scf file for carbon nanotube In-Reply-To: References: Message-ID: Hi everyone, I have a question. When I put my atom positions unde .xyz file, and input into xcrysden, they will generate a round carbon nanotube . However, when I put the same atomic positions under scf.in file, and then input them into xcrysden, I got departed four parts like four quarters of a nanotube, all outwards. I feel very stange about this. Can anyone tell me is there anything wrong with the scf file? I want a round carbon nanotube because it is more vivid and instinctive. my input files are like this: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/mems/espresso-4.2/tmp/' , pseudo_dir = '/home/mems/espresso-4.2/pseudo/' , prefix = 'cnt' , / &SYSTEM ibrav = 6, celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 24, ntyp = 1, ecutwfc = 75 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 K_POINTS automatic 4 4 4 1 1 1 and my .xyz file are like 24 (6,6) Nanotube -- TubeGen 3.3, J T Frey, University of Delaware C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 ------- Chengyu Yang Graduate student Material Science and Engineering. U of Central Florida Chengyu.young at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/e1eb7521/attachment.htm From leommj at usp.br Fri Jun 18 00:01:46 2010 From: leommj at usp.br (Leonardo Matheus) Date: Fri, 18 Jun 2010 00:01:46 +0200 Subject: [Pw_forum] Fwd: different structure under xyz file and scf file for carbon nanotube In-Reply-To: References: Message-ID: Hi, There is no problem on the coordinates, it's just a visualization "problem". In XCrysden change "Display -> Unit of Repetition -> Translational Asymmetric Unit". Keep in mind that in Espresso you have periodic boundary conditions, and so what you was seeing were the periodic images of each "quarter". Leonardo Jorge PhD Student USP - Brazil From suza.rri at gmail.com Fri Jun 18 00:33:50 2010 From: suza.rri at gmail.com (Suza W) Date: Fri, 18 Jun 2010 00:33:50 +0200 Subject: [Pw_forum] Pseudo Ba Message-ID: Dear all, On QE website, only following two GGA pseudos are available for Ba: Ba.pbe-nsp-van.UPF Ba.pw91-nsp-van.UPF > > Does anyone have a PZ LDA ultrasoft pseudo potential for Ba ? > > Thanking you all, > > Suza W > PhD student > Institute of Raman Research > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100618/d053c051/attachment.htm From chengyu.young at gmail.com Fri Jun 18 02:10:57 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 17 Jun 2010 20:10:57 -0400 Subject: [Pw_forum] Fwd: different structure under xyz file and scf file for carbon nanotube In-Reply-To: References: Message-ID: Thanks! That really helps. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/200b4c8b/attachment.htm From chengyu.young at gmail.com Fri Jun 18 02:42:02 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 17 Jun 2010 20:42:02 -0400 Subject: [Pw_forum] carbon nanotube & copper chain Message-ID: Dear everyone, i am trying to creat a carbon nanotube with a cu chain in its center, but i am not sure if my parameter settings are correct:I don't know if under the &system item, i should use the only cnt's data, and i am not sure the setting of k points. Because it will cost a lot of time to calculate, I want to make it as correct as possible. Would you plz have a look at my script and give some suggestions?Thank you. As following: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/mems/espresso-4.2/tmp/' , pseudo_dir = '/home/mems/espresso-4.2/pseudo/' , prefix = 'cnt' , / &SYSTEM ibrav = 6, celldm(1) = 108.82270564,celldm(3)=0.213765379 nat = 125, ntyp = 2, ecutwfc = 75 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -6.155049 C 3.838021 1.399343 -6.155049 C 3.537856 2.042582 -4.924040 C 2.624152 3.130877 -4.924040 C 2.042582 3.537856 -6.155049 C 0.707144 4.023496 -6.155049 C 0.000000 4.085165 -4.924040 C -1.399343 3.838021 -4.924040 C -2.042582 3.537856 -6.155049 C -3.130877 2.624152 -6.155049 C -3.537856 2.042582 -4.924040 C -4.023496 0.707144 -4.924040 C -4.085165 0.000000 -6.155049 C -3.838021 -1.399343 -6.155049 C -3.537856 -2.042582 -4.924040 C -2.624152 -3.130877 -4.924040 C -2.042582 -3.537856 -6.155049 C -0.707144 -4.023496 -6.155049 C -0.000000 -4.085165 -4.924040 C 1.399343 -3.838021 -4.924040 C 2.042582 -3.537856 -6.155049 C 3.130877 -2.624152 -6.155049 C 3.537856 -2.042582 -4.924040 C 4.023496 -0.707144 -4.924040 C 4.085165 -0.000000 -3.693030 C 3.838021 1.399343 -3.693030 C 3.537856 2.042582 -2.462020 C 2.624152 3.130877 -2.462020 C 2.042582 3.537856 -3.693030 C 0.707144 4.023496 -3.693030 C 0.000000 4.085165 -2.462020 C -1.399343 3.838021 -2.462020 C -2.042582 3.537856 -3.693030 C -3.130877 2.624152 -3.693030 C -3.537856 2.042582 -2.462020 C -4.023496 0.707144 -2.462020 C -4.085165 0.000000 -3.693030 C -3.838021 -1.399343 -3.693030 C -3.537856 -2.042582 -2.462020 C -2.624152 -3.130877 -2.462020 C -2.042582 -3.537856 -3.693030 C -0.707144 -4.023496 -3.693030 C -0.000000 -4.085165 -2.462020 C 1.399343 -3.838021 -2.462020 C 2.042582 -3.537856 -3.693030 C 3.130877 -2.624152 -3.693030 C 3.537856 -2.042582 -2.462020 C 4.023496 -0.707144 -2.462020 C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 C 4.085165 -0.000000 1.231010 C 3.838021 1.399343 1.231010 C 3.537856 2.042582 2.462020 C 2.624152 3.130877 2.462020 C 2.042582 3.537856 1.231010 C 0.707144 4.023496 1.231010 C 0.000000 4.085165 2.462020 C -1.399343 3.838021 2.462020 C -2.042582 3.537856 1.231010 C -3.130877 2.624152 1.231010 C -3.537856 2.042582 2.462020 C -4.023496 0.707144 2.462020 C -4.085165 0.000000 1.231010 C -3.838021 -1.399343 1.231010 C -3.537856 -2.042582 2.462020 C -2.624152 -3.130877 2.462020 C -2.042582 -3.537856 1.231010 C -0.707144 -4.023496 1.231010 C -0.000000 -4.085165 2.462020 C 1.399343 -3.838021 2.462020 C 2.042582 -3.537856 1.231010 C 3.130877 -2.624152 1.231010 C 3.537856 -2.042582 2.462020 C 4.023496 -0.707144 2.462020 C 4.085165 -0.000000 3.693030 C 3.838021 1.399343 3.693030 C 3.537856 2.042582 4.924040 C 2.624152 3.130877 4.924040 C 2.042582 3.537856 3.693030 C 0.707144 4.023496 3.693030 C 0.000000 4.085165 4.924040 C -1.399343 3.838021 4.924040 C -2.042582 3.537856 3.693030 C -3.130877 2.624152 3.693030 C -3.537856 2.042582 4.924040 C -4.023496 0.707144 4.924040 C -4.085165 0.000000 3.693030 C -3.838021 -1.399343 3.693030 C -3.537856 -2.042582 4.924040 C -2.624152 -3.130877 4.924040 C -2.042582 -3.537856 3.693030 C -0.707144 -4.023496 3.693030 C -0.000000 -4.085165 4.924040 C 1.399343 -3.838021 4.924040 C 2.042582 -3.537856 3.693030 C 3.130877 -2.624152 3.693030 C 3.537856 -2.042582 4.924040 C 4.023496 -0.707144 4.924040 Cu 0 0 -6.184547225 Cu 0 0 -3.710728335 Cu 0 0 -1.236909445 Cu 0 0 1.236909445 Cu 0 0 3.710728335 K_POINTS automatic 4 4 4 1 1 1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/ed8be431/attachment.htm From nkxirainbow at gmail.com Fri Jun 18 03:07:56 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Jun 2010 09:07:56 +0800 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: Message-ID: Dear Yang: 1:Why you choose C.pz-vbc.UPF and Cu.pz-d-rrkjus.UPF. Cu.pz-d-rrkjus.UPF is Ultrasoft pseudopotential However, C.pz-vbc.UPF is Norm - Conserving pseudopotential. You should set all atoms to the same kind of PP. 2:Kpoints?4 4 4 1 1 1 If you are going to deal with isolated nanotube, you should set Kpints to 1 1 X. X is a integer. On Fri, Jun 18, 2010 at 8:42 AM, chengyu yang wrote: > Dear everyone, > i am trying to creat a carbon nanotube with a cu chain in its center, > but i am not sure if my parameter settings are correct:I don't know if under > the &system item, i should use the only cnt's data, and i am not sure the > setting of k points. Because it will cost a lot of time to calculate, I want > to make it as correct as possible. Would you plz have a look at my script > and give some suggestions?Thank you. > As following: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/mems/espresso-4.2/tmp/' , > pseudo_dir = '/home/mems/espresso-4.2/pseudo/' , > prefix = 'cnt' , > / > &SYSTEM > ibrav = 6, > celldm(1) = 108.82270564,celldm(3)=0.213765379 > nat = 125, > ntyp = 2, > ecutwfc = 75 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > C 12.01100 C.pz-vbc.UPF > Cu 63.55 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS angstrom > C 4.085165 -0.000000 -6.155049 > C 3.838021 1.399343 -6.155049 > C 3.537856 2.042582 -4.924040 > C 2.624152 3.130877 -4.924040 > C 2.042582 3.537856 -6.155049 > C 0.707144 4.023496 -6.155049 > C 0.000000 4.085165 -4.924040 > C -1.399343 3.838021 -4.924040 > C -2.042582 3.537856 -6.155049 > C -3.130877 2.624152 -6.155049 > C -3.537856 2.042582 -4.924040 > C -4.023496 0.707144 -4.924040 > C -4.085165 0.000000 -6.155049 > C -3.838021 -1.399343 -6.155049 > C -3.537856 -2.042582 -4.924040 > C -2.624152 -3.130877 -4.924040 > C -2.042582 -3.537856 -6.155049 > C -0.707144 -4.023496 -6.155049 > C -0.000000 -4.085165 -4.924040 > C 1.399343 -3.838021 -4.924040 > C 2.042582 -3.537856 -6.155049 > C 3.130877 -2.624152 -6.155049 > C 3.537856 -2.042582 -4.924040 > C 4.023496 -0.707144 -4.924040 > C 4.085165 -0.000000 -3.693030 > C 3.838021 1.399343 -3.693030 > C 3.537856 2.042582 -2.462020 > C 2.624152 3.130877 -2.462020 > C 2.042582 3.537856 -3.693030 > C 0.707144 4.023496 -3.693030 > C 0.000000 4.085165 -2.462020 > C -1.399343 3.838021 -2.462020 > C -2.042582 3.537856 -3.693030 > C -3.130877 2.624152 -3.693030 > C -3.537856 2.042582 -2.462020 > C -4.023496 0.707144 -2.462020 > C -4.085165 0.000000 -3.693030 > C -3.838021 -1.399343 -3.693030 > C -3.537856 -2.042582 -2.462020 > C -2.624152 -3.130877 -2.462020 > C -2.042582 -3.537856 -3.693030 > C -0.707144 -4.023496 -3.693030 > C -0.000000 -4.085165 -2.462020 > C 1.399343 -3.838021 -2.462020 > C 2.042582 -3.537856 -3.693030 > C 3.130877 -2.624152 -3.693030 > C 3.537856 -2.042582 -2.462020 > C 4.023496 -0.707144 -2.462020 > C 4.085165 -0.000000 -1.231010 > C 3.838021 1.399343 -1.231010 > C 3.537856 2.042582 0.000000 > C 2.624152 3.130877 0.000000 > C 2.042582 3.537856 -1.231010 > C 0.707144 4.023496 -1.231010 > C 0.000000 4.085165 0.000000 > C -1.399343 3.838021 0.000000 > C -2.042582 3.537856 -1.231010 > C -3.130877 2.624152 -1.231010 > C -3.537856 2.042582 0.000000 > C -4.023496 0.707144 0.000000 > C -4.085165 0.000000 -1.231010 > C -3.838021 -1.399343 -1.231010 > C -3.537856 -2.042582 0.000000 > C -2.624152 -3.130877 0.000000 > C -2.042582 -3.537856 -1.231010 > C -0.707144 -4.023496 -1.231010 > C -0.000000 -4.085165 0.000000 > C 1.399343 -3.838021 0.000000 > C 2.042582 -3.537856 -1.231010 > C 3.130877 -2.624152 -1.231010 > C 3.537856 -2.042582 0.000000 > C 4.023496 -0.707144 0.000000 > C 4.085165 -0.000000 1.231010 > C 3.838021 1.399343 1.231010 > C 3.537856 2.042582 2.462020 > C 2.624152 3.130877 2.462020 > C 2.042582 3.537856 1.231010 > C 0.707144 4.023496 1.231010 > C 0.000000 4.085165 2.462020 > C -1.399343 3.838021 2.462020 > C -2.042582 3.537856 1.231010 > C -3.130877 2.624152 1.231010 > C -3.537856 2.042582 2.462020 > C -4.023496 0.707144 2.462020 > C -4.085165 0.000000 1.231010 > C -3.838021 -1.399343 1.231010 > C -3.537856 -2.042582 2.462020 > C -2.624152 -3.130877 2.462020 > C -2.042582 -3.537856 1.231010 > C -0.707144 -4.023496 1.231010 > C -0.000000 -4.085165 2.462020 > C 1.399343 -3.838021 2.462020 > C 2.042582 -3.537856 1.231010 > C 3.130877 -2.624152 1.231010 > C 3.537856 -2.042582 2.462020 > C 4.023496 -0.707144 2.462020 > C 4.085165 -0.000000 3.693030 > C 3.838021 1.399343 3.693030 > C 3.537856 2.042582 4.924040 > C 2.624152 3.130877 4.924040 > C 2.042582 3.537856 3.693030 > C 0.707144 4.023496 3.693030 > C 0.000000 4.085165 4.924040 > C -1.399343 3.838021 4.924040 > C -2.042582 3.537856 3.693030 > C -3.130877 2.624152 3.693030 > C -3.537856 2.042582 4.924040 > C -4.023496 0.707144 4.924040 > C -4.085165 0.000000 3.693030 > C -3.838021 -1.399343 3.693030 > C -3.537856 -2.042582 4.924040 > C -2.624152 -3.130877 4.924040 > C -2.042582 -3.537856 3.693030 > C -0.707144 -4.023496 3.693030 > C -0.000000 -4.085165 4.924040 > C 1.399343 -3.838021 4.924040 > C 2.042582 -3.537856 3.693030 > C 3.130877 -2.624152 3.693030 > C 3.537856 -2.042582 4.924040 > C 4.023496 -0.707144 4.924040 > Cu 0 0 -6.184547225 > Cu 0 0 -3.710728335 > Cu 0 0 -1.236909445 > Cu 0 0 1.236909445 > Cu 0 0 3.710728335 > > K_POINTS automatic > 4 4 4 1 1 1 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100618/19daec10/attachment-0001.htm From chengyu.young at gmail.com Fri Jun 18 03:39:24 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 17 Jun 2010 21:39:24 -0400 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: Message-ID: Dear Wang, 1, I don't know where to find the Cu.pz-vbc.UPF, I just download the pseudo from the web, in which no Cu's norm pseudopotential at all. 2, what do you mean by 1 1 X? There are only 3 parameters for K points? I am new to quantum espresso, and really don't know how to choose the right k points. Thank you. Chengyu Yang Graduate student Materials Science & Engineering > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/f005719b/attachment.htm From nkxirainbow at gmail.com Fri Jun 18 03:52:10 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Jun 2010 09:52:10 +0800 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: Message-ID: Dear Yang? On Fri, Jun 18, 2010 at 9:39 AM, chengyu yang wrote: > Dear Wang, > 1, I don't know where to find the Cu.pz-vbc.UPF, I just download the > pseudo from the web, in which no Cu's norm pseudopotential at all. > You can choose C.pz-rrkjus.UPF and Cu.pz-d-rrkjus.UPF. 2, what do you mean by 1 1 X? There are only 3 parameters for K points? > I am new to quantum espresso, and really don't know how to choose the right > k points. Thank you. > > You can find wonderful explanation about the meaning of kpoints in ?*Solid and Surface*: A Chemist's View of Bonding in Extended Structure ?*Roald Hoffmann. And there is a chinese version.* ____________________________________ 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/20100618/ff2175e6/attachment.htm From chengyu.young at gmail.com Fri Jun 18 04:12:01 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 17 Jun 2010 22:12:01 -0400 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: Message-ID: Dear Hui Wang, But under such a case, should I using what kind of k-point? As following: K_POINTS { tpiba | automatic | crystal | gamma } gamma : use k = 0 ( do not read anything after this card ) Note that a set of subroutines optimized for clculations at the gamma point are used so that both memory and cpu requirements are reduced automatic: automatically generated uniform grid of k-points next card: nk1, nk2, nk3, k1, k2, k3 generates ( nk1, nk2, nk3 ) mesh with ( k1, k2, k3 ) offset nk1, nk2, nk3 as in Monkhorst-Pack grids k1, k2, k3 must be 0 ( no offset ) or 1 ( grid displaced by half a grid step in the corresponding direction ) The mesh with offset may not work with tetrahedra. crystal : read k-points in crystal coordinates tpiba : read k-points in 2pi/a units ( default ) next card: nks number of supplied special points xk_x, xk_y, xk_z, wk special points in the irreducible Brillouin Zone of the lattice (with all symmetries) and weights If the symmetry is lower than the full symmetry of the lattice, additional points with appropriate weights are generated =================================== And to save the time, what should I put in here? k point 1 1 4 will be OK? Or either integer will be OK? I am sorry for my bluntness. Chengyu Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100617/f4c02634/attachment.htm From giannozz at democritos.it Fri Jun 18 08:57:22 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 Jun 2010 08:57:22 +0200 Subject: [Pw_forum] pseudo-potential for virtual atom In-Reply-To: References: Message-ID: <4C1B18D2.2020303@democritos.it> German Samolyuk wrote: > virtual.x can not read ps files because UPF format has > been changed. What should I do to solve this problem? please have a look at Modules/upf.f90, Modules/read_upf_v1.f90, Modules/read_upf_v2.f90. There you will find all you need to read the new upf format. The routines in upftools/ were intended to be stand-alone, but this wasn't such a great idea: it is more convenient to use the same modules everywhere to read and write pseudopotentials. If you update virtual.x so that it reads new upf files, please let us know P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From marzari at MIT.EDU Fri Jun 18 08:59:28 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 18 Jun 2010 07:59:28 +0100 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: Message-ID: <4C1B1950.3040000@mit.edu> Dear Yang, 1) start from something much simpler. you need to build some competence, or you'll get meaningless results. study diamond, graphite, graphene, and a few perfect nanotubes first. compare with literature. 2) contrary to what is said below, you CAN mix ultrasoft and norm-conserving pseudos. 3) for a isolated tube, use indeed a sampling 1 1 n, with n integer - but keep in mind that then the nanotube needs to be infinite in the z direction. if infinite along x, you need n 1 1 (and then a shift that is 1 1 1 or 0 0 0 or 1 0 0). there is no difference between a 1 0 0 shift and a 1 1 1 shift, for a tube along x. why ? nicola xirainbow wrote: > Dear Yang: > 1:Why you choose C.pz-vbc.UPF and Cu.pz-d-rrkjus.UPF. > Cu.pz-d-rrkjus.UPF is Ultrasoft pseudopotential > However, C.pz-vbc.UPF is Norm - Conserving pseudopotential. > You should set all atoms to the same kind of PP. > > 2:Kpoints?4 4 4 1 1 1 > If you are going to deal with isolated nanotube, > you should set Kpints to 1 1 X. X is a integer. > > > > On Fri, Jun 18, 2010 at 8:42 AM, chengyu yang > wrote: > > Dear everyone, > i am trying to creat a carbon nanotube with a cu chain in > its center, but i am not sure if my parameter settings are > correct:I don't know if under the &system item, i should use the > only cnt's data, and i am not sure the setting of k points. > Because it will cost a lot of time to calculate, I want to make it > as correct as possible. Would you plz have a look at my script and > give some suggestions?Thank you. > As following: > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From nkxirainbow at gmail.com Fri Jun 18 15:15:07 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Jun 2010 21:15:07 +0800 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: <4C1B1950.3040000@mit.edu> References: <4C1B1950.3040000@mit.edu> Message-ID: Dear Nicola Marzari*:* * * > 2) contrary to what is said below, you CAN mix ultrasoft and > norm-conserving > pseudos. > Can you tell me why it is allowable to mix US and NC pp? I never know it before. Sorry for troubling you. Thanks in advance?? ____________________________________ 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/20100618/092ba761/attachment.htm From baroni at sissa.it Fri Jun 18 15:40:57 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 18 Jun 2010 15:40:57 +0200 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: <4C1B1950.3040000@mit.edu> Message-ID: <3E6647EE-0C3C-4E58-94BC-97DDED1C1B91@sissa.it> Short answer: why not? Longer answer: in order to give a meaningful answer, why you think it should not be possible? Stefano B On Jun 18, 2010, at 3:15 PM, xirainbow wrote: > Dear Nicola Marzari: > > > 2) contrary to what is said below, you CAN mix ultrasoft and norm-conserving > pseudos. > > Can you tell me why it is allowable to mix US and NC pp? I never know it before. > Sorry for troubling you. > Thanks in advance?? > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100618/003e6e26/attachment.htm From sks.jnc at gmail.com Fri Jun 18 17:16:03 2010 From: sks.jnc at gmail.com (S. K. S.) Date: Fri, 18 Jun 2010 17:16:03 +0200 Subject: [Pw_forum] Wu-Cohen GGA Message-ID: Dear All, Is Wu-Cohen GGA implemented in QE? Would anyone then like to share his or her pseudopotentials? With my best regards, Saha S. K. R&D Assistant JNCASR Bangalore- 560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100618/eb2c7330/attachment.htm From lshulenburger at gmail.com Fri Jun 18 17:39:41 2010 From: lshulenburger at gmail.com (Luke Shulenburger) Date: Fri, 18 Jun 2010 11:39:41 -0400 Subject: [Pw_forum] Wu-Cohen GGA In-Reply-To: References: Message-ID: Hi, Wu-Cohen is implemented in the newer versions. I have made a couple of pp's that I could share with you. Which elements are you interested in? Luke Shulenburger Geophysical Laboratory Carnegie Institution of Washington On Fri, Jun 18, 2010 at 11:16 AM, S. K. S. wrote: > > > ? Dear All, > > ? Is? Wu-Cohen GGA implemented in QE? > ? Would anyone then like to share his or her pseudopotentials? > > ? With my best regards, > > ?? Saha S. K. > ?? R&D Assistant > ?? JNCASR > ?? Bangalore- 560012 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From vovi47 at yahoo.com Sat Jun 19 01:35:39 2010 From: vovi47 at yahoo.com (Vi Vo) Date: Fri, 18 Jun 2010 16:35:39 -0700 (PDT) Subject: [Pw_forum] B3LYP Message-ID: <55003.88958.qm@web114507.mail.gq1.yahoo.com> Dear PWSCF Users, Is B3LYP implemented in QE 4.2? Thank you, Vi Vo Chemical Engineering Department University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100618/c3be8e3a/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Sat Jun 19 13:52:21 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Sat, 19 Jun 2010 13:52:21 +0200 Subject: [Pw_forum] B3LYP In-Reply-To: <55003.88958.qm@web114507.mail.gq1.yahoo.com> References: <55003.88958.qm@web114507.mail.gq1.yahoo.com> Message-ID: <201006191352.21615.giuseppe.mattioli@mlib.ism.cnr.it> Dear Vi Vo > Is B3LYP implemented in QE 4.2? It is, but first have a look at this file /yourespresso-4.2/examples/EXX_example/README having in mind that hybrid functionals are not still straightforwardly implemented in QE... Yours Giuseppe On Saturday 19 June 2010 01:35:39 Vi Vo wrote: > Dear PWSCF Users, > > Is B3LYP implemented in QE 4.2? > > Thank you, > > Vi Vo > Chemical Engineering Department > University of Houston -- ******************************************************** - 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: From elahe_afrodit at yahoo.com Sun Jun 20 14:33:24 2010 From: elahe_afrodit at yahoo.com (eli) Date: Sun, 20 Jun 2010 05:33:24 -0700 (PDT) Subject: [Pw_forum] irreducible representations Message-ID: <781979.94930.qm@web32504.mail.mud.yahoo.com> dear all in phonon calculation in? output of ph.x, what is irreducible representations? "for example 2 modes -E-2u" Elahe Teimouri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Isfahan, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100620/539c8e9f/attachment.htm From nkxirainbow at gmail.com Sun Jun 20 14:44:04 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 20 Jun 2010 20:44:04 +0800 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: <3E6647EE-0C3C-4E58-94BC-97DDED1C1B91@sissa.it> References: <4C1B1950.3040000@mit.edu> <3E6647EE-0C3C-4E58-94BC-97DDED1C1B91@sissa.it> Message-ID: Dear Stefano Baroni and Stefano B: *Thanks very much for your correction. ??