<div dir="ltr"><div><div>Dear, Bahad?r SALMANKURT.<br><br></div>Thank you very much. <br><br></div>Best regard, <br><br></div><div class="gmail_extra"><br><div class="gmail_quote">2016-07-21 7:00 GMT-03:00 <span dir="ltr"><<a href="mailto:pw_forum-request@pwscf.org" target="_blank">pw_forum-request@pwscf.org</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Nickel doped graphene supercell scf calculation with<br>
nspin=2 stopped (?????? ?????????)<br>
2. How to get the real-space Hamiltonian by using wannier_ham.x<br>
? ( ?? )<br>
3. SCF do not converge (Regina Lelis de Sousa)<br>
4. Re: SCF do not converge (Bahad?r SALMANKURT)<br>
5. Re: SCF do not converge (Arles V. Gil Rebaza)<br>
6. Vc_Relax distorts the whole structure<br>
(Mofrad, Amir Mehdi (MU-Student))<br>
7. Fortran runtime error: Bad real number in item 13 of list<br>
input (efi dwi indari)<br>
8. Re: absorption spectrum &dielectric constant of turboTDDFT<br>
(Manu Hegde)<br>
9. Free computational material science consultancy (Gabriele Mogni)<br>
10. Re: absorption spectrum &dielectric constant of turboTDDFT<br>
(dario rocca)<br>
11. Subject: Relaxing a 2x2x2 supercell ...while reading input<br>
file getting "wrong number of columns in Atomic positions error"<br>
for silver atom created from Xcrysden (Md Mahabul Islam)<br>
12. Re: Subject: Relaxing a 2x2x2 supercell ...while reading<br>
input file getting "wrong number of columns in Atomic positions<br>
error" for silver atom created from Xcrysden (Matteo Cococcioni)<br>
13. Re: Subject: Relaxing a 2x2x2 supercell ...while reading<br>
input file getting "wrong number of columns in Atomic positions<br>
error" for silver atom created from Xcrysden (Phanikumar Pentyala)<br>
14. Re: Subject: Relaxing a 2x2x2 supercell ...while reading<br>
input file getting "wrong number of columns in Atomic positions<br>
error" for silver atom created from Xcrysden (Dae Kwang Jun)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 20 Jul 2016 15:44:18 +0400<br>
From: ?????? ????????? <<a href="mailto:ars21031960@gmail.com">ars21031960@gmail.com</a>><br>
Subject: Re: [Pw_forum] Nickel doped graphene supercell scf<br>
calculation with nspin=2 stopped<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAJ_PVdKK00e+FVr66bCyOEv_65=<a href="mailto:UJiUKPgD-dF21F%2BEFbKdFOQ@mail.gmail.com">UJiUKPgD-dF21F+EFbKdFOQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Rolly!<br>
I calculated the same object with SIESTA,<br>
<a href="https://www.researchgate.net/publication/285619763_Doping_graphene_with_a_monovacancy_bonding_and_magnetism" rel="noreferrer" target="_blank">https://www.researchgate.net/publication/285619763_Doping_graphene_with_a_monovacancy_bonding_and_magnetism</a><br>
and other 49 elements of periodic table<br>
interesting to compare (note spins are not correct).<br>
<br>
2016-07-19 19:00 GMT+04:00 Rolly Ng <<a href="mailto:rollyng@gmail.com">rollyng@gmail.com</a>>:<br>
<br>
> Dear Prof. Paolo,<br>
><br>
> I can confirm that pw.x with CPU works okay for nspin=2, so I would like<br>
> to report the bug for the pw-gpu.x (GPU version).<br>
><br>
> Thanks for your attention.<br>
><br>
> Regards,<br>
><br>
> Rolly<br>
><br>
><br>
> On 07/18/2016 02:16 PM, Paolo Giannozzi wrote:<br>
> > You are using the GPU-enabled version of QE. Try the normal version<br>
> > first. You do not need more than a few bands over the Fermi energy.<br>
> > Setting mixing_mode='TF-local- improves the convergency.<br>
> ><br>
> > Paolo<br>
> ><br>
> > On Sat, Jul 16, 2016 at 6:34 PM, Rolly Ng <<a href="mailto:rollyng@gmail.com">rollyng@gmail.com</a>> wrote:<br>
> >> Dear QE experts,<br>
> >><br>
> >> I would like to compute the DOS of Nickel doped graphene supercell with<br>
> QE<br>
> >> v5.3.0, and our group has already done that with DMol3.<br>
> >><br>
> >> Our previous publication can be found here, Ding, N., Lu, X., Wu,<br>
> C.-M.L.,<br>
> >> 2012. Comput. Mater. Sci. 51, 141?145.<br>
> >><br>
> >> Now, I like to refine the computation with QE, so at first I used<br>
> "relax" to<br>
> >> get the optimized structure of a graphene supercell with of 72 Carbon<br>
> atoms<br>
> >> and a Nickel atom was added at the center to replace one of the carbons.<br>
> >><br>
> >> Then I run scf with nspin=2 and starting magnetization (1) = 0.5 where<br>
> (1)<br>
> >> refers to the Nickel atom, the scf converged. However, at the very end<br>
> pw.x<br>
> >> stopped with the following error.<br>
> >><br>
> >> WARNING: integrated charge= 294.76903202, expected= 302.00000000<br>
> >><br>
> >><br>
> >><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> >> Error in routine electrons (1):<br>
> >> charge is wrong<br>
> >><br>
> >><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> >><br>
> >> stopping ...<br>
> >><br>
> >> I googled and found that it may be related to smearing and nbnd, I have<br>
> >> already set smearing to 0.002 Ry (312K) and I have increased nbnd to<br>
> 400 but<br>
> >> it is still running.<br>
> >><br>
> >> Can anyone help me to resolve the issue? Please find my input and output<br>
> >> attached.<br>
> >><br>
> >> Thank you very much,<br>
> >> Rolly<br>
> >><br>
> >> --<br>
> >> PhD. Research Fellow,<br>
> >> Dept. of Physics & Materials Science,<br>
> >> City University of Hong Kong<br>
> >> Tel: +852 3442 4000<br>
> >> Fax: +852 3442 0538<br>
> >><br>
> >><br>
> >> _______________________________________________<br>
> >> Pw_forum mailing list<br>
> >> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> >> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
> ><br>
> ><br>
><br>
> --<br>
> PhD. Research Fellow,<br>
> Dept. of Physics & Materials Science,<br>
> City University of Hong Kong<br>
> Tel: <a href="tel:%2B852%203442%204000" value="+85234424000">+852 3442 4000</a><br>
> Fax: <a href="tel:%2B852%203442%200538" value="+85234420538">+852 3442 0538</a><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
--<br>
Best wishes,<br>
Maxim Arsent'ev, Ph.D. (Chemistry)<br>
Laboratory of research of nanostructures<br>
Institute of Silicate Chemistry of RAS<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 20 Jul 2016 21:17:12 +0800<br>
From: " ?? " <<a href="mailto:863075773@qq.com">863075773@qq.com</a>><br>
Subject: [Pw_forum] How to get the real-space Hamiltonian by using<br>
wannier_ham.x ?<br>
To: " pw_forum " <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
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<br>
Hi there<br>
I try to construct the tight-binding model. It seems that the wannier_ham.x can generate hopping parameters. However, the output file "hamilt" only contains the Hamiltonian in k-space, where or how can I find the Hamiltonian elements in real space?<br>
Thanks<br>
<br>
<br>
------------------<br>
<br>
<br>
<br>
Liang Liu<br>
<br>
School of Physics , State Key Laboratory for Crystal Materials, Shandong University<br>
<br>
No.27, Shanda Nan Road, Jinan 250100, China<br>
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<br>
Message: 3<br>
Date: Wed, 20 Jul 2016 10:34:26 -0300<br>
From: Regina Lelis de Sousa <<a href="mailto:rlsousa@mail.uft.edu.br">rlsousa@mail.uft.edu.br</a>><br>
Subject: [Pw_forum] SCF do not converge<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAAz75G_BPG87nMBxUaT22OPaHhL7BungTLG0hFvu=<a href="mailto:P4zn-sKZw@mail.gmail.com">P4zn-sKZw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
I am studying Pt(111) and Pt(100) surfaces (using a slab model) with PWSCF.<br>
I ran a structural relaxations for slabs containing 4 - 9 atomic planes<br>
(layers) and everything was fine. In all calculations a vacuum region of<br>
the order of 15 Angstroms was used. However, in the calculations with 10<br>
atomic planes or more the SCF procedure does not converge and i do not<br>
understand the reason. I did some changes on SCF procedure (for example: I<br>
