[Pw_forum] Pseudoptential for Nd
Javier Antonio Montoya wrote: > Is there anyone in the forum who can provide me with a pseudo-potential > (nonlinear core-correction + ultrasoft + PBE) for any of the following > elements? : Sm, Nd, Pr, Ce . We are running experiments that include > those elements and I could provide feedback on how well those pseudos > reproduce experimental properties, such as vibrational spectra and > lattice parameters at different pressure conditions; in order to include > them in the PWscf.org web page. Nd is the one that we are going to > measure first, so, getting that one would be cool. as I already mentioned several times in this forum: the problem with such elements is not much the pseudopotential (which IS anyway a problem: generating ultrasoft PP's for those elements is a full-time job) but the reliability of the current DFT. Years ago I tried something with Pr, with less than moderate success. I'll try to locate those files if they still exists. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] Defining an antiferromagnetic graphene nanoribbon
Adriano.Mosca.Conte at roma2.infn.it wrote: > 3) I'm not sure at 100% that the symbols "-" and "+" are allowed to > specify atomic names. I think they are. They are read and treated as fortran character variables. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] Defining an antiferromagnetic graphene nanoribbon
It seems ok apart some details: 1) You have to define DIR. 2) The cell parameters with ibrav=8 have to be specified by: celldm(1)=a,celldm(2)=b/a,celldm(3)=c/a 3) I'm not sure at 100% that the symbols "-" and "+" are allowed to specify atomic names. > Dear PW users: > > I want to carry out a single point calculation of an antiferromagnetic > graphene nanoribbon with PWscf. Since such a system is magnetic, with a > specific magnetic orientation for the edge carbons, I have to perform a > spin-polarized calculation. I'd like to know if the following PW input is > suitable for such a calculation. > > >calculation = 'scf' , > restart_mode = 'from_scratch' , > pseudo_dir = '$DIR' , >/ > > ibrav = 8, > A = 17.482046 , > B = 20.00 , > C = 15.00 , >nat = 70 , > ntyp = 4, >ecutwfc = 20.00 , >ecutrho = 80.00 , >occupations = 'smearing' , >degauss = 0.01 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = -1.0 , > starting_magnetization(2) = 1.0 , > starting_magnetization(3) = 0.0 , > starting_magnetization(4) = 0.0 , >/ > > conv_thr = 1.0D-6 , >startingpot = 'atomic', >startingwfc = 'atomic', >mixing_mode = 'plain' , >mixing_beta = 0.25 , >diagonalization = 'david' , > / > ATOMIC_SPECIES > C-1 12.0107 C.pbe.UPF > C+1 12.0107 C.pbe.UPF > C 12.0107 C.pbe.UPF > H 1.0079 H.pbe.UPF > ATOMIC_POSITIONS angstrom > C+1 1.249543 -0.7110740.00 > C 0.000947 -0.016393 -0.01 > C 0.0008441.443145 -0.01 > C 1.2493812.1599540.01 > C 1.2494093.6089460.01 > C 0.0008434.325668 -0.01 > C 0.0009395.7852830.00 > C-1 1.2495156.479991 -0.01 > H 1.249981 -1.8256310.00 > H 1.2499817.5944130.00 > C+1 3.746978 -0.7110740.00 > C 2.498382 -0.016393 -0.01 > C 2.4982791.443145 -0.01 > C 3.7468162.1599540.01 > C 3.7468443.6089460.01 > C 2.4982784.325668 -0.01 > C 2.4983745.7852830.00 > C-1 3.7469506.479991 -0.01 > H 3.747416 -1.8256310.00 > H 3.7474167.5944130.00 > C+1 6.244413 -0.7110740.00 > C 4.995817 -0.016393 -0.01 > C 4.9957141.443145 -0.01 > C 6.2442512.1599540.01 > C 6.2442793.6089460.01 > C 4.9957134.325668 -0.01 > C 4.9958095.7852830.00 > C-1 6.2443856.479991 -0.01 > H 6.244851 -1.8256310.00 > H 6.2448517.5944130.00 > C+1 8.741849 -0.7110740.00 > C 7.493253 -0.016393 -0.01 > C 7.4931501.443145 -0.01 > C 8.7416872.1599540.01 > C 8.7417153.6089460.01 > C 7.4931494.325668 -0.01 > C 7.4932455.7852830.00 > C-1 8.7418216.479991 -0.01 > H 8.742287 -1.8256310.00 > H 8.7422877.5944130.00 > C+1 11.239284 -0.7110740.00 > C 9.990688 -0.016393 -0.01 > C 9.9905851.443145 -0.01 > C 11.2391222.1599540.01 > C 11.2391503.6089460.01 > C 9.9905844.325668 -0.01 > C 9.9906805.7852830.00 > C-1 11.2392566.479991 -0.01 > H 11.239722 -1.8256310.00 > H 11.2397227.5944130.00 > C+1 13.736719 -0.7110740.00 > C 12.488123 -0.016393 -0.01 > C 12.4880201.443145 -0.01 > C 13.7365572.1599540.01 > C 13.7365853.6089460.01 > C 12.4880194.325668 -0.01 > C 12.4881155.7852830.00 > C-1 13.7366916.479991 -0.01 > H 13.737157 -1.8256310.00 > H 13.7371577.5944130.00 > C+1 16.234154 -0.7110740.00 > C 14.985558 -0.016393 -0.01 > C 14.9854551.443145 -0.01 > C 16.2339922.1599540.01 > C 16.2340203.6089460.01 > C 14.9854544.325668 -0.01 > C 14.9855505.7852830.00 > C-1 16.2341266.479991 -0.01 >
[Pw_forum] Pseudoptential for Nd
Hi Paolo On Fri, May 9, 2008 at 11:05 AM, Paolo Giannozzi wrote: > Javier Antonio Montoya wrote: > as I already mentioned several times in this forum: the problem with > such elements is not much the pseudopotential (which IS anyway a > problem: generating ultrasoft PP's for those elements is a full-time > job) but the reliability of the current DFT. Years ago I tried something > with Pr, with less than moderate success. I'll try to locate those > files if they still exists. > > Paolo > -- Thanks a lot, I would really appreciate if you can find your Pr pseudo, I am willing to take that risk. Same regarding the other ones, in case somebody already have them. The matter is that experimentally we already have the Raman and Infrared peak positions, plus the lattice constants, therefore, it will be pretty easy to decide whether or not the results make some sense and then, to use them to support some microscopic analysis of the physics that is going on in our samples. Each material contains a single rare-earth element but it also contains oxygen and iron, I think there isn't a big risk on using the ones available from the repository in PWscf.org for those other two, therefore I just need to satisfy the NLCC, Van-US, PBE requirement also for the rare-earths in order to make them match. Cheers, Javier. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/f74a2e9f/attachment.htm
[Pw_forum] Pseudoptential for Nd
On Fri, 9 May 2008, Javier Antonio Montoya wrote: javier, JAM> Thanks a lot, I would really appreciate if you can find your Pr pseudo, I am JAM> willing to take that risk. Same regarding the other ones, in case somebody JAM> already have them. The matter is that experimentally we already have the JAM> Raman and Infrared peak positions, plus the lattice constants, therefore, it JAM> will be pretty easy to decide whether or not the results make some sense and what paolo was pointing out is that you have a _fundamental_ problem. so even if you get a match, it will be by accident and not by design. what would that prove? only that you got lucky! yes, you want to match the experiment, but you want to match it for right reasons. i've seen this with uranium for example. it was giving reasonable results for some uranium oxide compounds at some lattice constant values but then it would just give complete crap at some others. JAM> then, to use them to support some microscopic analysis of the physics that JAM> is going on in our samples. Each material contains a single rare-earth JAM> element but it also contains oxygen and iron, I think there isn't a big risk so if you get crap for one element out of many (and i would not be so certain about iron either, that can be pretty nasty, too), how does that make your results better than if all elements would be doubtful. the only difference is that the error will be less obvious. JAM> on using the ones available from the repository in PWscf.org for those other JAM> two, therefore I just need to satisfy the NLCC, Van-US, PBE requirement also JAM> for the rare-earths in order to make them match. why? all you have to match is the functional! ...and as paolo had pointed out in some other mail, it looks like the vanderbilt type ultrasofts don't perform so well for "tricky" elements. it is definitely tricky to even get those potentials created with the vanderbilt code in a way they look reasonable to begin with. cheers, axel. JAM> JAM> Cheers, JAM> JAM> Javier. JAM> -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] Defining an antiferromagnetic graphene nanoribbon
