[Pw_forum] a questoin about pressure and bulk modulus of system
Folks: a distinguished colleague of mine just made me notice that if I were a student I would probably fail the first-year thermodynamics exam. Some of my statements are right, but my claims of Meyasam being wrong are partially wrong (and he was therefore partially right!). Let me point out my own mistakes: >> I have another question :Is these terms are right? >> E=-PV+uN+TS Contrary to my claims, this equation is correct, as it is a consequence of Euler's theorem on homogeneous functions [E(?S,?V,?N)=?E(S,V,N) implies E= S ?E/?S + V ?E/?V +N ?E/?N] - Notice that you need Euler's theorem *AND* the definition of T,P,? as energy derivatives to establish the equation. >> => dE=-PdV-VdP+udN+Ndu+Tds+SdT > > NO - this is nonsense. Nor the energy, nor its differential are what you > write. As said in my previous post, the energy is an extensive function of > the three extensive quantities S,V,N: E=E(S,V,N) ? -PV+uN+TS. In calculating > its differential, you should vary only the variables it depends upon (i.e., > S,V,N). MY comment is wrong. As said, E=-PV+uN+TS is a consequence of Euler's theorem, and it is legitimate to take the formal differential the way Meyasam did. > >> and we know from first law of thermodynamics that dE=-PdV+udN+Tds > > This is correct, in fact it is different from the expression you gave before. > Form this relation you can conclude that P=-?E/?V; T=?E/?S, ?=?E/?N. The > first relation is what you need > >> and we conclude that -VdP+Ndu+SdT=0 > > NO - see above RIGHT for a more subtle reason than I was able to guess at first sight the above equation even has a distinguished name: its is know as the Gibbs-Duhem equation > >> and in zero temrature and fixed number of atoms >> we have dE=-PdV and P=-dE/dV > > right, for the wrong reason (i.e. your conclusion is correct, the argument > you use to derive it is not) my last negative statement is less wrong than others, in the sense that you do not need the Gibbs-Duhem equation to establish that P=-?E/?V. This relation is instead a definition of the pressure, as the derivative of the energy with respect to one of its natural variables, and it is indeed needed to establish the Gibbs-Duhem equation. Sorry for the mess I may have created. I can only conclude that I could have directed the recommendation to study more thermodynamics to myself in the first place ... In any event, I now know more than I did before, and so I hope will some of you. Thank you for making me (re-) learn something that I had long forgotten ... 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/20101015/56c640aa/attachment.htm
[Pw_forum] Bond-order-corrected (or BOLS) pseudopotentials
Sorry for forgetting it in my previous post; my affiliation (now) is: Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia
[Pw_forum] a questoin about pressure and bulk modulus of system
On Oct 15, 2010, at 4:18 PM, Stefano Baroni wrote: > dered in their ground state. In the BO approximations, electrons are kind of > slaves who keep atoms together, but do participate in the (thermo) what I meant here, of course is that " ... electrons ... do NOT participate ... " sorry for the misunderstanding I may have created 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/20101015/1d078663/attachment-0001.htm
[Pw_forum] Bond-order-corrected (or BOLS) pseudopotentials
We would like to understand better the so-called bond order length strength (BOLS) correlation approach [Chang Q. Sun an co-workers, basic ref. is Prog. Solid. State Chem. 35, pag. 1 (2007)] to structures with under-coordinated atoms (surfaces, ribbons, rods, etc.) Sometimes it is stated that the BOLS approach is incorportated with DFT calculations, and in particular quoting from [J. Phys. Chem. C, 112, 18927 (2008)] "...Unfortunately, the presence and polarization of the nonbonding states are hardly described from the self-consistent optimization in DFT or tight-binding approximations at the present because of the limitation of interatomic potentials. Potentials suitable for the broken-bond-induced local strain and quantum trapping that are sometimes several folds deeper than the potential at the usual atomic site in the bulk and potentials suitable for the weak interaction between the nonbonding and the polarized antibonding states are highly desirable for computations." It seems to me that they would call for pseudopotentials corrected by the fact of going to represent atoms with low coordination or nonbonding states/electrons. Typically, in such a situation, the neighboring bonds tend to shrink and the bonding energies (in magnitude) tend to increase. Should one then consider a "BOLS-corrected" pseudpotential? Are you aware of problems of this kind, or is the question correctly posed at all? Thanks again for your time. Cristian