tested cg method among other things). Does anyone notice some mistake with<br>
the input file or with my atomic coordinates? Any help would be<br>
appreciated.<br>
<br>
<br>
The inputs and outputs are:<br>
<br>
1 - First Try:<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
&control<br>
calculation = 'relax'<br>
restart_mode='from_scratch',<br>
prefix='Pt_100_12_layers_15_vacuo',<br>
tprnfor = .true.,<br>
tstress =.true.,<br>
verbosity ='high',<br>
pseudo_dir = '/home/rlsousa/Pseudopot',<br>
/<br>
&system<br>
ibrav= 6,<br>
A = 2.831157456,<br>
C=37.2,<br>
nat= 12,<br>
ntyp= 1,<br>
ecutwfc =35.0,<br>
ecutrho = 350.0,<br>
occupations='smearing',<br>
smearing='marzari-vanderbilt',<br>
degauss=0.01, !I tested this.<br>
/<br>
&electrons<br>
mixing_beta = 0.7,<br>
conv_thr = 1.0d-8<br>
electron_maxstep = 600,<br>
/<br>
&ions<br>
/<br>
ATOMIC_SPECIES<br>
Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
ATOMIC_POSITIONS {angstrom}<br>
Pt 0.000000 0.000000 0.000000<br>
Pt 1.414214 1.414214 2.000000<br>
Pt 0.000000 0.000000 4.000000<br>
Pt 1.414214 1.414214 6.000000<br>
Pt 0.000000 0.000000 8.000000<br>
Pt 1.414214 1.414214 10.000000<br>
Pt 0.000000 0.000000 12.000000<br>
Pt 1.414214 1.414214 14.000000<br>
Pt 0.000000 0.000000 16.000000<br>
Pt 1.414214 1.414214 18.000000<br>
Pt 0.000000 0.000000 20.000000<br>
Pt 1.414214 1.414214 22.000000<br>
K_POINTS AUTOMATIC<br>
16 16 1 1 1 1<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
OUTPUT:<br>
<br>
Program PWSCF v.5.0.1 starts on 3Mar2016 at 1:58: 2<br>
...<br>
<br>
...<br>
<br>
Self-consistent Calculation<br>
<br>
iteration # 1 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
ethr = 1.00E-02, avg # of iterations = 4.0<br>
<br>
total cpu time spent up to now is 212.7 secs<br>
<br>
total energy = -1037.38592080 Ry<br>
Harris-Foulkes estimate = -1039.73360971 Ry<br>
estimated scf accuracy < 2.83017780 Ry<br>
<br>
iteration # 2 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
ethr = 2.36E-03, avg # of iterations = 8.9<br>
<br>
total cpu time spent up to now is 627.5 secs<br>
<br>
total energy = -1004.47885510 Ry<br>
Harris-Foulkes estimate = -1113.67210149 Ry<br>
estimated scf accuracy < 4035.50057863<br>
<br>
...<br>
<br>
<br>
iteration #600 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
ethr = 2.92E-05, avg # of iterations = 11.5<br>
<br>
total cpu time spent up to now is 250301.6 secs<br>
<br>
total energy = -1025.14170975 Ry<br>
Harris-Foulkes estimate = -1050.93732899 Ry<br>
estimated scf accuracy < 312.87625423 Ry<br>
<br>
End of self-consistent calculation<br>
<br>
convergence NOT achieved after 600 iterations: stopping<br>
<br>
<br>
===================================================================================<br>
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>
= EXIT CODE: 1<br>
= CLEANING UP REMAINING PROCESSES<br>
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
===================================================================================<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
2 - Second Try:<br>
I did:<br>
&electrons<br>
diagonalization='cg'<br>
mixing_beta = 0.5,<br>
conv_thr = 1.0d-8<br>
electron_maxstep = 300,<br>
<br>
and this work fine only for Pt(100) with 10 atomic plane.<br>
<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
3 - Third Try:<br>
For Pt(111) with 10 atomic planes:<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
&control<br>
calculation = 'relax'<br>
restart_mode='from_scratch',<br>
prefix='Pt_111_10_layers',<br>
tprnfor = .true.,<br>
tstress =.true.,<br>
verbosity ='high',<br>
pseudo_dir = '/home/rlsousa/pseudo/'<br>
/<br>
&system<br>
ibrav= 4,<br>
A = 2.831157456,<br>
C=36.0,<br>
nat= 10,<br>
ntyp= 1,<br>
ecutwfc =35.0,<br>
ecutrho = 350.0,<br>
occupations='smearing',<br>
smearing='marzari-vanderbilt',<br>
degauss=0.01,<br>
/<br>
&electrons<br>
mixing_beta = 0.7,<br>
conv_thr = 1.0d-8<br>
electron_maxstep = 600,<br>
/<br>
&ions<br>
/<br>
ATOMIC_SPECIES<br>
Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
ATOMIC_POSITIONS {angstrom}<br>
Pt -0.000000000 -0.000000000 -20.784609691<br>
Pt 0.000000000 -0.000000000 -13.856406461<br>
Pt 0.000000000 -0.000000000 -6.928203230<br>
Pt 0.000000000 0.000000000 0.000000000<br>
Pt 1.414213562 0.816496581 -16.165807537<br>
Pt 1.414213562 0.816496581 -9.237604307<br>
Pt 1.414213562 0.816496581 -2.309401077<br>
Pt -0.000000000 1.632993162 -18.475208614<br>
Pt -0.000000000 1.632993162 -11.547005384<br>
Pt -0.000000000 1.632993162 -4.618802154<br>
K_POINTS AUTOMATIC<br>
16 16 1 1 1 1<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
And the output is:<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
Self-consistent Calculation<br>
<br>
iteration # 1 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
ethr = 1.00E-02, avg # of iterations = 3.7<br>
<br>
total cpu time spent up to now is 619.8 secs<br>
<br>
total energy = -864.90667968 Ry<br>
Harris-Foulkes estimate = -866.46381391 Ry<br>
estimated scf accuracy < 1.92161923 Ry<br>
<br>
iteration # 2 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
ethr = 1.92E-03, avg # of iterations = 8.8<br>
<br>
total cpu time spent up to now is 1789.4 secs<br>
<br>
total energy = -834.69092069 Ry<br>
Harris-Foulkes estimate = -912.73406647 Ry<br>
estimated scf accuracy < 3297.67106012 Ry<br>
iteration #154 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
ethr = 8.37E-05, avg # of iterations = 7.2<br>
<br>
negative rho (up, down): 0.577E-07 0.000E+00<br>
<br>
total cpu time spent up to now is 143089.7 secs<br>
<br>
total energy = -862.54326840 Ry<br>
Harris-Foulkes estimate = -876.81955048 Ry<br>
estimated scf accuracy < 354.34333068 Ry<br>
<br>
iteration #155 ecut= 35.00 Ry beta=0.70<br>
Davidson diagonalization with overlap<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
<br>
4 - fourth Try:<br>
The atomic positions for input file was optimized with a PCFF force field:<br>
a - For Pt(100) with 16 atomic planes, the atomic positions for input were:<br>
Pt 0.000001863 -0.000006550 1.917081940<br>
Pt -0.000000583 -0.000002969 5.858730954<br>
Pt -0.000001806 0.000000728 9.775507899<br>
Pt -0.000003453 0.000006845 13.688807549<br>
Pt -0.000001863 0.000006007 17.601709335<br>
Pt -0.000000324 0.000000339 21.516053222<br>
Pt 0.000003440 -0.000003229 25.439026038<br>
Pt 0.000005016 -0.000002994 29.455726011<br>
Pt 1.382821195 1.382814326 -0.121704445<br>
Pt 1.382818575 1.382816058 3.895001445<br>
Pt 1.382817093 1.382818978 7.817973036<br>
Pt 1.382816565 1.382824166 11.732314256<br>
Pt 1.382814960 1.382827050 15.645213637<br>
Pt 1.382818406 1.382822391 19.558517247<br>
Pt 1.382820459 1.382816862 23.475296312<br>
Pt 1.382823964 1.382815499 27.416943612<br>
<br>
But I get the same result.<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
5 - fifth try - I did not have any throuble for these cases.<br>
a - For Pt(100) with 9 atomic planes:<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
.....<br>
&system<br>
ibrav= 6,<br>
A = 2.831157456,<br>
C=33.2,<br>
nat= 9,<br>
ntyp= 1,<br>
ecutwfc =35.0,<br>
ecutrho = 350.0,<br>
occupations='smearing',<br>
smearing='marzari-vanderbilt',<br>
degauss=0.01,<br>
/<br>
&electrons<br>
diagonalization='cg'<br>
mixing_beta = 0.5,<br>
conv_thr = 1.0d-8<br>
electron_maxstep = 300,<br>
/<br>
&ions<br>
/<br>
ATOMIC_SPECIES<br>
Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
ATOMIC_POSITIONS {angstrom}<br>
Pt 0.000000000 -0.000000000 2.001930636<br>
Pt 0.000000000 -0.000000000 6.005791907<br>
Pt 0.000000000 -0.000000000 10.009653178<br>
Pt 0.000000000 -0.000000000 14.013514450<br>
Pt 1.415578728 1.415578728 -0.000000000<br>
Pt 1.415578728 1.415578728 4.003861271<br>
Pt 1.415578728 1.415578728 8.007722543<br>
Pt 1.415578728 1.415578728 12.011583814<br>
Pt 1.415578728 1.415578728 16.015445086<br>
<br>