Hi, Konstantin: thank you very much. Such a large cutoff (80 Ry) is necessary for convergence? Or maybe I'm using one quite small (20 Ry)... []s, Roberto Konstantin Kudin wrote: Hi Roberto, Here is a ribbon input that works for sure: https://kiev.princeton.edu/misc/rg_07.scf.in (get PPs from the PWSCF website) Good luck! Kostya Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/7fb147dd/attachment.htm
[Pw_forum] openmp vs mpich performance with MKL 10.x
Thank you Axel, for all the time and the explanations of the deep numerical details. I will give up at his point. I am satisfied to know that I am not wasting CPU resources due to bad configuration, and I will keep both MPI and OpenMP compilations.. I will try to add to the benchmark of Nicola with CP. Best regards -- Eduardo Menendez -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/e749495a/attachment-0001.htm
[Pw_forum] Au relaxation error
Dear Axel, Thanks for pointing this out! I am already aware of it. I thought that we only need to specify the single unit cell parameter. For my case, I have like 6 unit cell aligned in one direction. How can I find out the new lattice parameter and symmetry of the nanostructure (6 unit cell)? Your suggestions are welcomed! Thanks in advance for your help! Mohamed Sabri Majdoub PhD candidate Mechanical Engineering University of Houston, TX,USA - Original Message - From: Axel Kohlmeyer <akohl...@cmm.chem.upenn.edu> Date: Thursday, May 8, 2008 2:34 pm Subject: Re: [Pw_forum] Au relaxation error To: Mohamed.Majdoub at mail.uh.edu Cc: pw_forum at pwscf.org > On Thu, 8 May 2008, Mohamed.Majdoub at mail.uh.edu wrote: > > MM> Dear users, > > mohamed, > > please _first_ study the online documentation, troubleshooting > tips and the mailing list archives. this error is one of the > most frequently reported ones... > > cheers, > ?? axel. > > > p.s.: ...and while you are at it, please consider the policy here > to state your name and affiliation. thanks. > > MM> > MM> - > ---? > MM> ?? warning: symmetry operation #? 2 not allowed.?? > fractional translation: > MM> ?? 0.0139992 -0.0139992? 0.000? in crystal coordinates > MM> warning: symmetry operation #? 7 not allowed.?? > fractional translation: > MM> ?? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates > MM> warning: symmetry operation #? 8 not allowed.?? > fractional translation: > MM> ?? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates > MM> warning: symmetry operation # 27 not allowed.?? > fractional translation: > MM> ?? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates > MM> warning: symmetry operation # 28 not allowed.?? > fractional translation: > MM> ?? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates > MM> warning: symmetry operation # 29 not allowed.?? > fractional translation: > MM> ?? 0.0139992 -0.0139992? 0.000? in crystal coordinates > MM> ... > MM> > MM> ? Initial potential from superposition of free atoms > MM> > MM> starting charge? 395.74037, renormalised to? 396.0 > MM> Starting wfc are atomic > MM> > MM> > ?%%MM> > from cdiaghg : error #?? 325 > MM> info =/= 0 > MM> > ?%%MM> > > MM> stopping ... > MM> - > --- > MM> > MM> > MM> > > -- > === > Axel Kohlmeyer?? > akohlmey at cmm.chem.upenn.edu?? http://www.cmm.upenn.edu > ?? Center for Molecular Modeling?? -- > ?? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582,? fax: 1-215-573-6233,? office- > tel: 1-215-898-5425 > === > If you make something idiot-proof, the universe creates a better > idiot. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/38adc6ab/attachment.htm
