[Pw_forum] A problem with average.x
Hi, My understanding is that average.x needs to be run on single processor (serial submission) and not multiple CPUs in parallel. So if you run average.x as mpirun -np 1 path/to/average.x ..it should work. Hope it helps! Regards, Rajan Rajan K. Pandey, Ph.D. Advisory Research Engineer, Semiconductor Research & Development Center India Systems & Technology Engineering Lab IBM India Pvt. Ltd. MD3 1F B354 Manyata Embassy Business Park Nagawara, Outer Ring Road Bangalore - 560045, India Phone: +91-80-28061262 Mobile: +91-9901850981 Email: rajapand at in.ibm.com rajanpandey at gmail.com On Thu, Apr 21, 2011 at 4:34 PM, meysam pazoki wrote: > Dear Pwscf users > > I have a problem in using average.x, > after DFT ground state calculations i use pp.x for saving the V_bare + V_H > potential in "fermipot.dat" file. > I want to use average.x for average the data saved in the file for > obtaining the fermi level(follow the instruction of work_FCT example of > espresso) > i use the following input file for average.in: > > > 1 > fermirefpot > 1.D0 > 500 > 3 > 55.809 > > > where if i am not wrong,*55.809 is my lattice constant in bohr and i want > to get 500 data finally. > but the program average.x is steel running after two days for a 16 > processor server and in .out file i see: > > Reading header from file fermirefpot.dat > > the cpu is fully engaged but the memory usage is 0%! > i think there is something wrong in my input file.*I try to change some > parameters like "3->2 or 1" and "500->1000 or 300" but the result is the > same. > > i would be really grateful *if you could help me, > Thanks indeed for your time and kindness > Meysam* > ___ > 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/20110421/86ab2fb0/attachment.htm
[Pw_forum] why are there two Fermi energies?
Hello 2011/4/21 Eduardo Ariel Menendez Proupin > Hi, > Let me clarify that I found no difference between version 4.2.1 and others. > I have used only 4.2.1. > > I suspected that the Fermi level was a way to control the occupations. > However, using different fermi levels will produce different charge > densities because the occupation numbers will be different. If both types of > calculations produce the same energy, then the ground state is degenerate, > but the one with two Fermi energies seems incompatible with thermodynamics. > I used Fermi smearing, by the way. > > I am committed to teaching duties today. Thanks for your answers, and I > will come back tomorrow, or maybe late today, and I will look at the > occupations using verbosity = .true. > > Mathematically it seems logical that to control the number of electron > (one degree of freedom) one needs one parameter, which is the Fermi level. > To control an additional degree of freedom, the magnetization, one needs an > additional parameter, then it is reasonable to use two Fermi levels or an > equivalent set of two parameters. > For example, one could define a single Fermi level and apply a shift to the > spin down eigenvalues. This needs a physical interpretation, as well as > having to Fermi levels. > Shift in eigenvalues can be seen as produced by external magnetic fiels (a Zeeman term) then the state with two different Fermi energies may be thought of a true ground state with only one Fermi level but in the presence of this stabilizing magnetic field proportional to the difference in Fermi energies. The true ground state with equal Efs do not need of course this magnetic field. regards, Alexander > > Moreover, reversing the reasoning, I wonder why or how one gets the same > number of electrons and magnetization using only one parameter (Fermi level) > in the case of not using tot_magnetization. Is it a hazard or is there a > trick that bias the calculation to the integer magnetization? > > Best regards > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > ___ > 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/20110421/389322cb/attachment.htm
[Pw_forum] One minor bug, one not minor and two questions
On Sun, 2011-04-10 at 16:13 -0500, Laurence Marks wrote: > Another quick one: line 1766 of install/configure.ac nulls out > scalapack_libs and the lines below look like they are special tests, > which seems to be inconsistent with line 150 and standard protocols of > letting the user define input variables. (hopefully) fixed in the development version: http://qe-forge.org/scm/browser.php?group_id=10 > at least on the cluster where I have PWSCF installed it complains that > at configure.ac:30 the language is set as C not Fortran. this happens on my macintosh as well, after some recent change. It must be somethiing related to the version of "autoconf" P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] new bfgs: strange behavior doing vc-relax
On Apr 20, 2011, at 10:21 PM, Stefano de Gironcoli wrote: >>> With QE I have always seen the energy to decrease when the cutoffs are >>> increased, but with VASP, I always see an oscillation in the total >>> energy >>> when the cutoff is incremented. >> just guessing: it might be a consequence of real-space treatment of >> augmentation >> functions. > > actually it can happen for US pseudo, if the cutoff for the density is > not large enough, that the energy increases with increasing cutoff.. > just because the augmentation charges are not integrated correctly and > the error can have any sign. If ecutrho is sufficient to integrate > correctly augmentation charges the energy should be variational w.r.t. > ecutwfc . Just a short, half-philosphoc comment, in the hope to make the whole issue even more clear. DFT is variational with respect to the size of the 1-electron basis set (irrespective of the fact that ionic potentials are local or not), if the numerics of the calculation is otherwise well converged with respect to any possible parameter of the calculation. When it is not, no guarantee of variational bounds. This is obvious in a sense. Stealthy problems may arise when some of the auxiliary numerical parameters of the calculations are surreptitiously correlated with the size of the basis set (such as, e.g. the number of plane waves in the Fourier expansion of the [augmented] charge density or the number of mesh points used for the real-space integration of different functions). Hope this halps Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110421/b1dd24cd/attachment.htm
[Pw_forum] TDDFT approach for periodic system
** > >Giuseppe Mattioli >CNR - ISTITUTO DI STRUTTURA DELLA MATERIA >v. Salaria Km 29,300 - C.P. 10 >I 00015 - Monterotondo Stazione (RM) >Tel + 39 06 90672836 - Fax +39 06 90672316 >E-mail: > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20110421/e907e171/attachment-0001.htm
[Pw_forum] why are there two Fermi energies?