.....<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
<br>
Atomic positions for Pt(100) with 9 atomic planes:<br>
$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
b - For Pt(111) with 9 atomic planes:<br>
&system<br>
ibrav= 4,<br>
A = 2.831157456,<br>
C=36.0,<br>
nat= 9,<br>
ntyp= 1,<br>
ecutwfc =35.0,<br>
ecutrho = 350.0,<br>
occupations='smearing',<br>
smearing='marzari-vanderbilt',<br>
degauss=0.01,<br>
/<br>
&electrons<br>
mixing_beta = 0.7,<br>
conv_thr = 1.0d-8<br>
electron_maxstep = 600,<br>
/<br>
&ions<br>
/<br>
ATOMIC_SPECIES<br>
Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
ATOMIC_POSITIONS {angstrom}<br>
Pt 0.000000000 -0.000000000 -13.856406461<br>
Pt 0.000000000 -0.000000000 -6.928203230<br>
Pt 0.000000000 0.000000000 0.000000000<br>
Pt 1.414213562 0.816496581 -16.165807537<br>
Pt 1.414213562 0.816496581 -9.237604307<br>
Pt 1.414213562 0.816496581 -2.309401077<br>
Pt -0.000000000 1.632993162 -18.475208614<br>
Pt -0.000000000 1.632993162 -11.547005384<br>
Pt -0.000000000 1.632993162 -4.618802154<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
Thanks in advance,<br>
regards<br>
<br>
R. Lelis-Sousa.<br>
UFT/TO/Brazil.<br>
<br>
<br>
<br>
--<br>
Tenha uma ?tima semana,<br>
<br>
Atenciosamente,<br>
<br>
<br>
Dra. Regina L?lis de Sousa<br>
Professor Adjunto -- Universidade Federal do Tocantins<br>
Campus de Aragua?na<br>
Rua Paraguai SN -- Esquina com a Urixamas<br>
Telefone: +55(63)2112-2283<br>
Caixa Postal 132<br>
CEP: 77.838-824<br>
Tocantins.<br>
"Success is knowing that you have done your best and have exploited your<br>
God-given or gene-given abilities to the next maximum extent. More than<br>
this, no<br>
one can do...". Prof. Alan Graham MacDiarmid<br>
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<br>
Message: 4<br>
Date: Wed, 20 Jul 2016 17:11:03 +0300<br>
From: Bahad?r SALMANKURT <<a href="mailto:bsalmankurt@gmail.com">bsalmankurt@gmail.com</a>><br>
Subject: Re: [Pw_forum] SCF do not converge<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CADT9cuvUhyuBYxgVxPRwR6JPN2hVtb29gZ1nObjvZ-fuQBY%2Bkw@mail.gmail.com">CADT9cuvUhyuBYxgVxPRwR6JPN2hVtb29gZ1nObjvZ-fuQBY+kw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Regina,<br>
<br>
Please add the following to the &electrons section and reduce mixing_beta<br>
to 0.5 or less<br>
<br>
* mixing_mode='local-TF'*<br>
<br>
I calculated this with 6x6x1 mesh in order to gain time.<br>
<br>
result;<br>
<br>
one-electron contribution = -9188.05659192 Ry<br>
hartree contribution = 4706.16324373 Ry<br>
xc contribution = -553.52233265 Ry<br>
ewald contribution = 3996.04511660 Ry<br>
smearing contrib. (-TS) = -0.00116989 Ry<br>
<br>
convergence has been achieved in 21 iterations<br>
<br>
<br>
Bests<br>
<br>
<br>
2016-07-20 16:34 GMT+03:00 Regina Lelis de Sousa <<a href="mailto:rlsousa@mail.uft.edu.br">rlsousa@mail.uft.edu.br</a>>:<br>
<br>
> Dear all,<br>
> I am studying Pt(111) and Pt(100) surfaces (using a slab model) with<br>
> PWSCF. I ran a structural relaxations for slabs containing 4 - 9 atomic<br>
> planes (layers) and everything was fine. In all calculations a vacuum<br>
> region of the order of 15 Angstroms was used. However, in the calculations<br>
> with 10 atomic planes or more the SCF procedure does not converge and i do<br>
> not understand the reason. I did some changes on SCF procedure (for<br>
> example: I tested cg method among other things). Does anyone notice some<br>
> mistake with the input file or with my atomic coordinates? Any help would<br>
> be appreciated.<br>
><br>
><br>
> The inputs and outputs are:<br>
><br>
> 1 - First Try:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> &control<br>
> calculation = 'relax'<br>
> restart_mode='from_scratch',<br>
> prefix='Pt_100_12_layers_15_vacuo',<br>
> tprnfor = .true.,<br>
> tstress =.true.,<br>
> verbosity ='high',<br>
> pseudo_dir = '/home/rlsousa/Pseudopot',<br>
> /<br>
> &system<br>
> ibrav= 6,<br>
> A = 2.831157456,<br>
> C=37.2,<br>
> nat= 12,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01, !I tested this.<br>
> /<br>
> &electrons<br>
> mixing_beta = 0.7,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 600,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt 0.000000 0.000000 0.000000<br>
> Pt 1.414214 1.414214 2.000000<br>
> Pt 0.000000 0.000000 4.000000<br>
> Pt 1.414214 1.414214 6.000000<br>
> Pt 0.000000 0.000000 8.000000<br>
> Pt 1.414214 1.414214 10.000000<br>
> Pt 0.000000 0.000000 12.000000<br>
> Pt 1.414214 1.414214 14.000000<br>
> Pt 0.000000 0.000000 16.000000<br>
> Pt 1.414214 1.414214 18.000000<br>
> Pt 0.000000 0.000000 20.000000<br>
> Pt 1.414214 1.414214 22.000000<br>
> K_POINTS AUTOMATIC<br>
> 16 16 1 1 1 1<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> OUTPUT:<br>
><br>
> Program PWSCF v.5.0.1 starts on 3Mar2016 at 1:58: 2<br>
> ...<br>
><br>
> ...<br>
><br>
> Self-consistent Calculation<br>
><br>
> iteration # 1 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 1.00E-02, avg # of iterations = 4.0<br>
><br>
> total cpu time spent up to now is 212.7 secs<br>
><br>
> total energy = -1037.38592080 Ry<br>
> Harris-Foulkes estimate = -1039.73360971 Ry<br>
> estimated scf accuracy < 2.83017780 Ry<br>
><br>
> iteration # 2 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 2.36E-03, avg # of iterations = 8.9<br>
><br>
> total cpu time spent up to now is 627.5 secs<br>
><br>
> total energy = -1004.47885510 Ry<br>
> Harris-Foulkes estimate = -1113.67210149 Ry<br>
> estimated scf accuracy < 4035.50057863<br>
><br>
> ...<br>
><br>
><br>
> iteration #600 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 2.92E-05, avg # of iterations = 11.5<br>
><br>
> total cpu time spent up to now is 250301.6 secs<br>
><br>
> total energy = -1025.14170975 Ry<br>
> Harris-Foulkes estimate = -1050.93732899 Ry<br>
> estimated scf accuracy < 312.87625423 Ry<br>
><br>
> End of self-consistent calculation<br>
><br>
> convergence NOT achieved after 600 iterations: stopping<br>
><br>
><br>
><br>
> ===================================================================================<br>
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>
> = EXIT CODE: 1<br>
> = CLEANING UP REMAINING PROCESSES<br>
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
><br>
> ===================================================================================<br>
><br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> 2 - Second Try:<br>
> I did:<br>
> &electrons<br>
> diagonalization='cg'<br>
> mixing_beta = 0.5,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 300,<br>
><br>
> and this work fine only for Pt(100) with 10 atomic plane.<br>
><br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> 3 - Third Try:<br>
> For Pt(111) with 10 atomic planes:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> &control<br>
> calculation = 'relax'<br>
> restart_mode='from_scratch',<br>
> prefix='Pt_111_10_layers',<br>
> tprnfor = .true.,<br>
> tstress =.true.,<br>
> verbosity ='high',<br>
> pseudo_dir = '/home/rlsousa/pseudo/'<br>
> /<br>
> &system<br>
> ibrav= 4,<br>
> A = 2.831157456,<br>
> C=36.0,<br>
> nat= 10,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01,<br>
> /<br>
> &electrons<br>
> mixing_beta = 0.7,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 600,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt -0.000000000 -0.000000000 -20.784609691<br>
> Pt 0.000000000 -0.000000000 -13.856406461<br>
> Pt 0.000000000 -0.000000000 -6.928203230<br>
> Pt 0.000000000 0.000000000 0.000000000<br>
> Pt 1.414213562 0.816496581 -16.165807537<br>
> Pt 1.414213562 0.816496581 -9.237604307<br>
> Pt 1.414213562 0.816496581 -2.309401077<br>
> Pt -0.000000000 1.632993162 -18.475208614<br>
> Pt -0.000000000 1.632993162 -11.547005384<br>
> Pt -0.000000000 1.632993162 -4.618802154<br>
> K_POINTS AUTOMATIC<br>
