[Pw_forum] about the quantum tunneling of diffusing atoms
Dear Prof. Baroni: Thank you for your kind attention! Yes, I totally agree with you. But the coordinates for the "quantum tunneling" are different from that for the adiabatic diffusion, and it seems not easy to find to fulfil the realistic processes. So what I need now is well accepted model to find this kind of coordinates. I have found some papers related to quantum tunneling, but I am still wondering: are there some widely accepted model to find the configurations for quantum tunneling? Could you please introduce me some good papers related or expertise advice? Thank you very much! Best Wishes! Yours Sincerely L. F. Huang > From: Stefano Baroni > > Dear LF Huang, > > no code will ever be a substitute of common sense. What you need is > simply the potential energy (i.e. "total energy" in the usual DFT > parlance) of a system, as a function of the coordinates of the > diffusing atom. As simple (or as complicated) as that! > > 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 > -- == L.F.Huang(???) lfhuang at theory.issp.ac.cn == 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/20090331/8b95cec9/attachment.htm
[Pw_forum] Choice of irreducible representations with ph.x
I would like to perform a phonon calculation at Gamma making a choice of only a selected number of irreducible representations. After a proper scf calculation I use with ph.x with an input file like the following one: Phononic spectrum (1) of CoM (at Gamma) &inputph amass(1)=1.00794, amass(2)=12.011, amass(3)=14.007, amass(4)=15.999, amass(5)=55.845, prefix='CoM', outdir='/scratch/userinfm/cne0fm4a/CoM/results/', iverbosity=1, epsil=.false., fildyn='CoM.dm', nrapp=1, / 0.0 0.0 0.0 1 The problem is that the calculation seems to proceed ignoring the nrapp value and the list of numbers I put in the last line and all the irreps are considered. This happens both for nrapp=1 (one value in the list) or nrapp>1 (nrapp values in the list). pw.x and ph.x are run on the CINECA cluster where there appears to be QE ver. 4.1CVS and I would liketo save cpu time by excluding the undesired irreps. Using the same syntax (nrapp and the list of irreps at the end) to modify the scripts of example02 I successfully select only one of the two irreps for Si with QE ver. 3.2 installed on a desktop pc (reporting the message "Not done in this run"). Might it be a version issue? Thanks a lot for your help and time. -- ___ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web:http://www.df.unibo.it/fismat/theory ___
[Pw_forum] about the quantum tunneling of diffusing atoms
Dear Tone Kokalj: First thank you for your kind attention to my previous poster: "about the logical parameter use_masses in IONS card" Now I have another question: How to calculate the potential barrier for the quantum tunneling of diffusing atoms in PWSCF? Any technical method suggested ? If PWSCF can't calculate this kind of things, where should I get a start to edit the code ? PS: In an excellent paper: P. G. Sundell etc., PRL 92, 155901, the authors found a "symmetrically weighted" method to calculate the "coincidence configuration". Best Wishes! Yours Sincerely L. F. Huang -- == L.F.Huang(???) lfhuang at theory.issp.ac.cn == 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/20090331/51db9e80/attachment.htm
[Pw_forum] PP for Planar average of all |psi|^2
sujata Paul wrote: > Dear Dr. Giannozzi, > Thanks for your reply. I set the prefix properly from > scf to PP calculation. When I wrote you earlier I just wanted to write > the namelist and parameters I used for my calculations. Sorry for the > inconvenience. > So could you please tell me how can I make the post processing work when > I want to use plot_num=9? It was written in the error message you posted at the beginning: %% from punch_plot : error # 1 no longer implemented, see PP/plan_avg.f90 %% So I guessed "plot_num=9" is not implemented in post processing. You have to use the program plan_avg.x in place of pp.x for this task. Though I never used it, from a glance to the source I guess it should be simple to use: NAMELIST / inputpp / outdir, prefix, filplot You simply need to specify these three strings... GS > > Thanks and Regards > Sujata Paul > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | |via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o o
[Pw_forum] about the quantum tunneling of diffusing atoms
On Tue, 2009-03-31 at 08:07 +0200, Stefano Baroni wrote: > Dear LF Huang, > > > no code will ever be a substitute of common sense. What you need is > simply the potential energy (i.e. "total energy" in the usual DFT > parlance) of a system, as a function of the coordinates of the > diffusing atom. As simple (or as complicated) as that! please let me add my 2 cents to this. you can go back to a quantum mechanics text book and look up for example the discussions of quantum particle vs. wall cases. the potential doesn't change whether the particle is quantum or classical! what you seem to be looking for is some kind of "barrier crossing probability". now, wrt to that i'd have several concerns: - how accurate is your "classical" barrier potential to begin with? you are doing graphite and hydrogen and use plain DFT. the interaction between a benzene molecule and a hydrogen molecule is a frequently used test case for methods that add dispersion interactions corrections to DFT. hmmm... - is tunneling relevant at all? at T > 0K the carbon