On Thu, 2011-04-21 at 11:28 +0200, Gabriele Sclauzero wrote: > Yes, I know there have been some changes in the last versions. > I think Paolo can be more helpful here. I don't think so. There are no substantial differences in the last version wrt the previous one in this case. I do not see anything anomalous in Eduardo's results, by the way. The results with constrained and unconstrained magnetizations are the same => the constrained-magnetization result is the ground state. The "two Fermi energies" of the constrained case need not to be exactly the same as the (single) Fermi energy of the unconstrained case, as long as the occupancies for spin-up and spin-down are the same in the two cases. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] why are there two Fermi energies?
Hello, I'm also interested in going deeper into this topic. I tell what (I think) I've understood, so maybe we can trigger a discussion with Paolo or Stefano ;) Il giorno 21/apr/2011, alle ore 01.35, Eduardo Ariel Menendez Proupin ha scritto: > Hi, > Why are there two Fermi energies in certain spin-polarized calculations ? It's just a practical way to deal with spin polarized calculations when you fix a net non-zero total magnetization in the unit cell. Since you know the total charge and the total magnetization, you can determine univocally the number of spin up and of spin down electrons. This in turns allows you to treat the up and down Fermi energies independently, using the same techniques for spin-unpolarized calculations to determine the two Fermi energies. > > input starting_magnetization(1) = 0.0, > starting_magnetization(2) = 0.5, > output the Fermi energy is 6.1598 ev >!total energy =-502.92538790 Ry > > input tot_magnetization = 1 > output the spin up/dw Fermi energies are 6.38216.1598 ev > !total energy =-502.92538790 Ry > > What is the meaning of the spin up Fermi level in the second case? Did you get this with smearing? Otherwise the Fermi energy should not be printed. Specifying starting_magnetization or tot_magnetization is not equivalent, the former is just used to break the symmetry. You might end with a different magnetization, if that set by tot_magnetization does not correspond to the ground state. In your case it looks like the GS has M_tot=1, since you got exactly the same energy. What do you get as total magnetization in the first case? At first glance I don't see why in the first case you get the lowest of the two Fermi energies, I would rather expect the other. What changes between the two calculations is how the occupations are computed (see PW/weights.f90). You can print them on output by specifying verbosity='high'. > > This numbers are for a 64 atoms Si unit cell with one Si replaced by Al, and > only one k-point, but the same happens with more k-points. I also used Fermi > smearing with a very low smearing. > There is a difference if I set the starting magnetization or the total > magnetization, with pw.x version 4.2.1. However, despite reporting different > Fermi levels, the total energy and magnetization are equal. Also are equal KS > energies, at least around the Fermi levels. Yes, I know there have been some changes in the last versions. I think Paolo can be more helpful here. HTH GS > > Thanks, > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > ___ > 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/20110421/63369d32/attachment.htm
[Pw_forum] Generating ultra soft pseudopotential
On Thu, 2011-04-21 at 09:50 +0200, Gabriele Sclauzero wrote: > (you might have a look into Paolo's notes, there should be something: > http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf) an updated version of this document is in atomic_doc/pseudo-gen.pdf P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] why are there two Fermi energies?