* On Fri, Jun 18, 2010 at 9:40 PM, Stefano Baroni wrote: > Short answer: why not? > Longer answer: in order to give a meaningful answer, why you think it > should not be possible? > Stefano B > > On Jun 18, 2010, at 3:15 PM, xirainbow wrote: > -- ____________________________________ 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/20100620/eedc3096/attachment.htm From nkxirainbow at gmail.com Sun Jun 20 14:49:55 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 20 Jun 2010 20:49:55 +0800 Subject: [Pw_forum] irreducible representations In-Reply-To: <781979.94930.qm@web32504.mail.mud.yahoo.com> References: <781979.94930.qm@web32504.mail.mud.yahoo.com> Message-ID: Dear eli: "*E*" means it is a double-degenerate mode. "*u*" means it is antisymmetry under inversion operation. You will find more information in books about "lattice dynamics" On Sun, Jun 20, 2010 at 8:33 PM, eli wrote: > dear all > in phonon calculation in output of ph.x, what is irreducible > representations? "for example 2 modes -E-2u" > Elahe Teimouri > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology, Isfahan, Iran > > ____________________________________ 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/20100620/c1388152/attachment.htm From baroni at sissa.it Sun Jun 20 18:14:53 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 20 Jun 2010 18:14:53 +0200 Subject: [Pw_forum] irreducible representations In-Reply-To: <781979.94930.qm@web32504.mail.mud.yahoo.com> References: <781979.94930.qm@web32504.mail.mud.yahoo.com> Message-ID: <974154C3-0FA5-4CDD-ABC6-11C0776E2A14@sissa.it> See chapter XII of Landau's "Quantum mechanics" or any other textbook of quantum mechanics / molecular physics / condensed matter physics. If all this takes too much time, google may also help ... Stefano B On Jun 20, 2010, at 2:33 PM, eli wrote: > dear all > in phonon calculation in output of ph.x, what is irreducible representations? "for example 2 modes -E-2u" > Elahe Teimouri > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology, Isfahan, Iran > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100620/72e8d2af/attachment.htm From kazempoor2000 at yahoo.com Mon Jun 21 08:00:49 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Sun, 20 Jun 2010 23:00:49 -0700 (PDT) Subject: [Pw_forum] GWW for metal Message-ID: <922195.96119.qm@web114403.mail.gq1.yahoo.com> Dear all Can GWW be used for obtaining? QP spectra in metals or unpaired states? 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/20100620/cbabe0c9/attachment.htm From gianluca.giovannetti at gmail.com Mon Jun 21 08:04:42 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Mon, 21 Jun 2010 08:04:42 +0200 Subject: [Pw_forum] consistent Fe,Se,Te pseudopotential files Message-ID: Dear All, i want to make calculations with PBE functional for a system including Fe,Se,Te elements. At the webpage: http://www.quantum-espresso.org/pseudo.php i can find for Se: Se.pbe-van.UPF ( details) Perdew-Burke-Ernzerhof (PBE) exch-corr Vanderbilt ultrasoft then for Fe: Fe.pbe-sp-mt_gipaw.UPF (details ) Perdew-Burke-Ernzerhof (PBE) exch-corr semicore state s in valence semicore state p in valence Martins-Troullier author: gipaw Perdew-Wang 91 gradient-corrected functional Fe.pbe-sp-van.UPF ( details) Perdew-Burke-Ernzerhof (PBE) exch-corr semicore state s in valence semicore state p in valence Vanderbilt ultrasoft Fe.pbe-sp-van_mit.UPF ( details) Perdew-Burke-Ernzerhof (PBE) exch-corr semicore state s in valence semicore state p in valence Vanderbilt ultrasoft author: mit Fe.pbe-nd-rrkjus.UPF ( details) Perdew-Burke-Ernzerhof (PBE) exch-corr nonlinear core-correction semicore state d in valence Rabe Rappe Kaxiras Joannopoulos (ultrasoft) Fe.pbe-sp-van_ak.UPF ( details) Perdew-Burke-Ernzerhof (PBE) exch-corr semicore state s in valence semicore state p in valence Vanderbilt ultrasoft author: ak and then for Te: Te.pbe-rrkj.UPF ( details) Perdew-Burke-Ernzerhof (PBE) exch-corr Rabe Rappe Kaxiras Joannopoulos (norm-conserving) basically i cannot find same type of these pseudopotentials. :-) I think in principle it is not really good to mix types of pseudopotentials. however i have checked that doing calculation with PW and using pseudo: Fe.pbe-sp-van.UPF Te.pbe-rrkj.UPF Se.pbe-van.UPF i can get good band structures very close to another dft code (all-electron). moreover i would appreciate much more to have Te Vanderbilt ultrasoft pseudopotential. Before going to generate it (i must confess i`m not an expert :-).... ), i ask you if here there is someone who generated already this pseudo and he could share it with me or if you know if i can download it from some website. i thank you in advance. cheers, Gianluca Giovannetti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/fa51b7d2/attachment-0001.htm From baroni at sissa.it Mon Jun 21 08:52:39 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 21 Jun 2010 08:52:39 +0200 Subject: [Pw_forum] GWW for metal In-Reply-To: <922195.96119.qm@web114403.mail.gq1.yahoo.com> References: <922195.96119.qm@web114403.mail.gq1.yahoo.com> Message-ID: <64AF2A78-38B6-400D-9467-F6E272573738@sissa.it> NO - SB On Jun 21, 2010, at 8:00 AM, ali kazempour wrote: > Dear all > Can GWW be used for obtaining QP spectra in metals or unpaired states? > 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 --- 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/20100621/06dc104d/attachment.htm From kazempoor2000 at yahoo.com Mon Jun 21 09:47:31 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 21 Jun 2010 00:47:31 -0700 (PDT) Subject: [Pw_forum] GWW for metal In-Reply-To: <64AF2A78-38B6-400D-9467-F6E272573738@sissa.it> Message-ID: <885891.79828.qm@web114406.mail.gq1.yahoo.com> Dear Stefano Thanks for reply. I have another question: In GW calculation the number of empty states is important, But as I found in GWW It is independent of empty states Unlike SAX( that the nbnd is 4*valence band)? Am I right? Thanks 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 --- On Sun, 6/20/10, Stefano Baroni wrote: From: Stefano Baroni Subject: Re: [Pw_forum] GWW for metal To: "PWSCF Forum" Date: Sunday, June 20, 2010, 11:52 PM NO - SB On Jun 21, 2010, at 8:00 AM, ali kazempour wrote: Dear all Can GWW be used for obtaining? QP spectra in metals or unpaired states? 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 ---Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Triestehttp://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 attachmentsWhy? See:??http://www.gnu.org/philosophy/no-word-attachments.html -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/3692da35/attachment.htm From giannozz at democritos.it Mon Jun 21 09:59:01 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Jun 2010 09:59:01 +0200 Subject: [Pw_forum] consistent Fe,Se,Te pseudopotential files In-Reply-To: References: Message-ID: <201006210959.02250.giannozz@democritos.it> On Monday 21 June 2010 08:04, Gianluca Giovannetti wrote: > i would appreciate much more to have Te Vanderbilt ultrasoft > pseudopotential. why? the big advantage of ultrasoft PPs is to require a much smaller cutoff. In the case of Fe-Te-Se systems, Fe is by far the hardest element. The cutoff needed for ultrasoft Fe might well be sufficient for norm-conserving Te (and Se as well). P. -- Paolo Giannozzi, Democritos and Udine University From mahkameh_va at yahoo.com Mon Jun 21 10:26:06 2010 From: mahkameh_va at yahoo.com (raheleh vaziri) Date: Mon, 21 Jun 2010 01:26:06 -0700 (PDT) Subject: [Pw_forum] offset Message-ID: <817903.31172.qm@web32906.mail.mud.yahoo.com> Dear all, ? I have two input files. The difference between these input files is offset. Which of them is the best? Please find the attached input files. ?I am pleased if you could tell me the criterion of the determination of offset. ? Thanks in advance. ? &CONTROL ? calculation? ="scf", ? pseudo_dir?? = "./", ? outdir?? = "./", ? prefix?? = "2", / &SYSTEM ? ibrav= 4, ? celldm(1) = 13.9452, ? celldm(3) = 0.50220, ? nat = 21, ? ntyp= 2 , ? ecutwfc? = 25.0, ? ecutrho = 105.0, ? occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05, / &electrons ? diagonalization='cg', ? conv_thr? = 1.0e-7, ? mixing_beta = 0.5, / ATOMIC_SPECIES C? 12.00?? C.pw91-van_ak.UPF Li 6.914?? Li.pw91-s-van_ak.UPF ATOMIC_POSITIONS {angstrom}??? ?C???????????????? -2.31375055??? 5.60380930??? 1.97749928 ?C????????????????? 2.60873529??? 5.59894992??? 1.97827588 ?C????????????????? 1.37111491??? 4.88605088??? 1.98071055 ?C????????????????? 0.14749316??? 5.60138230??? 1.98026831 ?C???????????????? -1.09012567??? 4.88849231??? 1.98354393 ?C???????????? ????-1.08523445??? 3.47114506??? 1.99210730 ?C????????????????? 3.83236102??? 4.88362824??? 1.98354902 ?C????????????????? 3.83725009??? 3.46629018??? 1.99363246 ?C????????????????? 2.59963288??? 2.75339819??? 1.99851730 ?C????????????????? 1.37600716??? 3.46871987??? 1.99324416 ?C????????????????? 0.13838997??? 2.75582789??? 1.99812899 ?C????????????????? 0.14327905??? 1.33848981??? 2.00821243 ?C????????????????? 5.06087580??? 2.75096849??? 1.99890559 ?C????????????????? 5.06576489??? 1.33363043??? 2.00898904 ?C????????????????? 3.82814767??? 0.62073845??? 2.01387388 ?C????????????????? 2.60452196??? 1.33606013??? 2.00860075 ?C????????????????? 1.36690476??? 0.62316813??? 2.01348557 ?C????????????????? 6.28939060??? 0.61830875??? 2.01426218 ?Li???????????? ????1.35277313??? 6.31968764??? 0.12525022 ?Li??????????????? -2.31676697??? 4.21513012??? 0.13346760 ?Li???????????????? 1.35260170??? 2.08833760??? 0.15666888 K_POINTS {automatic} 2 2 5 0 0 0 Or K_POINTS {automatic} 2 2 5 1 1 1 ? Mahkameh Vaziri physical chemistry department K.N.Toosi university of technology,Tehran,Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/a97e79ae/attachment-0001.htm From archygu at gmail.com Mon Jun 21 10:07:35 2010 From: archygu at gmail.com (archygu) Date: Mon, 21 Jun 2010 16:07:35 +0800 Subject: [Pw_forum] pseudopotential Message-ID: <201006211607328745576@gmail.com> hi Pwscf user, can you share a tested Hs pseudopotential with me? many thakns, archy GU NTU, Singapore 2010-06-21 archygu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/58bae2b8/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Mon Jun 21 11:35:26 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 21 Jun 2010 11:35:26 +0200 Subject: [Pw_forum] pseudopotential In-Reply-To: <201006211607328745576@gmail.com> References: <201006211607328745576@gmail.com> Message-ID: <201006211135.26387.giuseppe.mattioli@mlib.ism.cnr.it> Hs is not present on my periodic table... G. On Monday 21 June 2010 10:07:35 archygu wrote: > hi Pwscf user, > > can you share a tested Hs pseudopotential with me? > many thakns, > archy GU > NTU, Singapore > > 2010-06-21 > > > > archygu -- ******************************************************** - 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: From paulatto at sissa.it Mon Jun 21 11:54:03 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 21 Jun 2010 11:54:03 +0200 Subject: [Pw_forum] pseudopotential In-Reply-To: <201006211135.26387.giuseppe.mattioli@mlib.ism.cnr.it> References: <201006211607328745576@gmail.com> <201006211135.26387.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: On Mon, 21 Jun 2010 11:35:26 +0200, Giuseppe Mattioli wrote: > Hs is not present on my periodic table... > G. Hassium, formerly known as unniloctium or eka-osmium is an artificial element; from wikipedia: <> If anybody had a pseudopotential for it, it would be by far the element with the highest ratio for the number of available pseudopotentials over the number of available atoms. Honestly, I doubt there is any serious application for it in the field of condensed matter physics. regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From giuseppe.mattioli at mlib.ism.cnr.it Mon Jun 21 12:10:44 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 21 Jun 2010 12:10:44 +0200 Subject: [Pw_forum] pseudopotential In-Reply-To: References: <201006211607328745576@gmail.com> <201006211135.26387.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201006211210.44798.giuseppe.mattioli@mlib.ism.cnr.it> A typo...? On Monday 21 June 2010 11:54:03 Lorenzo Paulatto wrote: > On Mon, 21 Jun 2010 11:35:26 +0200, Giuseppe Mattioli > > wrote: > > Hs is not present on my periodic table... > > G. > > Hassium, formerly known as unniloctium or eka-osmium is an artificial > element; from wikipedia: > < 269Hs being the longest-lived with a half-life of ~10 s. There is also > tentative evidence for an isotope 277bHs with a measured half-life of > ~16.5 minutes, which would make it one of the longest-lived superheavy > nuclides. More than 100 atoms of hassium have been synthesized to date in > various cold and hot fusion reactions, both as a parent nucleus and decay > product.>> > > If anybody had a pseudopotential for it, it would be by far the element > with the highest ratio for the number of available pseudopotentials over > the number of available atoms. Honestly, I doubt there is any serious > application for it in the field of condensed matter physics. > > regards -- ******************************************************** - 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: From gianluca.giovannetti at gmail.com Mon Jun 21 13:19:30 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Mon, 21 Jun 2010 13:19:30 +0200 Subject: [Pw_forum] consistent Fe,Se,Te pseudopotential files In-Reply-To: <201006210959.02250.giannozz@democritos.it> References: <201006210959.02250.giannozz@democritos.it> Message-ID: Dear Paolo, thank you for the reply. Probably i`m missing something in your statement. :-) Are you suggesting to use Fe.pbe-sp-van.UPF Te.pbe-rrkj.UPF Se.pbe-van.UPF pseudopotential files evenif there are belonging to different types? cheers, Gianluca On Mon, Jun 21, 2010 at 9:59 AM, Paolo Giannozzi wrote: > On Monday 21 June 2010 08:04, Gianluca Giovannetti wrote: > > > i would appreciate much more to have Te Vanderbilt ultrasoft > > pseudopotential. > > why? the big advantage of ultrasoft PPs is to require a much > smaller cutoff. In the case of Fe-Te-Se systems, Fe is by far > the hardest element. The cutoff needed for ultrasoft Fe might > well be sufficient for norm-conserving Te (and Se as well). > > P. > -- > Paolo Giannozzi, Democritos and Udine University > _______________________________________________ > 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/20100621/df4bb41e/attachment.htm From degironc at sissa.it Mon Jun 21 13:47:30 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 21 Jun 2010 13:47:30 +0200 Subject: [Pw_forum] consistent Fe,Se,Te pseudopotential files In-Reply-To: References: <201006210959.02250.giannozz@democritos.it> Message-ID: <4C1F5152.6080008@sissa.it> The reason why USPP have been introduced is not for some form of masochism but because for certain elements of the first row (C-N-O-F) or for first row transition metals or rare earths NCPP would require very high cutoff. Most other elements (including Se,Te) can be treated with much lower cutoffs and do not need USPP construction... It is convenient therefore to use USPP for the hard elements while you can stick to NCPP when this is not needed. And you CAN mix different types. And always test convergence of your calculations. stefano Gianluca Giovannetti wrote: > Dear Paolo, > > thank you for the reply. > Probably i`m missing something in your statement. :-) > Are you suggesting to use > > Fe.pbe-sp-van.UPF > > Te.pbe-rrkj.UPF > Se.pbe-van.UPF > > pseudopotential files evenif there are belonging to different types? > > cheers, > > Gianluca > > On Mon, Jun 21, 2010 at 9:59 AM, Paolo Giannozzi wrote: > > >> On Monday 21 June 2010 08:04, Gianluca Giovannetti wrote: >> >> >>> i would appreciate much more to have Te Vanderbilt ultrasoft >>> pseudopotential. >>> >> why? the big advantage of ultrasoft PPs is to require a much >> smaller cutoff. In the case of Fe-Te-Se systems, Fe is by far >> the hardest element. The cutoff needed for ultrasoft Fe might >> well be sufficient for norm-conserving Te (and Se as well). >> >> P. >> -- >> Paolo Giannozzi, Democritos and Udine University >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From gianluca.giovannetti at gmail.com Mon Jun 21 13:53:18 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Mon, 21 Jun 2010 13:53:18 +0200 Subject: [Pw_forum] consistent Fe,Se,Te pseudopotential files In-Reply-To: <4C1F5152.6080008@sissa.it> References: <201006210959.02250.giannozz@democritos.it> <4C1F5152.6080008@sissa.it> Message-ID: Dear All, now it is clear. i thank you all of you for the discussions. cheers, Gianluca On Mon, Jun 21, 2010 at 1:47 PM, Stefano de Gironcoli wrote: > The reason why USPP have been introduced is not for some form of > masochism but because for certain elements of the first row (C-N-O-F) or > for first row transition metals or rare earths NCPP would require very > high cutoff. Most other elements (including Se,Te) can be treated with > much lower cutoffs and do not need USPP construction... > It is convenient therefore to use USPP for the hard elements while you > can stick to NCPP when this is not needed. > And you CAN mix different types. > > And always test convergence of your calculations. > > stefano > > Gianluca Giovannetti wrote: > > Dear Paolo, > > > > thank you for the reply. > > Probably i`m missing something in your statement. :-) > > Are you suggesting to use > > > > Fe.pbe-sp-van.UPF< > http://www.quantum-espresso.org/pseudo/1.3/UPF/Fe.pbe-sp-van.UPF> > > > > Te.pbe-rrkj.UPF< > http://www.quantum-espresso.org/pseudo/1.3/UPF/Te.pbe-rrkj.UPF> > > Se.pbe-van.UPF< > http://www.quantum-espresso.org/pseudo/1.3/UPF/Se.pbe-van.UPF> > > > > pseudopotential files evenif there are belonging to different types? > > > > cheers, > > > > Gianluca > > > > On Mon, Jun 21, 2010 at 9:59 AM, Paolo Giannozzi >wrote: > > > > > >> On Monday 21 June 2010 08:04, Gianluca Giovannetti wrote: > >> > >> > >>> i would appreciate much more to have Te Vanderbilt ultrasoft > >>> pseudopotential. > >>> > >> why? the big advantage of ultrasoft PPs is to require a much > >> smaller cutoff. In the case of Fe-Te-Se systems, Fe is by far > >> the hardest element. The cutoff needed for ultrasoft Fe might > >> well be sufficient for norm-conserving Te (and Se as well). > >> > >> P. > >> -- > >> Paolo Giannozzi, Democritos and Udine University > >> _______________________________________________ > >> 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 > > > > _______________________________________________ > 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/20100621/4fc71b42/attachment-0001.htm From kazempoor2000 at yahoo.com Mon Jun 21 14:08:10 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 21 Jun 2010 05:08:10 -0700 (PDT) Subject: [Pw_forum] elestic constant for Hexagonal Message-ID: <653496.86681.qm@web114410.mail.gq1.yahoo.com> Dear All Has anyone suitable reference about elastic constant matrix for Hexagonal lattice . In principle does this elastic constants differ in each Hexagonal shape crystals?( I mean for example between NiAs-type material that has Hexagonal lattice and? HCP lattice )? . Another question: is any reffernce about how to connect the elestic constant of Hexagonal to phonon frequency? 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/20100621/dc4e773a/attachment.htm From nnlinh at sissa.it Mon Jun 21 15:37:05 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 21 Jun 2010 15:37:05 +0200 Subject: [Pw_forum] offset In-Reply-To: <817903.31172.qm@web32906.mail.mud.yahoo.com> References: <817903.31172.qm@web32906.mail.mud.yahoo.com> Message-ID: <4C1F6B01.5080607@sissa.it> I think in this question you can figure it out by yourself. Hint: with offset of kpoint, in your case, you can increase the number of k points in Brillouin Zone. And the calculation for some quantities, such as Li absorption energy, will approach a convergence if the number of k points is increased. Good luck, Linh raheleh vaziri wrote: > > Dear all, > > > > I have two input files. The difference between these input files is > offset. Which of them is the best? Please find the attached input files. > > I am pleased if you could tell me the criterion of the determination > of offset. > > > > Thanks in advance. > > > > &CONTROL > > calculation ="scf", > > pseudo_dir = "./", > > outdir = "./", > > prefix = "2", > > / > > &SYSTEM > > ibrav= 4, > > celldm(1) = 13.9452, > > celldm(3) = 0.50220, > > nat = 21, > > ntyp= 2 , > > ecutwfc = 25.0, > > ecutrho = 105.0, > > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05, > > / > > &electrons > > diagonalization='cg', > > conv_thr = 1.0e-7, > > mixing_beta = 0.5, > > / > > ATOMIC_SPECIES > > C 12.00 C.pw91-van_ak.UPF > > Li 6.914 Li.pw91-s-van_ak.UPF > > ATOMIC_POSITIONS {angstrom} > > C -2.31375055 5.60380930 1.97749928 > > C 2.60873529 5.59894992 1.97827588 > > C 1.37111491 4.88605088 1.98071055 > > C 0.14749316 5.60138230 1.98026831 > > C -1.09012567 4.88849231 1.98354393 > > C -1.08523445 3.47114506 1.99210730 > > C 3.83236102 4.88362824 1.98354902 > > C 3.83725009 3.46629018 1.99363246 > > C 2.59963288 2.75339819 1.99851730 > > C 1.37600716 3.46871987 1.99324416 > > C 0.13838997 2.75582789 1.99812899 > > C 0.14327905 1.33848981 2.00821243 > > C 5.06087580 2.75096849 1.99890559 > > C 5.06576489 1.33363043 2.00898904 > > C 3.82814767 0.62073845 2.01387388 > > C 2.60452196 1.33606013 2.00860075 > > C 1.36690476 0.62316813 2.01348557 > > C 6.28939060 0.61830875 2.01426218 > > Li 1.35277313 6.31968764 0.12525022 > > Li -2.31676697 4.21513012 0.13346760 > > Li 1.35260170 2.08833760 0.15666888 > > K_POINTS {automatic} > > 2 2 5 0 0 0 > > Or > > K_POINTS {automatic} > > 2 2 5 1 1 1 > > > > Mahkameh Vaziri > > physical chemistry department > > K.N.Toosi university of technology,Tehran,Iran. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From gianluca.giovannetti at gmail.com Mon Jun 21 16:12:47 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Mon, 21 Jun 2010 16:12:47 +0200 Subject: [Pw_forum] occupancies of density matrix in LDA+U vs output polarization in Lowdin Charges Message-ID: Dear All, i have a question for you. I made the following self-consistent calculation: ------------------------------------------------------------- FeSe &control calculation = 'scf' restart_mode = 'from_scratch' prefix = 'fese' tprnfor = .true. pseudo_dir = './' outdir = './' iprint = 2 / &system ibrav = 8 celldm(1) = 10.0852834932257 celldm(2) = 1.00000000000000 celldm(3) = 1.03521095322306 nat = 8 ntyp = 5 ecutwfc = 35.0 ecutrho = 350.0 nbnd = 120 occupations = 'smearing' smearing = 'methfessel-paxton' degauss = 0.01 nspin = 2 starting_magnetization(1) = -1.0 starting_magnetization(2) = 1.0 starting_magnetization(3) = -1.0 starting_magnetization(4) = 1.0 starting_magnetization(5) = 0.0 lda_plus_u =.true. lda_plus_u =.true. Hubbard_U(1) = 1.d-8 Hubbard_U(2) = 1.d-8 Hubbard_U(3) = 1.d-8 Hubbard_U(4) = 1.d-8 Hubbard_alpha(1) = 1.d-8 Hubbard_alpha(2) = 1.d-8 Hubbard_alpha(3) = 1.d-8 Hubbard_alpha(4) = 1.d-8 / &electrons conv_thr = 1.0d-8 diagonalization = 'cg' / ATOMIC_SPECIES Fe1 55.845 Fe.pbe-sp-van.UPF Fe2 55.845 Fe.pbe-sp-van.UPF Fe3 55.845 Fe.pbe-sp-van.UPF Fe4 55.845 Fe.pbe-sp-van.UPF Se 78.96 Se.pbe-van.UPF ATOMIC_POSITIONS { crystal } Fe1 0.00000000 0.50000000 0.00000000 Fe2 1.00000000 0.00000000 0.00000000 Fe3 0.50000000 0.50000000 0.00000000 Fe4 0.50000000 0.00000000 0.00000000 Se 0.24999979 0.74999981 0.73480000 Se 0.75000021 0.74999981 0.26520000 Se 0.75000021 0.25000019 0.73480000 Se 0.24999979 0.25000019 0.26520000 K_POINTS {automatic} 10 10 8 0 0 0 ------------------------------------------------------------- Calculations are fine. In the output i can find at the last electronic iteration: atom 4 spin 1 eigenvalues: 0.9283366 0.9383877 0.9483978 0.9712519 0.9740784 eigenvectors 1 -0.1720270 0.0000000 0.0000000 -0.9850922 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 -1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 0.0000000 -1.0000000 5 -0.9850922 0.0000000 0.0000000 0.1720270 0.0000000 occupations 0.973 0.000 0.000 -0.008 0.000 0.000 0.938 0.000 0.000 0.000 0.000 0.000 0.948 0.000 0.000 -0.008 0.000 0.000 0.930 0.000 0.000 0.000 0.000 0.000 0.971 atom 4 spin 2 eigenvalues: 0.3553238 0.3753074 0.4625234 0.5670451 0.6892263 eigenvectors 1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 2 0.0000000 -1.0000000 0.0000000 0.0000000 0.0000000 3 0.7516066 0.0000000 0.0000000 0.6596117 0.0000000 4 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 5 0.6596117 0.0000000 0.0000000 -0.7516066 0.0000000 occupations 0.561 0.000 0.000 -0.112 0.000 0.000 0.375 0.000 0.000 0.000 0.000 0.000 0.567 0.000 0.000 -0.112 0.000 0.000 0.591 0.000 0.000 0.000 0.000 0.000 0.355 nsum = 28.8394618 If i sum up the eigenvalues of spin 1 i get: 4.7604524 If i sum up the eigenvalues of spin 2 i get: 2.449426. The difference is: 2.3110264. This difference is the polarization at Fe sites. Then i can use projwfc.x to calculate the polarization at each atom. I get in output file: Atom # 4: total charge = 16.3558, s = 2.3950, p = 7.2026, d = 6.7582, spin up = 9.4347, s = 1.2029, p = 3.6081, d = 4.6237, spin down = 6.9211, s = 1.1921, p = 3.5945, d = 2.1345, polarization = 2.5136, s = 0.0108, p = 0.0135, d = 2.4892, Now: 2.3110264 is different from 2.5136. Can someone explain me this difference? :-) Is this due to the broadening of DOS? Is it correct to consider numbers coming from eigenvalues of density matrix of LDA+U (calculated with U=0)? In this latter case if my system of reference is correct they are solved respect to l=1,2,3,4,5. :-) i thank you in advance. cheers, Gianluca Giovannetti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/a5df5ad7/attachment.htm From max.n.popov at gmail.com Mon Jun 21 16:24:15 2010 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Mon, 21 Jun 2010 16:24:15 +0200 Subject: [Pw_forum] elestic constant for Hexagonal In-Reply-To: <653496.86681.qm@web114410.mail.gq1.yahoo.com> References: <653496.86681.qm@web114410.mail.gq1.yahoo.com> Message-ID: Dear Ali, here is a great book on tensorial properties including elasticity: J.F. Nye, Physical Properties of Crystals, Clarendon Press, Oxford, 1998. It includes forms of elastic matrices for all possible crystal systems. -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. 