[Pw_forum] a questoin about pressure and bulk modulus of system
On Oct 15, 2010, at 11:27 AM, meysam pazoki wrote: > > Dear Stefano > > Thanks for your good answer.I am an experimentalist and I learn good new > things from your answer. > My mistake was that I didnt know in calculation of pressure,we neglect > electronic degrres of freedom(I will be thankfull to you,if you introduce a > reference about this subject). I am sorry to keep correcting you. I don't think I ever said that you can disregard the electronic degrees of freedom when calculating the pressure. I said you can neglect them *in the BO approximation*, when dealing with thermodynamics. I could have been more precise by saying that when doing thermodynamics in the BO approximation, you can safely assume that the "electronic temperature" is zero, i.e. that electrons can be considered in their ground state. In the BO approximations, electrons are kind of slaves who keep atoms together, but do participate in the (thermo) dynamics. The fact that they are slave does imply that you can do without them ... > I have another question :Is these terms are right? > E=-PV+uN+TS => dE=-PdV-VdP+udN+Ndu+Tds+SdT NO - this is nonsense. Nor the energy, nor its differential are what you write. As said in my previous post, the energy is an extensive function of the three extensive quantities S,V,N: E=E(S,V,N) ? -PV+uN+TS. In calculating its differential, you should vary only the variables it depends upon (i.e., S,V,N). > and we know from first law of thermodynamics that dE=-PdV+udN+Tds This is correct, in fact it is different from the expression you gave before. Form this relation you can conclude that P=-?E/?V; T=?E/?S, ?=?E/?N. The first relation is what you need > and we conclude that -VdP+Ndu+SdT=0 NO - see above > and in zero temrature and fixed number of atoms > we have dE=-PdV and P=-dE/dV right, for the wrong reason (i.e. your conclusion is correct, the argument you use to derive it is not) > Thanks You are welcome. You asked a well posed question, and it is a pleasure to answer well posed questions. I think you should study some basic thermodynamics / statistical mechanics. Chandler's book is a very good starting point. Regards - 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/20101015/b53e3557/attachment.htm
[Pw_forum] a questoin about pressure and bulk modulus of system
Dear Stefano Thanks for your good answer.I am an experimentalist and I learn good new things from your answer. My mistake was that I didnt know in calculation of pressure,we neglect electronic degrres of freedom(I will be thankfull to you,if you introduce a reference about this subject). I have another question :Is these terms are right? E=-PV+uN+TS => dE=-PdV-VdP+udN+Ndu+Tds+SdT and we know from first law of thermodynamics that dE=-PdV+udN+Tds and we conclude that -VdP+Ndu+SdT=0 and in zero temrature and fixed number of atoms we have dE=-PdV and P=-dE/dV Thanks Meysam pazoki SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/acd26890/attachment.htm
[Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell
Dear mohnish and Prasenjit Thanks for your good answers ,I have another question :"Is enthalpy of adsorbtion equals to energy of adsorbtion?" I want to calculate enthalpy of adsorbtion and your answers are about energy of adsorbtion. Regards Meysam Pazoki SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/f31de22a/attachment.htm
[Pw_forum] problem in generation of PP with semicore states?
Dear All QE users and developers, I have problems with generation of PP for Cu(+0.5) with TM pseudization scheme , when i include semicore states. Without semicore state, i don't have any problem. But when i include 3s and 3p states in valence, error comes like- negative rho, problem in finding qi coeffs. Rho problem is solved with PSQ aug functions, but finding of qi coeffs is still there. Please see below for input file title='Cu' zed=29, eminld=-10.0, emaxld=3.0, rlderiv=2.5, nld=3, iswitch=3, config="[Ar] 3d9.0 4s1.3 4p0.2" dft='LDA' rel=1, / pseudotype=3, nlcc=.true., new_core_ps = .true. rcore=0.6000 lloc=-1, rcloc=2., file_pseudopw='Cu_1.UPF' zval=19, lpaw=.false. lnc2paw=.false. which_augfun ='PSQ', rmatch_augfun= 2., author='sk', tm =.true. !rho0=0.01, !nX n l occ nrg rmin rcut / 8 3S 1 0 2.000.000.6503. 1 3P 2 1 6.000.000.6503. 1 3D 3 2 9.000.000.6502. 1 !1.9000 1 3D 3 2 0.000.100.6502. 1 !1.9000 1 4S 1 0 1.300.002.0003.2000 1 4S 1 0 0.001.952.0003.2000 1 4P 2 1 0.200.002.6003.6000 1 4P 2 1 0.000.052.6003.6000 1 ! doubt: ! !is it ok if I take one 3s and one 4s so that two proj/angular !momentum. similarly for for 3p and 4p ? -input file end--- i shall be very thankful to you for your help. With Kind regards, Sonu Kumar Phd Student, Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/
[Pw_forum] perdew zunger pseudo potential for Sc,Cr and V.
