[Pw_forum] convergence not achieved .related problem
Dear users
I have been trying to relax a graphene structure with a vacancy but
many erros stoped optimization and convergence not achieved.like
1. Efermy cannot braket :
2. to0 many bands not coveraged
for solving the errors I have chenged these parametrs
increasing ecutoff to 60 and ecuthro to 720 .increasing edeguss to
0.07 and changing diagnolization from cg to david . I have tested
smearing for m-v and mp .increasing nbands from 70 to 120 too .but
optimization didnt achived .I appreciate if any one helpe me .
my input file is :
calculation='relax',
prefix='graphene'
pseudo_dir = '/media/espresso-4.2/pseudo/',
outdir='./tmp/',
etot_conv_thr=1.0D-3 ,
forc_conv_thr=1.0D-2 ,
/
ibrav= 4, celldm(1) =13.9506, celldm(3)=1.667,nat=35, ntyp= 1,nbnd=120
ecutwfc =80.0,ecutrho = 900,
occupations='smearing',smearing='m-v',degauss=0.07,
/
diagonalization='cg',
conv_thr=1.D-8 ,
mixing_beta=0.1,
/
upscale=20,
/
ATOMIC_SPECIES
C 1.00 C.blyp-mt.UPF
ATOMIC_POSITIONS {angstrom}
C0.00716832700.00413863801.674000
.
..
K_POINTS AUTOMATIC
8 8 1 0 0 0
.
I am not sure about these questions to0 :.
1.in example 3 the atomic weight for different atoms is set to 1 in
relax process.is this correct? as I did for carbon (ATOMIC_SPECIES
C 1.00 C.blyp-mt.UPF)
I am not sure about k-point .is 8 8 1 0 0 0 enough for this structure
with 10 A` vaccum .
how many nbands I should for coverage ?
wich diagnbolization is better david or cg ?
mixing_beta should be around 0.1-0.3?
thanks alot
Melika Rostami
Master Student of Sharif University
[Pw_forum] pw bands calculation crash
On Fri, 2012-04-27 at 15:04 +0100, Davide Tiana wrote: > Application 1981542 exit codes: 139 > Application 1981542 exit signals: Killed it looks like an out-of-bounds memory error > Any suggestion? 0) the usual suggestions apply: http://www.quantum-espresso.org/?page_id=26#2.0 1) locate where the code crashes, either with a debugger or the dumb way, with print statements. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] convergence NOT achieved after 100 iterations: stopping
How about trying to fix the movement for BN-sheet and just move H atoms. The
BN-sheet may achieve a concavity during "relax" process. For the absorption of
H2, the concavity will vanish and a plane-BN finally be obtained. But for
single H atom, I am not sure whether one can ignore such an effect.
By the way, is it reasonable that only one H atom was absorped instead of
diatom H2 molecule?
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-04-27 09:20:20,"Cao TF" wrote:
Dear QE users
Recently, I have done some calculation of BN sheet with hydrogen atoms adsorbed
on it. The problem is that when I let hydrogen atoms adsorb on the N atoms. The
calculation is hard to converge. Although, I have changed mixing_beta and the
number of K points. The problem have not been solved. Dose anyone have some
experience on such kind of calculations? Any suggestions will be greatly
appreciated. Here is my input file.