2010/6/21 ali kazempour > Dear All > Has anyone suitable reference about elastic constant matrix for Hexagonal > lattice . > In principle does this elastic constants differ in each Hexagonal shape > crystals?( I mean for example between NiAs-type material that has > Hexagonal lattice and HCP lattice ) . > Another question: is any reffernce about how to connect the elestic > constant of Hexagonal to phonon frequency? > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/73e5430f/attachment.htm From dmitry at korotin.name Mon Jun 21 17:09:13 2010 From: dmitry at korotin.name (Dmitry Korotin) Date: Mon, 21 Jun 2010 21:09:13 +0600 Subject: [Pw_forum] occupancies of density matrix in LDA+U vs output polarization in Lowdin Charges In-Reply-To: References: Message-ID: Dear Gianluca, as I remember, in projwfc.x atomic states are orthogonalized and normalized in pw.x atomic states are used as in PP try to set U_projection_type='ortho-atomic' in the input file. 2010/6/21 Gianluca Giovannetti : > Dear All, > > i have a question for you. > > I made the following self-consistent calculation: > > ------------------------------------------------------------- > FeSe > ?&control > ??? calculation???? =? 'scf' > ??? restart_mode??? =? 'from_scratch' > ??? prefix????????? =? 'fese' > ??? tprnfor???????? =? .true. > ??? pseudo_dir????? =? './' > ??? outdir????????? =? './' > ??? iprint????????? =?? 2 > / > ?&system > ??? ibrav?????????? =? 8 > ??? celldm(1)?????? =? 10.0852834932257 > ??? celldm(2)?????? =? 1.00000000000000 > ??? celldm(3)?????? =? 1.03521095322306 > ??? nat???????????? =? 8 > ??? ntyp??????????? =? 5 > ??? ecutwfc???????? =? 35.0 > ??? ecutrho???????? =? 350.0 > ??? nbnd??????????? =? 120 > ??? occupations???? =? 'smearing' > ??? smearing??????? =? 'methfessel-paxton' > ??? degauss???????? =? 0.01 > ??? nspin = 2 > ??? starting_magnetization(1) = -1.0 > ??? starting_magnetization(2) = 1.0 > ??? starting_magnetization(3) = -1.0 > ??? starting_magnetization(4) = 1.0 > ??? starting_magnetization(5) =? 0.0 > ??? lda_plus_u????? =.true. > ??? lda_plus_u????? =.true. > ??? Hubbard_U(1)??? =? 1.d-8 > ??? Hubbard_U(2)??? =? 1.d-8 > ??? Hubbard_U(3)??? =? 1.d-8 > ??? Hubbard_U(4)??? =? 1.d-8 > ??? Hubbard_alpha(1) = 1.d-8 > ??? Hubbard_alpha(2) = 1.d-8 > ??? Hubbard_alpha(3) = 1.d-8 > ??? Hubbard_alpha(4) = 1.d-8 > / > ?&electrons > ??? conv_thr??????? =?? 1.0d-8 > ??? diagonalization =? 'cg' > / > ATOMIC_SPECIES > ?Fe1 55.845?? Fe.pbe-sp-van.UPF > ?Fe2 55.845?? Fe.pbe-sp-van.UPF > ?Fe3 55.845?? Fe.pbe-sp-van.UPF > ?Fe4 55.845?? Fe.pbe-sp-van.UPF > ?Se 78.96??? Se.pbe-van.UPF > ATOMIC_POSITIONS { crystal } > Fe1?? 0.00000000? 0.50000000? 0.00000000 > Fe2?? 1.00000000? 0.00000000? 0.00000000 > Fe3?? 0.50000000? 0.50000000? 0.00000000 > Fe4?? 0.50000000? 0.00000000? 0.00000000 > Se?? 0.24999979? 0.74999981? 0.73480000 > Se?? 0.75000021? 0.74999981? 0.26520000 > Se?? 0.75000021? 0.25000019? 0.73480000 > Se?? 0.24999979? 0.25000019? 0.26520000 > K_POINTS {automatic} > 10 10 8 0 0 0 > > ------------------------------------------------------------- > Calculations are fine. > In the output i can find at the last electronic iteration: > > atom? 4? spin? 1 > eigenvalues:? 0.9283366 0.9383877 0.9483978 0.9712519 0.9740784 > ?eigenvectors > ?1? -0.1720270? 0.0000000? 0.0000000 -0.9850922? 0.0000000 > ?2?? 0.0000000? 1.0000000? 0.0000000? 0.0000000? 0.0000000 > ?3?? 0.0000000? 0.0000000 -1.0000000? 0.0000000? 0.0000000 > ?4?? 0.0000000? 0.0000000? 0.0000000? 0.0000000 -1.0000000 > ?5? -0.9850922? 0.0000000? 0.0000000? 0.1720270? 0.0000000 > ?occupations > ?0.973? 0.000? 0.000 -0.008? 0.000 > ?0.000? 0.938? 0.000? 0.000? 0.000 > ?0.000? 0.000? 0.948? 0.000? 0.000 > -0.008? 0.000? 0.000? 0.930? 0.000 > ?0.000? 0.000? 0.000? 0.000? 0.971 > atom? 4? spin? 2 > eigenvalues:? 0.3553238 0.3753074 0.4625234 0.5670451 0.6892263 > ?eigenvectors > ?1?? 0.0000000? 0.0000000? 0.0000000? 0.0000000? 1.0000000 > ?2?? 0.0000000 -1.0000000? 0.0000000? 0.0000000? 0.0000000 > ?3?? 0.7516066? 0.0000000? 0.0000000? 0.6596117? 0.0000000 > ?4?? 0.0000000? 0.0000000? 1.0000000? 0.0000000? 0.0000000 > ?5?? 0.6596117? 0.0000000? 0.0000000 -0.7516066? 0.0000000 > ?occupations > ?0.561? 0.000? 0.000 -0.112? 0.000 > ?0.000? 0.375? 0.000? 0.000? 0.000 > ?0.000? 0.000? 0.567? 0.000? 0.000 > -0.112? 0.000? 0.000? 0.591? 0.000 > ?0.000? 0.000? 0.000? 0.000? 0.355 > nsum =? 28.8394618 > > If i sum up the eigenvalues of spin 1 i get: 4.7604524 > If i sum up the eigenvalues of spin 2 i get: 2.449426. > The difference is: 2.3110264. > This difference is the polarization at Fe sites. > Then i can use projwfc.x to calculate the polarization at each atom. > I get in output file: > > ???? Atom #?? 4: total charge =? 16.3558, s =? 2.3950, p =? 7.2026, d = > 6.7582, > ???????????????? spin up????? =?? 9.4347, s =? 1.2029, p =? 3.6081, d = > 4.6237, > ???????????????? spin down??? =?? 6.9211, s =? 1.1921, p =? 3.5945, d = > 2.1345, > ???????????????? polarization =?? 2.5136, s =? 0.0108, p =? 0.0135, d = > 2.4892, > > Now: 2.3110264 is different from 2.5136. > > Can someone explain me this difference? :-) > Is this due to the broadening of DOS? > Is it correct to consider numbers coming from eigenvalues of density matrix > of LDA+U (calculated with U=0)? > In this latter case if my system of reference is correct they are solved > respect to l=1,2,3,4,5. :-) > > i thank you in advance. > > cheers, > > Gianluca Giovannetti > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best regards, Dmitry Korotin Ph. D. Student, Institute of Metal Physics S. Kovalevskaya, 18 620041 Ekaterinburg GSP-170 Russia From baroni at sissa.it Mon Jun 21 18:47:57 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 21 Jun 2010 18:47:57 +0200 Subject: [Pw_forum] GWW for metal In-Reply-To: <885891.79828.qm@web114406.mail.gq1.yahoo.com> References: <885891.79828.qm@web114406.mail.gq1.yahoo.com> Message-ID: <738DE8C9-485C-49AF-95EB-4BFD13255018@sissa.it> I am a bit confused about the names of the oces. in any case. the number of empty states is always important in GW calculations. recent implementations of GW in QE (I do not know how they are called, GWW, or maybe GWL) use implicit methods that sum over all of the empty states. when emty states are explicitly summed, the number of them is never a god measure of the quality of the calculation. the energy cutoff below which empty states are included in the sum should be used instead, IMHO. SB On Jun 21, 2010, at 9:47 AM, ali kazempour wrote: > Dear Stefano > Thanks for reply. I have another question: > In GW calculation the number of empty states is important, But as I found in GWW It is independent of empty states Unlike SAX( that the nbnd is 4*valence band)? Am I right? > Thanks > > 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 > > --- On Sun, 6/20/10, Stefano Baroni wrote: > > From: Stefano Baroni > Subject: Re: [Pw_forum] GWW for metal > To: "PWSCF Forum" > Date: Sunday, June 20, 2010, 11:52 PM > > NO - SB > > On Jun 21, 2010, at 8:00 AM, ali kazempour wrote: > >> Dear all >> Can GWW be used for obtaining QP spectra in metals or unpaired states? >> 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 > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > 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/20100621/8616a2a5/attachment.htm From chengyu.young at gmail.com Tue Jun 22 00:02:58 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 21 Jun 2010 18:02:58 -0400 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: <4C1B1950.3040000@mit.edu> References: <4C1B1950.3040000@mit.edu> Message-ID: Dear Professor and everyone, I have successfully run the scf calculation for a (6,6) cnt, and get converged. Thanks for all your advice. Now my boss want me to add a copper atom in it, and do more calculations. I added one, but the copper atom cannot show in xcrysden, although again show in .xyz files. I don't know what the problem is , and I don't know if my script is right for a cnt+ copper calculation, may anyone have a look at it?At least I need to find the copper atom out first. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , prefix = 'cnt' , / &SYSTEM ibrav = 6, celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 25, ntyp = 2, ecutwfc = 75 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 Cu 0 0 0 K_POINTS automatic 1 1 5 0 0 0 Best regards. Sincerely, Chengyu Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/3068ddac/attachment.htm From lfhuang at theory.issp.ac.cn Tue Jun 22 02:37:54 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 22 Jun 2010 8:37:54 +0800 Subject: [Pw_forum] =?utf-8?q?occupancies_of_density_matrix_in_LDA+U_vs_ou?= =?utf-8?q?tput_polarization_in_Lowdin_Charges?= Message-ID: <20100622003754.26859.qmail@ms.hfcas.ac.cn> Dear G. Giovannetti: The small numerical difference between the two methods by you is reasonable and allowable because: (1) The Lowdin population analysis is used in PWSCF; (2) There may be some effect from the hybridization of orbitals. (Partial DOS maybe helpful.) In my opinion, the difference is so small that it can be deemed that the magnetic moment is localized at the Fe site (as you think). Best Wishes Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) 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/20100622/d32e2a7c/attachment-0001.htm From usagi at alumni.rice.edu Tue Jun 22 05:19:43 2010 From: usagi at alumni.rice.edu (Bryan M. Wong) Date: Mon, 21 Jun 2010 20:19:43 -0700 Subject: [Pw_forum] problem with vc-relax and spin-polarization Message-ID: Hi, I seem to have a problem doing "vc-relax" with the "starting_magnetization" initialization turned on. I can always do a regular "relax" with the starting_magnetization guess, and the structure will relax with a magnetic state constrained to my *fixed* unit cell dimensions. However, when I do a *vc-relax* with starting_magnetization set to any non-zero value, the 2nd step in the cell relaxation always reverts to the spin-unpolarized case (and the optimization will continue with the spin-unpolarized case). I have attached an example of this behavior for a simple graphene nanoribbon. After the first step, the nanoribbon is magnetic and nonzero, but the 2nd step reverts back to a non-magnetic initial condition. Is there any way around this (without constraining the magnetization to a fixed value for all steps)? Thanks, Bryan &CONTROL calculation = 'vc-relax' , etot_conv_thr = 1.0e-4 , forc_conv_thr = 1.0e-3 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 8, celldm(1) = 4.644592221, celldm(2) = 6.70720764, celldm(3) = 4.393200375, nat = 10, ntyp = 4, ecutwfc = 60.D0 , nosym = .false. , nbnd = 28, nelec = 34, tot_charge = 0.000000, occupations = 'smearing' , degauss = 0.02 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 1.0, starting_magnetization(2) = -1.0, starting_magnetization(3) = 1.0, starting_magnetization(4) = -1.0, / &ELECTRONS conv_thr = 1.D-6 , mixing_beta = 0.7D0 , / &IONS ion_dynamics = 'bfgs' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , trust_radius_ini = 0.2D0 , / ATOMIC_SPECIES H1 1.00000 H.pbe-rrkjus.UPF C1 12.00000 C.pbe-rrkjus.UPF C2 12.00000 C.pbe-rrkjus.UPF H2 1.00000 H.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal H1 0.000000000 0.218692155 0.000000000 1 1 0 C1 0.000000000 0.284883518 0.000000000 1 1 0 C2 0.500000000 0.326062773 0.000000000 1 1 0 C1 0.500000000 0.413734370 0.000000000 1 1 0 C2 0.000000000 0.456468822 0.000000000 1 1 0 C1 0.000000000 0.543530576 0.000000000 1 1 0 C2 0.500000000 0.586265119 0.000000000 1 1 0 C1 0.500000000 0.673937250 0.000000000 1 1 0 C2 0.000000000 0.715116935 0.000000000 1 1 0 H2 0.000000000 0.781308481 0.000000000 1 1 0 K_POINTS automatic 13 1 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100621/2c9bdac6/attachment.htm From acicek at akdeniz.edu.tr Tue Jun 22 07:25:19 2010 From: acicek at akdeniz.edu.tr (Ahmet Cicek) Date: Tue, 22 Jun 2010 08:25:19 +0300 Subject: [Pw_forum] Freezing computation during geometry optimization using BFGS Message-ID: Dear all, I am carrying out geometry optimization on 6H-SiC slabs comprising 12 or 24 atoms using BFGS algorithm. However, computations freeze at some point for either LDA or GGA without any error. Since the computations freeze at the same iteration when restarted from the same configuration, I think I have a problem related to my input but not to network connection. Could anyone help me resolve this issue? Thank you very much, Ahmet Cicek Department of Physics Faculty of Arts and Sciences Akdeniz University Campus, 07058 Antalya/Turkey Phone: +90-242-3102283 Fax: +90-242-3102283 e-mail: acicek at akdeniz.edu.tr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100622/0dcccab3/attachment.htm From baroni at sissa.it Tue Jun 22 07:28:08 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 22 Jun 2010 07:28:08 +0200 Subject: [Pw_forum] Freezing computation during geometry optimization using BFGS In-Reply-To: References: Message-ID: <4F74D130-DC2E-432C-962F-9EAA1A4F20A5@sissa.it> how can anybody, without knowing what the system is, what the input is, what the output is? SB On Jun 22, 2010, at 7:25 AM, Ahmet Cicek wrote: > Dear all, > > I am carrying out geometry optimization on 6H-SiC slabs comprising 12 or 24 atoms using BFGS algorithm. However, computations freeze at some point for either LDA or GGA without any error. Since the computations freeze at the same iteration when restarted from the same configuration, I think I have a problem related to my input but not to network connection. Could anyone help me resolve this issue? > > Thank you very much, > > Ahmet Cicek > Department of Physics > Faculty of Arts and Sciences > Akdeniz University > Campus, 07058 > Antalya/Turkey > > Phone: +90-242-3102283 > Fax: +90-242-3102283 > e-mail: acicek at akdeniz.edu.tr > _______________________________________________ > 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/20100622/6df4d8ce/attachment.htm From mighfar at jncasr.ac.in Tue Jun 22 08:44:33 2010 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Tue, 22 Jun 2010 12:14:33 +0530 (IST) Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: References: <4C1B1950.3040000@mit.edu> Message-ID: <65df4eddff29baf8228091e056e7dd5c.squirrel@mercury.jncasr.ac.in> Dear Chengyu, your Cu atom is quite showing up in xcrysden! It is a Cu chain along the axis of your cnt. > Dear Professor and everyone, > I have successfully run the scf > calculation for a (6,6) cnt, and get > converged. Thanks for all your advice. Now my > boss want me to add a copper > atom in it, and do more calculations. I added > one, but the copper atom > cannot show in xcrysden, although again show in > .xyz files. I don't know > what the problem is , and I don't know if my > script is right for a cnt+ > copper calculation, may anyone have a look at > it?At least I need to find the > copper atom out first. > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > prefix = 'cnt' , > / > &SYSTEM > ibrav = 6, > celldm(1) = > 21.764541128,celldm(3)=0.213765379 > nat = 25, > ntyp = 2, > ecutwfc = 75 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > C 12.01100 C.pz-vbc.UPF > Cu 63.55 Cu.pz-d-rrkjus.UPF > > ATOMIC_POSITIONS angstrom > C 4.085165 -0.000000 -1.231010 > C 3.838021 1.399343 -1.231010 > C 3.537856 2.042582 0.000000 > C 2.624152 3.130877 0.000000 > C 2.042582 3.537856 -1.231010 > C 0.707144 4.023496 -1.231010 > C 0.000000 4.085165 0.000000 > C -1.399343 3.838021 0.000000 > C -2.042582 3.537856 -1.231010 > C -3.130877 2.624152 -1.231010 > C -3.537856 2.042582 0.000000 > C -4.023496 0.707144 0.000000 > C -4.085165 0.000000 -1.231010 > C -3.838021 -1.399343 -1.231010 > C -3.537856 -2.042582 0.000000 > C -2.624152 -3.130877 0.000000 > C -2.042582 -3.537856 -1.231010 > C -0.707144 -4.023496 -1.231010 > C -0.000000 -4.085165 0.000000 > C 1.399343 -3.838021 0.000000 > C 2.042582 -3.537856 -1.231010 > C 3.130877 -2.624152 -1.231010 > C 3.537856 -2.042582 0.000000 > C 4.023496 -0.707144 0.000000 > Cu 0 0 0 > > K_POINTS automatic > 1 1 5 0 0 0 > > > Best regards. > > Sincerely, > Chengyu Yang > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bipulrr at gmail.com Tue Jun 22 11:39:41 2010 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 22 Jun 2010 15:09:41 +0530 Subject: [Pw_forum] pressure derivative of elastic constant Message-ID: Dear PWSCF user, I want to calculate the pressure derivative of elastic constant for some of my cubic materials (ScP, ScN in NaCl phase). Please anybody tell me the procedure or refer any paper, where i get the method of calculating the pressure derivative of elastic constants (C11, C12, C44) regards -- 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/20100622/817fdc96/attachment.htm From baroni at sissa.it Tue Jun 22 13:02:31 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 22 Jun 2010 13:02:31 +0200 Subject: [Pw_forum] pressure derivative of elastic constant In-Reply-To: References: Message-ID: <164AB2EC-A8CE-48E9-9C04-F3ED5E211BB3@sissa.it> 1) Calculate C11, C12, and C44 for different volumes 2) Calculate numerically their volume derivatives 3) Use the chain rule to express the pressure derivatives in terms of the volume derivatives hope this helps - Stefano B On Jun 22, 2010, at 11:39 AM, Bipul Rakshit wrote: > Dear PWSCF user, > I want to calculate the pressure derivative of elastic constant for some of my cubic materials (ScP, ScN in NaCl phase). Please anybody tell me the procedure or refer any paper, where i get the method of calculating the pressure derivative of elastic constants (C11, C12, C44) > > > regards > > -- > Bipul Rakshit > Research Fellow, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20100622/a3630245/attachment.htm From irida at ims.demokritos.gr Tue Jun 22 12:41:10 2010 From: irida at ims.demokritos.gr (Iris Theophilou) Date: Tue, 22 Jun 2010 13:41:10 +0300 Subject: [Pw_forum] LDA+U Ti Message-ID: <201006221041.o5MAfAHJ005905@mail.ims.demokritos.gr> Dear users, I would like to perform a scf calulation for TiO2 with LDA+U and I get the following error message: psd = Ti %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from set_hubbard_l : error # 1 pseudopotential not yet inserted %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I added to set_hubbard_l.f90 subroutine "CASE( 'Ti' ) ! hubbard_l = 2 " but nothing changed. Can anyone help me with this? Thank you in advance. Iris Theophilou PhD Student National Center for Scientific Research "Demokritos" Theoretical Physics of Multielectron and Magnetic Systems Group Athens, Greece From irida at ims.demokritos.gr Tue Jun 22 12:42:14 2010 From: irida at ims.demokritos.gr (Iris Theophilou) Date: Tue, 22 Jun 2010 13:42:14 +0300 Subject: [Pw_forum] LDA+U Ti Message-ID: <201006221042.o5MAgEn1006149@mail.ims.demokritos.gr> Dear users, I would like to perform a scf calulation for TiO2 with LDA+U and I get the following error message: psd = Ti %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from set_hubbard_l : error # 1 pseudopotential not yet inserted %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I added to set_hubbard_l.f90 subroutine "CASE( 'Ti' ) ! hubbard_l = 2 " but nothing changed. Can anyone help me with this? Thank you in advance. Iris Theophilou PhD Student National Center for Scientific Research "Demokritos" Theoretical Physics of Multielectron and Magnetic Systems Group Athens, Greece From giuseppe.mattioli at mlib.ism.cnr.it Tue Jun 22 13:28:38 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 22 Jun 2010 13:28:38 +0200 Subject: [Pw_forum] LDA+U Ti In-Reply-To: <201006221042.o5MAgEn1006149@mail.ims.demokritos.gr> References: <201006221042.o5MAgEn1006149@mail.ims.demokritos.gr> Message-ID: <201006221328.38584.giuseppe.mattioli@mlib.ism.cnr.it> You must insert by hand the 'Ti' label in two files: yourespresso/PW/tabd.f90 yourespresso/PW/set_hubbard_l.f90 and recompile the code Giuseppe On Tuesday 22 June 2010 12:42:14 Iris Theophilou wrote: > Dear users, > I would like to perform a scf calulation for TiO2 with LDA+U and I get > the following error message: > psd = Ti > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% from set_hubbard_l : error # 1 > pseudopotential not yet inserted > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% > > stopping ... > I added to set_hubbard_l.f90 subroutine > "CASE( 'Ti' ) > ! > hubbard_l = 2 " > > but nothing changed. Can anyone help me with this? > Thank you in advance. > Iris Theophilou > PhD Student > National Center for Scientific Research "Demokritos" > Theoretical Physics of Multielectron and Magnetic Systems Group > Athens, > Greece > _______________________________________________ > 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: From chengyu.young at gmail.com Tue Jun 22 16:30:59 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Tue, 22 Jun 2010 10:30:59 -0400 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: <65df4eddff29baf8228091e056e7dd5c.squirrel@mercury.jncasr.ac.in> References: <4C1B1950.3040000@mit.edu> <65df4eddff29baf8228091e056e7dd5c.squirrel@mercury.jncasr.ac.in> Message-ID: Well, Dear Mighfar, What I am talking about is the new script, there are only one Cu atom in it, while the only one didn't show up under scf.in file. Thanks all the same. 2010/6/22 Mighfar Imam > Dear Chengyu, > your Cu atom is quite showing up in xcrysden! It > is a Cu chain along the axis of your cnt. > > > > > > Dear Professor and everyone, > > I have successfully run the scf > > calculation for a (6,6) cnt, and get > > converged. Thanks for all your advice. Now my > > boss want me to add a copper > > atom in it, and do more calculations. I added > > one, but the copper atom > > cannot show in xcrysden, although again show in > > .xyz files. I don't know > > what the problem is , and I don't know if my > > script is right for a cnt+ > > copper calculation, may anyone have a look at > > it?At least I need to find the > > copper atom out first. > > > > &CONTROL > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > prefix = 'cnt' , > > / > > &SYSTEM > > ibrav = 6, > > celldm(1) = > > 21.764541128,celldm(3)=0.213765379 > > nat = 25, > > ntyp = 2, > > ecutwfc = 75 , > > / > > &ELECTRONS > > conv_thr = 1.0d-8 , > > mixing_beta = 0.7 , > > / > > ATOMIC_SPECIES > > C 12.01100 C.pz-vbc.UPF > > Cu 63.55 Cu.pz-d-rrkjus.UPF > > > > ATOMIC_POSITIONS angstrom > > C 4.085165 -0.000000 -1.231010 > > C 3.838021 1.399343 -1.231010 > > C 3.537856 2.042582 0.000000 > > C 2.624152 3.130877 0.000000 > > C 2.042582 3.537856 -1.231010 > > C 0.707144 4.023496 -1.231010 > > C 0.000000 4.085165 0.000000 > > C -1.399343 3.838021 0.000000 > > C -2.042582 3.537856 -1.231010 > > C -3.130877 2.624152 -1.231010 > > C -3.537856 2.042582 0.000000 > > C -4.023496 0.707144 0.000000 > > C -4.085165 0.000000 -1.231010 > > C -3.838021 -1.399343 -1.231010 > > C -3.537856 -2.042582 0.000000 > > C -2.624152 -3.130877 0.000000 > > C -2.042582 -3.537856 -1.231010 > > C -0.707144 -4.023496 -1.231010 > > C -0.000000 -4.085165 0.000000 > > C 1.399343 -3.838021 0.000000 > > C 2.042582 -3.537856 -1.231010 > > C 3.130877 -2.624152 -1.231010 > > C 3.537856 -2.042582 0.000000 > > C 4.023496 -0.707144 0.000000 > > Cu 0 0 0 > > > > K_POINTS automatic > > 1 1 5 0 0 0 > > > > > > Best regards. > > > > Sincerely, > > Chengyu Yang > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100622/ce784fcd/attachment-0001.htm From chengyu.young at gmail.com Tue Jun 22 16:47:09 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Tue, 22 Jun 2010 10:47:09 -0400 Subject: [Pw_forum] carbon nanotube & copper chain In-Reply-To: <65df4eddff29baf8228091e056e7dd5c.squirrel@mercury.jncasr.ac.in> References: <4C1B1950.3040000@mit.edu> <65df4eddff29baf8228091e056e7dd5c.squirrel@mercury.jncasr.ac.in> Message-ID: Thanks, Mighfar, I found my mistake. uhhh, really should blame my worrying heart. I used a different script.:P Have a nice day. 2010/6/22 Mighfar Imam > Dear Chengyu, > your Cu atom is quite showing up in xcrysden! It > is a Cu chain along the axis of your cnt. > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100622/f6119425/attachment.htm From degironc at sissa.it Tue Jun 22 17:51:51 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 22 Jun 2010 17:51:51 +0200 Subject: [Pw_forum] problem with vc-relax and spin-polarization In-Reply-To: References: Message-ID: <4C20DC17.7030901@sissa.it> I repeated your calculation on my computer and vc-relax was maintaining a finite value of absolute magnetization till the end of the relaxation. double check your results and in case you can confirm it for a recent version include your output and more information on the run (parallel or serial, machine, compiler, libraries...) stefano Bryan M. Wong wrote: > Hi, > > I seem to have a problem doing "vc-relax" with the > "starting_magnetization" initialization turned on. > > I can always do a regular "relax" with the starting_magnetization > guess, and the structure will relax with a magnetic state constrained to my > *fixed* unit cell dimensions. However, when I do a *vc-relax* with > starting_magnetization set to any non-zero value, the 2nd step in the cell > relaxation always reverts to the spin-unpolarized case (and the optimization > will continue with the spin-unpolarized case). > > I have attached an example of this behavior for a simple graphene > nanoribbon. After the first step, the nanoribbon is magnetic and nonzero, > but the 2nd step reverts back to a non-magnetic initial condition. > > Is there any way around this (without constraining the magnetization to > a fixed value for all steps)? > > Thanks, > Bryan > > > > &CONTROL > calculation = 'vc-relax' , > etot_conv_thr = 1.0e-4 , > forc_conv_thr = 1.0e-3 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 8, > celldm(1) = 4.644592221, > celldm(2) = 6.70720764, > celldm(3) = 4.393200375, > nat = 10, > ntyp = 4, > ecutwfc = 60.D0 , > nosym = .false. , > nbnd = 28, > nelec = 34, > tot_charge = 0.000000, > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = 1.0, > starting_magnetization(2) = -1.0, > starting_magnetization(3) = 1.0, > starting_magnetization(4) = -1.0, > / > &ELECTRONS > conv_thr = 1.D-6 , > mixing_beta = 0.7D0 , > / > &IONS > ion_dynamics = 'bfgs' , > pot_extrapolation = 'second_order' , > wfc_extrapolation = 'second_order' , > trust_radius_ini = 0.2D0 , > / > ATOMIC_SPECIES > H1 1.00000 H.pbe-rrkjus.UPF > C1 12.00000 C.pbe-rrkjus.UPF > C2 12.00000 C.pbe-rrkjus.UPF > H2 1.00000 H.pbe-rrkjus.UPF > ATOMIC_POSITIONS crystal > H1 0.000000000 0.218692155 0.000000000 1 1 0 > C1 0.000000000 0.284883518 0.000000000 1 1 0 > C2 0.500000000 0.326062773 0.000000000 1 1 0 > C1 0.500000000 0.413734370 0.000000000 1 1 0 > C2 0.000000000 0.456468822 0.000000000 1 1 0 > C1 0.000000000 0.543530576 0.000000000 1 1 0 > C2 0.500000000 0.586265119 0.000000000 1 1 0 > C1 0.500000000 0.673937250 0.000000000 1 1 0 > C2 0.000000000 0.715116935 0.000000000 1 1 0 > H2 0.000000000 0.781308481 0.000000000 1 1 0 > K_POINTS automatic > 13 1 1 0 0 0 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From tkaloni at gmail.com Wed Jun 23 05:32:13 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Wed, 23 Jun 2010 09:17:13 +0545 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 63 In-Reply-To: References: Message-ID: Dear All, I am getting error like below, please help anyone. Sincerely T P Kaloni S N B N C B S, Kolkata Program PWSCF v.4.1.2 starts ... Today is 23Jun2010 at 8:56:40 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... bravais-lattice index = 4 lattice parameter (a_0) = 4.9000 a.u. unit-cell volume = 277.1327 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 1 number of electrons = 8.00 number of Kohn-Sham states= 4 kinetic-energy cutoff = 65.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-09 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW TPSS TPSS (1476) celldm(1)= 4.900000 celldm(2)= 0.000000 celldm(3)= 2.720000 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) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 2.720000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.577350 0.000000 ) b(2) = ( 0.000000 1.154701 0.000000 ) b(3) = ( 0.000000 0.000000 0.367647 ) PseudoPot. # 1 for C read from file C.tpss-mt.UPF Pseudo is Norm-conserving, Zval = 4.0 Generated by new atomic code, or converted to UPF format Using radial grid of 1983 points, 1 beta functions with: l(1) = 0 atomic species valence mass pseudopotential C 4.00 12.01070 C ( 1.00) Starting magnetic structure atomic species magnetization C 0.700 24 Sym.Ops. (with inversion) Cartesian axes site n. atom positions (a_0 units) 1 C tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) 2 C tau( 2) = ( 0.5000000 0.2886751 0.0000000 ) number of k points= 48 gaussian broad. (Ry)= 0.0200 ngauss = 0 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0833333 0.1443376 0.0459559), wk = 0.0277778 k( 2) = ( 0.0833333 0.1443376 0.1378676), wk = 0.0277778 k( 3) = ( 0.0833333 0.3367877 0.0459559), wk = 0.0555556 k( 4) = ( 0.0833333 0.3367877 0.1378676), wk = 0.0555556 k( 5) = ( 0.0833333 0.5292377 0.0459559), wk = 0.0555556 k( 6) = ( 0.0833333 0.5292377 0.1378676), wk = 0.0555556 k( 7) = ( 0.0833333 -0.4330127 0.0459559), wk = 0.0555556 k( 8) = ( 0.0833333 -0.4330127 0.1378676), wk = 0.0555556 k( 9) = ( 0.0833333 -0.2405626 0.0459559), wk = 0.0555556 k( 10) = ( 0.0833333 -0.2405626 0.1378676), wk = 0.0555556 k( 11) = ( 0.0833333 -0.0481125 0.0459559), wk = 0.0277778 k( 12) = ( 0.0833333 -0.0481125 0.1378676), wk = 0.0277778 k( 13) = ( 0.2500000 0.4330127 0.0459559), wk = 0.0277778 k( 14) = ( 0.2500000 0.4330127 0.1378676), wk = 0.0277778 k( 15) = ( 0.2500000 0.6254628 0.0459559), wk = 0.0555556 k( 16) = ( 0.2500000 0.6254628 0.1378676), wk = 0.0555556 k( 17) = ( 0.2500000 -0.3367877 0.0459559), wk = 0.0555556 k( 18) = ( 0.2500000 -0.3367877 0.1378676), wk = 0.0555556 k( 19) = ( 0.2500000 -0.1443376 0.0459559), wk = 0.0277778 k( 20) = ( 0.2500000 -0.1443376 0.1378676), wk = 0.0277778 k( 21) = ( 0.4166667 0.7216878 0.0459559), wk = 0.0277778 k( 22) = ( 0.4166667 0.7216878 0.1378676), wk = 0.0277778 k( 23) = ( 0.4166667 -0.2405626 0.0459559), wk = 0.0277778 k( 24) = ( 0.4166667 -0.2405626 0.1378676), wk = 0.0277778 k( 25) = ( 0.0833333 0.1443376 0.0459559), wk = 0.0277778 k( 26) = ( 0.0833333 0.1443376 0.1378676), wk = 0.0277778 k( 27) = ( 0.0833333 0.3367877 0.0459559), wk = 0.0555556 k( 28) = ( 0.0833333 0.3367877 0.1378676), wk = 0.0555556 k( 29) = ( 0.0833333 0.5292377 0.0459559), wk = 0.0555556 k( 30) = ( 0.0833333 0.5292377 0.1378676), wk = 0.0555556 k( 31) = ( 0.0833333 -0.4330127 0.0459559), wk = 0.0555556 k( 32) = ( 0.0833333 -0.4330127 0.1378676), wk = 0.0555556 k( 33) = ( 0.0833333 -0.2405626 0.0459559), wk = 0.0555556 k( 34) = ( 0.0833333 -0.2405626 0.1378676), wk = 0.0555556 k( 35) = ( 0.0833333 -0.0481125 0.0459559), wk = 0.0277778 k( 36) = ( 0.0833333 -0.0481125 0.1378676), wk = 0.0277778 k( 37) = ( 0.2500000 0.4330127 0.0459559), wk = 0.0277778 k( 38) = ( 0.2500000 0.4330127 0.1378676), wk = 0.0277778 k( 39) = ( 0.2500000 0.6254628 0.0459559), wk = 0.0555556 k( 40) = ( 0.2500000 0.6254628 0.1378676), wk = 0.0555556 k( 41) = ( 0.2500000 -0.3367877 0.0459559), wk = 0.0555556 k( 42) = ( 0.2500000 -0.3367877 0.1378676), wk = 0.0555556 k( 43) = ( 0.2500000 -0.1443376 0.0459559), wk = 0.0277778 k( 44) = ( 0.2500000 -0.1443376 0.1378676), wk = 0.0277778 k( 45) = ( 0.4166667 0.7216878 0.0459559), wk = 0.0277778 k( 46) = ( 0.4166667 0.7216878 0.1378676), wk = 0.0277778 k( 47) = ( 0.4166667 -0.2405626 0.0459559), wk = 0.0277778 k( 48) = ( 0.4166667 -0.2405626 0.1378676), wk = 0.0277778 G cutoff = 182.4541 ( 24355 G-vectors) FFT grid: ( 30, 30, 75) G cutoff = 158.1269 ( 19701 G-vectors) smooth grid: ( 25, 25, 72) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.15 Mb ( 2467, 4) NL pseudopotentials 0.08 Mb ( 2467, 2) Each V/rho on FFT grid 2.06 Mb ( 67500, 2) Each G-vector array 0.19 Mb ( 24355) G-vector shells 0.01 Mb ( 1262) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 0.60 Mb ( 2467, 16) Each subspace H/S matrix 0.00 Mb ( 16, 16) Each matrix 0.00 Mb ( 2, 4) Arrays for rho mixing 8.24 Mb ( 67500, 8) Initial potential from superposition of free atoms starting charge 7.99991, renormalised to 8.00000 Starting wfc are random total cpu time spent up to now is 4.96 secs per-process dynamical memory: 18.2 Mb Self-consistent Calculation iteration # 1 ecut= 65.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 8.2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from efermig : error # 1 internal error, cannot braket Ef %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... On Tue, Jun 22, 2010 at 8:16 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. pressure derivative of elastic constant (Bipul Rakshit) > 2. Re: pressure derivative of elastic constant (Stefano Baroni) > 3. LDA+U Ti (Iris Theophilou) > 4. LDA+U Ti (Iris Theophilou) > 5. Re: LDA+U Ti (Giuseppe Mattioli) > 6. Re: carbon nanotube & copper chain (chengyu yang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Jun 2010 15:09:41 +0530 > From: Bipul Rakshit > Subject: [Pw_forum] pressure derivative of elastic constant > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear PWSCF user, > I want to calculate the pressure derivative of elastic constant for some of > my cubic materials (ScP, ScN in NaCl phase). Please anybody tell me the > procedure or refer any paper, where i get the method of calculating the > pressure derivative of elastic constants (C11, C12, C44) > > > regards > > -- > 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/20100622/817fdc96/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Tue, 22 Jun 2010 13:02:31 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] pressure derivative of elastic constant > To: PWSCF Forum > Message-ID: <164AB2EC-A8CE-48E9-9C04-F3ED5E211BB3 at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > 1) Calculate C11, C12, and C44 for different volumes > 2) Calculate numerically their volume derivatives > 3) Use the chain rule to express the pressure derivatives in terms of the > volume derivatives > hope this helps - Stefano B > > On Jun 22, 2010, at 11:39 AM, Bipul Rakshit wrote: > > > Dear PWSCF user, > > I want to calculate the pressure derivative of elastic constant for some > of my cubic materials (ScP, ScN in NaCl phase). Please anybody tell me the > procedure or refer any paper, where i get the method of calculating the > pressure derivative of elastic constants (C11, C12, C44) > > > > > > regards > > > > -- > > Bipul Rakshit > > Research Fellow, > > S N Bose Centre for Basic Sciences, > > Salt Lake, > > Kolkata 700 098 > > India > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > 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/20100622/a3630245/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Tue, 22 Jun 2010 13:41:10 +0300 > From: "Iris Theophilou" > Subject: [Pw_forum] LDA+U Ti > To: pw_forum at pwscf.org > Message-ID: <201006221041.o5MAfAHJ005905 at mail.ims.demokritos.gr> > Content-Type: text/plain; charset=iso-8859-1 > > Dear users, > I would like to perform a scf calulation for TiO2 with LDA+U and I get > the following error message: > psd = Ti > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from set_hubbard_l : error # 1 > pseudopotential not yet inserted > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > I added to set_hubbard_l.f90 subroutine > "CASE( 'Ti' ) > ! > hubbard_l = 2 " > > but nothing changed. Can anyone help me with this? > Thank you in advance. > Iris Theophilou > PhD Student > National Center for Scientific Research "Demokritos" > Theoretical Physics of Multielectron and Magnetic Systems Group > Athens, > Greece > > > ------------------------------ > > Message: 4 > Date: Tue, 22 Jun 2010 13:42:14 +0300 > From: "Iris Theophilou" > Subject: [Pw_forum] LDA+U Ti > To: pw_forum at pwscf.org > Message-ID: <201006221042.o5MAgEn1006149 at mail.ims.demokritos.gr> > Content-Type: text/plain; charset=iso-8859-1 > > Dear users, > I would like to perform a scf calulation for TiO2 with LDA+U and I get > the following error message: > psd = Ti > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from set_hubbard_l : error # 1 > pseudopotential not yet inserted > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > I added to set_hubbard_l.f90 subroutine > "CASE( 'Ti' ) > ! > hubbard_l = 2 " > > but nothing changed. Can anyone help me with this? > Thank you in advance. > Iris Theophilou > PhD Student > National Center for Scientific Research "Demokritos" > Theoretical Physics of Multielectron and Magnetic Systems Group > Athens, > Greece > > > ------------------------------ > > Message: 5 > Date: Tue, 22 Jun 2010 13:28:38 +0200 > From: Giuseppe Mattioli > Subject: Re: [Pw_forum] LDA+U Ti > To: PWSCF Forum > Message-ID: <201006221328.38584.giuseppe.mattioli at mlib.ism.cnr.it> > Content-Type: text/plain; charset="iso-8859-1" > > You must insert by hand the 'Ti' label in two files: > > yourespresso/PW/tabd.f90 > yourespresso/PW/set_hubbard_l.f90 > > and recompile the code > > Giuseppe > > On Tuesday 22 June 2010 12:42:14 Iris Theophilou wrote: > > Dear users, > > I would like to perform a scf calulation for TiO2 with LDA+U and I get > > the following error message: > > psd = Ti > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >%%% from set_hubbard_l : error # 1 > > pseudopotential not yet inserted > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >%%% > > > > stopping ... > > I added to set_hubbard_l.f90 subroutine > > "CASE( 'Ti' ) > > ! > > hubbard_l = 2 " > > > > but nothing changed. Can anyone help me with this? > > Thank you in advance. > > Iris Theophilou > > PhD Student > > National Center for Scientific Research "Demokritos" > > Theoretical Physics of Multielectron and Magnetic Systems Group > > Athens, > > Greece > > _______________________________________________ > > 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: > > > ------------------------------ > > Message: 6 > Date: Tue, 22 Jun 2010 10:30:59 -0400 > From: chengyu yang > Subject: Re: [Pw_forum] carbon nanotube & copper chain > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Well, Dear Mighfar, > What I am talking about is the new script, there are only one Cu > atom in it, while the only one didn't show up under scf.in file. > Thanks all the same. > > > > 2010/6/22 Mighfar Imam > > > Dear Chengyu, > > your Cu atom is quite showing up in xcrysden! It > > is a Cu chain along the axis of your cnt. > > > > > > > > > > > Dear Professor and everyone, > > > I have successfully run the scf > > > calculation for a (6,6) cnt, and get > > > converged. Thanks for all your advice. Now my > > > boss want me to add a copper > > > atom in it, and do more calculations. I added > > > one, but the copper atom > > > cannot show in xcrysden, although again show in > > > .xyz files. I don't know > > > what the problem is , and I don't know if my > > > script is right for a cnt+ > > > copper calculation, may anyone have a look at > > > it?At least I need to find the > > > copper atom out first. > > > > > > &CONTROL > > > calculation = 'scf' , > > > restart_mode = 'from_scratch' , > > > prefix = 'cnt' , > > > / > > > &SYSTEM > > > ibrav = 6, > > > celldm(1) = > > > 21.764541128,celldm(3)=0.213765379 > > > nat = 25, > > > ntyp = 2, > > > ecutwfc = 75 , > > > / > > > &ELECTRONS > > > conv_thr = 1.0d-8 , > > > mixing_beta = 0.7 , > > > / > > > ATOMIC_SPECIES > > > C 12.01100 C.pz-vbc.UPF > > > Cu 63.55 Cu.pz-d-rrkjus.UPF > > > > > > ATOMIC_POSITIONS angstrom > > > C 4.085165 -0.000000 -1.231010 > > > C 3.838021 1.399343 -1.231010 > > > C 3.537856 2.042582 0.000000 > > > C 2.624152 3.130877 0.000000 > > > C 2.042582 3.537856 -1.231010 > > > C 0.707144 4.023496 -1.231010 > > > C 0.000000 4.085165 0.000000 > > > C -1.399343 3.838021 0.000000 > > > C -2.042582 3.537856 -1.231010 > > > C -3.130877 2.624152 -1.231010 > > > C -3.537856 2.042582 0.000000 > > > C -4.023496 0.707144 0.000000 > > > C -4.085165 0.000000 -1.231010 > > > C -3.838021 -1.399343 -1.231010 > > > C -3.537856 -2.042582 0.000000 > > > C -2.624152 -3.130877 0.000000 > > > C -2.042582 -3.537856 -1.231010 > > > C -0.707144 -4.023496 -1.231010 > > > C -0.000000 -4.085165 0.000000 > > > C 1.399343 -3.838021 0.000000 > > > C 2.042582 -3.537856 -1.231010 > > > C 3.130877 -2.624152 -1.231010 > > > C 3.537856 -2.042582 0.000000 > > > C 4.023496 -0.707144 0.000000 > > > Cu 0 0 0 > > > > > > K_POINTS automatic > > > 1 1 5 0 0 0 > > > > > > > > > Best regards. > > > > > > Sincerely, > > > Chengyu Yang > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100622/ce784fcd/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 36, Issue 63 > **************************************** > -- ################################### ****************************************** Thaneshwor Prashad Kaloni TWAS-BOSE FELLOW /JRF S N Bose national Centre for Basic Sciences Kolkata 700098, INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100623/aab41477/attachment-0001.htm From bipulrr at gmail.com Wed Jun 23 07:19:35 2010 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 23 Jun 2010 10:49:35 +0530 Subject: [Pw_forum] pressure derivative of elastic constant In-Reply-To: <164AB2EC-A8CE-48E9-9C04-F3ED5E211BB3@sissa.it> References: <164AB2EC-A8CE-48E9-9C04-F3ED5E211BB3@sissa.it> Message-ID: Dear Stefano, Thanks for yr kind reply. For calculating the elastic constant i am refering the following paper. S K R Patil et. al Phys. Rev. B *73*, 104118 (2006). So in this paper, they generally fit a parabola equation in terms of energy as a function of strain and thus finds the C11, C12 and C44 etc. But as u suggested to find the C11 etc at different volume, but change in volume cause the change in pressure. So the minimum of the parabola is not minimum at high pressure. So i need an equation like Murnaghan equation of state, in which the the pressure derivative is included. On Tue, Jun 22, 2010 at 4:32 PM, Stefano Baroni wrote: > 1) Calculate C11, C12, and C44 for different volumes > 2) Calculate numerically their volume derivatives > 3) Use the chain rule to express the pressure derivatives in terms of the > volume derivatives > hope this helps - Stefano B > > On Jun 22, 2010, at 11:39 AM, Bipul Rakshit wrote: > > Dear PWSCF user, > I want to calculate the pressure derivative of elastic constant for some of > my cubic materials (ScP, ScN in NaCl phase). Please anybody tell me the > procedure or refer any paper, where i get the method of calculating the > pressure derivative of elastic constants (C11, C12, C44) > > > regards > > -- > Bipul Rakshit > Research Fellow, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100623/be38bb34/attachment.htm From nnlinh at sissa.it Wed Jun 23 10:23:10 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 23 Jun 2010 10:23:10 +0200 Subject: [Pw_forum] internal error, cannot braket Ef In-Reply-To: References: Message-ID: <4C21C46E.2030107@sissa.it> Thaneshwor Kaloni wrote: > Dear All, > I am getting error like below, please help anyone. > Sincerely > T P Kaloni > S N B N C B S, Kolkata > Program PWSCF v.4.1.2 starts ... > Today is 23Jun2010 at 8:56:40 > > 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... > > > bravais-lattice index = 4 > lattice parameter (a_0) = 4.9000 a.u. > unit-cell volume = 277.1327 (a.u.)