[Pw_forum] Au relaxation error
Dear Mohamed Majdoub, have you checked your structure with some visualization tool like xcrysden or similar ? remember that celldm(1) is given in bohr radii (7.6 a.u., about 4 Angstrom) while your atomic positions, given in angstrom, extend from 0 to 14 Angstrom.. it seems to me quite unlikely that your structure is what you think it is. hope it helps, stefano de Gironcoli - SISSA and DEMOCRITOS Mohamed.Majdoub at mail.uh.edu wrote: > Dear users, > > Thanks professor > I am a new pwscf user. I have been trying to do a geometry relaxation > of a gold nanocluster (few wunit cells of Au). The objective is to put > this metal in contact with an MgO insulator and relax the 2 structures > to find out the optimal interface configuration. As a first trial, I > am relaxing only the Au alone. But I keep getting error message. The > Au has fcc unit cell with lattice constant 4.0783 angstrom = 7.70687 a.u. > > calculation = "relax", > pseudo_dir = "/pwscf/pseudo", > outdir = "/pwscf/pwscftemp", > / > > ibrav = 2, > celldm(1) = 7.6533D0, > nat = 36, > ntyp= 1, > ecutwfc = 30.D0, > occupations = "smearing", > smearing= "gaussian", > degauss = 0.005D0, > / > > conv_thr= 1.D-6, > mixing_beta = 0.3D0, > / > > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", > / > ATOMIC_SPECIES > Au 196.96655 Au.pz-d-van.UPF > ATOMIC_POSITIONS angstrom > Au 0.00.0 -0.0 > Au 0.02.039152.03915 > Au 2.039150.02.03915 > Au 2.039152.039150.0 > Au 4.078300.0 -0.0 > Au 4.078302.039152.03915 > Au 0.04.07830 -0.0 > Au 2.039154.078302.03915 > Au 0.00.04.07830 > Au 0.02.039156.11745 > Au 2.039150.06.11745 > Au 2.039152.039154.07830 > Au 0.04.078304.07830 > Au 2.039154.078306.11745 > Au 4.078300.04.07830 > Au 4.078302.039156.11745 > Au 4.078304.07830 -0.0 > Au 4.078304.078304.07830 > Au 0.00.08.15660 > Au 0.02.03915 10.19575 > Au 2.039150.0 10.19575 > Au 2.039152.039158.15660 > Au 0.00.0 12.23490 > Au 0.02.03915 14.27405 > Au 2.039150.0 14.27405 > Au 2.039152.03915 12.23490 > Au 0.04.078308.15660 > Au 2.039154.07830 10.19575 > Au 0.04.07830 12.23490 > Au 2.039154.07830 14.27405 > Au 4.078300.08.15660 > Au 4.078302.03915 10.19575 > Au 4.078300.0 12.23490 > Au 4.078302.03915 14.27405 > Au 4.078304.078308.15660 > Au 4.078304.07830 12.23490 > K_POINTS automatic > 6 6 1 0 0 0 > > > > >warning: symmetry operation # 2 not allowed. fractional translation: >0.0139992 -0.0139992 0.000 in crystal coordinates > warning: symmetry operation # 7 not allowed. fractional > translation: >0.0069996 -0.0069996 -0.0069996 in crystal coordinates > warning: symmetry operation # 8 not allowed. fractional > translation: >0.0069996 -0.0069996 0.0069996 in crystal coordinates > warning: symmetry operation # 27 not allowed. fractional > translation: >0.0069996 -0.0069996 -0.0069996 in crystal coordinates > warning: symmetry operation # 28 not allowed. fractional > translation: >0.0069996 -0.0069996 0.0069996 in crystal coordinates > warning: symmetry operation # 29 not allowed. fractional > translation: >0.0139992 -0.0139992 0.000 in crystal coordinates > ... > > Initial potential from superposition of free atoms > > starting charge 395.74037, renormalised to 396.0 > Starting wfc are atomic > > > %% > from cdiaghg : error # 325 > info =/= 0 > > %% > > stopping ... > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org >
[Pw_forum] Defining an antiferromagnetic graphene nanoribbon
Hi Roberto, Here is a ribbon input that works for sure: https://kiev.princeton.edu/misc/rg_07.scf.in (get PPs from the PWSCF website) Good luck! Kostya Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
[Pw_forum] Definition of the projector function output in the "file_beta" file by LD1.
