[Pw_forum] plane averaged local potential
2009/10/28 Eduardo Ariel Menendez Proupin > Hello, > I need to calculate plane averaged local potentials, and charges, for a > heterostructure. I.e., > V(z)=1/(Lx*Ly) \int\int V(x,y,z) dx dy > > I think I can do it using PP to get V(x,y,z) in the 3D FFT grid and a > write a program that makes the average. Then I want to obtain the > macroscopic average, as defined in a triestine paper by Baldereschi, Baroni > and Resta PRL 61 ,734 (1988). > > Before spending one or two days writing the program and become sure that > is works fine, I would like to confirm that this is not already implemented > in PP or in other utility of Quantum-ESPRESSO. > > Hi Eduardo, The executable average.x can do the jobfor the input file you can see the example on Work function calculation.. However, if you want to calculate the planar average of charge density, you need to multiply it with the area of the xy plane, assuming you want to plot along the z-direction. Also I think (I'm not sure) it works only if the z- is perpendicular to the xy-plane. With regards, Prasenjit. -- 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) -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091028/b81cdc30/attachment.htm
[Pw_forum] (no subject)
kajal jindal wrote: > Hii, > > I am working on ZnO doped with Nitrogen .I have used 2*2*2 ZnO > supercell ..If i replace 1 Zn atom by 1 N atom in that supercell,doped > N atom does not make any bonds with the surrounding atoms even after > optimizing the lattice constants and atomic positions..It remains at > that position as an isolated atom only...So can anybody plz suggest me > what should i do in this caseAlso i want to know that whether > this will affect my band structure calculations??? > > sincerely, > Miss Kajal > (UTA)(University of Delhi) Dear Miss Kajal, it probably made some bonds - simplest way to tell would be to look at the charge density, or the charge density difference between the two cases (use the unit cell of the doped system, but relax fully the atoms in both cases). Sure, the N will affect your band structures. Might be worth studying the media.quantum-espresso.org lectures. nicola -- - 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
[Pw_forum] About gaussian cubic format
with regards to the Tone comments, infact i am using guassian cubic so that i can do bader population analysis. I am thankful to all for your timely help. with best regards saqib University of strasbourg, France.
[Pw_forum] About gaussian cubic format
On Wed, 2009-10-28 at 16:55 +0100, Lorenzo Paulatto wrote: > In data 28 ottobre 2009 alle ore 16:49:42, saqib javaid > ha scritto: > > i found that > > inter atomic distances are the same as in SCF input file, but origin for > > plotting has changed. I hope i am clear enough this time... > > Dear Saqib, > it does not come from the Gaussian file, but from XCrysDen itself, which > translates all the atoms inside the primitive unit cell. If you want all > the atoms in they original positions follow the menu Displa -> Unit of > repetition -> translational asymmetric unit. To add to this comment, which raises two issues: (1) if your system is periodic (i.e. crystal or surface), use XSF file instead of gaussian cube file as to have the possibility to use/generate periodic images (2) if your system is a molecule "in the box", put the molecule in the center of the box, as this will avoid the "translational" problem discussed above. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] About gaussian cubic format
In data 28 ottobre 2009 alle ore 16:49:42, saqib javaid ha scritto: > i found that > inter atomic distances are the same as in SCF input file, but origin for > plotting has changed. I hope i am clear enough this time... Dear Saqib, it does not come from the Gaussian file, but from XCrysDen itself, which translates all the atoms inside the primitive unit cell. If you want all the atoms in they original positions follow the menu Displa -> Unit of repetition -> translational asymmetric unit. best 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/
[Pw_forum] About gaussian cubic format
Thanks a lot for your reply. What i mean by "do not match" is the fact that atomic coordinates are different from what i gave in SCF input file. When i load the guassina cubic file in the Xcrysden, i found that inter atomic distances are the same as in SCF input file, but origin for plotting has changed. I hope i am clear enough this time... with best regards saqib javaid University of strasbourg, France
[Pw_forum] About gaussian cubic format
saqib javaid wrote: > the xyz coordinates of the atoms given in the output file (...) > do not match the coordinates used in SCF input file. what do you mean by "do not match"? if you visualize the charge and the atoms, do they look misplaced? > Secondly, is there any way to increase the no. of mesh points in this > format. the number of mesh points is determined by the size of the FFT grid. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] About gaussian cubic format