^3 > number of atoms/cell = 2 > number of atomic types = 1 > number of electrons = 8.00 > number of Kohn-Sham states= 4 > kinetic-energy cutoff = 65.0000 Ry > charge density cutoff = 300.0000 Ry > convergence threshold = 1.0E-09 > mixing beta = 0.7000 > number of iterations used = 8 plain mixing > Exchange-correlation = SLA PW TPSS TPSS (1476) > > celldm(1)= 4.900000 celldm(2)= 0.000000 celldm(3)= 2.720000 > 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) = ( -0.500000 0.866025 0.000000 ) > a(3) = ( 0.000000 0.000000 2.720000 ) > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > b(1) = ( 1.000000 0.577350 0.000000 ) > b(2) = ( 0.000000 1.154701 0.000000 ) > b(3) = ( 0.000000 0.000000 0.367647 ) > > > PseudoPot. # 1 for C read from file C.tpss-mt.UPF > Pseudo is Norm-conserving, Zval = 4.0 > Generated by new atomic code, or converted to UPF format > Using radial grid of 1983 points, 1 beta functions with: > l(1) = 0 > > atomic species valence mass pseudopotential > C 4.00 12.01070 C ( 1.00) > > Starting magnetic structure > atomic species magnetization > C 0.700 > > 24 Sym.Ops. (with inversion) > > > Cartesian axes > > site n. atom positions (a_0 units) > 1 C tau( 1) = ( 0.0000000 0.0000000 > 0.0000000 ) > 2 C tau( 2) = ( 0.5000000 0.2886751 > 0.0000000 ) > > number of k points= 48 gaussian broad. (Ry)= 0.0200 > ngauss = 0 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0833333 0.1443376 0.0459559), wk = > 0.0277778 > k( 2) = ( 0.0833333 0.1443376 0.1378676), wk = > 0.0277778 > k( 3) = ( 0.0833333 0.3367877 0.0459559), wk = > 0.0555556 > k( 4) = ( 0.0833333 0.3367877 0.1378676), wk = > 0.0555556 > k( 5) = ( 0.0833333 0.5292377 0.0459559), wk = > 0.0555556 > k( 6) = ( 0.0833333 0.5292377 0.1378676), wk = > 0.0555556 > k( 7) = ( 0.0833333 -0.4330127 0.0459559), wk = > 0.0555556 > k( 8) = ( 0.0833333 -0.4330127 0.1378676), wk = > 0.0555556 > k( 9) = ( 0.0833333 -0.2405626 0.0459559), wk = > 0.0555556 > k( 10) = ( 0.0833333 -0.2405626 0.1378676), wk = > 0.0555556 > k( 11) = ( 0.0833333 -0.0481125 0.0459559), wk = > 0.0277778 > k( 12) = ( 0.0833333 -0.0481125 0.1378676), wk = > 0.0277778 > k( 13) = ( 0.2500000 0.4330127 0.0459559), wk = > 0.0277778 > k( 14) = ( 0.2500000 0.4330127 0.1378676), wk = > 0.0277778 > k( 15) = ( 0.2500000 0.6254628 0.0459559), wk = > 0.0555556 > k( 16) = ( 0.2500000 0.6254628 0.1378676), wk = > 0.0555556 > k( 17) = ( 0.2500000 -0.3367877 0.0459559), wk = > 0.0555556 > k( 18) = ( 0.2500000 -0.3367877 0.1378676), wk = > 0.0555556 > k( 19) = ( 0.2500000 -0.1443376 0.0459559), wk = > 0.0277778 > k( 20) = ( 0.2500000 -0.1443376 0.1378676), wk = > 0.0277778 > k( 21) = ( 0.4166667 0.7216878 0.0459559), wk = > 0.0277778 > k( 22) = ( 0.4166667 0.7216878 0.1378676), wk = > 0.0277778 > k( 23) = ( 0.4166667 -0.2405626 0.0459559), wk = > 0.0277778 > k( 24) = ( 0.4166667 -0.2405626 0.1378676), wk = > 0.0277778 > k( 25) = ( 0.0833333 0.1443376 0.0459559), wk = > 0.0277778 > k( 26) = ( 0.0833333 0.1443376 0.1378676), wk = > 0.0277778 > k( 27) = ( 0.0833333 0.3367877 0.0459559), wk = > 0.0555556 > k( 28) = ( 0.0833333 0.3367877 0.1378676), wk = > 0.0555556 > k( 29) = ( 0.0833333 0.5292377 0.0459559), wk = > 0.0555556 > k( 30) = ( 0.0833333 0.5292377 0.1378676), wk = > 0.0555556 > k( 31) = ( 0.0833333 -0.4330127 0.0459559), wk = > 0.0555556 > k( 32) = ( 0.0833333 -0.4330127 0.1378676), wk = > 0.0555556 > k( 33) = ( 0.0833333 -0.2405626 0.0459559), wk = > 0.0555556 > k( 34) = ( 0.0833333 -0.2405626 0.1378676), wk = > 0.0555556 > k( 35) = ( 0.0833333 -0.0481125 0.0459559), wk = > 0.0277778 > k( 36) = ( 0.0833333 -0.0481125 0.1378676), wk = > 0.0277778 > k( 37) = ( 0.2500000 0.4330127 0.0459559), wk = > 0.0277778 > k( 38) = ( 0.2500000 0.4330127 0.1378676), wk = > 0.0277778 > k( 39) = ( 0.2500000 0.6254628 0.0459559), wk = > 0.0555556 > k( 40) = ( 0.2500000 0.6254628 0.1378676), wk = > 0.0555556 > k( 41) = ( 0.2500000 -0.3367877 0.0459559), wk = > 0.0555556 > k( 42) = ( 0.2500000 -0.3367877 0.1378676), wk = > 0.0555556 > k( 43) = ( 0.2500000 -0.1443376 0.0459559), wk = > 0.0277778 > k( 44) = ( 0.2500000 -0.1443376 0.1378676), wk = > 0.0277778 > k( 45) = ( 0.4166667 0.7216878 0.0459559), wk = > 0.0277778 > k( 46) = ( 0.4166667 0.7216878 0.1378676), wk = > 0.0277778 > k( 47) = ( 0.4166667 -0.2405626 0.0459559), wk = > 0.0277778 > k( 48) = ( 0.4166667 -0.2405626 0.1378676), wk = > 0.0277778 > > G cutoff = 182.4541 ( 24355 G-vectors) FFT grid: ( 30, 30, 75) > G cutoff = 158.1269 ( 19701 G-vectors) smooth grid: ( 25, 25, 72) > > Largest allocated arrays est. size (Mb) dimensions > Kohn-Sham Wavefunctions 0.15 Mb ( 2467, 4) > NL pseudopotentials 0.08 Mb ( 2467, 2) > Each V/rho on FFT grid 2.06 Mb ( 67500, 2) > Each G-vector array 0.19 Mb ( 24355) > G-vector shells 0.01 Mb ( 1262) > Largest temporary arrays est. size (Mb) dimensions > Auxiliary wavefunctions 0.60 Mb ( 2467, 16) > Each subspace H/S matrix 0.00 Mb ( 16, 16) > Each matrix 0.00 Mb ( 2, 4) > Arrays for rho mixing 8.24 Mb ( 67500, 8) > > Initial potential from superposition of free atoms > > starting charge 7.99991, renormalised to 8.00000 > Starting wfc are random > > total cpu time spent up to now is 4.96 secs > > per-process dynamical memory: 18.2 Mb > > Self-consistent Calculation > > iteration # 1 ecut= 65.00 Ry beta=0.70 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 8.2 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from efermig : error # 1 > internal error, cannot braket Ef > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... Hardly to say anythings about problem if you don't send a input file. Linh P/s: As reminded many times that you should not post the question by replying with many questions in Digest. > > > > -- > ################################### > ****************************************** > Thaneshwor Prashad Kaloni > TWAS-BOSE FELLOW /JRF > S N Bose national Centre for Basic Sciences > Kolkata 700098, > INDIA > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From giannozz at democritos.it Wed Jun 23 10:31:43 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Jun 2010 10:31:43 +0200 Subject: [Pw_forum] Bad input (and bad manners) Was: Pw_forum Digest In-Reply-To: References: Message-ID: <4C21C66F.8020808@democritos.it> First of all: - Please USE THE "Subject:" LINE TO SPECIFY THE SUBJECT OF YOUR POST. This is the N-th time that you are requested to do so. - please DO NOT POST ONLY IRRELEVANT INFORMATION such as quoted lines of a digest. If you specify a broadening, you should also specify a number of bands larger than the strict minimum for an insulator. When in doubt, do not specify the number of bands: the code will choose an appropriate value. "nbnd=4" in your case is not an appropriate value, since you also specified a broadening. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From amit99266 at rediffmail.com Wed Jun 23 14:27:21 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 23 Jun 2010 12:27:21 -0000 Subject: [Pw_forum] =?utf-8?q?About_phonon_lifetimes?= Message-ID: <20100623122721.8135.qmail@f4mail-235-129.rediffmail.com> Dear All Can anyone tell me about how to calculate the phonon lifetimes using QE? (Please forgive me for my ignorance.) Warm Regards Amit N. Harode CRL INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100623/d1c73f5a/attachment.htm From nnlinh at sissa.it Wed Jun 23 15:06:17 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 23 Jun 2010 15:06:17 +0200 Subject: [Pw_forum] About phonon lifetimes In-Reply-To: <20100623122721.8135.qmail@f4mail-235-129.rediffmail.com> References: <20100623122721.8135.qmail@f4mail-235-129.rediffmail.com> Message-ID: <4C2206C9.9070300@sissa.it> Someday before, a question about phonon lifetime was posted. Let refer that discussion. Linh Yamit wrote: > Dear All > > Can anyone tell me about how to calculate the phonon lifetimes using > QE? (Please forgive me for my ignorance.) > > Warm Regards > Amit N. Harode > CRL INDIA > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From quantumdft at gmail.com Wed Jun 23 18:08:35 2010 From: quantumdft at gmail.com (vega lew) Date: Thu, 24 Jun 2010 00:08:35 +0800 Subject: [Pw_forum] Do you think QE could get a considerable improved performance on AMD 6100 series CPUs Message-ID: Dear all, We are considering a plan on building a small cluster (about 6 servers) for QE. New version of AMD Opteron labeled with 6100 comes into market earlier in this year. It is said the bandwidth of memory and number of cores of CPU are improved greatly in the new architecture of AMD. We just wondering whether QE could get a considerable improved performance on AMD 6100 series CPUs. Is Opteron 6100 series with 12 cores or 8 cores CPU more suitable for QE than intel XEON 5600 Series? Do you think 2.67G memory per core is feasible? We also want to use InfiniBand to connect servers? Do you think the infiniband with 20G bandwidth is suitable for the parallel computation task of QE? or we should purchase more advanced infiniband with 40G bandwith and a small improved delay of network. Is there any benchmark on the performance of QE on Opteron CPUs? 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/20100624/407a1d70/attachment.htm From chengyu.young at gmail.com Wed Jun 23 19:36:53 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Wed, 23 Jun 2010 13:36:53 -0400 Subject: [Pw_forum] plotrho.x error Message-ID: Hello everyone, I am now running the plotrho.x, and found the same problem. When I input the .rho.dat file, and then I answered the interactive questions like in the example 5, I found nothing came out. In fact, there was no run at all. When I checked the status, it said At line 114 of file plotrho.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 3 in list input And the item 3 is a zero(0.000000). I cannot figure out why, as a matter of fact, I found this when I try to run the example 5. No result came out neither. I cannot find the answer from beforehand discussion, so hope anyone could help me.Thanks in advance. Input file > cntcu.rho.dat r0 : 0.0000 0.0000 0.0000 tau1 : 1.0000 1.0000 0.0000 tau2 : 0.0000 0.0000 1.0000 read 25 atomic positions output file > cntcu.rho.ps Read 56 * 40 grid Logarithmic scale (y/n)? > Bounds: 0.000002 1.372000 min, max, # of levels > 0.000000 1.38000 Then dead. Chengyu Yang MSE PhD student -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100623/cfbc30b2/attachment.htm From degironc at sissa.it Wed Jun 23 19:47:16 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 23 Jun 2010 19:47:16 +0200 Subject: [Pw_forum] plotrho.x error In-Reply-To: References: Message-ID: <4C2248A4.6020703@sissa.it> chengyu yang wrote: > min, max, # of levels > 0.000000 1.38000 > > the code is asking THREE data min, max AND number of levels ... if you provide only two data the code will patiently waits stefano > Then dead. > > Chengyu Yang > MSE PhD student > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From chengyu.young at gmail.com Wed Jun 23 19:57:31 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Wed, 23 Jun 2010 13:57:31 -0400 Subject: [Pw_forum] plotrho.x error In-Reply-To: <4C2248A4.6020703@sissa.it> References: <4C2248A4.6020703@sissa.it> Message-ID: Dear Stefano, Thanks. You are certainly right. And then what's the meaning of min,max and number of levels? I just set them arbitrarily. Chengyu Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100623/268c1fda/attachment-0001.htm From giannozz at democritos.it Wed Jun 23 20:14:29 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Jun 2010 20:14:29 +0200 Subject: [Pw_forum] plotrho.x error In-Reply-To: References: <4C2248A4.6020703@sissa.it> Message-ID: <773BDE7B-9876-4367-A7B9-6DCE9528BF1B@democritos.it> On Jun 23, 2010, at 19:57 , chengyu yang wrote: > what's the meaning of min,max and number of levels? if you want a contour plot, you need to specify the number of contour levels and their values. If you specify min,max,N, the code will plot N contours at z_i = min + i*(max-min)/(N-1), i=0,N-1 (or whatever is appropriate for logarithmic scale). The code prints the minimum and maximum value of the quantity to be plotted, in the line: Bounds: 0.000002 1.372000 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 chengyu.young at gmail.com Wed Jun 23 20:16:04 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Wed, 23 Jun 2010 14:16:04 -0400 Subject: [Pw_forum] plotrho.x error In-Reply-To: <773BDE7B-9876-4367-A7B9-6DCE9528BF1B@democritos.it> References: <4C2248A4.6020703@sissa.it> <773BDE7B-9876-4367-A7B9-6DCE9528BF1B@democritos.it> Message-ID: Thanks. Learned much from you. :) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100623/a56335cd/attachment.htm From vovi47 at yahoo.com Wed Jun 23 21:12:02 2010 From: vovi47 at yahoo.com (Vi Vo) Date: Wed, 23 Jun 2010 12:12:02 -0700 (PDT) Subject: [Pw_forum] B3LYP In-Reply-To: <201006191352.21615.giuseppe.mattioli@mlib.ism.cnr.it> References: <55003.88958.qm@web114507.mail.gq1.yahoo.com> <201006191352.21615.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <572303.79859.qm@web114517.mail.gq1.yahoo.com> Dear Giuseppe, Thank you very much! Vi ________________________________ From: Giuseppe Mattioli To: PWSCF Forum Sent: Sat, June 19, 2010 4:52:21 AM Subject: Re: [Pw_forum] B3LYP Dear Vi Vo > Is B3LYP implemented in QE 4.2? It is, but first have a look at this file /yourespresso-4.2/examples/EXX_example/README having in mind that hybrid functionals are not still straightforwardly implemented in QE... Yours Giuseppe On Saturday 19 June 2010 01:35:39 Vi Vo wrote: > Dear PWSCF Users, > > Is B3LYP implemented in QE 4.2? > > Thank you, > > Vi Vo > Chemical Engineering Department > University of Houston -- ******************************************************** - 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: _______________________________________________ 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/20100623/e8b5f855/attachment.htm From alex968873 at yahoo.com.cn Thu Jun 24 04:40:44 2010 From: alex968873 at yahoo.com.cn (=?gb2312?B?wO6x8w==?=) Date: Thu, 24 Jun 2010 10:40:44 +0800 (CST) Subject: [Pw_forum] Is there PBE or LDA UPF for Rb element? Message-ID: <321888.16879.qm@web15103.mail.cnb.yahoo.com> Dear all, I need a UPF using PBE or LDA Exchange-Correlation for Rb element in my calculation. But I can't find Rb...UPF file in pseudo folder or QE website. I try to convert the FHI file to UPF but not very sure about that. So who can provide it to me? Or give me some suggestion? Thanks a lot! ************************** Li Bin Department of Physics, Southeast University, PRC. *********************************************** From amit99266 at rediffmail.com Thu Jun 24 05:38:12 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 24 Jun 2010 03:38:12 -0000 Subject: [Pw_forum] =?utf-8?q?_About_phonon_lifetimes?= In-Reply-To: <4C2206C9.9070300@sissa.it> Message-ID: <1277298376.S.5483.10090.F.H.Tk5nb2MgTGluaCBOZ3V5ZW4AUmU6IFtQd19mb3J1bV0gQWJvdXQgcGhvbm9uIGxpZmV0aW1lcw__.f4-235-215.1277350691.7871@webmail.rediffmail.com> Dear Mr Nguyen Ngoc Linh Thank you for your reply !(may be a blind pointer as it was not discussed that time.) I sincerely request to describe about phonon lifetime calculation using QE? Warm Regards Amit N Harode CR Labs INDIA On Wed, 23 Jun 2010 18:36:16 +0530 wrote >Someday before, a question about phonon lifetime was posted. Let refer that discussion. Linh Yamit wrote: > Dear All > > Can anyone tell me about how to calculate the phonon lifetimes using > QE? (Please forgive me for my ignorance.) > > Warm Regards > Amit N. Harode > CRL INDIA > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" _______________________________________________ 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/20100624/fb82a855/attachment.htm From gbilalbegovic at gmail.com Thu Jun 24 07:14:16 2010 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Thu, 24 Jun 2010 07:14:16 +0200 Subject: [Pw_forum] About phonon lifetimes In-Reply-To: <1277298376.S.5483.10090.F.H.Tk5nb2MgTGluaCBOZ3V5ZW4AUmU6IFtQd19mb3J1bV0gQWJvdXQgcGhvbm9uIGxpZmV0aW1lcw__.f4-235-215.1277350691.7871@webmail.rediffmail.com> References: <4C2206C9.9070300@sissa.it> <1277298376.S.5483.10090.F.H.Tk5nb2MgTGluaCBOZ3V5ZW4AUmU6IFtQd19mb3J1bV0gQWJvdXQgcGhvbm9uIGxpZmV0aW1lcw__.f4-235-215.1277350691.7871@webmail.rediffmail.com> Message-ID: On Thu, Jun 24, 2010 at 5:38 AM, Yamit wrote: > > Dear Mr Nguyen Ngoc Linh > > Thank you for your reply !(may be a blind pointer as it was not discussed > that time.) > > I sincerely request to describe about phonon lifetime calculation using QE? > > > > Dear Amit, As Linh wrote, it is possible to find a search engine on the page: http://www.quantum-espresso.org/contacts.php then to write "phonon lifetime" and get: http://tinyurl.com/3x8nfw3 Pleaese read first two messages. In addition, there is a possibility to download the thesis of Alberto Debernardi, Anharmonic Properties of Semiconductors from Density Functional Perturbation Theory: http://www.sissa.it/cm/thesis/1995/debernardi.ps.gz Best regards -- Goranka Bilalbegovic, Department of Physics, Faculty of Science, University of Zagreb, Croatia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/c5c47fe9/attachment.htm From amit99266 at rediffmail.com Thu Jun 24 08:13:27 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 24 Jun 2010 06:13:27 -0000 Subject: [Pw_forum] =?utf-8?q?About_phonon_lifetimes?= In-Reply-To: Message-ID: <1277356462.S.5746.61311.H.WUdvcmFua2EgQmlsYWxiZWdvdmljAFJlOiBbUHdfZm9ydW1dIEFib3V0IHBob25vbiBsaWZldGltZXM_.f4-234-204.1277360007.1624@webmail.rediffmail.com> Dear Prof. Goranka Bilalbegovic Thank for your inputs! Thanks & Regards Amit On Thu, 24 Jun 2010 10:44:22 +0530 wrote > On Thu, Jun 24, 2010 at 5:38 AM, Yamit wrote: Dear Mr Nguyen Ngoc Linh Thank you for your reply !(may be a blind pointer as it was not discussed that time.) I sincerely request to describe about phonon lifetime calculation using QE? ??Dear Amit, As Linh wrote, it is possible to find a search engine on the page: http://www.quantum-espresso.org/contacts.php then to write "phonon lifetime" and get: http://tinyurl.com/3x8nfw3Pleaese read first two messages. In addition, there is a possibility to download the thesis of Alberto Debernardi, Anharmonic Properties of Semiconductors from Density Functional Perturbation Theory: http://www.sissa.it/cm/thesis/1995/debernardi.ps.gz Best regards ? ? -- Goranka Bilalbegovic, Department of Physics, Faculty of Science, University of Zagreb, Croatia _______________________________________________ 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/20100624/b5092fc2/attachment.htm From giannozz at democritos.it Thu Jun 24 10:15:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Jun 2010 10:15:16 +0200 Subject: [Pw_forum] B3LYP In-Reply-To: <572303.79859.qm@web114517.mail.gq1.yahoo.com> References: <55003.88958.qm@web114507.mail.gq1.yahoo.com> <201006191352.21615.giuseppe.mattioli@mlib.ism.cnr.it> <572303.79859.qm@web114517.mail.gq1.yahoo.com> Message-ID: On Jun 23, 2010, at 21:12 , Vi Vo wrote: > > [...] hybrid functionals are not still straightforwardly > implemented in QE... actually the implementation of hybrid functionals *is* straightforward. The problem is that this "straigthforward" implementation is quite slow... 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 gianluca.giovannetti at gmail.com Thu Jun 24 10:17:11 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Thu, 24 Jun 2010 10:17:11 +0200 Subject: [Pw_forum] occupancies of density matrix in LDA+U vs output polarization in Lowdin Charges In-Reply-To: <20100622003754.26859.qmail@ms.hfcas.ac.cn> References: <20100622003754.26859.qmail@ms.hfcas.ac.cn> Message-ID: Dear All, thank you for your comments. cheers, Gianluca On Tue, Jun 22, 2010 at 2:37 AM, lfhuang wrote: > Dear G. Giovannetti: > The small numerical difference between the two methods by you is reasonable > and allowable because: > (1) The Lowdin population analysis is used in PWSCF; > (2) There may be some effect from the hybridization of orbitals. (Partial > DOS maybe helpful.) > > In my opinion, the difference is so small that it can be deemed that the > magnetic moment is localized at the Fe site (as you think). > > Best Wishes > > Yours Sincerely > L. F. Huang > > ------ > ====================================================================== > L.F.Huang(???) 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/750559f4/attachment.htm From Norbert.Nemec.List at gmx.de Thu Jun 24 14:51:36 2010 From: Norbert.Nemec.List at gmx.de (Norbert Nemec) Date: Thu, 24 Jun 2010 14:51:36 +0200 Subject: [Pw_forum] Energy conservation in Verlet-MD? Message-ID: <20100624125136.137030@gmx.net> Hi there, I am trying a very simple MD calculation (optical phonon mode of Silicon, similar to the original Car-Parinello paper). I am surprised that the total energy is not constant but oscillates with about 10% of the amplitude of the potential energy. This oscillation is *independent* of the MD time step. Furthermore it did not change with the k-grid, the energy cutoff, the functional or the pseudopotentials. Attached is one of the input files that I used. Does anyone know what might cause this behavior? Greetings, Norbert -- GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl. Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl -------------- next part -------------- A non-text attachment was scrubbed... Name: in.pwscf Type: application/octet-stream Size: 704 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100624/02db3d98/attachment.obj From alex968873 at yahoo.com.cn Thu Jun 24 15:41:24 2010 From: alex968873 at yahoo.com.cn (=?utf-8?B?5p2O5paM?=) Date: Thu, 24 Jun 2010 21:41:24 +0800 (CST) Subject: [Pw_forum] lambda.x problem, espresso 4.2 Message-ID: <482276.89710.qm@web15108.mail.cnb.yahoo.com> Dear all, When i run the example07 in espresso 4.2, got?the following?message at the end: *************************************************** running lambda.x for lambda calculation...forrtl: No such file or directory forrtl: severe (29): file not found, unit 4, file /home/jyding/espresso/examples/example07/results/fort.4 Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? lambda.x?????????? 0000000000674AE6? Unknown?????????????? Unknown? Unknown lambda.x?????????? 0000000000673612? Unknown?????????????? Unknown? Unknown lambda.x?????????? 00000000006351BC? Unknown?????????????? Unknown? Unknown lambda.x?????????? 0000000000602FF1? Unknown?????????????? Unknown? Unknown lambda.x?????????? 00000000006035C9? Unknown?????????????? Unknown? Unknown lambda.x?????????? 000000000061D1A2? Unknown?????????????? Unknown? Unknown lambda.x?????????? 000000000040A275? Unknown?????????????? Unknown? Unknown lambda.x?????????? 0000000000409DEA? Unknown?????????????? Unknown? Unknown Unknown??????????? 0000003CC191C40B? Unknown?????????????? Unknown? Unknown lambda.x?????????? 0000000000409D2A? Unknown?????????????? Unknown? Unknown Error condition encountered during test: exit status = 29 Aborting *********************************** lambda.out is empty, but i can get the elph.**** files. i want to know what had happened and how to fix it? From wangqj1 at 126.com Thu Jun 24 15:15:10 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Thu, 24 Jun 2010 21:15:10 +0800 (CST) Subject: [Pw_forum] matdyn.x Message-ID: <74154a11.1bdb8.1296a190199.Coremail.wangqj1@126.com> Dear all When I use matdyn.x in version 4.2? it turns up : 'At line 284 of file matdyn.f90 Fortran runtime error: End of file' So I want to know how I can solve this problem? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/01d53f19/attachment.htm From ouuing at gmail.com Thu Jun 24 15:51:15 2010 From: ouuing at gmail.com (Hanyu) Date: Thu, 24 Jun 2010 21:51:15 +0800 Subject: [Pw_forum] lambda.x problem, espresso 4.2 In-Reply-To: <482276.89710.qm@web15108.mail.cnb.yahoo.com> References: <482276.89710.qm@web15108.mail.cnb.yahoo.com> Message-ID: in lambda.in file you will find the lines of elph.***. you need to delete the signs behind the elph.***. in order words, you must delete the characters that from #. I feel the # is not like in shell script. best regards! On Thu, Jun 24, 2010 at 9:41 PM, ?? wrote: > Dear all, > > When i run the example07 in espresso 4.2, got the following message at the end: > > *************************************************** > running lambda.x for lambda calculation...forrtl: No such file or directory > forrtl: severe (29): file not found, unit 4, file /home/jyding/espresso/examples/example07/results/fort.4 > Image PC Routine Line Source > lambda.x 0000000000674AE6 Unknown Unknown Unknown > lambda.x 0000000000673612 Unknown Unknown Unknown > lambda.x 00000000006351BC Unknown Unknown Unknown > lambda.x 0000000000602FF1 Unknown Unknown Unknown > lambda.x 00000000006035C9 Unknown Unknown Unknown > lambda.x 000000000061D1A2 Unknown Unknown Unknown > lambda.x 000000000040A275 Unknown Unknown Unknown > lambda.x 0000000000409DEA Unknown Unknown Unknown > Unknown 0000003CC191C40B Unknown Unknown Unknown > lambda.x 0000000000409D2A Unknown Unknown Unknown > Error condition encountered during test: exit status = 29 > Aborting > > *********************************** > lambda.out is empty, but i can get the elph.**** files. i want to know what had happened and how to fix it? > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), grad State key Laboratory of Superhard Materials, Jilin University, China Email: liuhanyu08 at mails.jlu.edu.cn or ouuing at gmail.com skype: ouuing From degironc at sissa.it Thu Jun 24 15:55:06 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 24 Jun 2010 15:55:06 +0200 Subject: [Pw_forum] lambda.x problem, espresso 4.2 In-Reply-To: <482276.89710.qm@web15108.mail.cnb.yahoo.com> References: <482276.89710.qm@web15108.mail.cnb.yahoo.com> Message-ID: <4C2363BA.2000005@sissa.it> the input for lambda.x in run_example has been modified adding comments after a couple of file names ... something like >>> elph. 0.000000. 0.000000. 0.000000 ! elph output file names, elph.-0.250000. 0.250000.-0.250000 ! in the same order as the q-points before elph. 0.500000.-0.500000. 0.500000 elph. 0.000000. 0.500000. 0.000000 elph. 0.750000.