[Pw_forum] How to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO?
On 05/28/2011 10:18 AM, mohnish pandey wrote:
>
>
> On Sun, May 29, 2011 at 4:33 AM, Hongsheng Zhao
> mailto:zhaohscas at yahoo.com.cn>> wrote:
>
> On 05/28/2011 02:44 AM, mohnish pandey wrote:
>
> Dear Hongsheng,
> All the four bonds in ZnO wurtzite are equivalent.
>
> But the four bonds have different bond lengths: the bond length
> parallel to c axis is different from that of the other two bonds.
> Why can you say are equivalent?
> They have different orientation but the length are same. You can
> check it by calculating the bond length using crystal convention.
> Just give the coordinate in crystal-convention in Xcrysden and you
> can measure it.You will get all the bonds as same.
>
The Xcrysden is not so intuitive for measuring the bond lengths. I use
materials studio's visualizer to do this test. And find they have
different bond lengths. Please see the snapshot for this from here:
http://h1.ripway.com/zhaohs/ZnO-b4-bond-length.tif
I also give you the corresponding cif file which I used to measure the
bond lengths, just for your information. To obtain the cif file, from
here: http://h1.ripway.com/zhaohs/ZnO.cif
<http://h1.ripway.com/zhaohs/ZnO.cif>
>
> So to calculate the binding energy you have to use the below
> formula :
>
> E_{binding-ZnO}=E{calculated-ZnO-wurtzite}-E_{Zn_{crystal-total}}-E_{E(1/2*O2}}.
> Remember that you have to do spin-polarised calculation for
> O2 otherwise it will give wrong answer.
>
> I've learned that this is due to O atom's open-shell
> configuration. Than what is the initial spin should I use for O2?
>
> Furthermore, for ZnO wurtzite, should I do spin-polarised
> calculation or not?
>
> No for ZnO you dont have to. I said for O2 only. You can do both the
> unpolarised and polarised calculation, and you will find the
> difference in bond energy and bond length too.
This is just the things that I cann't figure them out completely. Let
me give more detail descriptions of my understanding and my confusion:
1- For most open-shell atoms, there are non-spherical density due to
unfilled shells and a non-zero spin state, say, for O atom. In this case,
if we want to obtain the atom energy via DFT calculation by using the
big box model, a spin-polarised calculation should be used.
2- When the open-shell atoms combined together to form molecular, say, O
to O2, then open-shell orbitals will form covalent bonds. In this case,
does it mean that the open-shell atoms configurations will be changed
into close-shelled configurations? If so, I think we should not do a
spin-polarised calculation for O2, just a non spin-polarised calculation
should be OK.
3- For the Wurtsite ZnO, the Zn atom is a closed subshell atom, but the
O atom is a open subshell atom. When they combine to form Wurtsite
ZnO, how we know the Wurtsite ZnO molecule should be open-shell or
close-shell?
4- In one word, when we calculate the total energy for a atom/molecule,
what's the criteria that determine the spin-polarised calculation should
be done or not?
Regards.
>
>
> Binding energy definition is same as above. And cohesive
> energy is the difference in energy between the energy of
> crystal and corresponding species in isolated phases. Below
> are the some references.
>
> Do you mean, for the calculation of cohesive energy, I should use
> the big box model, then put one Zn in the big box, and O atom in
> another box to obtain the total energy of each isolated phases?
> Yea you have to use box model as you correctly mentioned.
>
> http://arxiv.org/ftp/cond-mat/papers/0610/0610002.pdf
> http://prb.aps.org/pdf/PRB/v70/i5/e054104
>
>
> Regards.