> 16 16 1 1 1 1<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> And the output is:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> Self-consistent Calculation<br>
><br>
> iteration # 1 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 1.00E-02, avg # of iterations = 3.7<br>
><br>
> total cpu time spent up to now is 619.8 secs<br>
><br>
> total energy = -864.90667968 Ry<br>
> Harris-Foulkes estimate = -866.46381391 Ry<br>
> estimated scf accuracy < 1.92161923 Ry<br>
><br>
> iteration # 2 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 1.92E-03, avg # of iterations = 8.8<br>
><br>
> total cpu time spent up to now is 1789.4 secs<br>
><br>
> total energy = -834.69092069 Ry<br>
> Harris-Foulkes estimate = -912.73406647 Ry<br>
> estimated scf accuracy < 3297.67106012 Ry<br>
> iteration #154 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 8.37E-05, avg # of iterations = 7.2<br>
><br>
> negative rho (up, down): 0.577E-07 0.000E+00<br>
><br>
> total cpu time spent up to now is 143089.7 secs<br>
><br>
> total energy = -862.54326840 Ry<br>
> Harris-Foulkes estimate = -876.81955048 Ry<br>
> estimated scf accuracy < 354.34333068 Ry<br>
><br>
> iteration #155 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
><br>
> 4 - fourth Try:<br>
> The atomic positions for input file was optimized with a PCFF force field:<br>
> a - For Pt(100) with 16 atomic planes, the atomic positions for input were:<br>
> Pt 0.000001863 -0.000006550 1.917081940<br>
> Pt -0.000000583 -0.000002969 5.858730954<br>
> Pt -0.000001806 0.000000728 9.775507899<br>
> Pt -0.000003453 0.000006845 13.688807549<br>
> Pt -0.000001863 0.000006007 17.601709335<br>
> Pt -0.000000324 0.000000339 21.516053222<br>
> Pt 0.000003440 -0.000003229 25.439026038<br>
> Pt 0.000005016 -0.000002994 29.455726011<br>
> Pt 1.382821195 1.382814326 -0.121704445<br>
> Pt 1.382818575 1.382816058 3.895001445<br>
> Pt 1.382817093 1.382818978 7.817973036<br>
> Pt 1.382816565 1.382824166 11.732314256<br>
> Pt 1.382814960 1.382827050 15.645213637<br>
> Pt 1.382818406 1.382822391 19.558517247<br>
> Pt 1.382820459 1.382816862 23.475296312<br>
> Pt 1.382823964 1.382815499 27.416943612<br>
><br>
> But I get the same result.<br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> 5 - fifth try - I did not have any throuble for these cases.<br>
> a - For Pt(100) with 9 atomic planes:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> .....<br>
> &system<br>
> ibrav= 6,<br>
> A = 2.831157456,<br>
> C=33.2,<br>
> nat= 9,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01,<br>
> /<br>
> &electrons<br>
> diagonalization='cg'<br>
> mixing_beta = 0.5,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 300,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt 0.000000000 -0.000000000 2.001930636<br>
> Pt 0.000000000 -0.000000000 6.005791907<br>
> Pt 0.000000000 -0.000000000 10.009653178<br>
> Pt 0.000000000 -0.000000000 14.013514450<br>
> Pt 1.415578728 1.415578728 -0.000000000<br>
> Pt 1.415578728 1.415578728 4.003861271<br>
> Pt 1.415578728 1.415578728 8.007722543<br>
> Pt 1.415578728 1.415578728 12.011583814<br>
> Pt 1.415578728 1.415578728 16.015445086<br>
><br>
> .....<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
><br>
> Atomic positions for Pt(100) with 9 atomic planes:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> b - For Pt(111) with 9 atomic planes:<br>
> &system<br>
> ibrav= 4,<br>
> A = 2.831157456,<br>
> C=36.0,<br>
> nat= 9,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01,<br>
> /<br>
> &electrons<br>
> mixing_beta = 0.7,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 600,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt 0.000000000 -0.000000000 -13.856406461<br>
> Pt 0.000000000 -0.000000000 -6.928203230<br>
> Pt 0.000000000 0.000000000 0.000000000<br>
> Pt 1.414213562 0.816496581 -16.165807537<br>
> Pt 1.414213562 0.816496581 -9.237604307<br>
> Pt 1.414213562 0.816496581 -2.309401077<br>
> Pt -0.000000000 1.632993162 -18.475208614<br>
> Pt -0.000000000 1.632993162 -11.547005384<br>
> Pt -0.000000000 1.632993162 -4.618802154<br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
><br>
> Thanks in advance,<br>
> regards<br>
><br>
> R. Lelis-Sousa.<br>
> UFT/TO/Brazil.<br>
><br>
><br>
><br>
> --<br>
> Tenha uma ?tima semana,<br>
><br>
> Atenciosamente,<br>
><br>
><br>
> Dra. Regina L?lis de Sousa<br>
> Professor Adjunto -- Universidade Federal do Tocantins<br>
> Campus de Aragua?na<br>
> Rua Paraguai SN -- Esquina com a Urixamas<br>
> Telefone: +55(63)2112-2283<br>
> Caixa Postal 132<br>
> CEP: 77.838-824<br>
> Tocantins.<br>
> "Success is knowing that you have done your best and have exploited your<br>
> God-given or gene-given abilities to the next maximum extent. More than<br>
> this, no<br>
> one can do...". Prof. Alan Graham MacDiarmid<br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
--<br>
<br>
Bahad?r SALMANKURT<br>
Ph.D. Candidate<br>
Department of Physics, Sakarya University, TURKEY<br>
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------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 20 Jul 2016 11:18:13 -0300<br>
From: "Arles V. Gil Rebaza" <<a href="mailto:arvifis@gmail.com">arvifis@gmail.com</a>><br>
Subject: Re: [Pw_forum] SCF do not converge<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CABEdBFNNwmnANC_7CJLR5Gp3zVufAhAzpdmZMGUzxb8LYFH0AA@mail.gmail.com">CABEdBFNNwmnANC_7CJLR5Gp3zVufAhAzpdmZMGUzxb8LYFH0AA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Regina, Pt have a FCC crystal structure, so if you are studing Pt(111)<br>
surface, you need 3 layer to have 1 slab, i.e. to describe the Pt(111)<br>
surface in general you should use 3, 6, 9 or 12, .etc.. layers. In the case<br>
of Pt(100) surface are 2, 4, 6,.. layers. May be this is the reason that<br>
your calculation does not converge.<br>
<br>
Best<br>
<br>
Dr. Arles V. Gil Rebaza<br>
Instituto de F?sica La Plata<br>
La Plata - Argentina<br>
<br>
2016-07-20 10:34 GMT-03:00 Regina Lelis de Sousa <<a href="mailto:rlsousa@mail.uft.edu.br">rlsousa@mail.uft.edu.br</a>>:<br>
<br>
> Dear all,<br>
> I am studying Pt(111) and Pt(100) surfaces (using a slab model) with<br>
> PWSCF. I ran a structural relaxations for slabs containing 4 - 9 atomic<br>
> planes (layers) and everything was fine. In all calculations a vacuum<br>
> region of the order of 15 Angstroms was used. However, in the calculations<br>
> with 10 atomic planes or more the SCF procedure does not converge and i do<br>
> not understand the reason. I did some changes on SCF procedure (for<br>
> example: I tested cg method among other things). Does anyone notice some<br>
> mistake with the input file or with my atomic coordinates? Any help would<br>
> be appreciated.<br>
><br>
><br>
> The inputs and outputs are:<br>
><br>
> 1 - First Try:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> &control<br>
> calculation = 'relax'<br>
> restart_mode='from_scratch',<br>
> prefix='Pt_100_12_layers_15_vacuo',<br>
> tprnfor = .true.,<br>
> tstress =.true.,<br>
> verbosity ='high',<br>
> pseudo_dir = '/home/rlsousa/Pseudopot',<br>
> /<br>
> &system<br>
> ibrav= 6,<br>
> A = 2.831157456,<br>
> C=37.2,<br>
> nat= 12,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01, !I tested this.<br>
> /<br>
> &electrons<br>
> mixing_beta = 0.7,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 600,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt 0.000000 0.000000 0.000000<br>
> Pt 1.414214 1.414214 2.000000<br>
> Pt 0.000000 0.000000 4.000000<br>
> Pt 1.414214 1.414214 6.000000<br>
> Pt 0.000000 0.000000 8.000000<br>
> Pt 1.414214 1.414214 10.000000<br>
> Pt 0.000000 0.000000 12.000000<br>
> Pt 1.414214 1.414214 14.000000<br>
> Pt 0.000000 0.000000 16.000000<br>
> Pt 1.414214 1.414214 18.000000<br>
> Pt 0.000000 0.000000 20.000000<br>
> Pt 1.414214 1.414214 22.000000<br>
> K_POINTS AUTOMATIC<br>