-0.250000. 0.750000 elph. 0.500000. 0.000000. 0.500000 elph. 0.000000.-1.000000. 0.000000 elph.-0.500000.-1.000000. 0.000000 <<< lambda.x does not like these extra character in exclamation marks. remove the comments and run lambda.x again In the cvs version this problem has been solved. stefano ?? wrote: > Dear all, > > When i run the example07 in espresso 4.2, got the following message at the end: > > *************************************************** > running lambda.x for lambda calculation...forrtl: No such file or directory > forrtl: severe (29): file not found, unit 4, file /home/jyding/espresso/examples/example07/results/fort.4 > Image PC Routine Line Source > lambda.x 0000000000674AE6 Unknown Unknown Unknown > lambda.x 0000000000673612 Unknown Unknown Unknown > lambda.x 00000000006351BC Unknown Unknown Unknown > lambda.x 0000000000602FF1 Unknown Unknown Unknown > lambda.x 00000000006035C9 Unknown Unknown Unknown > lambda.x 000000000061D1A2 Unknown Unknown Unknown > lambda.x 000000000040A275 Unknown Unknown Unknown > lambda.x 0000000000409DEA Unknown Unknown Unknown > Unknown 0000003CC191C40B Unknown Unknown Unknown > lambda.x 0000000000409D2A Unknown Unknown Unknown > Error condition encountered during test: exit status = 29 > Aborting > > *********************************** > lambda.out is empty, but i can get the elph.**** files. i want to know what had happened and how to fix it? > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From prasenjit.jnc at gmail.com Thu Jun 24 16:01:35 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 24 Jun 2010 16:01:35 +0200 Subject: [Pw_forum] matdyn.x In-Reply-To: <74154a11.1bdb8.1296a190199.Coremail.wangqj1@126.com> References: <74154a11.1bdb8.1296a190199.Coremail.wangqj1@126.com> Message-ID: it means that the file which the code is reading is not complete. Most probably in the input file you have mentioned fewer q-vectors than nq (no. of q-vectors). Please check your input. With regards, Prasenjit. 2010/6/24 Q.J.Wang : > Dear all > ?? When I use matdyn.x in version 4.2? it turns up : > 'At line 284 of file matdyn.f90 > Fortran runtime error: End of file' > So I want to know? how I can solve this problem? > -- > Best regards > > Q.J.Wang > > XiangTan University > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh From degironc at sissa.it Thu Jun 24 16:05:43 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 24 Jun 2010 16:05:43 +0200 Subject: [Pw_forum] Energy conservation in Verlet-MD? In-Reply-To: <20100624125136.137030@gmx.net> References: <20100624125136.137030@gmx.net> Message-ID: <4C236637.5020209@sissa.it> with your input on my computer the "constant" is oscillating within a range of the order of 3e-6 . the potential energy varies on a scale that is 1000 times larger stefano Norbert Nemec wrote: > Hi there, > > I am trying a very simple MD calculation (optical phonon mode of Silicon, similar to the original Car-Parinello paper). I am surprised that the total energy is not constant but oscillates with about 10% of the amplitude of the potential energy. > > This oscillation is *independent* of the MD time step. Furthermore it did not change with the k-grid, the energy cutoff, the functional or the pseudopotentials. > > Attached is one of the input files that I used. > > Does anyone know what might cause this behavior? > > Greetings, > Norbert > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From chengyu.young at gmail.com Thu Jun 24 17:30:38 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 24 Jun 2010 11:30:38 -0400 Subject: [Pw_forum] no interaction in my 2-D charge density contour Message-ID: Dear everyone, I am now facing a problem. My charge density contour has little interactions. Although I changed the # of level, I found little difference. Can anybody have a look at my script and point out my mistake? I really want to get a contour with interactions, in which they should be there. 1)rho_pp.in &inputpp prefix = 'cntcu' filplot = 'cntcucharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'cntcucharge' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'cntcu.rho.dat' e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, nx=56, ny=40 / 2) The interactive process: Input file > cntcu.rho.dat r0 : 0.0000 0.0000 0.0000 tau1 : 1.0000 0.0000 0.0000 tau2 : 0.0000 1.0000 0.0000 read 25 atomic positions output file > test.rho.ps Read 56 * 40 grid Logarithmic scale (y/n)? > n Bounds: 0.000004 1.403000 min, max, # of levels > 0 1.41 6 3)the rho.ps as attached. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/dff705f8/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: cntcu.rho.ps Type: application/postscript Size: 124472 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100624/dff705f8/attachment-0001.ps From giannozz at democritos.it Thu Jun 24 17:41:25 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Jun 2010 17:41:25 +0200 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: References: Message-ID: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> On Jun 24, 2010, at 17:30 , chengyu yang wrote: > output file > test.rho.ps > the rho.ps as attached. > "test.rho.ps" .ne. "rho.ps" .ne. "cntcu.rho.ps" 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 Norbert.Nemec.List at gmx.de Thu Jun 24 17:42:49 2010 From: Norbert.Nemec.List at gmx.de (Norbert Nemec) Date: Thu, 24 Jun 2010 17:42:49 +0200 Subject: [Pw_forum] Energy conservation in Verlet-MD? In-Reply-To: <4C236637.5020209@sissa.it> References: <20100624125136.137030@gmx.net> <4C236637.5020209@sissa.it> Message-ID: <20100624154249.323380@gmx.net> Thanks, Stefano -- inspired by your information I tried various versions of PWSCF and finally found out that a uncommitted patch that I had believed to be completely independent actually slightly messed up the forces during the SCF loop. Will not be easy to fix the problem, but at least I have identified it now... -------- Original-Nachricht -------- > Datum: Thu, 24 Jun 2010 16:05:43 +0200 > Von: Stefano de Gironcoli > An: PWSCF Forum > Betreff: Re: [Pw_forum] Energy conservation in Verlet-MD? > with your input on my computer the "constant" is oscillating within a > range of the order of 3e-6 . > the potential energy varies on a scale that is 1000 times larger > stefano > > Norbert Nemec wrote: > > Hi there, > > > > I am trying a very simple MD calculation (optical phonon mode of > Silicon, similar to the original Car-Parinello paper). I am surprised that the > total energy is not constant but oscillates with about 10% of the amplitude of > the potential energy. > > > > This oscillation is *independent* of the MD time step. Furthermore it > did not change with the k-grid, the energy cutoff, the functional or the > pseudopotentials. > > > > Attached is one of the input files that I used. > > > > Does anyone know what might cause this behavior? > > > > Greetings, > > Norbert > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 -- GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl. Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl From chengyu.young at gmail.com Thu Jun 24 17:45:40 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 24 Jun 2010 11:45:40 -0400 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> Message-ID: All right, I now change the parameters, and found some ideal change. Maybe it is because I set the # of levels too low. My another question is , how can I get a contour as a whole carbon nanotube, rather than a quarter ? It is more intuitive. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/d3e0fac3/attachment.htm From baroni at sissa.it Thu Jun 24 17:55:03 2010 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 24 Jun 2010 17:55:03 +0200 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> Message-ID: signature? affiliation? On Jun 24, 2010, at 5:45 PM, chengyu yang wrote: > All right, I now change the parameters, and found some ideal change. Maybe it is because I set the # of levels too low. > > My another question is , how can I get a contour as a whole carbon nanotube, rather than a quarter ? It is more intuitive. > > > > _______________________________________________ > 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/20100624/f4793494/attachment.htm From chengyu.young at gmail.com Thu Jun 24 18:00:18 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 24 Jun 2010 12:00:18 -0400 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> Message-ID: Sorry. My another question is , how can I get a contour as a whole carbon nanotube, rather than a quarter ? It is more intuitive then. Chengyu Yang MSE sudent, UCF -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/80aadbe4/attachment.htm From giannozz at democritos.it Thu Jun 24 18:09:25 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Jun 2010 18:09:25 +0200 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> Message-ID: <4F9BC078-913B-4942-BE33-574F3AC1F6F6@democritos.it> On Jun 24, 2010, at 18:00 , chengyu yang wrote: > how can I get a contour as a whole carbon nanotube, > rather than a quarter ? you get what you ask for. See the definition of variables x0, e1, e2, in the input of pp.x . 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 chengyu.young at gmail.com Thu Jun 24 19:51:16 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 24 Jun 2010 13:51:16 -0400 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: <4F9BC078-913B-4942-BE33-574F3AC1F6F6@democritos.it> References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> <4F9BC078-913B-4942-BE33-574F3AC1F6F6@democritos.it> Message-ID: Dear Paolo, Thanks for your answer. However, I still cannot quite understand it. In my script I defined the plane as (001), which is , e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0; e2(1) =0.0, e2(2)=1.0, e2(3) = 0.0; I didn't define x(i). In my scf file, the unit cell is just like quarter, is that the reason for my quarter like charge density contour? Thanks for your patience. Chengyu Yang UCF PhD student. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/7e9bc794/attachment.htm From giannozz at democritos.it Thu Jun 24 20:46:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Jun 2010 20:46:06 +0200 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> <4F9BC078-913B-4942-BE33-574F3AC1F6F6@democritos.it> Message-ID: <5B7A8A02-E691-479A-B8F1-04E330961EEC@democritos.it> On Jun 24, 2010, at 19:51 , chengyu yang wrote: > I still cannot quite understand it. In my script I defined the > plane as (001), which is , > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0; > e2(1) =0.0, e2(2)=1.0, e2(3) = 0.0; > I didn't define x(i) default is x0 = (0,0,0), e1, e2 are in units of the lattice parameter a. You are plotting square with corners (0,0,0), (a,0,0), (0,0,a), (a,a,0). So if the axis of your nanotube is along (0,0,z), you will see 1/4 of nanotube in each corner 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 chengyu.young at gmail.com Thu Jun 24 21:18:22 2010 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 24 Jun 2010 15:18:22 -0400 Subject: [Pw_forum] no interaction in my 2-D charge density contour In-Reply-To: <5B7A8A02-E691-479A-B8F1-04E330961EEC@democritos.it> References: <90C19937-3F57-4304-A0BB-3CBE17D6FC54@democritos.it> <4F9BC078-913B-4942-BE33-574F3AC1F6F6@democritos.it> <5B7A8A02-E691-479A-B8F1-04E330961EEC@democritos.it> Message-ID: Thanks Paolo. It works. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/35127555/attachment-0001.htm From wangqj1 at 126.com Fri Jun 25 02:01:06 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Fri, 25 Jun 2010 08:01:06 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 68 In-Reply-To: References: Message-ID: <3091a97.63c.1296c685e1d.Coremail.wangqj1@126.com> Dear Prasenjit, Thank you very much. With your help, the problem has been solved. -- Best regards Q.J.Wang XiangTan University ?2010-06-24 22:01:56?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: B3LYP (Paolo Giannozzi) > 2. Re: occupancies of density matrix in LDA+U vs output > polarization in Lowdin Charges (Gianluca Giovannetti) > 3. Energy conservation in Verlet-MD? (Norbert Nemec) > 4. lambda.x problem, espresso 4.2 (??) > 5. matdyn.x (Q.J.Wang) > 6. Re: lambda.x problem, espresso 4.2 (Hanyu) > 7. Re: lambda.x problem, espresso 4.2 (Stefano de Gironcoli) > 8. Re: matdyn.x (Prasenjit Ghosh) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 24 Jun 2010 10:15:16 +0200 >From: Paolo Giannozzi >Subject: Re: [Pw_forum] B3LYP >To: PWSCF Forum >Message-ID: >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > >On Jun 23, 2010, at 21:12 , Vi Vo wrote: > >> > [...] hybrid functionals are not still straightforwardly >> implemented in QE... > >actually the implementation of hybrid functionals *is* straightforward. >The problem is that this "straigthforward" implementation is quite >slow... > >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: 2 >Date: Thu, 24 Jun 2010 10:17:11 +0200 >From: Gianluca Giovannetti >Subject: Re: [Pw_forum] occupancies of density matrix in LDA+U vs > output polarization in Lowdin Charges >To: PWSCF Forum >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Dear All, > >thank you for your comments. > >cheers, > >Gianluca > >On Tue, Jun 22, 2010 at 2:37 AM, lfhuang wrote: > >> Dear G. Giovannetti: >> The small numerical difference between the two methods by you is reasonable >> and allowable because: >> (1) The Lowdin population analysis is used in PWSCF; >> (2) There may be some effect from the hybridization of orbitals. (Partial >> DOS maybe helpful.) >> >> In my opinion, the difference is so small that it can be deemed that the >> magnetic moment is localized at the Fe site (as you think). >> >> Best Wishes >> >> Yours Sincerely >> L. F. Huang >> >> ------ >> ====================================================================== >> L.F.Huang(???) 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 >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/750559f4/attachment-0001.htm > >------------------------------ > >Message: 3 >Date: Thu, 24 Jun 2010 14:51:36 +0200 >From: "Norbert Nemec" >Subject: [Pw_forum] Energy conservation in Verlet-MD? >To: PWSCF Forum >Message-ID: <20100624125136.137030 at gmx.net> >Content-Type: text/plain; charset="utf-8" > >Hi there, > >I am trying a very simple MD calculation (optical phonon mode of Silicon, similar to the original Car-Parinello paper). I am surprised that the total energy is not constant but oscillates with about 10% of the amplitude of the potential energy. > >This oscillation is *independent* of the MD time step. Furthermore it did not change with the k-grid, the energy cutoff, the functional or the pseudopotentials. > >Attached is one of the input files that I used. > >Does anyone know what might cause this behavior? > >Greetings, >Norbert >-- >GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl. >Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: in.pwscf >Type: application/octet-stream >Size: 704 bytes >Desc: not available >Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100624/02db3d98/attachment-0001.obj > >------------------------------ > >Message: 4 >Date: Thu, 24 Jun 2010 21:41:24 +0800 (CST) >From: ?? >Subject: [Pw_forum] lambda.x problem, espresso 4.2 >To: pw_forum at pwscf.org >Message-ID: <482276.89710.qm at web15108.mail.cnb.yahoo.com> >Content-Type: text/plain; charset=utf-8 > >Dear all, > >When i run the example07 in espresso 4.2, got?the following?message at the end: > >*************************************************** >running lambda.x for lambda calculation...forrtl: No such file or directory >forrtl: severe (29): file not found, unit 4, file /home/jyding/espresso/examples/example07/results/fort.4 >Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? >lambda.x?????????? 0000000000674AE6? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 0000000000673612? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 00000000006351BC? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 0000000000602FF1? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 00000000006035C9? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 000000000061D1A2? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 000000000040A275? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 0000000000409DEA? Unknown?????????????? Unknown? Unknown >Unknown??????????? 0000003CC191C40B? Unknown?????????????? Unknown? Unknown >lambda.x?????????? 0000000000409D2A? Unknown?????????????? Unknown? Unknown >Error condition encountered during test: exit status = 29 >Aborting > >*********************************** >lambda.out is empty, but i can get the elph.**** files. i want to know what had happened and how to fix it? > > > > > > >------------------------------ > >Message: 5 >Date: Thu, 24 Jun 2010 21:15:10 +0800 (CST) >From: "Q.J.Wang" >Subject: [Pw_forum] matdyn.x >To: pw_forum >Message-ID: <74154a11.1bdb8.1296a190199.Coremail.wangqj1 at 126.com> >Content-Type: text/plain; charset="gbk" > >Dear all > When I use matdyn.x in version 4.2? it turns up : >'At line 284 of file matdyn.f90 >Fortran runtime error: End of file' >So I want to know how I can solve this problem? >-- > >Best regards > >Q.J.Wang > >XiangTan University >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/01d53f19/attachment-0001.htm > >------------------------------ > >Message: 6 >Date: Thu, 24 Jun 2010 21:51:15 +0800 >From: Hanyu >Subject: Re: [Pw_forum] lambda.x problem, espresso 4.2 >To: PWSCF Forum >Message-ID: > >Content-Type: text/plain; charset=GB2312 > >in lambda.in file you will find the lines of elph.***. you need to >delete the signs behind the elph.***. in order words, you must delete >the characters that from #. I feel the # is not like in shell script. > >best regards! > > >On Thu, Jun 24, 2010 at 9:41 PM, ?? wrote: >> Dear all, >> >> When i run the example07 in espresso 4.2, got the following message at the end: >> >> *************************************************** >> running lambda.x for lambda calculation...forrtl: No such file or directory >> forrtl: severe (29): file not found, unit 4, file /home/jyding/espresso/examples/example07/results/fort.4 >> Image PC Routine Line Source >> lambda.x 0000000000674AE6 Unknown Unknown Unknown >> lambda.x 0000000000673612 Unknown Unknown Unknown >> lambda.x 00000000006351BC Unknown Unknown Unknown >> lambda.x 0000000000602FF1 Unknown Unknown Unknown >> lambda.x 00000000006035C9 Unknown Unknown Unknown >> lambda.x 000000000061D1A2 Unknown Unknown Unknown >> lambda.x 000000000040A275 Unknown Unknown Unknown >> lambda.x 0000000000409DEA Unknown Unknown Unknown >> Unknown 0000003CC191C40B Unknown Unknown Unknown >> lambda.x 0000000000409D2A Unknown Unknown Unknown >> Error condition encountered during test: exit status = 29 >> Aborting >> >> *********************************** >> lambda.out is empty, but i can get the elph.**** files. i want to know what had happened and how to fix it? >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > >-- >-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > grad > State key Laboratory of Superhard Materials, Jilin University, China > Email: liuhanyu08 at mails.jlu.edu.cn or ouuing at gmail.com > skype: ouuing > > >------------------------------ > >Message: 7 >Date: Thu, 24 Jun 2010 15:55:06 +0200 >From: Stefano de Gironcoli >Subject: Re: [Pw_forum] lambda.x problem, espresso 4.2 >To: PWSCF Forum >Message-ID: <4C2363BA.2000005 at sissa.it> >Content-Type: text/plain; charset=UTF-8; format=flowed > >the input for lambda.x in run_example has been modified adding comments >after a couple of file names ... >something like > >>> >elph. 0.000000. 0.000000. 0.000000 ! elph output file names, >elph.-0.250000. 0.250000.-0.250000 ! in the same order as the q-points >before >elph. 0.500000.-0.500000. 0.500000 >elph. 0.000000. 0.500000. 0.000000 >elph. 0.750000.-0.250000. 0.750000 >elph. 0.500000. 0.000000. 0.500000 >elph. 0.000000.-1.000000. 0.000000 >elph.-0.500000.-1.000000. 0.000000 ><<< >lambda.x does not like these extra character in exclamation marks. > >remove the comments and run lambda.x again > >In the cvs version this problem has been solved. > >stefano > > >?? wrote: >> Dear all, >> >> When i run the example07 in espresso 4.2, got the following message at the end: >> >> *************************************************** >> running lambda.x for lambda calculation...forrtl: No such file or directory >> forrtl: severe (29): file not found, unit 4, file /home/jyding/espresso/examples/example07/results/fort.4 >> Image PC Routine Line Source >> lambda.x 0000000000674AE6 Unknown Unknown Unknown >> lambda.x 0000000000673612 Unknown Unknown Unknown >> lambda.x 00000000006351BC Unknown Unknown Unknown >> lambda.x 0000000000602FF1 Unknown Unknown Unknown >> lambda.x 00000000006035C9 Unknown Unknown Unknown >> lambda.x 000000000061D1A2 Unknown Unknown Unknown >> lambda.x 000000000040A275 Unknown Unknown Unknown >> lambda.x 0000000000409DEA Unknown Unknown Unknown >> Unknown 0000003CC191C40B Unknown Unknown Unknown >> lambda.x 0000000000409D2A Unknown Unknown Unknown >> Error condition encountered during test: exit status = 29 >> Aborting >> >> *********************************** >> lambda.out is empty, but i can get the elph.**** files. i want to know what had happened and how to fix it? >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > >------------------------------ > >Message: 8 >Date: Thu, 24 Jun 2010 16:01:35 +0200 >From: Prasenjit Ghosh >Subject: Re: [Pw_forum] matdyn.x >To: PWSCF Forum >Message-ID: > >Content-Type: text/plain; charset=UTF-8 > >it means that the file which the code is reading is not complete. > >Most probably in the input file you have mentioned fewer q-vectors >than nq (no. of q-vectors). > >Please check your input. > >With regards, >Prasenjit. > >2010/6/24 Q.J.Wang : >> Dear all >> ?? When I use matdyn.x in version 4.2? it turns up : >> 'At line 284 of file matdyn.f90 >> Fortran runtime error: End of file' >> So I want to know? how I can solve this problem? >> -- >> Best regards >> >> Q.J.Wang >> >> XiangTan University >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > >-- >PRASENJIT GHOSH, >POST-DOC, >ROOM NO: 265, MAIN BUILDING, >CM SECTION, ICTP, >STRADA COSTERIA 11, >TRIESTE, 34104, >ITALY >PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) >URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh > > >------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End of Pw_forum Digest, Vol 36, Issue 68 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100625/a9812c48/attachment-0001.htm From jperaltac at gmail.com Fri Jun 25 03:39:38 2010 From: jperaltac at gmail.com (joaquin peralta) Date: Thu, 24 Jun 2010 20:39:38 -0500 Subject: [Pw_forum] Example-29, NOTE : eigenvalues are not computed without ortho. Message-ID: Dear espresso users, I'm running some examples of espresso, in order to understand some variables and settings used principally in MD capabilities. I ran the example-29 in order to understand more about the ensemble-DFT and the correct way to use them. I ran the example, and work fine, however if I augmented the number of steps and run again (cleaning all previous information) I obtain the message (each iprint step): ...... Step 9 10 -7.57021 -7.70233 -7.70223 6 NOTE: eigenvalues are not computed without ortho Occupations : 1.999950 1.999437 1.627765 0.938538 0.938528 0.241211 0.241203 0.013369 nfi tempp E -T.S-mu.nbsp +K_p #Iter Step 10 12 -7.57024 -7.70236 -7.70223 6 ...... The eigenvalues are not calculated, but why?, it's correct? if the example use the option : orthogonalization = 'Gram-Schmidt' I remove the orthogonalization option in order to see what happen and the message disappear, however i don't understand because the reference and README file show that eigenvalues are calculated. Surely I forget something or have a mistake with input_file, but i don't see that. Thanks in Advance Joaqu?n Peralta Post-Doc position in Iowa State University. Materials Science and Engineering. -- ---------------------------------------------------- Group of NanoMaterials ---------------------------------------------------- http://www.gnm.cl ---------------------------------------------------- Joaqu?n Andr?s Peralta Camposano ---------------------------------------------------- http://zeth.ciencias.uchile.cl/~jperalta In a world without frontiers, who needs Gates and Win. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100624/47e02c08/attachment.htm From suza.rri at gmail.com Fri Jun 25 09:27:40 2010 From: suza.rri at gmail.com (Suza W) Date: Fri, 25 Jun 2010 09:27:40 +0200 Subject: [Pw_forum] ultrasoft Cs pseudopotential Message-ID: Dear QE USERS, QE pseudo site does not have Cs ultrasoft pseudo-potential. Can you anybody help me to get the ultasoft (LDA&GGA) pseudo-potential for Cs? I have got the following link in the forum : http://www.fisica.uniud.it/~giannozz/public/Cs.tar.gz but not able to open this. It seems that the above link is dead. Any help in this regard will be highly appreciated. Yours sincerely, Suza W. Ph. D. student Institute of Raman Research, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100625/44d36069/attachment.htm From sclauzer at sissa.it Fri Jun 25 10:20:00 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 25 Jun 2010 10:20:00 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 36, Issue 68 In-Reply-To: <3091a97.63c.1296c685e1d.Coremail.wangqj1@126.com> References: <3091a97.63c.1296c685e1d.Coremail.wangqj1@126.com> Message-ID: <4C2466B0.2060902@sissa.it> On 06/25/2010 02:01 AM, Q.J.Wang wrote: > Dear Prasenjit, > Thank you very much. With your help, the problem has been solved. But you have NOT yet solved the problem described here below (read carefully the last line quoted). Please make some effort to extirpate the vice of hitting reply to a Forum digest... for the peace of mind of all the forum community. Thanks GS > > -- > Best regards > Q.J.Wang > XiangTan University > > ??2010-06-24 22:01:56??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..." > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From eyvaz_isaev at yahoo.com Fri Jun 25 11:42:55 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 25 Jun 2010 02:42:55 -0700 (PDT) Subject: [Pw_forum] lambda.x problem, espresso 4.2 In-Reply-To: <4C2363BA.2000005@sissa.it> Message-ID: <794676.8135.qm@web65708.mail.ac4.yahoo.com> Dear all, In fact, lambda.x is now obsolete, as I have included log_w calculations into matdyn.f90 which should be replaced soon. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 6/24/10, Stefano de Gironcoli wrote: > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] lambda.x problem, espresso 4.2 > To: "PWSCF Forum" > Date: Thursday, June 24, 2010, 5:55 PM > the input for lambda.x in run_example > has been modified adding comments > after a couple of file names? ... > something like > >>> > elph. 0.000000. 0.000000. 0.000000 ! elph output file > names, > elph.-0.250000. 0.250000.-0.250000 ! in the same order as > the q-points > before > elph. 0.500000.-0.500000. 0.500000 > elph. 0.000000. 0.500000. 0.000000 > elph. 0.750000.-0.250000. 0.750000 > elph. 0.500000. 0.000000. 0.500000 > elph. 0.000000.-1.000000. 0.000000 > elph.-0.500000.-1.000000. 0.000000 > <<< > lambda.x does not like these extra character in exclamation > marks. > > remove the comments and run lambda.x again > > In the cvs version this problem? has been solved. > > stefano > > > ?? wrote: > > Dear all, > > > > When i run the example07 in espresso 4.2, got the > following message at the end: > > > > *************************************************** > > running lambda.x for lambda calculation...forrtl: No > such file or directory > > forrtl: severe (29): file not found, unit 4, file > /home/jyding/espresso/examples/example07/results/fort.4 > > Image? ? ? ? ? ? ? > PC? ? ? ? ? ? ? ? > Routine? ? ? ? ? ? Line? > ? ? ? Source? ? ? ? > ? ??? > > lambda.x? ? ? ? > ???0000000000674AE6? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???0000000000673612? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???00000000006351BC? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???0000000000602FF1? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???00000000006035C9? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???000000000061D1A2? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???000000000040A275? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > lambda.x? ? ? ? > ???0000000000409DEA? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > Unknown? ? ? ? ? ? > 0000003CC191C40B? Unknown? ? ? ? > ? ? ???Unknown? Unknown > > lambda.x? ? ? ? > ???0000000000409D2A? Unknown? > ? ? ? ? ? > ???Unknown? Unknown > > Error condition encountered during test: exit status = > 29 > > Aborting > > > > *********************************** > > lambda.out is empty, but i can get the elph.**** > files. i want to know what had happened and how to fix it? > > > > > >? ? ??? > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > >??? > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From gianluca.giovannetti at gmail.com Fri Jun 25 12:33:07 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Fri, 25 Jun 2010 12:33:07 +0200 Subject: [Pw_forum] PW interfaced with DMFT code Message-ID: Dear All, i have some question i would like to post in order to use PW and the DMFT code http://qe-forge.org/projects/dmft/ Is that a project "working"? the DMFT code works well as i tested on SrVO3 (it is given as example...) but changing system i would like to know more about its use. Do you know where i can post questions? thank you in advance. cheers, Gianluca Giovannetti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100625/ff0fc194/attachment.htm From sks.jnc at gmail.com Fri Jun 25 14:02:06 2010 From: sks.jnc at gmail.com (S. K. S.) Date: Fri, 25 Jun 2010 14:02:06 +0200 Subject: [Pw_forum] Eu or Sm Pseudo Potential Message-ID: > Dear All, > > Does anybody have Eu or Sm (LDA/GGA and Ultra-soft/Norm-conserving) pseudopotential? > > Looking forward to your kind reply. > > Thanking you and with my best regards, > > Saha SK > R&D assistant > JNCASR > Jakkur 560012 > India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100625/9a018c2b/attachment.htm From jperaltac at gmail.com Fri Jun 25 18:09:28 2010 From: jperaltac at gmail.com (joaquin peralta) Date: Fri, 25 Jun 2010 11:09:28 -0500 Subject: [Pw_forum] Example-29, "NOTE : eigenvalues are not computed without ortho." Message-ID: Dear espresso users, I'm running some examples of espresso, in order to understand some variables and settings used principally in MD capabilities. I ran the example-29 in order to understand more about the ensemble-DFT and the correct way to use them. I ran the example, and work fine, however if I augmented the number of steps and run again (cleaning all previous information) I obtain the message (each iprint step): ...... Step 9 10 -7.57021 -7.70233 -7.70223 6 NOTE: eigenvalues are not computed without ortho Occupations : 1.999950 1.999437 1.627765 0.938538 0.938528 0.241211 0.241203 0.013369 nfi tempp E -T.S-mu.nbsp +K_p #Iter Step 10 12 -7.57024 -7.70236 -7.70223 6 ...... The eigenvalues are not calculated, but why?, it's correct? if the example use the option : orthogonalization = 'Gram-Schmidt' I remove the orthogonalization option in order to see what happen and the message disappear, however i don't understand because the reference and README file show that eigenvalues are calculated. Surely I forget something or have a mistake with input_file, but i don't see that. Thanks in Advance Joaqu?n Peralta Post-Doc position in Iowa State University. Materials Science and Engineering. PD : I send the e-mail again, because previously was in a sub-thread, excuse me if is not correct. -- ---------------------------------------------------- Group of NanoMaterials ---------------------------------------------------- http://www.gnm.cl ---------------------------------------------------- Joaqu?n Andr?s Peralta Camposano ---------------------------------------------------- http://zeth.ciencias.uchile.cl/~jperalta In a world without frontiers, who needs Gates and Win. -- ---------------------------------------------------- Group of NanoMaterials ---------------------------------------------------- http://www.gnm.cl ---------------------------------------------------- Joaqu?n Andr?s Peralta Camposano ---------------------------------------------------- http://zeth.ciencias.uchile.cl/~jperalta In a world without frontiers, who needs Gates and Win. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100625/cc69ddb4/attachment.htm From giannozz at democritos.it Fri Jun 25 18:20:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 25 Jun 2010 18:20:30 +0200 Subject: [Pw_forum] Example-29, "NOTE : eigenvalues are not computed without ortho." In-Reply-To: References: Message-ID: <4C24D74E.20004@democritos.it> joaquin peralta wrote: > The eigenvalues are not calculated, but why? I know close to nothing on this specific subject, but, as a rule, in CP the eigenvalues are obtained as a byproduct of iterative orthonormalization (from diagonalization of the "Lambda" matrices, i.e. Lagrange multipliers enforcing orthonormalization constraints). If you use Gram-Schmidt orthonormalization, you do not have these matrices. Nothing would prevent the calculation of eigenvalues by some other algorithms (e.g. Davidson diagonalization), but as a matter of facts, this is not currently implemented in CP. It is a problem of "tradition", so to speak. Gram-Schmidt is inefficient and should nbot be used anyway, except in the first few time steps. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From b.janesko at tcu.edu Fri Jun 25 19:34:46 2010 From: b.janesko at tcu.edu (Janesko, Benjamin) Date: Fri, 25 Jun 2010 12:34:46 -0500 Subject: [Pw_forum] Cannot reproduce standard CO/Au(111) adsorption energy calculations Message-ID: Dear QE experts, I am just starting to use pwscf for surface chemistry research. I've begun by attempting to reproduce the CO/Au(111) adsorption energy in de Gironcoli et al, PRB 77, 085414 (2008). My problem is that my PBE adsorption energy is an order of magnitude lower than any I've seen in the literature! And I can't figure out what I'm doing wrong. I've prepared a 5-layer slab of Au(111) at the experimental bulk lattice parameter (2.884 Angstrom Au-Au spacing): --------------------------------------- &control calculation='relax' prefix='au5-3x3', pseudo_dir = '/home/bjanesko2/espresso/pseudo//', outdir='/tmp/espresso/' / &system ibrav=4, celldm(1)=9.439624066, celldm(3)=8.0, nat=15, ntyp=1, ecutwfc = 40.0, ecutrho = 250.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 / &electrons conv_thr=0.0000001 / &ions ion_dynamics='bfgs', path_thr=0.03 / ATOMIC_SPECIES Au 196.966 Au.pbe-nd-van.UPF ATOMIC_POSITIONS alat Au 0.000000 0.000000 4.000000 1 1 1 Au 0.500000 0.288675 4.000000 1 1 1 Au 1.000000 0.577350 4.000000 1 1 1 Au 0.333333 0.000000 3.528595 1 1 1 Au 0.833333 0.288675 3.528595 1 1 1 Au 1.333333 0.577350 3.528595 1 1 1 Au 0.666667 0.000000 3.057191 0 0 0 Au 1.166667 0.288675 3.057191 0 0 0 Au 1.666667 0.577350 3.057191 0 0 0 Au 1.000000 0.000000 2.585786 0 0 0 Au 1.500000 0.288675 2.585786 0 0 0 Au 2.000000 0.577350 2.585786 0 0 0 Au 1.333333 0.000000 2.114382 0 0 0 Au 1.833333 0.288675 2.114382 0 0 0 Au 2.333333 0.577350 2.114382 0 0 0 K_POINTS automatic 8 8 1 0 0 0 ---------------------------------------------------- and CO adsorbed to the fcc site, in a sqrt(3) x sqrt(3) overlayer (1/3 ML coverage) ------------------------------------------------------- &control calculation='relax' prefix='coau5-3x3-hcp', pseudo_dir = '/home/bjanesko2/espresso/pseudo//', outdir='/tmp/espresso/' / &system ibrav=4, celldm(1)=9.439624066, celldm(3)=8.0, nat=17, ntyp=3, ecutwfc = 40.0, ecutrho = 250.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 / &electrons conv_thr=0.0000001 / &ions ion_dynamics='bfgs', path_thr=0.03 / ATOMIC_SPECIES Au 196.966 Au.pbe-nd-van.UPF C 12.0107 C-pbe-van_ak.UPF O 15.9994 O-pbe-van_ak.UPF ATOMIC_POSITIONS alat Au 0.000000 0.000000 4.000000 1 1 1 Au 0.500000 0.288675 4.000000 1 1 1 Au 1.000000 0.577350 4.000000 1 1 1 Au 0.333333 0.000000 3.528595 1 1 1 Au 0.833333 0.288675 3.528595 1 1 1 Au 1.333333 0.577350 3.528595 1 1 1 Au 0.666667 0.000000 3.057191 0 0 0 Au 1.166667 0.288675 3.057191 0 0 0 Au 1.666667 0.577350 3.057191 0 0 0 Au 1.000000 0.000000 2.585786 0 0 0 Au 1.500000 0.288675 2.585786 0 0 0 Au 2.000000 0.577350 2.585786 0 0 0 Au 1.333333 0.000000 2.114382 0 0 0 Au 1.833333 0.288675 2.114382 0 0 0 Au 2.333333 0.577350 2.114382 0 0 0 C 0.333333333 0.000000000 5.309331423 1 1 1 O 0.333333333 0.000000000 5.544873192 1 1 1 K_POINTS automatic 8 8 1 0 0 0 --------------------------------------------------- The pseudopotentials are all from the Quantum Espresso website, and are used without modification. I get total energies at optimized geometries of -43.3739979804 Ry for an isolated CO molecule, -1530.4827281024 Ry for the Au slab, and -1573.8569359340 Ry for CO on the slab. Everything looks reasonable in XCrysDen. Am I doing something obviously wrong? Thanks, Ben J. =================== Benjamin G. Janesko Assistant Professor Department of Chemistry Texas Christian University Office: SWR 428 http://personal.tcu.edu/bjanesko/ b.janesko at tcu.edu Phone: 1-817-257-6202 Fax: 1-817-257-5851 (attn:janesko) From ynwuyang at gmail.com Sat Jun 26 00:04:30 2010 From: ynwuyang at gmail.com (yuning wu) Date: Sat, 26 Jun 2010 06:04:30 +0800 Subject: [Pw_forum] meta-GGA (TPSS) PP generation code Message-ID: <4C2527EE.8050904@gmail.com> Hello, all, Does anybody have this meta-GGA (TPSS) PP generation code which was implemented in old version? I need it to generate PP and do test. Thanks in advance. Yuning Wu Graduate student in Physics Department of Physics and Quantum Theory Project University of Florida Gainesville, FL 32611 U. S. A. From mohnish.iitk at gmail.com Sat Jun 26 07:10:19 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 26 Jun 2010 10:40:19 +0530 Subject: [Pw_forum] Is there a way to fix the c of supercell and vary only a and b Message-ID: Dear QE users, I am doing supercell calculation for some systems. But I want to change the a and b parameter for the supercell but want to fix the c for that because the in plane lattice parameter(xy plane) should change on relaxation process. Right now I am using 'vc-relax' calculation for the same. But many times its given error " Enough space not allocated to fft grid". I am increasing the cell_factor to 1.8 which I think is very large value and this also makes the relaxation computationally expensive. Can anybody suggest a way to resolve it, I was thinking of the way to vary a and b and fix the c. Thanks a lot in advance. -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100626/581e8325/attachment.htm From giannozz at democritos.it Sat Jun 26 17:51:47 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Jun 2010 17:51:47 +0200 Subject: [Pw_forum] Is there a way to fix the c of supercell and vary only a and b In-Reply-To: References: Message-ID: <1EEFE9EF-0D7E-491C-878D-F081398D9B09@democritos.it> On Jun 26, 2010, at 7:10 , mohnish pandey wrote: > many times its given error " Enough space not allocated to fft grid" this means that you are starting from an initial cell that is too different from the final one. > I was thinking of the way to vary a and b and fix the c. look at "cell_dofree" variables and how they are used. 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 Jun 26 18:01:56 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Jun 2010 18:01:56 +0200 Subject: [Pw_forum] meta-GGA (TPSS) PP generation code In-Reply-To: <4C2527EE.8050904@gmail.com> References: <4C2527EE.8050904@gmail.com> Message-ID: <9553A220-C385-4BDF-9900-27B448EBB0B7@democritos.it> On Jun 26, 2010, at 24:04 , yuning wu wrote: > Does anybody have this meta-GGA (TPSS) PP generation code which was > implemented in old version? I need it to generate PP and do test. once upon a time I wrote an extension of the pseudopotential generation code to the meta-GGA case. It went missing when I moved back to Pisa. Not a big loss, though: that code was numerically unstable. Later Xiaofei Wang, then PhD student in Princeton, wrote a new version that he later sent to me for inclusion in the QE distribution, but I never found the time and the will to do it. I'll send you a copy of it. 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 Jun 26 18:50:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Jun 2010 18:50:06 +0200 Subject: [Pw_forum] Cannot reproduce standard CO/Au(111) adsorption energy calculations In-Reply-To: References: Message-ID: On Jun 25, 2010, at 19:34 , Janesko, Benjamin wrote: > Everything looks reasonable in XCrysDen and what is the C-Au or O-Au distance? it seems to me that the CO molecule is very far away from the gold surface. If so, it is normal to find very small binding energies 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 asubedi at gmail.com Sun Jun 27 03:45:20 2010 From: asubedi at gmail.com (asubedi) Date: Sat, 26 Jun 2010 21:45:20 -0400 Subject: [Pw_forum] npool and electron phonon calculation Message-ID: Dear All, I was wondering if it is possible to do electron phonon calculation with npool > 1. Apparently, this was implemented in some previous version but I cannot find it. Is this hard to implement in the current version of QE? Thanks, Alaska From mohnish.iitk at gmail.com Sun Jun 27 07:43:08 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 27 Jun 2010 11:13:08 +0530 Subject: [Pw_forum] Is there a way to fix the c of supercell and vary only a and b In-Reply-To: <1EEFE9EF-0D7E-491C-878D-F081398D9B09@democritos.it> References: <1EEFE9EF-0D7E-491C-878D-F081398D9B09@democritos.it> Message-ID: Dear Prof. Paolo, Sorry to bug you again but I am using 'cell_dofree" as 'xy' in the supercell calculation but even after using this flag the 'c' is varying at every step. I am attaching my input and output file(output file is not complete but it contains 3 iterations). On Sat, Jun 26, 2010 at 9:21 PM, Paolo Giannozzi wrote: > > On Jun 26, 2010, at 7:10 , mohnish pandey wrote: > > > many times its given error " Enough space not allocated to fft grid" > > this means that you are starting from an initial cell that is too > different > from the final one. > > > I was thinking of the way to vary a and b and fix the c. > > look at "cell_dofree" variables and how they are used. > > 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 > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100627/2ff559e4/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mnse.scf.in Type: application/octet-stream Size: 864 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100627/2ff559e4/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: mnse.scf.out Type: application/octet-stream Size: 93714 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100627/2ff559e4/attachment-0003.obj From sd.wang000 at gmail.com Sun Jun 27 13:15:00 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Sun, 27 Jun 2010 19:15:00 +0800 Subject: [Pw_forum] norm-conserving potential of Fluorine Message-ID: Dear all: How can I get the norm-conserving potential of Fluorine? Who has it and please help me. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100627/549e0e4d/attachment.htm From giannozz at democritos.it Sun Jun 27 20:43:14 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 Jun 2010 20:43:14 +0200 Subject: [Pw_forum] npool and electron phonon calculation In-Reply-To: References: Message-ID: <6A29C34D-504D-454B-9F41-649B59A171AD@democritos.it> On Jun 27, 2010, at 3:45 , asubedi wrote: > I was wondering if it is possible to do electron phonon calculation > with npool > 1. Apparently, this was implemented in some previous > version I don't think so > but I cannot find it. Is this hard to implement in the current > version of QE? I wouldn't say it is hard, but it is not trivial and this is why it was never implemented. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Jun 27 20:45:01 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 Jun 2010 20:45:01 +0200 Subject: [Pw_forum] Is there a way to fix the c of supercell and vary only a and b In-Reply-To: References: <1EEFE9EF-0D7E-491C-878D-F081398D9B09@democritos.it> Message-ID: <0AD4A4E2-EDB8-4717-82C2-F250D564D862@democritos.it> I don't think the version of the code you are using implements constraints ihn variable-cell optimization. It was implemented quite recently, I think P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Jun 27 20:48:51 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 Jun 2010 20:48:51 +0200 Subject: [Pw_forum] npool and electron phonon calculation In-Reply-To: <6A29C34D-504D-454B-9F41-649B59A171AD@democritos.it> References: <6A29C34D-504D-454B-9F41-649B59A171AD@democritos.it> Message-ID: <173239B7-722E-49DB-8F4F-7C4E35B4A1CB@democritos.it> On Jun 27, 2010, at 20:43 , Paolo Giannozzi wrote: > I wouldn't say it is hard, but it is not trivial and this is why it > was > never implemented. actually there is also another reason. The current implementation of electron-phonon coefficients is not satisfactory. There are better algorithms around, thus investing in the old algorithm doesn't seem such a great idea. Software implementing Wannier interpolation for electron-phonon calculations has been released recently and works in conjunction with QE: see epw.org.uk 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 cjobrien at ncsu.edu Sun Jun 27 20:54:56 2010 From: cjobrien at ncsu.edu (Christopher O'Brien) Date: Sun, 27 Jun 2010 14:54:56 -0400 Subject: [Pw_forum] PW very sensitive to number of processors and pools Message-ID: <2AB930F8-9661-4B33-B538-1CF4908EFBCA@ncsu.edu> I am trying to do benchmarks and determine how best to parallelize pw.x for scf calculations using a toy system consisting of a single Cu unit cell. However it seems as if there are 'magic' combinations of processors and pools that determine if a run will work. Is there a pattern to choosing these parameters? As an example, I used ewcut=35Ry, ecutrho=350Ry and a monkhorst-pack k-points grid. I have an older beowulf cluster with 2 single-core procs per node and 1GB RAM each. As an example of the sensitivity two cases are shown: kpoints nprocs npool nr3 nr3s npp npps Working 10x10x10 20 10 30 20 15 12 Working 20x20x20 32 2 30 20 2 2 Failing 30x30x30 20 2 30 20 4 3 Failing 30x30x30 64 8 30 20 4 3 As you can tell I am randomly guessing here. Even the 10x10x10 case took a lot of guessing to get it to work. All of the crashes occur in one of two places: 1.) During writing of the k-points, or 2.) while writing the band energies at each k-point. Case 1) > k( 282) = ( 0.7833333 -0.0500000 0.8166667), wk = 0.0008889 > k( 283) = ( 0.7500000 -0.0166667 0.7833333), wk = 0.0008889 > p1_8011: p4_error: net_recv read: probable EOF on socket: 1 > p7_25354: p4_error: net_recv read: probable EOF on socket: 1 > p19_22825: p4_error: net_recv read: probable EOF on socket: 1 Case 2) > k = 0.4500-0.4500 1.3500 ( 271 PWs) bands (ev): > > 7.6764 9.3915 9.6220 10.1803 10.9132 12.6419 16.5014 30.5475 > 33.0769 33.8058 Thanks in advance. =================================================================== Christopher J. O'Brien cjobrien at ncsu.edu Ph.D. Candidate Computational Materials Group Department of Materials Science & Engineering North Carolina State University __________________________________________________________________ Please send all documents in PDF, HTML, RTF, DVI, PS or plain text. For Word documents: Please use the 'Save as PDF' option before sending. =================================================================== From giannozz at democritos.it Sun Jun 27 21:46:25 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 Jun 2010 21:46:25 +0200 Subject: [Pw_forum] PW very sensitive to number of processors and pools In-Reply-To: <2AB930F8-9661-4B33-B538-1CF4908EFBCA@ncsu.edu> References: <2AB930F8-9661-4B33-B538-1CF4908EFBCA@ncsu.edu> Message-ID: On Jun 27, 2010, at 20:54 , Christopher O'Brien wrote: >> p1_8011: p4_error: net_recv read: probable EOF on socket: 1 can you reproduce these errors on other machines? If no, these are due, with (1-\epsilon) probability, to compiler or MPI library or system library bugs. 