Dear PWSCF users, I have a question regarding gaussian cubic format (output_format=6 in pp input file). I have used this format to get charge density. However, the xyz coordinates of the atoms given in the output file (which should be in bohr as per a previous post) do not match the coordinates used in SCF input file. I would appreciate if you can clarify this problem. Secondly, is there any way to increase the no. of mesh points in this format. Thanks in advance for your kind reply with best regards, saqib Javaid Unviersity of Strasbourg, France
[Pw_forum] about the nelec in the outputfile
Dear Duy Le: Thanks very much for your kind reply! Because just a small amount of charges are added to my system, so that I did not noticed the small difference in the values. Thanks very much! Best Wishes! Yours Sincerely L.F.Huang > From: Duy Le > Subject: Re: [Pw_forum] about the nelec in the outputfile > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Did you check carefully? If you change the tot_charge, the number of > electron must be charged accordingly. The starting charge is generated to be > a non-charge system but then will be renormalized accordingly. > > That number 200 is the total electron in your unit cell corresponding to the > neutral system. > -- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" -- == L.F.Huang(???) ph.D candidate, 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/20091028/f4a96efe/attachment.htm
[Pw_forum] plane averaged local potential
Hello, I need to calculate plane averaged local potentials, and charges, for a heterostructure. I.e., V(z)=1/(Lx*Ly) \int\int V(x,y,z) dx dy I think I can do it using PP to get V(x,y,z) in the 3D FFT grid and a write a program that makes the average. Then I want to obtain the macroscopic average, as defined in a triestine paper by Baldereschi, Baroni and Resta PRL 61 ,734 (1988). Before spending one or two days writing the program and become sure that is works fine, I would like to confirm that this is not already implemented in PP or in other utility of Quantum-ESPRESSO. Thank you -- 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/20091028/6f36f848/attachment.htm
[Pw_forum] electronic-phonon coupling error
Thanks for your reply, I find the reason of this problem. When I erase the following control parameter ,verything is ok . wf_collect=.true. Thank you very much . 2009-10-28 Y.M.Qian Paolo Giannozzi ? 2009-10-26 16:32:50 PWSCF Forum ??? ??? Re: [Pw_forum] electronic-phonon coupling error Y.M.Qian wrote: > But there is still mistake > from openfilq : error # 1 > file nm-type.wfc not found it is not there. Check your input data. 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 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091028/28a05bcd/attachment.htm
[Pw_forum] About Debye Temp.
Hi I am trying to investigate the Debye Temp. of two polymorphs of a non-metal case, by calculating the heat capacity,?c_v?(using the phonon DOS) at very low temperatures. But the polymorph with higher Bulk Modulus, gets the lower Debye Temp. I think, as the acoustic frequencies have more important role in both stiffness and "c_v in low temps", the higher the Bulk Modulus, may get the higher Debye temp. Am i right? Is there anything wrong in my calculation? Thanks for any comment R. Ebraahimi Grad. Student Tehran University -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091028/9855250f/attachment.htm
[Pw_forum] convergence problems using GIPAW
Davide, > is your system metallic? > the material I am studying is Li2MnO3. It is an insulator, at low temperature there might exist a weak antiferromagnetic interaction between Mn ions. In this material I predominantley wanted to calculate the hyperfine interaction between Mn ion and Li nucleus. Therefore I performed spin-polarized calculation. The input file is given below. Nevertheless, I was also interested in the magnitude of Li chemical shifts. calculation = 'scf' , restart_mode = 'from_scratch' , outdir = './scratch/' , pseudo_dir = './pseudo/' , prefix = 'Li2MnO3' , tstress = .true. , tprnfor = .true. , verbosity = 'high' , / ibrav = 14, A = 4.929200 , B = 8.531500 , C = 5.025100 , cosAB = 0 , cosAC = -0.3311 , cosBC = 0 , nat = 24, ntyp = 3, ecutwfc = 80.0 , ecutrho = 320.0 , occupations = 'smearing' , degauss = 0.02 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(2) = 0.7, / conv_thr = 1.0d-10 , mixing_mode = 'plain' , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES Li6.94100 Li_pbe-20090916.UPF Mn 54.93800 Mn.pbe-rrkj-semi-gipaw.UPF O 15.99900 O.pbe-tm-gipaw.UPF ATOMIC_POSITIONS crystal Li 0.0 0.5 0.0 . . . K_POINTS automatic 4 3 4 1 1 1 Gregor
[Pw_forum] about the nelec in the outputfile