> 16 16 1 1 1 1<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> OUTPUT:<br>
><br>
> Program PWSCF v.5.0.1 starts on 3Mar2016 at 1:58: 2<br>
> ...<br>
><br>
> ...<br>
><br>
> Self-consistent Calculation<br>
><br>
> iteration # 1 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 1.00E-02, avg # of iterations = 4.0<br>
><br>
> total cpu time spent up to now is 212.7 secs<br>
><br>
> total energy = -1037.38592080 Ry<br>
> Harris-Foulkes estimate = -1039.73360971 Ry<br>
> estimated scf accuracy < 2.83017780 Ry<br>
><br>
> iteration # 2 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 2.36E-03, avg # of iterations = 8.9<br>
><br>
> total cpu time spent up to now is 627.5 secs<br>
><br>
> total energy = -1004.47885510 Ry<br>
> Harris-Foulkes estimate = -1113.67210149 Ry<br>
> estimated scf accuracy < 4035.50057863<br>
><br>
> ...<br>
><br>
><br>
> iteration #600 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 2.92E-05, avg # of iterations = 11.5<br>
><br>
> total cpu time spent up to now is 250301.6 secs<br>
><br>
> total energy = -1025.14170975 Ry<br>
> Harris-Foulkes estimate = -1050.93732899 Ry<br>
> estimated scf accuracy < 312.87625423 Ry<br>
><br>
> End of self-consistent calculation<br>
><br>
> convergence NOT achieved after 600 iterations: stopping<br>
><br>
><br>
><br>
> ===================================================================================<br>
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>
> = EXIT CODE: 1<br>
> = CLEANING UP REMAINING PROCESSES<br>
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
><br>
> ===================================================================================<br>
><br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> 2 - Second Try:<br>
> I did:<br>
> &electrons<br>
> diagonalization='cg'<br>
> mixing_beta = 0.5,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 300,<br>
><br>
> and this work fine only for Pt(100) with 10 atomic plane.<br>
><br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> 3 - Third Try:<br>
> For Pt(111) with 10 atomic planes:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> &control<br>
> calculation = 'relax'<br>
> restart_mode='from_scratch',<br>
> prefix='Pt_111_10_layers',<br>
> tprnfor = .true.,<br>
> tstress =.true.,<br>
> verbosity ='high',<br>
> pseudo_dir = '/home/rlsousa/pseudo/'<br>
> /<br>
> &system<br>
> ibrav= 4,<br>
> A = 2.831157456,<br>
> C=36.0,<br>
> nat= 10,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01,<br>
> /<br>
> &electrons<br>
> mixing_beta = 0.7,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 600,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt -0.000000000 -0.000000000 -20.784609691<br>
> Pt 0.000000000 -0.000000000 -13.856406461<br>
> Pt 0.000000000 -0.000000000 -6.928203230<br>
> Pt 0.000000000 0.000000000 0.000000000<br>
> Pt 1.414213562 0.816496581 -16.165807537<br>
> Pt 1.414213562 0.816496581 -9.237604307<br>
> Pt 1.414213562 0.816496581 -2.309401077<br>
> Pt -0.000000000 1.632993162 -18.475208614<br>
> Pt -0.000000000 1.632993162 -11.547005384<br>
> Pt -0.000000000 1.632993162 -4.618802154<br>
> K_POINTS AUTOMATIC<br>
> 16 16 1 1 1 1<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> And the output is:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> Self-consistent Calculation<br>
><br>
> iteration # 1 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 1.00E-02, avg # of iterations = 3.7<br>
><br>
> total cpu time spent up to now is 619.8 secs<br>
><br>
> total energy = -864.90667968 Ry<br>
> Harris-Foulkes estimate = -866.46381391 Ry<br>
> estimated scf accuracy < 1.92161923 Ry<br>
><br>
> iteration # 2 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 1.92E-03, avg # of iterations = 8.8<br>
><br>
> total cpu time spent up to now is 1789.4 secs<br>
><br>
> total energy = -834.69092069 Ry<br>
> Harris-Foulkes estimate = -912.73406647 Ry<br>
> estimated scf accuracy < 3297.67106012 Ry<br>
> iteration #154 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> ethr = 8.37E-05, avg # of iterations = 7.2<br>
><br>
> negative rho (up, down): 0.577E-07 0.000E+00<br>
><br>
> total cpu time spent up to now is 143089.7 secs<br>
><br>
> total energy = -862.54326840 Ry<br>
> Harris-Foulkes estimate = -876.81955048 Ry<br>
> estimated scf accuracy < 354.34333068 Ry<br>
><br>
> iteration #155 ecut= 35.00 Ry beta=0.70<br>
> Davidson diagonalization with overlap<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
><br>
> 4 - fourth Try:<br>
> The atomic positions for input file was optimized with a PCFF force field:<br>
> a - For Pt(100) with 16 atomic planes, the atomic positions for input were:<br>
> Pt 0.000001863 -0.000006550 1.917081940<br>
> Pt -0.000000583 -0.000002969 5.858730954<br>
> Pt -0.000001806 0.000000728 9.775507899<br>
> Pt -0.000003453 0.000006845 13.688807549<br>
> Pt -0.000001863 0.000006007 17.601709335<br>
> Pt -0.000000324 0.000000339 21.516053222<br>
> Pt 0.000003440 -0.000003229 25.439026038<br>
> Pt 0.000005016 -0.000002994 29.455726011<br>
> Pt 1.382821195 1.382814326 -0.121704445<br>
> Pt 1.382818575 1.382816058 3.895001445<br>
> Pt 1.382817093 1.382818978 7.817973036<br>
> Pt 1.382816565 1.382824166 11.732314256<br>
> Pt 1.382814960 1.382827050 15.645213637<br>
> Pt 1.382818406 1.382822391 19.558517247<br>
> Pt 1.382820459 1.382816862 23.475296312<br>
> Pt 1.382823964 1.382815499 27.416943612<br>
><br>
> But I get the same result.<br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> 5 - fifth try - I did not have any throuble for these cases.<br>
> a - For Pt(100) with 9 atomic planes:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> .....<br>
> &system<br>
> ibrav= 6,<br>
> A = 2.831157456,<br>
> C=33.2,<br>
> nat= 9,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01,<br>
> /<br>
> &electrons<br>
> diagonalization='cg'<br>
> mixing_beta = 0.5,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 300,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt 0.000000000 -0.000000000 2.001930636<br>
> Pt 0.000000000 -0.000000000 6.005791907<br>
> Pt 0.000000000 -0.000000000 10.009653178<br>
> Pt 0.000000000 -0.000000000 14.013514450<br>
> Pt 1.415578728 1.415578728 -0.000000000<br>
> Pt 1.415578728 1.415578728 4.003861271<br>
> Pt 1.415578728 1.415578728 8.007722543<br>
> Pt 1.415578728 1.415578728 12.011583814<br>
> Pt 1.415578728 1.415578728 16.015445086<br>
><br>
> .....<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
><br>
> Atomic positions for Pt(100) with 9 atomic planes:<br>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$<br>
> b - For Pt(111) with 9 atomic planes:<br>
> &system<br>
> ibrav= 4,<br>
> A = 2.831157456,<br>
> C=36.0,<br>
> nat= 9,<br>
> ntyp= 1,<br>
> ecutwfc =35.0,<br>
> ecutrho = 350.0,<br>
> occupations='smearing',<br>
> smearing='marzari-vanderbilt',<br>
> degauss=0.01,<br>
> /<br>
> &electrons<br>
> mixing_beta = 0.7,<br>
> conv_thr = 1.0d-8<br>
> electron_maxstep = 600,<br>
> /<br>
> &ions<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pt 0.000000000 -0.000000000 -13.856406461<br>
> Pt 0.000000000 -0.000000000 -6.928203230<br>
> Pt 0.000000000 0.000000000 0.000000000<br>
> Pt 1.414213562 0.816496581 -16.165807537<br>
> Pt 1.414213562 0.816496581 -9.237604307<br>
> Pt 1.414213562 0.816496581 -2.309401077<br>
> Pt -0.000000000 1.632993162 -18.475208614<br>
> Pt -0.000000000 1.632993162 -11.547005384<br>
> Pt -0.000000000 1.632993162 -4.618802154<br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
><br>
> Thanks in advance,<br>
> regards<br>
><br>
> R. Lelis-Sousa.<br>
> UFT/TO/Brazil.<br>
><br>
><br>
><br>
> --<br>
> Tenha uma ?tima semana,<br>
><br>
> Atenciosamente,<br>
><br>
><br>
> Dra. Regina L?lis de Sousa<br>
> Professor Adjunto -- Universidade Federal do Tocantins<br>
> Campus de Aragua?na<br>
> Rua Paraguai SN -- Esquina com a Urixamas<br>