> --
>
> Hongsheng Zhaomailto:zhaohscas at
> yahoo.com.cn>>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
>
>
>
> --
> Regards,
> MOHNISH,
> -
> Mohnish Pandey
> Y6927262,5th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR, UP, INDIA
> -
--
Hongsheng Zhao
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China
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[Pw_forum] error in running the espresso-4.3 examples
Dear PWSCF users I installed mpich2 in my machine and the i ran the espresso-4.3_examples. Many programme were succesfully done but many showed error. Foe eg. /home/Software/espresso-4.3_ examples/examples/example14 : starting This example shows how to use pw.x, ph.x and d3.x to calculate the third-order expansion coefficients of the total energy of Si. executables directory: /home/Software/espresso-4.3/bin pseudo directory: /home/Software/pseudo temporary directory: ./tmp checking that needed directories and files exist... done running pw.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/pw.x running ph.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/ph.x running d3.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/d3.x cleaning ./tmp... done running the scf calculation for Si... done running the phonon calculation for Si at Gamma...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3 application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 Error condition encountered during test: exit status = 15 Aborting many eg (15,18, ..) showed the same error. what can be the possible error. thanks in advance Vicky singh research student Bangalore -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/b40b09e8/attachment.htm
[Pw_forum] Pseudo-potential testing
H-1015 Lausanne > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > 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/20110530/1a290525/attachment.htm
[Pw_forum] sumpdos.x
[gabriele at macgurlo:~]$ sumpdos.x -h USAGE: sumpdos [-h] [-f ] [ ... ] Sum the pdos from the file specified in input and write the sum to stdout -h : write this manual -f : takes the list of pdos files from (one per line) instead of command line : the M-th pdos file Il giorno 29/mag/2011, alle ore 13.52, Farzad Molani ha scritto: > Hi QE users, > I want to sum resalts from projwfc.x by sumpdos.x. I should say I read > pwforum and examples and usergide from PWSCF site, but I don't know how make > an input file for sumpdos.x. please help me and give an example clearly. > thanks in advance. > > Farzad Molani, > Ph.D Student, > Department of Theoretical Physical Chemistry, > K. N. Toosi University of Technology, > Tehran, Iran. > Tel.: 009891 4442 3308 > Tel.: 009821 2306 4280 > Fax: 009821 2285 3650 > Web: http://www.chem.kntu.ac.ir/~sjalili:/ > ___ > 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/20110530/a6137b77/attachment.htm
[Pw_forum] question about the convergence of eigenvalues
Hello, well, in my opinion it depends on what you have to do with those eigenvalues. If you include many empty bands, then probably the eigenvalues that did not converge will be at very high energies and you should not care about them if you just want to plot the DOS, for instance. HTH GS Il giorno 28/mag/2011, alle ore 18.42, Lun Yue ha scritto: > Hello, dear pwscf users: > > I have a question about the convergence of eigenvalues. > > In section 11.1.0.24 of the user guide, it is mentioned that a warning of N > eigenvectors not converged may signal serious trouble if it's presented in > the last steps of self-consistency. > (http://www.quantum-espresso.org/user_guide/node52.html#SECTION0001210240) > > But how about the non-scf calculations? > > In the bands and nscf calculations I got warning messanges as following: > > > > **example in band calculation (calculation = 'bands'): > > Computing kpt #:28 > c_bands: 1 eigenvalues not converged > > > **example in nscf calculation (calculation = 'nscf'): > > Computing kpt #: 144 > c_bands: 2 eigenvalues not converged > > > > Are they acceptable? > > > Thank you and best regards, > > Lun Yue > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > ___ > 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/20110530/1f58c25d/attachment-0001.htm
[Pw_forum] NEB error: unexpected dimension in ngg
.674681741
Fe 0.667703621 0.000536574 -0.00017
Fe 0.674316264 0.006943229 0.325683651
Fe 0.674316318 0.006943262 0.674316412