On Thu, May 8, 2008 23:39, Wei Chen (weic at Princeton.EDU) wrote: > Am I right about the output in the "file_beta" file? Dear Wei Chen, you are right, the condition is: <\beta_i|\psi^PS_j> = \delta_{i,j}. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/
[Pw_forum] Defining an antiferromagnetic graphene nanoribbon
2566.479991 -0.01 > H 11.239722 -1.8256310.00 > H 11.2397227.5944130.00 > C+1 13.736719 -0.7110740.00 > C 12.488123 -0.016393 -0.01 > C 12.4880201.443145 -0.01 > C 13.7365572.1599540.01 > C 13.7365853.6089460.01 > C 12.4880194.325668 -0.01 > C 12.4881155.7852830.00 > C-1 13.7366916.479991 -0.01 > H 13.737157 -1.8256310.00 > H 13.7371577.5944130.00 > C+1 16.234154 -0.7110740.00 > C 14.985558 -0.016393 -0.01 > C 14.9854551.443145 -0.01 > C 16.2339922.1599540.01 > C 16.2340203.6089460.01 > C 14.9854544.325668 -0.01 > C 14.9855505.7852830.00 > C-1 16.2341266.479991 -0.01 > H 16.234592 -1.8256310.00 > H 16.2345927.5944130.00 > K_POINTS automatic > 2 1 1 0 0 0 > > Regards, > > Roberto Veiga > PhD student > INSA-Lyon > > > - > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it > now.___ > 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 - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/71deaa06/attachment.htm
[Pw_forum] Defining an antiferromagnetic graphene nanoribbon
Dear PW users: I want to carry out a single point calculation of an antiferromagnetic graphene nanoribbon with PWscf. Since such a system is magnetic, with a specific magnetic orientation for the edge carbons, I have to perform a spin-polarized calculation. I'd like to know if the following PW input is suitable for such a calculation. calculation = 'scf' , restart_mode = 'from_scratch' , pseudo_dir = '$DIR' , / ibrav = 8, A = 17.482046 , B = 20.00 , C = 15.00 , nat = 70 , ntyp = 4, ecutwfc = 20.00 , ecutrho = 80.00 , occupations = 'smearing' , degauss = 0.01 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = -1.0 , starting_magnetization(2) = 1.0 , starting_magnetization(3) = 0.0 , starting_magnetization(4) = 0.0 , / conv_thr = 1.0D-6 , startingpot = 'atomic', startingwfc = 'atomic', mixing_mode = 'plain' , mixing_beta = 0.25 , diagonalization = 'david' , / ATOMIC_SPECIES C-1 12.0107 C.pbe.UPF C+1 12.0107 C.pbe.UPF C 12.0107 C.pbe.UPF H 1.0079 H.pbe.UPF ATOMIC_POSITIONS angstrom C+1 1.249543 -0.7110740.00 C 0.000947 -0.016393 -0.01 C 0.0008441.443145 -0.01 C 1.2493812.1599540.01 C 1.2494093.6089460.01 C 0.0008434.325668 -0.01 C 0.0009395.7852830.00 C-1 1.2495156.479991 -0.01 H 1.249981 -1.8256310.00 H 1.2499817.5944130.00 C+1 3.746978 -0.7110740.00 C 2.498382 -0.016393 -0.01 C 2.4982791.443145 -0.01 C 3.7468162.1599540.01 C 3.7468443.6089460.01 C 2.4982784.325668 -0.01 C 2.4983745.7852830.00 C-1 3.7469506.479991 -0.01 H 3.747416 -1.8256310.00 H 3.7474167.5944130.00 C+1 6.244413 -0.7110740.00 C 4.995817 -0.016393 -0.01 C 4.9957141.443145 -0.01 C 6.2442512.1599540.01 C 6.2442793.6089460.01 C 4.9957134.325668 -0.01 C 4.9958095.7852830.00 C-1 6.2443856.479991 -0.01 H 6.244851 -1.8256310.00 H 6.2448517.5944130.00 C+1 8.741849 -0.7110740.00 C 7.493253 -0.016393 -0.01 C 7.4931501.443145 -0.01 C 8.7416872.1599540.01 C 8.7417153.6089460.01 C 7.4931494.325668 -0.01 C 7.4932455.7852830.00 C-1 8.7418216.479991 -0.01 H 8.742287 -1.8256310.00 H 8.7422877.5944130.00 C+1 11.239284 -0.7110740.00 C 9.990688 -0.016393 -0.01 C 9.9905851.443145 -0.01 C 11.2391222.1599540.01 C 11.2391503.6089460.01 C 9.9905844.325668 -0.01 C 9.9906805.7852830.00 C-1 11.2392566.479991 -0.01 H 11.239722 -1.8256310.00 H 11.2397227.5944130.00 C+1 13.736719 -0.7110740.00 C 12.488123 -0.016393 -0.01 C 12.4880201.443145 -0.01 C 13.7365572.1599540.01 C 13.7365853.6089460.01 C 12.4880194.325668 -0.01 C 12.4881155.7852830.00 C-1 13.7366916.479991 -0.01 H 13.737157 -1.8256310.00 H 13.7371577.5944130.00 C+1 16.234154 -0.7110740.00 C 14.985558 -0.016393 -0.01 C 14.9854551.443145 -0.01 C 16.2339922.1599540.01 C 16.2340203.6089460.01 C 14.9854544.325668 -0.01 C 14.9855505.7852830.00 C-1 16.2341266.479991 -0.01 H 16.234592 -1.8256310.00 H 16.2345927.5944130.00 K_POINTS automatic 2 1 1 0 0 0 Regards, Roberto Veiga PhD student INSA-Lyon - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/43ac76ce/attachment.htm