Dear PWSCF Developers: I am calculating the electronic structure of charged systems, and there is one thing that has confused me: Whatever how much "tot_charge"(in unit of 1 electron, am I right?) I set in the input files, the "nelec" or the " starting charge" in the output files always appears to be about 200.0. It seems this is not related to the problem of unit transformation, am I right? Then, what does the number "200.0" means? Any kind-hearted reply would be highly appreciated! Thanks very much! Best Wishes! Yours Sincerely L. F. Huang -- == L.F.Huang(???) ph.D candidate, 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/20091028/b1694f5a/attachment-0001.htm
[Pw_forum] Charge ordering with QE
Dear QE community, I am currently studying charge-density wave ordered materials form the theoretical point of view. In my system, VS2, the Vanadium planes order in an hexagonal 2D lattice and are sandwiched by two Sulfur planes. As a basic approach, an hexagonal unit cell with one V and two S atoms produces a band structure that is in fair agreement with the experimental data and is consistent with other all-electron calculations. But both theoretically and experimentally there are hints that the system is orbital-ordered, i.e. that the d electrons on the Vanadium sites occupy orbitals of different symmetry on different Vanadium sites. In order to calculate the electronic structure of an orbitally-ordered system I think I have to use a supercell and specify different occupation numbers for the different Vanadium sites. The problem is that I don't know how to do that. I tried specifying the starting_ns_eigenvalue variable on different sites, but the converged calculation is identical to the calculation with starting_ns_eigenvalue left unspecified. In the INPUT_PW it is written that the occupation matrices can be specified only when the LDA+U scheme is used. However, I cannot use the LDA+U on my system (Mac OS X 10.5.6) because every time I use the Vanadium pseudopotential (either the one I generated, ether the one on the QE database) I find a "segmentation fault" that I cannot solve. BTW, the segmentation fault error does not appear for Co or Fe or Ni pseudopotentials. Thanks everybody for the help, Mattia Mulazzi FPR Fellow of RIKEN at Spring8 Excitation Order Research Team 1-1-1 Sayo-cho Sayo-gun, Hyogo Japan
[Pw_forum] mixing_mode: "local-TF" and "TF".
Dear Users, Recently, when i did some calculations of molecular dynamics using pwscf code, i found that the mixing_mode of local-TF and TF can improve the convergence greatly. However, i did not understand how it works. Could anybody tell me? I know the Thomas-Fermi theory, which is the foundation of DFT. So, the TF here is the same as the Thomas-Fermi theory? Are there any references about it? And is there any limitation for the usage of this mixing_mode? Thanks a lot. Jiayu -- --- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China -
[Pw_forum] mixing_mode: "local-TF" and "TF".
Jiayu Dai wrote: > i found that the mixing_mode of local-TF and TF can improve the > convergence greatly.[...] Are there any references about it? there is some explanation in the paper describing QE: J. Phys.: Condens. Matter 21, 395502 (2009). The relevant reference is D. Raczkowski, A. Canning, and L. W. Wang, Phys. Rev. B64, R121101 (2001) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] Left and right going Bloch's states from PWCOND
Dear Alexander,
You are correct, left and right moving states are in general not
related. I was wrong about trying to create a pair. Thanks for
clarification.
I have a few more questions.
1. I want to find out the reflection coefficient in the code. In
transmit.f90, transmission coefficient is |tmat(ig,n)|^2, where tmat is
vec1(ntran-n2d-npol*nocrosr+ig,n). (line 206, of version 4.0.5).
Reflection is not explicitly calculated in the code, but it should be
modulus square of vec1(2*n2d+npol*norbs+ig,n) (line 234). Am I correct?
2. In the code reflection and transmission coefficients are calculated
for one direction lets say t++ and t+-, which is transmission and
reflection coefficient for Bloch' state moving from - to + , or in other
words, left to right. To calculate transmission and reflection for Bloch's
state going from right to left, what should I do? Should i just rotate my
system 180 degree, that way leads get interchanged and also scattering
area has orientation 180 different from before.
3. In the subroutine sunitary.f90, is raux measure of conservation of
flux? If I sum all the transmission and reflecion coefficient for
a particular Bloch's state, I should get 1, and computationally a number
close to 1. How large could it be for S matrix not to be unitary, i m
getting raux more than one e.g. 1.0011 but code still considers smatrix
to be unitary.
Regards,
Manoj Srivastava
University of Florida, Gainesville, FL
On Thu, 22
Oct 2009, Alexander Smogunov wrote:
> On Thu, 2009-10-22 at 11:34 -0400, Manoj Srivastava wrote:
> > Dear Alexander,
> > Thanks for your answer. I just want to make sure. Imagine we have total
> > number of channels in the left lead 2, so total number of Bloch's state
> > are 4. 2 of them left going say a and b, and 2 right going say c and d.