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 cjobrien at ncsu.edu Mon Jun 28 04:50:14 2010 From: cjobrien at ncsu.edu (Christopher O'Brien) Date: Sun, 27 Jun 2010 22:50:14 -0400 Subject: [Pw_forum] PW very sensitive to number of processors and pools In-Reply-To: References: <2AB930F8-9661-4B33-B538-1CF4908EFBCA@ncsu.edu> Message-ID: <7B569CAD-8028-4F6F-BFDE-B771244E87A6@ncsu.edu> Paolo, Thank you for the quick reply. I was able to run some tests on another cluster without any dependence on the number of processors or pools. For reference, the combination that failed was: ifort 9.0 with Intel's MPICH The working cluster used: ifort 10.1.022 with Intel's MPICH2 1.3a2 Thanks again. =================================================================== Christopher J. O'Brien Ph.D. Candidate Computational Materials Group Department of Materials Science & Engineering North Carolina State University __________________________________________________________________ Please send all documents in PDF, HTML, RTF, DVI, PS or plain text. For Word documents: Please use the 'Save as PDF' option before sending. =================================================================== On Jun 27, 2010, at 3:46 PM, Paolo Giannozzi wrote: > > On Jun 27, 2010, at 20:54 , Christopher O'Brien wrote: > >>> p1_8011: p4_error: net_recv read: probable EOF on socket: 1 > > can you reproduce these errors on other machines? If no, these > are due, with (1-\epsilon) probability, to compiler or MPI library or > system library bugs. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From wangqj1 at 126.com Mon Jun 28 11:16:21 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Mon, 28 Jun 2010 17:16:21 +0800 (CST) Subject: [Pw_forum] Diagonal values are not equivalent of dielectric tensor and effective charge Message-ID: <129eab2.b6b6.1297dd7ccb6.Coremail.wangqj1@126.com> Dear all When I calculated phonons dispersion with pwscf, I found the diagonal values are not equivalent of dielectric tensor and effective charge. It as follows: Dielectric Tensor: -214542629.159461200237 -0.000000017208 0.000000000000 -0.000000017208 -214542629.159430831671 0.000000000000 0.000000000000 0.000000000000 5.116454120232 Effective Charges E-U: Z_{alpha}{s,beta} atom # 1 1.000246806754 0.000000000000 0.000000000000 0.000000000000 1.000246806755 0.000000000000 0.000000000000 0.000000000000 2.497025839024 atom # 2 -0.753096041524 0.000000000000 0.000000000000 0.000000000000 -0.753096041523 0.000000000000 0.000000000000 0.000000000000 -1.984411167723 atom # 3 1.000246806754 0.000000000000 0.000000000000 0.000000000000 1.000246806755 0.000000000000 0.000000000000 0.000000000000 2.497025839024 atom # 4 -0.753096041524 0.000000000000 0.000000000000 0.000000000000 -0.753096041523 0.000000000000 0.000000000000 0.000000000000 -1.984411167723 Why the diagonal values are not equivalent ? How to solve this problem ? Any comments and suggestions will be highly appreciated! -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100628/26066ccd/attachment.htm From paulatto at sissa.it Mon Jun 28 12:19:58 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 28 Jun 2010 12:19:58 +0200 Subject: [Pw_forum] Diagonal values are not equivalent of dielectric tensor and effective charge In-Reply-To: <129eab2.b6b6.1297dd7ccb6.Coremail.wangqj1@126.com> References: <129eab2.b6b6.1297dd7ccb6.Coremail.wangqj1@126.com> Message-ID: On Mon, 28 Jun 2010 11:16:21 +0200, Q.J.Wang wrote: > -214542629.159461200237 Dear Q.J.Wang, from the ridiculous magnitude of this values I can guess there is something wrong with you system. What it is, nobody can say without seeing the input file. best regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From huazhorg at 163.com Tue Jun 29 05:14:10 2010 From: huazhorg at 163.com (=?gbk?B?wfW7qtbS?=) Date: Tue, 29 Jun 2010 11:14:10 +0800 (CST) Subject: [Pw_forum] What's real imaginary frequency of the transition state? Message-ID: <59886114.48eb.12981b28ff5.Coremail.huazhorg@163.com> Hi, dear all, There are always some imaginary frequencies in the output of ph.x, whether it is in the calculation of transition states or not. why? In searching transition states, there are also many imaginary frequencies in the output file,usually. I'm confused. How I can pick out the real imaginary frequency of the transition state? Below is an example of a part of transition state calculation output: ************************************************************************** omega( 1) = -6.576208 [THz] = -219.360155 [cm-1] omega( 2) = -4.209028 [THz] = -140.398981 [cm-1] omega( 3) = -2.230600 [THz] = -74.405297 [cm-1] omega( 4) = -0.970684 [THz] = -32.378747 [cm-1] omega( 5) = -0.867754 [THz] = -28.945364 [cm-1] omega( 6) = 1.971578 [THz] = 65.765185 [cm-1] omega( 7) = 2.101039 [THz] = 70.083572 [cm-1] omega( 8) = 2.527013 [THz] = 84.292637 [cm-1] omega( 9) = 3.283256 [THz] = 109.518370 [cm-1] omega(10) = 3.705495 [THz] = 123.602844 [cm-1] omega(11) = 4.142298 [THz] = 138.173116 [cm-1] omega(12) = 4.503254 [THz] = 150.213369 [cm-1] omega(13) = 5.135967 [THz] = 171.318563 [cm-1] omega(14) = 5.632122 [THz] = 187.868601 [cm-1] omega(15) = 5.854701 [THz] = 195.293098 [cm-1] omega(16) = 6.304154 [THz] = 210.285335 [cm-1] omega(17) = 6.549402 [THz] = 218.465998 [cm-1] omega(18) = 7.221822 [THz] = 240.895661 [cm-1] omega(19) = 7.319292 [THz] = 244.146926 [cm-1] omega(20) = 7.657549 [THz] = 255.430048 [cm-1] omega(21) = 7.695989 [THz] = 256.712278 [cm-1] omega(22) = 8.930698 [THz] = 297.898015 [cm-1] omega(23) = 9.323473 [THz] = 310.999665 [cm-1] omega(24) = 9.878343 [THz] = 329.508231 [cm-1] omega(25) = 10.581080 [THz] = 352.949188 [cm-1] omega(26) = 11.214091 [THz] = 374.064288 [cm-1] omega(27) = 11.299609 [THz] = 376.916881 [cm-1] omega(28) = 11.865318 [THz] = 395.787052 [cm-1] omega(29) = 12.016973 [THz] = 400.845740 [cm-1] omega(30) = 12.304312 [THz] = 410.430402 [cm-1] omega(31) = 13.491423 [THz] = 450.028405 [cm-1] omega(32) = 14.502625 [THz] = 483.758708 [cm-1] omega(33) = 14.635485 [THz] = 488.190483 [cm-1] omega(34) = 15.048602 [THz] = 501.970660 [cm-1] omega(35) = 15.776018 [THz] = 526.234805 [cm-1] omega(36) = 17.267246 [THz] = 575.977162 [cm-1] omega(37) = 17.900635 [THz] = 597.104868 [cm-1] omega(38) = 18.180537 [THz] = 606.441468 [cm-1] omega(39) = 18.197251 [THz] = 606.998978 [cm-1] omega(40) = 18.545524 [THz] = 618.616204 [cm-1] omega(41) = 20.317191 [THz] = 677.713051 [cm-1] omega(42) = 23.728955 [THz] = 791.517987 [cm-1] omega(43) = 34.015744 [THz] = 1134.650635 [cm-1] omega(44) = 35.280937 [THz] = 1176.853218 [cm-1] omega(45) = 42.068145 [THz] = 1403.251608 [cm-1] omega(46) = 46.532727 [THz] = 1552.175006 [cm-1] omega(47) = 86.122480 [THz] = 2872.755808 [cm-1] omega(48) = 89.220661 [THz] = 2976.100690 [cm-1] ************************************************************************** Mode symmetry, C_1 (1) point group: omega( 1 - 1) = -219.4 [cm-1] --> A I+R omega( 2 - 2) = -140.4 [cm-1] --> A I+R omega( 3 - 3) = -74.4 [cm-1] --> A I+R omega( 4 - 4) = -32.4 [cm-1] --> A I+R omega( 5 - 5) = -28.9 [cm-1] --> A I+R omega( 6 - 6) = 65.8 [cm-1] --> A I+R omega( 7 - 7) = 70.1 [cm-1] --> A I+R omega( 8 - 8) = 84.3 [cm-1] --> A I+R omega( 9 - 9) = 109.5 [cm-1] --> A I+R omega( 10 - 10) = 123.6 [cm-1] --> A I+R omega( 11 - 11) = 138.2 [cm-1] --> A I+R omega( 12 - 12) = 150.2 [cm-1] --> A I+R omega( 13 - 13) = 171.3 [cm-1] --> A I+R omega( 14 - 14) = 187.9 [cm-1] --> A I+R omega( 15 - 15) = 195.3 [cm-1] --> A I+R omega( 16 - 16) = 210.3 [cm-1] --> A I+R omega( 17 - 17) = 218.5 [cm-1] --> A I+R omega( 18 - 18) = 240.9 [cm-1] --> A I+R omega( 19 - 19) = 244.1 [cm-1] --> A I+R omega( 20 - 20) = 255.4 [cm-1] --> A I+R omega( 21 - 21) = 256.7 [cm-1] --> A I+R omega( 22 - 22) = 297.9 [cm-1] --> A I+R omega( 23 - 23) = 311.0 [cm-1] --> A I+R omega( 24 - 24) = 329.5 [cm-1] --> A I+R omega( 25 - 25) = 352.9 [cm-1] --> A I+R omega( 26 - 26) = 374.1 [cm-1] --> A I+R omega( 27 - 27) = 376.9 [cm-1] --> A I+R omega( 28 - 28) = 395.8 [cm-1] --> A I+R omega( 29 - 29) = 400.8 [cm-1] --> A I+R omega( 30 - 30) = 410.4 [cm-1] --> A I+R omega( 31 - 31) = 450.0 [cm-1] --> A I+R omega( 32 - 32) = 483.8 [cm-1] --> A I+R omega( 33 - 33) = 488.2 [cm-1] --> A I+R omega( 34 - 34) = 502.0 [cm-1] --> A I+R omega( 35 - 35) = 526.2 [cm-1] --> A I+R omega( 36 - 36) = 576.0 [cm-1] --> A I+R omega( 37 - 37) = 597.1 [cm-1] --> A I+R omega( 38 - 38) = 606.4 [cm-1] --> A I+R omega( 39 - 39) = 607.0 [cm-1] --> A I+R omega( 40 - 40) = 618.6 [cm-1] --> A I+R omega( 41 - 41) = 677.7 [cm-1] --> A I+R omega( 42 - 42) = 791.5 [cm-1] --> A I+R omega( 43 - 43) = 1134.7 [cm-1] --> A I+R omega( 44 - 44) = 1176.9 [cm-1] --> A I+R omega( 45 - 45) = 1403.3 [cm-1] --> A I+R omega( 46 - 46) = 1552.2 [cm-1] --> A I+R omega( 47 - 47) = 2872.8 [cm-1] --> A I+R omega( 48 - 48) = 2976.1 [cm-1] --> A I+R ************************************************************************** ?????? the ecutwfc of neb calculation is 30.0 Ry, the tr2_ph of vibration calculation is 1.0d-14. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100629/ebe078e1/attachment-0001.htm From masoudnahali at live.com Tue Jun 29 08:06:43 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Tue, 29 Jun 2010 06:06:43 +0000 Subject: [Pw_forum] electrochemical potential Message-ID: Dear QE users How can one apply electrochemical potential to a metal in quantum espresso? for example +0.2 or +1.0 that is proper for oxidation and also negative extents like -0.3 and -1.5. I think that it may related to fermi level but I can not apply. I appreciate to your help. very best wishes Masoud Nahali Sharif University of Technology Ph. D student of physical chemistry _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100629/c43316d5/attachment.htm From baroni at sissa.it Tue Jun 29 08:16:57 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 29 Jun 2010 08:16:57 +0200 Subject: [Pw_forum] What's real imaginary frequency of the transition state? In-Reply-To: <59886114.48eb.12981b28ff5.Coremail.huazhorg@163.com> References: <59886114.48eb.12981b28ff5.Coremail.huazhorg@163.com> Message-ID: <5F4AB787-08B4-4062-B3ED-4594B9A4BD34@sissa.it> Dear Mr X, if your SCF calculation is well done (i.e. everything is well converged) you are not at a saddle point. In any case, it is always a good idea to attached the input file and relevant portions of the output file. Not to mention your signature and affiliation, which we have begged zillions of times to include. SB On Jun 29, 2010, at 5:14 AM, ??? wrote: > Hi, dear all, > There are always some imaginary frequencies in the output of ph.x, whether it is in the calculation of transition states or not. why? In searching transition states, there are also many imaginary frequencies in the output file,usually. I'm confused. How I can pick out the real imaginary frequency of the transition state? Below is an example of a part of transition state calculation output: --- 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/20100629/00ef6e38/attachment.htm From giannozz at democritos.it Tue Jun 29 14:41:03 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Jun 2010 14:41:03 +0200 Subject: [Pw_forum] norm-conserving potential of Fluorine In-Reply-To: References: Message-ID: <4C29E9DF.4030508@democritos.it> shudong wang wrote: > How can I get the norm-conserving potential of Fluorine? > Who has it and please help me. see atomic_doc/pseudo-gen.pdf P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Jun 29 14:42:04 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Jun 2010 14:42:04 +0200 Subject: [Pw_forum] Eu or Sm Pseudo Potential In-Reply-To: References: Message-ID: <4C29EA1C.5020209@democritos.it> S. K. S. wrote: > Does anybody have Eu or Sm (LDA/GGA and Ultra-soft/Norm-conserving) > pseudopotential? same as previoous message P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Jun 29 15:20:53 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Jun 2010 15:20:53 +0200 Subject: [Pw_forum] electrochemical potential In-Reply-To: References: Message-ID: <4C29F335.4010703@democritos.it> Masoud Nahali wrote: > How can one apply electrochemical potential to a metal in quantum > espresso? for example +0.2 or +1.0 that is proper for oxidation and also > negative extents like -0.3 and -1.5. > I think that it may related to fermi level but I can not apply. what you can do is to change the charge state of the (super-)cell, using variable "tot_charge" P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From limch at ihpc.a-star.edu.sg Wed Jun 30 09:43:52 2010 From: limch at ihpc.a-star.edu.sg (Lim Chiang Huay, Freda) Date: Wed, 30 Jun 2010 15:43:52 +0800 Subject: [Pw_forum] How to set nbnd value for berry phase calculations? Message-ID: Hi all, I'm doing Berry Phase calculations for the first time for BiFeO3. I met with some problems in setting nbnd values for the scf and nscf calculations. And I can't find an answer in previous forum post. I used the pseudopotentials available in the website http://www.pwscf.org/pseudo.php They are: Bi.pbe-d-mt.UPF Fe.pbe-nd-rrkjus.UPF O.pbe-mt.UPF and from the pseudopotentials, there should be 41 electrons in a cell. From the manual nbnd = nelect/2. I've tried different combinations of nbnd values for scf and nscf jobs and non was able to give me the polarization value. The following are the some selected cases and their error msg: Case(1) *.scf, nbnd=21; *.nscf, nbnd=21 Both jobs crash Error for scf: too few bands Error for nscf: starting and expected charges differ Case(2) *.scf, nbnd=43; *.nscf, nbnd=42 Scf converged. Nscf crashed. Error for nscf: Polarization only for insulators and no empty bands Case(3) *.scf, nbnd=42; *.nscf, nbnd=42 Scf converged. Nscf crashed. Error for scf: too few spin up bands Error for nscf: starting and expected charges differ My input files are as follows: SCF JOB: &control calculation = 'scf', restart_mode = 'from_scratch' pseudo_dir = '/Home6/cc/ihpclimc/BP_CAL/PPOT' outdir = '/Scratch/ihpclimc/BERRY_PHASE_CALCULATIONS/Try_BP/OUTDIR', / &system ibrav=5 celldm(1)=10.6523, celldm(4)=0.50988, nat=10 ntyp=3 nbnd=42 ecutwfc=50.0 occupations = 'fixed' degauss=0.00 nspin=2 multiplicity=5 lda_plus_u=.true. Hubbard_U(2)=6 / &electrons conv_thr = 1e-12, mixing_beta=0.3, diagonalization='cg', / ATOMIC_SPECIES Bi 209.0 Bi.pbe-d-mt.UPF Fe 55.85 Fe.pbe-nd-rrkjus.UPF O 16.00 O.pbe-mt.UPF ATOMIC_POSITIONS crystal Bi 0.000 0.000 0.000 0 0 0 Bi 0.500 0.500 0.500 0 0 0 Fe 0.219 0.219 0.219 Fe 0.719 0.719 0.719 O 0.445 0.032 0.897 O 0.897 0.445 0.032 O 0.032 0.897 0.445 O 1.397 0.532 0.945 O 0.532 0.945 1.397 O 0.945 1.397 0.532 K_POINTS {automatic} 1 1 1 1 1 1 NSCF JOB: &control calculation = 'nscf', pseudo_dir = '/Home6/cc/ihpclimc/BP_CAL/PPOT' outdir = '/Scratch/ihpclimc/BERRY_PHASE_CALCULATIONS/Try_BP/OUTDIR', lberry = .true. gdir = 3 nppstr = 7 / &system ibrav=5 celldm(1)=10.6523, celldm(4)=0.50988, nat=10 ntyp=3 nbnd=42 ecutwfc=50.0 occupations = 'fixed' degauss=0.00 nspin=2 multiplicity=5 lda_plus_u=.true. Hubbard_U(2)=6 / &electrons conv_thr = 1e-12, mixing_beta=0.3, diagonalization='cg', / ATOMIC_SPECIES Bi 209.0 Bi.pbe-d-mt.UPF Fe 55.85 Fe.pbe-nd-rrkjus.UPF O 16.00 O.pbe-mt.UPF ATOMIC_POSITIONS crystal Bi 0.000 0.000 0.000 0 0 0 Bi 0.500 0.500 0.500 0 0 0 Fe 0.219 0.219 0.219 Fe 0.719 0.719 0.719 O 0.445 0.032 0.897 O 0.897 0.445 0.032 O 0.032 0.897 0.445 O 1.397 0.532 0.945 O 0.532 0.945 1.397 O 0.945 1.397 0.532 K_POINTS {automatic} 4 4 4 1 1 1 Can anyone help? Thanks, Rgds Freda Lim Institute of High Performance Computing 1 Fusionopolis Way, #16-16 Connexis Singapore 138632 Email: limch at ihpc.a-star.edu.sg ________________________________ This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100630/ef30e50e/attachment-0001.htm From giannozz at democritos.it Wed Jun 30 10:08:55 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 30 Jun 2010 10:08:55 +0200 Subject: [Pw_forum] How to set nbnd value for berry phase calculations? In-Reply-To: References: Message-ID: <4C2AFB97.2090809@democritos.it> Lim Chiang Huay, Freda wrote: > and from the pseudopotentials, there should be 41 electrons in a cell. > From the manual nbnd = nelect/2. this is true for insulators without spin polarization. If you have an odd number of electrons, your system cannot be an insulator (and it should be treated as spin polarized) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From suza.rri at gmail.com Wed Jun 30 11:59:44 2010 From: suza.rri at gmail.com (Suza W) Date: Wed, 30 Jun 2010 11:59:44 +0200 Subject: [Pw_forum] ultrasoft Cs pseudopotential In-Reply-To: References: Message-ID: Dear QE USERS, QE pseudo site does not have Cs ultrasoft pseudo-potential. Can you anybody help me to get the ultasoft (LDA&GGA) pseudo-potential for Cs? I have got the following link in the forum : http://www.fisica.uniud.it/~giannozz/public/Cs.tar.gz but not able to open this. It seems that the above link is dead. Any help in this regard will be highly appreciated. Yours sincerely, Suza W. Ph. D. student RRI, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100630/be33ccd5/attachment.htm From seoman at yandex.ru Wed Jun 30 13:50:39 2010 From: seoman at yandex.ru (Oleg Sergeev) Date: Wed, 30 Jun 2010 15:50:39 +0400 Subject: [Pw_forum] electron-phonon coupling and pseudopotential choice Message-ID: <184671277898639@web104.yandex.ru> Dear all, calculating the electron-phonon coupling factor (lambda) for Aluminum i obtained that it depends very strongly on the PP i use. Trying different PPs from the QE package i got lambda values from 0 to 4.5 when the known value is about 0.4. To calculate lambda i just performed example07 with different pseudopotentials. What did i do wrong? Oleg Sergeev, JIHT RAS, Moscow. From degironc at sissa.it Wed Jun 30 14:17:15 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 30 Jun 2010 14:17:15 +0200 Subject: [Pw_forum] electron-phonon coupling and pseudopotential choice In-Reply-To: <184671277898639@web104.yandex.ru> References: <184671277898639@web104.yandex.ru> Message-ID: <4C2B35CB.7060603@sissa.it> example07 is meant to show the procedure to compute el-ph coupling NOT to represent a converged calculation of it. Have you checked convergence of your calculation w.r.t . cutoff, k-points and so on. Have you calculate consistently the lattice parameter of your system ? stefano Oleg Sergeev wrote: > Dear all, > > calculating the electron-phonon coupling factor (lambda) for Aluminum i obtained that it depends very strongly on the PP i use. > Trying different PPs from the QE package i got lambda values from 0 to 4.5 when the known value is about 0.4. To calculate > lambda i just performed example07 with different pseudopotentials. What did i do wrong? > > Oleg Sergeev, > JIHT RAS, Moscow. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From masoudnahali at live.com Wed Jun 30 15:11:04 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Wed, 30 Jun 2010 13:11:04 +0000 Subject: [Pw_forum] optimizing cell parameters and choosing k-points of graphite Message-ID: Dear Quantum Espresso users I have done a 'vc-relax' calculation to find the cell parameters of graphite. The selected k-points are (4*4*4) and automatic. obtained cell parameters: a = 2.469, b = 2.469, c = 7.069, then I used these values to 'relax' the atoms in cell (k-points were 4*4*4 too) . Finally I used the obtained cell parameters to find the proper k-points for graphite. I performed some 'scf' calculations with different k-points and in whole of them the cell parameters and positions were what is obtained from the relax part with 4*4*4 k-points. 'scf' energy with different k-points: k-points energy (4*4*4): -45.5732791969 Ry (5*5*5): -45.57637408 Ry (6*6*6): -45.57592043 Ry (7*7*7): -45.57420434 Ry (8*8*8): -45.57474553 Ry (9*9*9): -45.57500776 Ry (10*10*10): -45.57454272 Ry (11*11*11): -45.57464463 Ry (12*12*12): -45.57480118 Ry (13*13*13): -45.57462800 Ry (14*14*14): -45.57463705 Ry (15*15*15): -45.57473135 Ry (16*16*16): -45.57465384 Ry I appreciate if one help me to find the answers to these questions: 1. Is the whole procedure plausible ?2. why a energy convergence is not occurred after selecting these high values of k-points?3. How can I find the proper k-points safely? the input file for 'scf' calculation: &CONTROL calculation = "scf", pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo", outdir = "/home/koa/tmp", etot_conv_thr= 1.0D-4, forc_conv_thr= 1.0D-3, nstep=150, / &SYSTEM ibrav = 4, a = 2.469, b = 2.469, c = 7.069, cosab = -0.5, cosac = 1.0, cosbc = 1.0, nat = 4, ntyp = 1, ecutwfc = 30.D0, ecutrho = 200.D0 occupations = 'smearing' smearing ='mp', degauss = 0.01, nspin = 2, starting_magnetization(1)= 1.0, / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.7D0, diagonalization = "david", / &IONS ion_dynamics="bfgs" / ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF ATOMIC_POSITIONS {angstrom} C 0.000000000 0.000000000 0.000000000 C 0.000000000 1.425534302 0.000000000 C 0.000000000 0.000000000 3.534553118 C 1.234548920 0.712767151 3.534553118 K_POINTS {automatic} 16 16 16 1 1 1 the vc-relax input: &CONTROL calculation = "vc-relax", pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo", outdir = "/home/koa/tmp", etot_conv_thr= 1.0D-4, forc_conv_thr= 1.0D-3, dt=70, nstep=150, / &SYSTEM ibrav = 4, a = 2.456, b = 2.456, c = 6.696, cosab = -0.5, cosac = 1.0, cosbc = 1.0, nat = 4, ntyp = 1, ecutwfc = 30.D0, ecutrho = 200.D0 occupations = 'smearing' smearing ='mp', degauss = 0.01, nspin = 2, starting_magnetization(1)= 1.0, / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.7D0, diagonalization = "david", / &IONS ion_dynamics="bfgs" / &CELL cell_dynamics = 'damp-w', press = 0.0 , / ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF ATOMIC_POSITIONS {angstrom} C 0.00000000 0.00000000 0.00000000 C 0.00000000 1.41797226 0.00000000 C 0.00000000 0.00000000 3.34800000 C 1.22800000 0.70898613 3.34800000 K_POINTS {automatic} 4 4 4 1 1 1 very best wishes Many ThanksMasoud NahaliSharif University of Technology _________________________________________________________________ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100630/19e3127c/attachment.htm From seoman at yandex.ru Wed Jun 30 17:10:48 2010 From: seoman at yandex.ru (Oleg Sergeev) Date: Wed, 30 Jun 2010 19:10:48 +0400 Subject: [Pw_forum] electron-phonon coupling and pseudopotential choice In-Reply-To: <4C2B35CB.7060603@sissa.it> References: <184671277898639@web104.yandex.ru> <4C2B35CB.7060603@sissa.it> Message-ID: <261531277910649@web57.yandex.ru> stefano, thank you very much for the quick answer. i think my fault was that i didn't recalculate the lattice parameter for each new PP. i'll check it. Oleg Sergeev, JIHT RAS, Moscow. > example07 is meant to show the procedure to compute el-ph coupling NOT > to represent a converged calculation of it. > Have you checked convergence of your calculation w.r.t . cutoff, > k-points and so on. > Have you calculate consistently the lattice parameter of your system ? > stefano