atoms move and your barrier will fluctuate, that will affect the crossing probability. similarly, if your hydrogen has enough kinetic energy, tunneling is irrelevant. - what is the correlation length of your system? only if it is long quantum effects of the atom core matter. since you seem to be doing a solid state vacuum system, you should be good on that. after you've made sure that all of the above is not rendering any further studies of the quantum effects pointless, _then_ i would look into path-integral methods (e.g. the works of mark tuckerman and dominik marx) that allow studying probability distributions at finite temperature, albeit mostly in imaginary time. mind you, those calculations are hugely expensive and you may be best off to first make some tests with a classical potential. in fact, i would not be surprised if a suitably chosen classical potential would give you a better representation of the potential barrier than DFT. cheers, axel. > > > Stefano > > On Mar 31, 2009, at 7:38 AM, lfhuang wrote: > > > Dear Tone Kokalj: > > First thank you for your kind attention to my previous poster: > > "about the logical parameter use_masses in IONS > > card" Now I have another question: How to calculate the potential > > barrier for the quantum tunneling of diffusing > > atoms in PWSCF? Any technical method suggested ? If PWSCF can't > > calculate this kind of things, where should I > > get a start to edit the code ? > > PS: In an excellent paper: P. G. Sundell etc., PRL 92, 155901, the > > authors found a "symmetrically weighted" method > > to calculate the "coincidence configuration". > > > > Best Wishes! > > > > Yours Sincerely > > L. F. Huang > > -- > > == > > L.F.Huang(???) lfhuang at theory.issp.ac.cn > > == > > 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 > > > > --- > 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 -- === 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] about the quantum tunneling of diffusing atoms
Dear LF Huang, no code will ever be a substitute of common sense. What you need is simply the potential energy (i.e. "total energy" in the usual DFT parlance) of a system, as a function of the coordinates of the diffusing atom. As simple (or as complicated) as that! Stefano On Mar 31, 2009, at 7:38 AM, lfhuang wrote: > Dear Tone Kokalj: > First thank you for your kind attention to my previous poster: > "about the logical parameter use_masses in IONS > card" Now I have another question: How to calculate the potential > barrier for the quantum tunneling of diffusing > atoms in PWSCF? Any technical method suggested ? If PWSCF can't > calculate this kind of things, where should I > get a start to edit the code ? > PS: In an excellent paper: P. G. Sundell etc., PRL 92, 155901, the > authors found a "symmetrically weighted" method > to calculate the "coincidence configuration". > > Best Wishes! > > Yours Sincerely > L. F. Huang > -- > == > L.F.Huang(???) lfhuang at theory.issp.ac.cn > == > 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 --- 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/20090331/973f7b70/attachment-0001.htm
[Pw_forum] antiferromagnetism in ZB input file with 2 atoms
On Mar 31, 2009, at 1:23 AM, mazouz moulay wrote: > Dear Prof. Eyvaz > > > Also, I would like to ask you how your QHA code can be cited ? > > I would advise Eyvaz to set up an even rudimentary web page on qe- forge.org and encourage people to cite (at least) that page. regards - 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/20090331/6854d8de/attachment.htm
[Pw_forum] force and stress in the Berry phase method
Dear Hanghui Chen, On Mar 30, 2009, at 10:20 PM, hanghui chen wrote: > Dear PWSCF users, > In addition to my previous email, I would like to know: if I use > ultrasoft psedopotential, are the forces and stress correctly > calculated in the Berry phase method in the latest version 4.0.4? forgive my answering your question in a rather indirect and pedagogical way. this is a question that you could (actually, should) easily answer yourself. just repeat your calculation with (slightly) distorted atomic positions / cell parameters, calculate forces and stresses by finite differences, and compare with the results of the code. this way, you would do yourself and us a favor. yourself, because you would learn not to trust ANY code (not even the best, i.e. QE); us because if the code is supposed to give the right answer and id doesn't, then you will have helped discover a bug ... > Thank you very much. Good luck! 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/20090331/90571755/attachment.htm
[Pw_forum] QHA in qe-forge
Hi Stefano, In fact, I have started doing that, thanks. My thanks also go to Paolo he adviced me the same and my apologies not responding immediately to his e-mail. Hopefully I will annonce this soon. Bests, Eyvaz. --- On Tue, 3/31/09, Stefano Baroni wrote: > From: Stefano Baroni > Subject: Re: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms > To: "PWSCF Forum" > Date: Tuesday, March 31, 2009, 8:38 AM > On Mar 31, 2009, at 1:23 AM, mazouz moulay wrote: > > > Dear Prof. Eyvaz > > > > > > Also, I would like to ask you how your QHA code can be > cited ? > > > > > > I would advise Eyvaz to set up an even rudimentary web page > on qe-forge.org and encourage people to cite (at least) that > page. > > regards - 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 > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