> Telefone: +55(63)2112-2283<br>
> Caixa Postal 132<br>
> CEP: 77.838-824<br>
> Tocantins.<br>
> "Success is knowing that you have done your best and have exploited your<br>
> God-given or gene-given abilities to the next maximum extent. More than<br>
> this, no<br>
> one can do...". Prof. Alan Graham MacDiarmid<br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
--<br>
###---------> Arles V. <---------###<br>
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<br>
Message: 6<br>
Date: Wed, 20 Jul 2016 16:26:42 +0000<br>
From: "Mofrad, Amir Mehdi (MU-Student)" <<a href="mailto:amzf5@mail.missouri.edu">amzf5@mail.missouri.edu</a>><br>
Subject: [Pw_forum] Vc_Relax distorts the whole structure<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:BN3PR01MB13521C3312221B67D7347C93A7080@BN3PR01MB1352.prod.exchangelabs.com">BN3PR01MB13521C3312221B67D7347C93A7080@BN3PR01MB1352.prod.exchangelabs.com</a>><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear all,<br>
<br>
<br>
I want to do a cell optimization on sodalite (a type of zeolite), however, after I visualize the structure in xcrysden, not only it distorts the whole cell but also the final configuration is very different (not actually sodalite) from its initial one. I put my input file in case you might need to take a look at. Any help would be thoroughly appreciated.<br>
<br>
<br>
&CONTROL<br>
calculation = 'vc-relax' ,<br>
restart_mode = 'from_scratch' ,<br>
wf_collect = .true. ,<br>
outdir = './scratch' ,<br>
wfcdir = './scratch' ,<br>
pseudo_dir = '/global/espresso/pseudo' ,<br>
prefix = 'SOD' ,<br>
verbosity = 'high' ,<br>
etot_conv_thr = 1e-5 ,<br>
forc_conv_thr = 1e-4 ,<br>
nstep = 50 ,<br>
tstress = .true. ,<br>
tprnfor = .true. ,<br>
/<br>
&SYSTEM<br>
ibrav = 0,<br>
nat = 42,<br>
ntyp = 4,<br>
ecutwfc = 50 ,<br>
ecutrho = 500 ,<br>
/<br>
&ELECTRONS<br>
electron_maxstep = 100,<br>
conv_thr = 3e-8 ,<br>
mixing_mode = 'plain' ,<br>
mixing_beta = 0.7 ,<br>
diagonalization = 'david' ,<br>
/<br>
&IONS<br>
ion_dynamics = 'bfgs' ,<br>
trust_radius_ini = 0.5 ,<br>
/<br>
&CELL<br>
cell_dynamics = 'bfgs',<br>
/<br>
<br>
CELL_PARAMETERS bohr<br>
16.720296750 0.000000000 0.000000000<br>
0.000000000 16.720296750 0.000000000<br>
0.000000000 0.000000000 16.720296750<br>
<br>
ATOMIC_SPECIES<br>
Si 28.08600 Si.pbe-n-rrkjus_psl.0.1.UPF<br>
O 15.99940 O.pbe-n-rrkjus_psl.0.1.UPF<br>
Al 26.981539 Al.pbe-n-rrkjus_psl.0.1.UPF<br>
Na 22.989769 Na.pbe-sp-van_ak.UPF<br>
<br>
ATOMIC_POSITIONS angstrom<br>
Si 2.21200 0.00000 4.42400<br>
Si 6.63600 0.00000 4.42400<br>
Si 4.42400 2.21200 0.00000<br>
Si 4.42400 6.63600 0.00000<br>
Si 0.00000 4.42400 2.21200<br>
Si 0.00000 4.42400 6.63600<br>
Al 2.21200 4.42400 0.00000<br>
Al 6.63600 4.42400 0.00000<br>
Al 0.00000 2.21200 4.42400<br>
Al 0.00000 6.63600 4.42400<br>
Al 4.42400 0.00000 2.21200<br>
Al 4.42400 0.00000 6.63600<br>
O 1.20864 3.83826 1.31835<br>
O 7.63936 5.00974 1.31835<br>
O 7.63936 3.83826 7.52965<br>
O 1.20864 5.00974 7.52965<br>
O 1.31835 1.20864 3.83826<br>
O 1.31835 7.63936 5.00974<br>
O 7.52965 7.63936 3.83826<br>
O 7.52965 1.20864 5.00974<br>
O 3.83826 1.31835 1.20864<br>
O 5.00974 1.31835 7.63936<br>
O 3.83826 7.52965 7.63936<br>
O 5.00974 7.52965 1.20864<br>
O 8.26226 5.63264 5.74235<br>
O 0.58574 3.21536 5.74235<br>
O 8.26226 3.21536 3.10565<br>
O 0.58574 5.63264 3.10565<br>
O 5.63264 5.74235 8.26226<br>
O 3.21536 5.74235 0.58574<br>
O 3.21536 3.10565 8.26226<br>
O 5.63264 3.10565 0.58574<br>
O 5.74235 8.26226 5.63264<br>
O 5.74235 0.58574 3.21536<br>
O 3.10565 8.26226 3.21536<br>
O 3.10565 0.58574 5.63264<br>
Na 1.33074 1.33074 1.33074<br>
Na 7.51726 1.33074 7.51726<br>
Na 1.33074 7.51726 7.51726<br>
Na 5.75474 5.75474 5.75474<br>
Na 5.75474 3.09326 3.09326<br>
Na 3.09326 5.75474 3.09326<br>
<br>
<br>
K_POINTS automatic<br>
2 2 2 1 1 1<br>
<br>
<br>
<br>
<br>
Best,<br>
<br>
<br>
Amir M. Mofrad<br>
<br>
Graduate Research Assistant<br>
<br>
Chemical Engineering Department<br>
<br>
University of Missouri<br>
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<br>
Message: 7<br>
Date: Thu, 21 Jul 2016 00:12:48 +0700<br>
From: efi dwi indari <<a href="mailto:efidwiindari@gmail.com">efidwiindari@gmail.com</a>><br>
Subject: [Pw_forum] Fortran runtime error: Bad real number in item 13<br>
of list input<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAHN8Sf=<a href="mailto:Qj5oUJkS1N1MxKzd%2Bd5gu7XgpKEuc3%2BfqfZcTBSti0g@mail.gmail.com">Qj5oUJkS1N1MxKzd+d5gu7XgpKEuc3+fqfZcTBSti0g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear QE Users,<br>
<br>
I am using Espresso-5.2.0 in Ubuntu 14.04 and facing an issue about<br>
plotting the post-processing calculation.<br>
<br>
I have obtained the charge density files to be plotted. However, when I<br>
tried to run the command of plotrho.x, this following error appeared:<br>
<br>
At line 44 of file plotrho.f90 (unit = 1, file = 'MAPIss.rho.dat')<br>
Fortran runtime error: Bad real number in item 13 of list input<br>
<br>
I had checked the plotrho.f90 and could not identify a way to get rid of<br>
the problem. FYI, I have the output files of pp.x calculation without<br>
having a problem neither with memory usage or crash during the running<br>
process.<br>
<br>
Please kindly find both the input and plotrho.f90 files.<br>
<br>
Input file:<br>
&INPUTPP<br>
outdir='/home/efidwiindari/MAPI/',<br>
prefix='MAPIss'<br>
plot_num=0,<br>
filplot='MAPIss.rho.dat',<br>
/<br>
&PLOT<br>
nfile=1,<br>
iflag=3,<br>
output_format=5,<br>
fileout='MAPIsscontour3D.xsf'<br>
e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,<br>
e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,<br>
e3(1)=0.0, e3(2)=0.0, e3(3)=1.0,<br>
x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,<br>
nx=45, ny=45, nz=100,<br>
/<br>
<br>
plotrho.f90 file is attached below as the file is quite long. PS : line<br>
number 44 is about unit vector which I do not have any idea why the problem<br>
arose.<br>
<br>
Furthermore, I did three calculations for three different systems and<br>
unfortunately the problems were still the same. Any comment and/or<br>
suggestions would be really appreciated.<br>
<br>
Many thanks in advance.<br>
<br>
Best Regards,<br>
<br>
Efi Dwi Indari<br>
Research Assistant, Bandung Institute of Technology<br>
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<br>
Message: 8<br>
Date: Wed, 20 Jul 2016 13:49:11 -0400<br>
From: Manu Hegde <<a href="mailto:mhegde@uwaterloo.ca">mhegde@uwaterloo.ca</a>><br>
Subject: Re: [Pw_forum] absorption spectrum &dielectric constant of<br>
turboTDDFT<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CA+g44DuKcTWk14_0p=zhF+PJ8AgM_DWa=<a href="mailto:gbw2U%2BsxwGSWgMhYA@mail.gmail.com">gbw2U+sxwGSWgMhYA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello Dario,<br>
<br>
I have done the similar calculations, it went well, after running<br>
turbo_spectrum.x Do you have any code to extract S(E) or I have to do it<br>
manually?<br>
<br>
Manu<br>
(University of Waterloo)<br>
<br>
On Tue, Jul 19, 2016 at 8:24 PM, dario rocca <<a href="mailto:roccad@gmail.com">roccad@gmail.com</a>> wrote:<br>
<br>
> Dear SungHwan,<br>
> please refer to<br>
> <a href="http://arxiv.org/pdf/1402.0486.pdf" rel="noreferrer" target="_blank">http://arxiv.org/pdf/1402.0486.pdf</a><br>
> and<br>
><br>
> <a href="http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1" rel="noreferrer" target="_blank">http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1</a><br>
> for more details.<br>
><br>
> In the output of the postprocessing chi_1_1 is the xx component of the<br>
> dynamical polarizability, chi_1_2 the xy component, etc.<br>
> Often chi is indicated as \alpha in the papers.<br>
> Specifically you would have<br>
><br>
> Component energy of the perturbation real part of<br>
> chi imaginary<br>
> (indicated either as E or \omega)<br>