Fe 0.667708718 0.332776740 0.00048
Fe 0.674326689 0.326386676 0.325673271
Fe 0.674326586 0.326386572 0.674326591
Fe 0.666574671 0.62081 0.00087
S 0.50005 0.666584751 0.50002
Fe 0.674681834 0.63708 0.325318243
Fe 0.674681770 0.63861 0.674681713
Fe 0.163024413 0.166607159 0.163024430
Fe 0.163727069 0.12676 0.50008
Fe 0.163024383 0.166606989 0.836975609
Fe 0.164861935 0.499496907 0.164862035
Fe 0.165000320 0.497474731 0.49944
Fe 0.164862006 0.499497047 0.835137973
Fe 0.164906799 0.833775119 0.164906872
Fe 0.164999313 0.835864200 0.50137
Fe 0.164906819 0.833775188 0.835093037
Fe 0.50047 0.12740 0.163727088
Fe 0.49998 0.14603 0.49986
Fe 0.49968 0.12622 0.836272921
Fe 0.50044 0.497474704 0.165000336
Fe 0.50072 0.439226279 0.49816
Fe 0.49929 0.497474738 0.834999707
Fe 0.50075 0.835864185 0.164999302
Fe 0.49911 0.894163268 0.50163
Fe 0.49931 0.835864219 0.835000683
Fe 0.836975612 0.166607155 0.163024399
Fe 0.836272931 0.12710 0.49949
Fe 0.836975583 0.166607001 0.83697
Fe 0.835138037 0.499496958 0.164862120
Fe 0.834999679 0.497474714 0.49843
Fe 0.835138064 0.499497015 0.835137981
Fe 0.835093148 0.833775128 0.164906891
Fe 0.835000705 0.835864197 0.50007
Fe 0.835093210 0.833775249 0.835093104
CELL_PARAMETERS
1.00 0.0.0
0.0 1.0.0
0.0 0.1.0
K_POINTS {automatic}
3 3 3 0 0 0
--Output--
Program PWSCF v.4.2.1 starts on 30May2011 at 8:20: 6
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please acknowledge
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org";,
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
Parallel version (MPI), running on48 processors
path-images division: nimage=2
K-points division: npool =2
R & G space division: proc/pool = 12
wavefunctions fft division: fft/group =3
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 4
Max angular momentum in pseudopotentials (lmaxx) = 3
Waiting for input...
Message from routine iosys:
pot_extrapolation='second_order' not available, using 'atomic'
Message from routine iosys:
wfc_extrapolation='second_order' not available, using 'atomic'
reading file 'FeS_int_fixedPos_NEB.path'
calculation = neb
restart_mode = restart
opt_scheme= broyden
num_of_images = 6
nstep = 300
CI_scheme = no-CI
first_last_opt= F
coarse-grained phase-space= F
use_freezing = F
ds= 2. a.u.
k_max = 0.2000 a.u.
k_min = 0.0200 a.u.
suggested k_max = 0.1542 a.u.
suggested k_min = 0.0154 a.u.
path_thr = 0.0500 eV / A
-- iteration 1 --
rank 36 in job 1 node0308.int.hpc.ufs.ac.za_40349 caused collective abort of
all ranks
exit status of rank 36: return code 0
--ERROR MESSAGE--
%%
task #36
from igk_l2g_kdip : error # 1
unexpected dimension in ngg
%%
Thank you
Pieter Barnard
University of the Free State
South Africa
_
University of the Free State: This message and its contents are subject to a
disclaimer.
Please refer to http://www.ufs.ac.za/disclaimer for full details.
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[Pw_forum] total energy with GW
Hi, I wish to know if the GWW code calculates total energies of the ground state, such that can be used to obtain defect formation energies or elastic constants. If not GWW, is there any code with that capability? -- 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/20110530/5cc8d06b/attachment.htm
[Pw_forum] NEB error: unexpected dimension in ngg
Debugging such a big job, moreover after a restart, is going to be close to impossible ... P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] Born effective Charges
Hi dear user's Sorry about my last post. actually the born effective charges has transform according to symmetry. I didn't observe all the component of tensor, it is ok born effective charge are same for all the symmetry linked atom. Thanks -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA Office: 022-25595606 Home: 9920397437 / 9869834437
[Pw_forum] Using mixture of pseudo potential
Dear All, In my calculation, I used a mixture of pseudo potentials, ie. norm-conserving pp (NC pp) for one element and ultrasoft pp (US pp) for another. If I don't specify ecutrho in the input, what will be the default value for ecutrho for the ultrasoft pp. I know that for NC pp, ecutrho = 4*ecutwfc, but I do not know if the same value is used for US pp. On the other hand, if I specify ecutrho = 8*ecutwfc, then does the same value apply to the NC pp. Thank you very much, Vi University of Houston -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/eeb95881/attachment.htm