On Thu, 21 Apr 2011 01:35:39 +0200, Eduardo Ariel Menendez Proupin wrote: > Why are there two Fermi energies in certain spin-polarized calculations ? > > input starting_magnetization(1) = 0.0, > starting_magnetization(2) = 0.5, > output the Fermi energy is 6.1598 ev >!total energy =-502.92538790 Ry > > input tot_magnetization = 1 > output the spin up/dw Fermi energies are 6.38216.1598 ev > !total energy =-502.92538790 Ry > > What is the meaning of the spin up Fermi level in the second case? Dear Eduardo, if you force the system to have a certain magnetization (i.e. setting tot_magnetization) you are actually asking to occupy the "up" spin orbital more then the "down" spin ones, i.e. you have more up electrons then down electrons. This is achieved by filling the up orbitals up to a higher energy than the down orbitals, by setting two distinct Fermi energies. On the other hand, if you only set starting magnetization, you get the computational ground state, where up and down orbitals are be filled up to the same level; what changes is the KS eigenvalues. hth, lorenzo > > This numbers are for a 64 atoms Si unit cell with one Si replaced by Al, > and > only one k-point, but the same happens with more k-points. I also used > Fermi > smearing with a very low smearing. > There is a difference if I set the starting magnetization or the total > magnetization, with pw.x version 4.2.1. However, despite reporting > different > Fermi levels, the total energy and magnetization are equal. Also are > equal > KS energies, at least around the Fermi levels. > > Thanks, > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P Curie T23-C23/24-4e16 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/
[Pw_forum] Generating ultra soft pseudopotential
Dear Tram Bui, Il giorno 21/apr/2011, alle ore 00.25, Tram Bui ha scritto: > Dear Everyone, > I'm trying to complete my process of generating the Cesium PP (extremely > hard for a total new and have no experience with QE like me!!!). Have you tried with those available on the internet, before trying to generate it by yourself? > So far I have been helped with many other issues, and I'm very much getting > there. I still have couple more questions and hope you can spare me some time > to help me out. my questions are : > ---the number of logarithmic derivatives to be calculated, the "nld" > value, how does it determine? You determine. In principle it depends on how many angular momenta you include in the non-local part of the PP (i.e., if you include s and p, then choose nld=1, if you include also d then you need nld=2, ...). This does not influence the final PP data, but it helps you to understand if your PP is a good one or not. > Angular momentum of the local channel, the "lloc" value, how does it > determine? You determine. This flag is used to select how the local part of the PP is built (either from the smoothed all-electron KS potential - the default - or from a smoothed KS wavefunction - if lloc>=0). Different choices are possible here, it is not easy to give a general advice (you might have a look into Paolo's notes, there should be something: http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf) > my atom is : Cs with electron config. [Xe] 6s1, and i'm doing ultra-soft PP. > I have checked and it does have the bound state on the p orbital. so I guess > my electron config. should be "[Xe] 6s1 6p-1 ". What about 5d and 4f? Regards GS > > I appreciate any input you have for me! > Tram Bui > > On Tue, Apr 5, 2011 at 3:42 PM, Tram Bui wrote: > Dear Folks, P.S.: of course this forum is quite friendly and informal, but maybe not to this point :) > I'm trying to build an input file for generating the Cs pseudopotential. > when I run the ld1.x on my input file. I got an error message saying that i'm > using the wrong core. would you help me with extra information of where I can > find the help for how to choose the right core for some atoms such as in my > case it is Cs. > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > > > -- > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > ___ > 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/20110421/b454c9a3/attachment.htm
[Pw_forum] why are there two Fermi energies?
Hi, Let me clarify that I found no difference between version 4.2.1 and others. I have used only 4.2.1. I suspected that the Fermi level was a way to control the occupations. However, using different fermi levels will produce different charge densities because the occupation numbers will be different. If both types of calculations produce the same energy, then the ground state is degenerate, but the one with two Fermi energies seems incompatible with thermodynamics. I used Fermi smearing, by the way. I am committed to teaching duties today. Thanks for your answers, and I will come back tomorrow, or maybe late today, and I will look at the occupations using verbosity = .true. Mathematically it seems logical that to control the number of electron (one degree of freedom) one needs one parameter, which is the Fermi level. To control an additional degree of freedom, the magnetization, one needs an additional parameter, then it is reasonable to use two Fermi levels or an equivalent set of two parameters. For example, one could define a single Fermi level and apply a shift to the spin down eigenvalues. This needs a physical interpretation, as well as having to Fermi levels. Moreover, reversing the reasoning, I wonder why or how one gets the same number of electrons and magnetization using only one parameter (Fermi level) in the case of not using tot_magnetization. Is it a hazard or is there a trick that bias the calculation to the integer magnetization? Best regards -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110421/a7025c46/attachment.htm