> chi_1_1= 0.000000000000000E+00 0.955769346791472E+01<br>
> 0.000000000000000E+00<br>
> .........<br>
><br>
> As you correctly say the absorption spectrum is related to the imaginary<br>
> part of the average of chi multiplied by E (the energy E is often<br>
> indicated as \omega).<br>
> This averaged quantity is contained in S(E). Specifically S(E) is the<br>
> strength function defined as<br>
> S(E)=2m/(\pi*e^2*\hbar) * E*Im[chi(E)], where chi has been averaged over<br>
> the 3 spatial directions.<br>
> This definition is convenient because S(E) satisfies the f-sum rule.<br>
> So if you extract S(E) and plot it you will have the absorption spectrum.<br>
> Let me know if it's still not clear<br>
> Best,<br>
> Dario<br>
><br>
><br>
><br>
><br>
> On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi <<a href="mailto:sunghwanchoi91@gmail.com">sunghwanchoi91@gmail.com</a>><br>
> wrote:<br>
><br>
>> hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It was assume.<br>
>> Now I have prefix.plot_chi.dat file. then I don't know how to generate<br>
>> absorption spectrum from that file and dielectric constant values. As far<br>
>> as I understood, the absorption spectrum is related to imaginary part of<br>
>> average \chi value. but in the file there are 9 values<br>
>> chi_1_1<br>
>> chi_2_1<br>
>> chi_3_1<br>
>> chi_1_2<br>
>> chi_2_2<br>
>> chi_3_2<br>
>> chi_1_3<br>
>> chi_2_3<br>
>> chi_3_3<br>
>> This is 3*3*3 tensor. how do I get an absorption spectrum and dieletric<br>
>> constant values? by the way S(E) means what?<br>
>><br>
>> Sincerely<br>
>> Sunghwan Choi<br>
>><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>><br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
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Message: 9<br>
Date: Wed, 20 Jul 2016 23:07:08 +0200<br>
From: Gabriele Mogni <<a href="mailto:gabriele.mogni@gmail.com">gabriele.mogni@gmail.com</a>><br>
Subject: [Pw_forum] Free computational material science consultancy<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <<a href="mailto:ca512250-bf41-e1b0-d07f-9b5ce6eb9c0b@gmail.com">ca512250-bf41-e1b0-d07f-9b5ce6eb9c0b@gmail.com</a>><br>
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<br>
If you want to collaborate with me on a computational material science<br>
project as part of your research group or company please do not hesitate<br>
to contact me at my email address: <a href="mailto:gabriele.mogni@gmail.com">gabriele.mogni@gmail.com</a> or visit my<br>
website: <a href="http://gabrielemogni.wix.com/materialscience" rel="noreferrer" target="_blank">http://gabrielemogni.wix.com/materialscience</a><br>
<br>
Regards,<br>
<br>
Dr. Gabriele Mogni<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 10<br>
Date: Wed, 20 Jul 2016 17:09:42 -0700<br>
From: dario rocca <<a href="mailto:roccad@gmail.com">roccad@gmail.com</a>><br>
Subject: Re: [Pw_forum] absorption spectrum &dielectric constant of<br>
turboTDDFT<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAAEv5EX3XV19RW993TZKDBmiFZ3aRkEZaDT7gvx3N9JfU=<a href="mailto:AGOg@mail.gmail.com">AGOg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Manu,<br>
You can simply extract it with the command<br>
$ grep "S(E)" prefix.plot_chi.dat > file_for_plot<br>
and use your favorite program to plot it.<br>
Best,<br>
Dario<br>
<br>
On Wed, Jul 20, 2016 at 10:49 AM, Manu Hegde <<a href="mailto:mhegde@uwaterloo.ca">mhegde@uwaterloo.ca</a>> wrote:<br>
<br>
> Hello Dario,<br>
><br>
> I have done the similar calculations, it went well, after running<br>
> turbo_spectrum.x Do you have any code to extract S(E) or I have to do it<br>
> manually?<br>
><br>
> Manu<br>
> (University of Waterloo)<br>
><br>
> On Tue, Jul 19, 2016 at 8:24 PM, dario rocca <<a href="mailto:roccad@gmail.com">roccad@gmail.com</a>> wrote:<br>
><br>
>> Dear SungHwan,<br>
>> please refer to<br>
>> <a href="http://arxiv.org/pdf/1402.0486.pdf" rel="noreferrer" target="_blank">http://arxiv.org/pdf/1402.0486.pdf</a><br>
>> and<br>
>><br>
>> <a href="http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1" rel="noreferrer" target="_blank">http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1</a><br>
>> for more details.<br>
>><br>
>> In the output of the postprocessing chi_1_1 is the xx component of the<br>
>> dynamical polarizability, chi_1_2 the xy component, etc.<br>
>> Often chi is indicated as \alpha in the papers.<br>
>> Specifically you would have<br>
>><br>
>> Component energy of the perturbation real part of<br>
>> chi imaginary<br>
>> (indicated either as E or \omega)<br>
>> chi_1_1= 0.000000000000000E+00 0.955769346791472E+01<br>
>> 0.000000000000000E+00<br>
>> .........<br>
>><br>
>> As you correctly say the absorption spectrum is related to the imaginary<br>
>> part of the average of chi multiplied by E (the energy E is often<br>
>> indicated as \omega).<br>
>> This averaged quantity is contained in S(E). Specifically S(E) is the<br>
>> strength function defined as<br>
>> S(E)=2m/(\pi*e^2*\hbar) * E*Im[chi(E)], where chi has been averaged over<br>
>> the 3 spatial directions.<br>
>> This definition is convenient because S(E) satisfies the f-sum rule.<br>
>> So if you extract S(E) and plot it you will have the absorption spectrum.<br>
>> Let me know if it's still not clear<br>
>> Best,<br>
>> Dario<br>
>><br>
>><br>
>><br>
>><br>
>> On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi <<a href="mailto:sunghwanchoi91@gmail.com">sunghwanchoi91@gmail.com</a>><br>
>> wrote:<br>
>><br>
>>> hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It<br>
>>> was assume. Now I have prefix.plot_chi.dat file. then I don't know how<br>
>>> to generate absorption spectrum from that file and dielectric constant<br>
>>> values. As far as I understood, the absorption spectrum is related to<br>
>>> imaginary part of average \chi value. but in the file there are 9 values<br>
>>> chi_1_1<br>
>>> chi_2_1<br>
>>> chi_3_1<br>
>>> chi_1_2<br>
>>> chi_2_2<br>
>>> chi_3_2<br>
>>> chi_1_3<br>
>>> chi_2_3<br>
>>> chi_3_3<br>
>>> This is 3*3*3 tensor. how do I get an absorption spectrum and dieletric<br>
>>> constant values? by the way S(E) means what?<br>
>>><br>
>>> Sincerely<br>
>>> Sunghwan Choi<br>
>>><br>
>>> _______________________________________________<br>
>>> Pw_forum mailing list<br>
>>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
>>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>>><br>
>><br>
>><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>><br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
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Message: 11<br>
Date: Thu, 21 Jul 2016 12:33:58 +0530<br>
From: Md Mahabul Islam <<a href="mailto:mhblslm59@gmail.com">mhblslm59@gmail.com</a>><br>
Subject: [Pw_forum] Subject: Relaxing a 2x2x2 supercell ...while<br>
reading input file getting "wrong number of columns in Atomic<br>
positions error" for silver atom created from Xcrysden<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAGDebZTHqHxq+7nYvPhA-FKULG8M-chAuoSm=<a href="mailto:r4cm5-e7vsS_w@mail.gmail.com">r4cm5-e7vsS_w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi pwscf users & developers,<br>
I am trying to relax a silver atom with vacancy but while reading the input<br>
file I am getting "wrong number of columns in Atomic positions error".The<br>
atomic positions were created from Xcrysden for 2x2x2 supercell (asymmetric<br>
unit).<br>
Any help regarding this will be highly appreciated.<br>
Thank you,<br>
*Md Mahabul Islam*<br>
*PhD Candidate*<br>
<br>
*Department of Physics,*<br>
<br>
<br>
*Indian Institute of Technology Madras,Chennai-600036, India*Mobile- +91<br>
9087297118/+91-9593148106<br>
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<br>
Message: 12<br>
Date: Thu, 21 Jul 2016 09:33:56 +0200<br>
From: Matteo Cococcioni <<a href="mailto:matteo@umn.edu">matteo@umn.edu</a>><br>