> > So, are you saying that for left going state a, the corresponding right
> > going state is c? Are they ordered this way?
>
> what do you mean by corresponding? Left and right moving Bloch
> states are in general not related one to another, you can even have
> different number of them ... Only if you have some symmetry S which
> brings kz to -kz conserving k_parallel, then the state with
> \psi_{-kz} will be S \psi{kz}. This is true for example at 2D G point
> when you have time reversal operation.
>
> Now the code simply arranges the propagating states in the order of
> increasing |k_z|...
>
> Regards, Alexander
>
>
> >
> > Regards,
> > Manoj
> >
> >
> > On Thu, 22 Oct 2009, Alexander
> > Smogunov wrote:
> >
> > > Dear Manoj.
> > >
> > > The output of complex k vectors is performed in
> > > summary_band.f90 routine. If you want to see all
> > > the complex k vectors, not only propagating ones,
> > > you can change at the end of this routine:
> > >
> > > ---
> > > do i = 1, nchanl
> > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev
> > > enddo
> > > ---
> > >
> > > to
> > > ---
> > >
> > > do i = 1, 2*nstl
> > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev
> > > enddo
> > > ---
> > >
> > > Altogether there are 2*nstl (or 2*nstr) Bloch states in the left
> > > (or right) lead. First half, [1,nstl], are propagating or decaying to
> > > the right states, another half, [nstl+1,2*nstl], - propagating or
> > > decaying to the left. In each group, first nchanl states are propagating
> > > states.
> > >
> > > The propagating states are normalized by the current and are arranged in
> > > the above order at the end of jbloch.f90 routine, after the following
> > > lines:
> > >
> > > !
> > > ! Right ordering (+, >, -, <)
> > > !
> > >
> > >
> > >
> > > Notice, that in the last versions the code gives in output
> > > both propagating to the right and to the left states.
> > >
> > > Hope this helps,
> > > Alexander
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Wed, 2009-10-21 at 14:13 -0400, Manoj Srivastava wrote:
> > > > Dear All,
> > > > I am trying to figure out the left and right going Bloch's states in
> > > > the
> > > > lead from PWCOND. For a given (kx,ky)and energy we get kz. The code only
> > > > prints out Bloch's state moving in one direction. eg. in one of the
> > > > calculation-
> > > > k//=(0.375,-0.375)
> > > > Nchannels of the left tip =1
> > > > k1(2pi/a)k2(2pi/a) E-Ef (eV)
> > > >
> > > >0.3157801 0.000 0.000
> > > >
> > > > Now if I want Bloch's state moving in right as well as left direction, I
> > > > can go to kbloch.f90 subroutine, and print out all the eigen values of
> > > > AX=exp(ikd)BX, and out of those the ones with real solution would be our
> > > > Bloch's state, so I get for each channel two solutions-
> > > > kval (-0.275409421993275,1.823688001395235E-010)
> > > > kval (0.315780119742506,-3.611201785292708E-012)
> > > >
> > > > To figure out the direction, I can
[Pw_forum] Looking for Manganse pseudopotential
Hello world! I'm looking for a Manganse pseudopotencial. At the QE home page there is one but with semicore states in valence. Does anybody have a pseudo without semicore. Of course, Scalar-Relativistic Calculation and GGA ( the PBE one) and Ultrasoft are the main caracteristics Thanks everybody!! Lic. Christian Helman Gerencia de Investigaciones y Aplicaciones Centro At?mico Constituyentes-CNEA Argentina Tel:++54-11-6772-7102
[Pw_forum] about the nelec in the outputfile
Did you check carefully? If you change the tot_charge, the number of electron must be charged accordingly. The starting charge is generated to be a non-charge system but then will be renormalized accordingly. That number 200 is the total electron in your unit cell corresponding to the neutral system. -- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, Oct 27, 2009 at 10:17 PM, lfhuang wrote: > Dear PWSCF Developers: > > I am calculating the electronic structure of charged systems, and there > is one thing that has confused me: Whatever how much "tot_charge"(in unit of > 1 electron, am I right?) I set in the input files, the "nelec" or the " > starting charge" in the output files always appears to be about 200.0. It > seems this is not related to the problem of unit transformation, am I > right? Then, what does the number "200.0" means? > > Any kind-hearted reply would be highly appreciated! Thanks very much! > > Best Wishes! > > Yours Sincerely > > L. F. Huang > > -- > > == > L.F.Huang(???) ph.D candidate, 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/20091027/c1166f45/attachment.htm