title = 'graphene layer' ,
calculation = 'relax' ,
restart_mode = 'restart' ,
outdir = './tmp' ,
pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' ,
prefix = 'graphene' ,
tprnfor = .TRUE. ,
nstep = 400 ,
/
ibrav = 8 ,
a = 15.026832 , b = 13.014 , c = 15.0 ,
nat = 74 ,
ntyp = 3 ,
starting_magnetization(1) = 0.5 ,
occupations = 'smearing' ,
nosym = .TRUE. ,
degauss = 0.005 ,
smearing = 'mp' ,
nspin = 2 ,
ecutwfc = 30.0 ,
ecutrho = 300.0 ,
/
conv_thr = 1.0d-7 ,
mixing_mode = 'local-TF' ,
mixing_beta = 0.1 ,
diagonalization = 'cg' ,
/
ion_dynamics = 'bfgs' ,
pot_extrapolation = 'atomic' ,
/
ATOMIC_SPECIES
B 10.811 B.pbe-n-van.UPF
N 14.00674 N.pbe-rrkjus.UPF
H 1.0 H.pbe-rrkjus.UPF
ATOMIC_POSITIONS crystal
ATOMIC_POSITIONS crystal
N 0.000 0.000 0.5000 0 0 0
B 0.000 0.1100 0.5000
N 8.0005E-02 0.1700 0.5000
B 8.0005E-02 0.2800 0.5000
N 0.000 0.3299 0.5000
B 0.000 0.4400 0.5000
N 8.0005E-02 0.5000 0.5000
B 8.0005E-02 0.6099 0.5000
N 0.000 0.6597 0.5000
B 0.000 0.7696 0.5000
N 8.0005E-02 0.8296 0.5000
B 8.0005E-02 0.9394 0.5000
N 0.1700 0.000 0.5000
B 0.1700 0.1100 0.5000
N 0.2500 0.1700 0.5000
B 0.2500 0.2800 0.5000
N 0.1700 0.3299 0.5000
B 0.1700 0.4400 0.5000
N 0.2500 0.5000 0.5000
B 0.2500 0.6099 0.5000
N 0.1700 0.6597 0.5000
B 0.1700 0.7696 0.5000
N 0.2500 0.8296 0.5000
B 0.2500 0.9394 0.5000
N 0.3400 0.000 0.5000
B 0.3400 0.1100 0.5000
N 0.4198 0.1700 0.5000
B 0.4198 0.2800 0.5000
N 0.3400 0.3299 0.5000
B 0.3400 0.4400 0.5000
N 0.4198 0.5000 0.5000
B 0.4198 0.6099 0.5000
N 0.3400 0.6597 0.5000
B 0.3400 0.7696 0.5000
N 0.4198 0.8296 0.5000
B 0.4198 0.9394 0.5000
N 0.5101 0.000 0.5000
B 0.5101 0.1100 0.5000
N 0.58333403 0.1700 0.5000
B 0.58333403 0.2800 0.5000
N 0.5101 0.3299 0.5000
B 0.5101 0.4400 0.5000
N 0.58333403 0.5000 0.5000
B 0.58333403 0.6099 0.5000
N 0.5101 0.6597 0.5000
B 0.5101 0.7696 0.5000
N 0.58333403 0.8296 0.5000
B 0.58333403 0.9394 0.5000
N 0.6800 0.000 0.5000
B 0.6800 0.1100 0.5000
N 0.75000101 0.1700 0.5000
B 0.75000101 0.2800 0.5000
N 0.6800 0.3299 0.5000
B 0.6800 0.4400 0.5000
N 0.75000101 0.5000 0.5000
B 0.75000101 0.6099 0.5000
N 0.6800 0.6597 0.5000
B 0.6800 0.7696 0.5000
N 0.75000101 0.8296 0.5000
B 0.75000101 0.9394 0.5000
N 0.8498 0.000 0.5000
B 0.8498 0.1100 0.5000
N 0.91666800 0.1700 0.5000
B 0.91666800 0.2800 0.5000
N 0.8498 0.3299 0.5000
B 0.8498 0.4400 0.5000
N 0.91666800 0.5000 0.5000
B 0.91666800 0.6099 0.5000
N 0.8498 0.6597 0.5000
B 0.8498 0.7696 0.5000
N 0.91666800 0.8296 0.5000
B 0.91666800 0.9394 0.5000
H 0.5000 0.6600 0.56900670
H 0.6800 0.3300 0.56900670
K_POINTS {automatic}
8 8 1 0 0 0
==
Teng Fei Cao
==
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: 86-551-5591464-326(office)
Fax: 86-551-5591434
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[Pw_forum] pw bands calculation crash
Dear all,
After optimised a molecule I tried to calculate the band structure but
pw crashes and I can't figure out why.