Subject: Re: [Pw_forum] Subject: Relaxing a 2x2x2 supercell ...while<br>
reading input file getting "wrong number of columns in Atomic<br>
positions error" for silver atom created from Xcrysden<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAMZASgE%2BPHf8XQAjOX9aL5sPfgPf8MexOR8Rv6s2x-wuTEVhkw@mail.gmail.com">CAMZASgE+PHf8XQAjOX9aL5sPfgPf8MexOR8Rv6s2x-wuTEVhkw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
open your input file and check the atomic positions. there is something<br>
wrong there. maybe you forgot to specify the atomic species, or something<br>
else the code expects to find. I typically get this error when I fail to<br>
append the file with positions. I'm not sure this is the error you get if<br>
you indicate a wrong number of atoms. check that too.<br>
<br>
hope this helps.<br>
<br>
Matteo<br>
<br>
On Thu, Jul 21, 2016 at 9:03 AM, Md Mahabul Islam <<a href="mailto:mhblslm59@gmail.com">mhblslm59@gmail.com</a>><br>
wrote:<br>
<br>
> Hi pwscf users & developers,<br>
> I am trying to relax a silver atom with vacancy but while reading the<br>
> input file I am getting "wrong number of columns in Atomic positions<br>
> error".The atomic positions were created from Xcrysden for 2x2x2 supercell<br>
> (asymmetric unit).<br>
> Any help regarding this will be highly appreciated.<br>
> Thank you,<br>
> *Md Mahabul Islam*<br>
> *PhD Candidate*<br>
><br>
> *Department of Physics,*<br>
><br>
><br>
> *Indian Institute of Technology Madras,Chennai-600036, India*Mobile- +91<br>
> 9087297118/+91-9593148106<br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
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<br>
Message: 13<br>
Date: Thu, 21 Jul 2016 14:29:13 +0530<br>
From: Phanikumar Pentyala <<a href="mailto:phani12.chem@gmail.com">phani12.chem@gmail.com</a>><br>
Subject: Re: [Pw_forum] Subject: Relaxing a 2x2x2 supercell ...while<br>
reading input file getting "wrong number of columns in Atomic<br>
positions error" for silver atom created from Xcrysden<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAOgLYHEKOBDrr9zznZuNRcD=<a href="mailto:0tF_N%2B02FV28HGWvQMuUm769Tw@mail.gmail.com">0tF_N+02FV28HGWvQMuUm769Tw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
There are *TWO* possible mistakes for this problem<br>
<br>
1. In *ATOMIC_SPECIES* section may you forgot mentioning of one of element<br>
<br>
2. Number of atomic coordinates (cartesian) greater than the *nat* option<br>
<br>
<br>
<br>
Regards<br>
Phanikumar<br>
<br>
On Thu, Jul 21, 2016 at 1:03 PM, Matteo Cococcioni <<a href="mailto:matteo@umn.edu">matteo@umn.edu</a>> wrote:<br>
<br>
> open your input file and check the atomic positions. there is something<br>
> wrong there. maybe you forgot to specify the atomic species, or something<br>
> else the code expects to find. I typically get this error when I fail to<br>
> append the file with positions. I'm not sure this is the error you get if<br>
> you indicate a wrong number of atoms. check that too.<br>
><br>
> hope this helps.<br>
><br>
> Matteo<br>
><br>
> On Thu, Jul 21, 2016 at 9:03 AM, Md Mahabul Islam <<a href="mailto:mhblslm59@gmail.com">mhblslm59@gmail.com</a>><br>
> wrote:<br>
><br>
>> Hi pwscf users & developers,<br>
>> I am trying to relax a silver atom with vacancy but while reading the<br>
>> input file I am getting "wrong number of columns in Atomic positions<br>
>> error".The atomic positions were created from Xcrysden for 2x2x2 supercell<br>
>> (asymmetric unit).<br>
>> Any help regarding this will be highly appreciated.<br>
>> Thank you,<br>
>> *Md Mahabul Islam*<br>
>> *PhD Candidate*<br>
>><br>
>> *Department of Physics,*<br>
>><br>
>><br>
>> *Indian Institute of Technology Madras,Chennai-600036, India*Mobile- +91<br>
>> 9087297118/+91-9593148106<br>
>><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>><br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
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<br>
Message: 14<br>
Date: Thu, 21 Jul 2016 18:03:54 +0900<br>
From: Dae Kwang Jun <<a href="mailto:jdaekwang@gmail.com">jdaekwang@gmail.com</a>><br>
Subject: Re: [Pw_forum] Subject: Relaxing a 2x2x2 supercell ...while<br>
reading input file getting "wrong number of columns in Atomic<br>
positions error" for silver atom created from Xcrysden<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAC+GeGoR3K9jpe4BL49H6L=0RWe=<a href="mailto:MzU_bkano6771f1AzxSYJg@mail.gmail.com">MzU_bkano6771f1AzxSYJg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
It is possible that the number of atoms and nat do not match.<br>
<br>
On Thursday, 21 July 2016, Phanikumar Pentyala <<a href="mailto:phani12.chem@gmail.com">phani12.chem@gmail.com</a>><br>
wrote:<br>
<br>
> There are *TWO* possible mistakes for this problem<br>
><br>
> 1. In *ATOMIC_SPECIES* section may you forgot mentioning of one of element<br>
><br>
> 2. Number of atomic coordinates (cartesian) greater than the *nat* option<br>
><br>
><br>
><br>
> Regards<br>
> Phanikumar<br>
><br>
> On Thu, Jul 21, 2016 at 1:03 PM, Matteo Cococcioni <<a href="mailto:matteo@umn.edu">matteo@umn.edu</a><br>
> <javascript:_e(%7B%7D,'cvml','<a href="mailto:matteo@umn.edu">matteo@umn.edu</a>');>> wrote:<br>
><br>
>> open your input file and check the atomic positions. there is something<br>
>> wrong there. maybe you forgot to specify the atomic species, or something<br>
>> else the code expects to find. I typically get this error when I fail to<br>
>> append the file with positions. I'm not sure this is the error you get if<br>
>> you indicate a wrong number of atoms. check that too.<br>
>><br>
>> hope this helps.<br>
>><br>
>> Matteo<br>
>><br>
>> On Thu, Jul 21, 2016 at 9:03 AM, Md Mahabul Islam <<a href="mailto:mhblslm59@gmail.com">mhblslm59@gmail.com</a><br>
>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:mhblslm59@gmail.com">mhblslm59@gmail.com</a>');>> wrote:<br>
>><br>
>>> Hi pwscf users & developers,<br>
>>> I am trying to relax a silver atom with vacancy but while reading the<br>
>>> input file I am getting "wrong number of columns in Atomic positions<br>
>>> error".The atomic positions were created from Xcrysden for 2x2x2 supercell<br>
>>> (asymmetric unit).<br>
>>> Any help regarding this will be highly appreciated.<br>
>>> Thank you,<br>
>>> *Md Mahabul Islam*<br>
>>> *PhD Candidate*<br>
>>><br>
>>> *Department of Physics,*<br>
>>><br>
>>><br>
>>> *Indian Institute of Technology Madras,Chennai-600036, India*Mobile- +91<br>
>>> 9087297118/+91-9593148106<br>
>>><br>
>>> _______________________________________________<br>
>>> Pw_forum mailing list<br>
>>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a> <javascript:_e(%7B%7D,'cvml','<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a>');><br>
>>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>>><br>
>><br>
>><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a> <javascript:_e(%7B%7D,'cvml','<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a>');><br>
>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>><br>
><br>
><br>
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End of Pw_forum Digest, Vol 108, Issue 21<br>
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<span style="font-family:verdana,sans-serif">Tenha uma ótima semana,<br><br>Atenciosamente,<br><br><br>Dra. Regina Lélis de Sousa<br>Professor Adjunto -- Universidade Federal do Tocantins<br>Campus de Araguaína<br>Rua Paraguai SN -- Esquina com a Urixamas<br>Telefone: +55(63)2112-2283<br>Caixa Postal 132<br>CEP: <span>77.838-824</span><br>Tocantins.<br>"Success is knowing that you have done your best and have exploited your<br>God-given or gene-given abilities to the next maximum extent. More than this, no<br>one can do...". Prof. Alan Graham MacDiarmid<br></span><br></div></div></div></div>
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