Hi everyone, Does any one know where I can get perdew zunger pseudo potential for Sc,Cr and V.They are not included in the Quantum espresso pseudo potential package. Thanks G S .MANYALI POSTGRADUATE STUDENT KENYA -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/4b39f5ee/attachment.htm
[Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell
Dear Meysam, When you do a supercell calculation you do not need to relax the lattice parameters because the cell vectors perpendicular to the surface is ficticious in the sense that you simply use a value large enough so that the periodic images perpendicular to the surface do not interact with each other. The inplane lattice vectors are determined by your theoretically obtained bulk lattice parameter for ZnO. So you should follow the procedure suggested by Mohnish. Just another addition, all the calculations, the ZnO surface, O2+ZnO surface and the O2 molecule in vacuum (the gas phase) should be done using the same supercell. Also be careful when you do calculations for O2 molecule in gas phase, you should do a spin polarized calculation becase the ground state of O2 is spin triplet. Hope this helps. Prasenjit. On 14 October 2010 23:00, mohnish pandey wrote: > Dear Meysam, > ?? ? ? ? ? ? ? ? ? ? ? ?First you relax the supecell using "relax" > calculation, it will make all the atoms to attain an equilibrium position. > Then ?adsorb the atom (make it close enough so that your surface is > interacting with the adorbate) and make the "relaax" calculation again. The > energy that you get from latter step subtract the "former energy of the > supercell+energy of the isolated adsorbate"..This difference should give the > adsorption energy. In fact I have not done any adsorption calculations but > intuitively what I have said seems correct to me. > > On Thu, Oct 14, 2010 at 5:08 PM, meysam pazoki physics.sharif.edu> > wrote: >> >> Dear PWSCF users >> >> I want to calculte the enthalpy of adsorbtion of o2 molecule on the >> surface of a ZnO.Can i use variable cell relaxation for the supercell and >> use the enthalpy that printed in output file? >> I can also run a series of scf jobs with different cell volumes,and then >> calculate the pressure of system from E-V diagram and then calculate >> enthalpy by H=E+PV from my data.Is it also true? >> >> Thanks >> Best Regards >> Meysam Pazoki >> SUT >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Regards, > MOHNISH, > - > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > - > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790
[Pw_forum] a questoin about pressure and bulk modulus of system
Dear Meysam, your post seems the result of an intricate intertwining of thermodynamics, quantum mechanics, and condensed matter misunderstandings ... Let me try to sort them out. 1) In the Born-Oppenheimer approximation, which you are correctly referring too, you can just forget about electronic degrees of freedom, when dealing with the thermodynamics of the system. The chemical potential that may (or may not, see below) appear in your thermodynamics equation has nothing to do with the Fermi energy, in this case: it is the energy required to add or subtract one "particle" (atom, molecule) to/from your system. In fact, you should have one different chemical potential per atomic/molecular species. 2) When quoting any thermodynamic relation, you should always keep in mind which are the "natural" variables you are adopting. In standard treatments, the "natural" variables of the energy as an extensive quantity are the volume, the entropy, and the number of of particles: E=E(S,V,N) [see e.g. D. Chandler, Introduction to Modern Statistical Mechanics, Oxford University Press, New York (1987), Chapt. 1]. This being the case, the pressure is defined as p=-?E/?V - no other derivatives are involved in this definition. 2') The thermodynamic relation you are quoting looks very obscure to me. Where have you taken it from? Which "natural" variables would the energy depend on? 3) All the above is a complication of real life. In real-life DFT calculations (which, I presume, are what you are interested in) the number of atoms is fixed, and the temperature (and, hence, the entropy) is zero (unless you do molecular dynamics / Monte Carlo, which I understand is not the case). Hence the energy is a function of the volume alone (as well as of any other applied field, but this would open another thread), and the pressure is just the negative of the derivative of the energy with respect to the only extensive quantity it can depend on, i.e. the volume ... as simple as that! 4) The Fermi energy of any metal does depend on volume (think of the simple jellium model of simple metals), both at zero and at finite temperature, but, as said, this has nothing to do with the calculation of the pressure (but for the fact that when calculating the total energy of a metal as a function of volume, you should recalculate the Fermi energy for every volume you are considering). Hope this clarifies/helps a bit Stefano B. On Oct 14, 2010, at 1:27 PM, meysam pazoki wrote: > Dear PWSCF users > > I have a queston about bulk modulus and pressure of a system. > We know from thermodynamics that the energy of our electronic > system is E=TS-PV+? N.In the zero temrature(T=0) we have E=-PV+?N and > p=-?E/?v.In the limit of born openhimer approximation with freezed ions, we > can calculate the pressure of our system(electrons+ions) by partial > derrivative of energy with respect to volume of system.But in literature I > see that calculate pressure from this term: p=-dE/dV and neglect the ?E/?? > term.Is it correct? > In the zero temrature chemical potential is equal to fermi energy and We > should expect that the fermi energy have no changes by variation in volume > of system.Is it correct for finite temratures,too? > > Best Regards > Meysam Pazoki > SUT > ___ > 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/20101015/f2dcd4a6/attachment-0001.htm
[Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell
Dear Meysam, First you relax the supecell using "relax" calculation, it will make all the atoms to attain an equilibrium position. Then adsorb the atom (make it close enough so that your surface is interacting with the adorbate) and make the "relaax" calculation again. The energy that you get from latter step subtract the "former energy of the supercell+energy of the isolated adsorbate"..This difference should give the adsorption energy. In fact I have not done any adsorption calculations but intuitively what I have said seems correct to me. On Thu, Oct 14, 2010 at 5:08 PM, meysam pazoki wrote: > Dear PWSCF users > > I want to calculte the enthalpy of adsorbtion of o2 molecule on the surface > of a ZnO.Can i use variable cell relaxation for the supercell and use the > enthalpy that printed in output file? > I can also run a series of scf jobs with different cell volumes,and then > calculate the pressure of system from E-V diagram and then calculate > enthalpy by H=E+PV from my data.Is it also true? > > Thanks > Best Regards > Meysam Pazoki > SUT > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101014/880f149b/attachment.htm