The optimisation step should be fine(here it converge immediately
since I rerun my previous calculation):
BFGS Geometry Optimization
bfgs converged in 1 scf cycles and 0 bfgs steps
(criteria: energy < 0.10E-03, force < 0.10E-02)
Final energy =-646.2249695321 Ry
Begin final coordinates
ATOMIC_POSITIONS (crystal)
C0.953315090 0.000413805 0.235484404
..
..
H1.009939685 0.169442779 0.056058275
H1.044496546 0.158711398 -0.056214459
End final coordinates
Writing output data file mol_a.save
..
..
..
This run was terminated on: 13: 4:41 27Apr2012
=--=
JOB DONE.
=--=
"
but when I run pw.x to calculate bands it crashes
"
Atomic positions and unit cell read from directory:
./mol_a.save/
Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used
Application 1981542 exit codes: 139
Application 1981542 exit signals: Killed
Application 1981542 resources: utime ~2s, stime ~2s
"
My input should not contain any errors. I used it for other systems
similar to this one and it works. just in case:
"
calculation='bands',
title='mol_a',
wf_collect=.true.,
outdir='./',
prefix='mol_a'
etot_conv_thr=1.0d-4,
forc_conv_thr=1.0d-3,
/
ibrav=14,
celldm(1)=28.4693677,
celldm(2)=1.058648879,
celldm(3)=0.600431923,
celldm(4)=0,
celldm(5)=0,
celldm(6)=0,
nat=23,
ntyp=6,
nbnd=70
tot_charge=0.0,
ecutwfc=45.0,
ecutrho=450.0,
nosym=.false.,
nosym_evc=.false.,
london=.true.,
london_s6=0.75,
london_rcut=200,
/
electron_maxstep=80,
conv_thr=1.0d-6,
mixing_mode='plain',
mixing_beta=0.7,
mixing_ndim=8,
mixing_fixed_ns=0,
diagonalization='david',
/
ATOMIC_SPECIES
H 1.007 H.pw91-van_ak.UPF
...
Zn 65.409 Zn.pw91-n-van.UPF
ATOMIC_POSITIONS {crystal}
C 0.952835 0.50 0.826917
Zn 0.0.50 0.191590
K_POINTS {crystal}
11
0 0 0 1
0 0 .1 2
0 0 .2 3
0 0 .3 4
0 0 .4 5
0 0 .5 6
0 0 .6 7
0 0 .7 8
0 0 .8 9
0 0 .9 10
0 0 1 11
"
Any suggestion?
thanks a lot
Davide
[Pw_forum] convergence NOT achieved after 100 iterations --- related question
Dear Nicola, Many thanks for the prompt reply. > first question - would mp work? This we haven't tried. Since mv and mp give very similar numerical results for a given smearing width I guess I thought I should try something a bit different, i.e. gauss. > In terms of "structure" of the smearing function, gaussian is > the smoothest, then mv, then mp. So if there were an intrinsic problem > with states at the fermi energy, it should be even more apparent in > mp . I see. I'll surely take a look at mp then. > As a general comment, the role of smearing is to help improve the > accuracy of k-point sampling - and so the 0.01-.02 you are using > is exactly in the right ball park. Sure. Actually using a larger kpoint set sometimes helps but it gets a bit tricky because if you've run a number of calculations with a smaller kpoint set (say for a publication), then you want to stick to that. So sometimes we actually try with a larger set and then once (if) we see convergence revert back to the one we want. This only works about half the time though. Our g-Al2O3 + precious metal atom calculations were particularly notorious so we got to try this close to about 20-30 times. > A side effect (a positive one) for smearing is to help convergence > in iterative algorithms (as in PWSCF) - for that side effect, > 0.01-0.02 is actually small, and so the more "structure" of > mv or mp could hamper the iterative convergence. So you could try > converging first with a larger smearing (.04 to .08), and then restart > with the "right" one. I'd be somewhat surprised to see much difference > between gaussian/mp/mp for say 0.07 Ry ~ 1 eV of smearing. Of > course, such a large smearing shoudl be used only to help > get convergence, and then reduced. Oh, wow. We haven't done that since I'm a bit scared of large smearings but this is a great suggestion. We do make use of a similar trick though, namely going back and forth between an initial gauss shot followed by mv but I'm afraid this works even less than half the time. But I will definitely give this a shot and report back the result. Many thanks once again. Best wishes, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande
[Pw_forum] k-point
Dear all whether the number of k-points in final result of relax is effective?
[Pw_forum] convergence NOT achieved after 100 iterations --- related question
Dear PWSCF community, While we are on the subject of convergence, I would like to inquire about something that we have consistently been observing in a very large number of the systems we have studied (examples being metal atoms on g-Al2O3, CeO2 surfaces etc). While gaussian smearing consistently produces convergence without problems at first shot for a smearing width of 0.01-0.02, we frequently have problems with mv smearing (our favorite) for the same width. Systematically exploring a giant portion of 6 or 7-dimensional parameter space (kpoints, smearing width, vacuum length so forth) eventually results in convergence with mv but we usually have to fiddle a lot; with gauss instead, anything basically works. Would anyone be able to confirm this experience or better still provide some insight on the realtive ease of using mv vs gauss? Thank you very much in advance. Best regards, Hande Toffoli -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande
[Pw_forum] convergence NOT achieved after 100 iterations --- related question
Hi Hande, first question - would mp work? In terms of "structure" of the smearing function, gaussian is the smoothest, then mv, then mp. So if there were an intrinsic problem with states at the fermi energy, it should be even more apparent in mp . As a general comment, the role of smearing is to help improve the accuracy of k-point sampling - and so the 0.01-.02 you are using is exactly in the right ball park. A side effect (a positive one) for smearing is to help convergence in iterative algorithms (as in PWSCF) - for that side effect, 0.01-0.02 is actually small, and so the more "structure" of mv or mp could hamper the iterative convergence. So you could try converging first with a larger smearing (.04 to .08), and then restart with the "right" one. I'd be somewhat surprised to see much difference between gaussian/mp/mp for say 0.07 Ry ~ 1 eV of smearing. Of course, such a large smearing shoudl be used only to help get convergence, and then reduced. nicola On 27/04/2012 10:47, Hande Ustunel wrote: > Dear PWSCF community, > > While we are on the subject of convergence, I would like to inquire about > something that we have consistently been observing in a very large number > of the systems we have studied (examples being metal atoms on g-Al2O3, CeO2 > surfaces etc). While gaussian smearing consistently produces convergence > without problems at first shot for a smearing width of 0.01-0.02, we > frequently have problems with mv smearing (our favorite) for the same > width. Systematically exploring a giant portion of 6 or 7-dimensional > parameter space (kpoints, smearing width, vacuum length so forth) > eventually results in convergence with mv but we usually have to fiddle a > lot; with gauss instead, anything basically works. Would anyone be able to > confirm this experience or better still provide some insight on the > realtive ease of using mv vs gauss? > > Thank you very much in advance. > Best regards, > Hande Toffoli > > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- -- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
[Pw_forum] query on kpoints.x
On Wed, 2012-04-25 at 02:10 -0400, Ajit Vallabhaneni wrote: > I want to know whether the format for k points output by kpoints.x > is tpiba or not ? I think so. This is something you can easily verify P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] convergence NOT achieved after 100 iterations: stopping
On Fri, 2012-04-27 at 09:20 +0800, Cao TF wrote: > The problem is that when I let hydrogen atoms adsorb on the N atoms, > the calculation is hard to converge. you should start with a smaller, more manageable calculation, experiment a bit with parameters. It is hard to say anything for a relatively large system without investing a sizable amount of time and computer resources. > nosym = .TRUE. , you shouldn't use this unless you have a good reason > degauss = 0.005 , it looks small to me > nspin = 2 , you have 2 H atoms, so the system might be unpolarized. Try no spin first > starting_magnetization(1) = 0.5 , in any event, start with magnetization on H atoms, not on N or B > diagonalization = 'cg' , you shouldn't use this unless you have a good reason P, -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] convergence NOT achieved after 100 iterations: stopping
== 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: 86-551-5591464-326(office) Fax: 86-551-5591434 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120427/936a23a2/attachment.htm
