[Wien] lapw1 crash with SECLIT - Error in Cholesky
Pavel Ondracka
pavel.ondracka at email.cz
Fri Oct 10 11:03:20 CEST 2014
On Thu, 2014-10-09 at 08:02 -0500, Laurence Marks wrote:
> I am not sure what exactly you are trying to do. It looks like you
> have some approximation to a Si doped amorphous TiO2 structure. The
> BVS looks reasonable, so this may have come from some other code.
Yeah, the structure was produced by simulated annealing done by other
code and I want to calculate band gap and optical constants with Wien2k
using mBJ. At the moment I'm just trying to converge the case with LDA
before I initialize mBJ.
>
> One thing odd is the RMT for Si of 1.44 which may very well lead to
> problems. This is actually close to what setrmt is giving. I think
> there may be a bug here in setrmt, Peter can say more. The small Si
> RMT is why you are losing core electrons.
>
>
> One thing you can do is (after at least one pass) do "x RMTCheck".
> This will show the magnitude of the discontinuity at the RMT. I have
> seen that the discontinuities of different types of atoms should be
> roughly the same, and I suspect that in your case they are not.
>
Looking at the output of x RMTCheck (attached) the Si atom doesn't seem
to stand out too much, but I don't have any idea what "roughly the same"
means in this case. Can you have a look please? At the moment I have a
converged LDA case with the Si RMT = 1.44 and ecut -10.2 (no warnings)
and I'm wondering if I can continue with mBJ or rather restart with
different RMTs and higher ecut (e.g. -7.2).
>
> Without running your case myself, I would want to use
>
>
> cp case.struct Hold.struct
> setrmt case -a Ti:1.7,Si:1.6,O:1.4 ; cp *set* *.struct
>
>
> case is the name and the initial cp is because sometimes setrmt can be
> slightly buggy and get confused about decimal points.
>
>
> This initialized for me without warning with -ecut -7.2 and only the
> Si 2p as semicore not the 2s as well.
After playing with this a little bit more it seems that the old scheme
in setrmt is actually giving better results in my case:
new: O:1.57 Ti:1.74 Si:1.44
old: O:1.56 Ti:1.76 Si:1.56
The O and Ti RMTs are quite similar so I have no idea why the Si RMT is
so much lower with the new scheme.
BTW with the old scheme I can get no warning also with only 2p states.
>
> N.B., you may want to increase nband at the bottom of case.in1c to
> something like 480 or 512, increase emin to 2.5, only use one k-point
> and for LDA with these RMTs I suspect that a RKMAX of 6 is fine.
Did you meant increase emax to 2.5?
Anyway this is really helpful, thank you very much.
>
>
> On Thu, Oct 9, 2014 at 7:01 AM, Pavel Ondracka
> <pavel.ondracka at email.cz> wrote:
> On Thu, 2014-10-09 at 06:23 -0500, Laurence Marks wrote:
> > Why are you using P1? You have made everything much slower
> and less
> > efficient.
> >
> > Beyond this it is hard to guess.
> >
> Well, P1 is what I get during the initialization with sgrup.
>
> In the meantime I managed to get it running by removing -it
> switch (two
> successful iterations so far), so will see if it actually
> stays working.
>
> Best regards
> Pavel Ondračka
>
> > __________________________
> > Professor Laurence Marks
> > Department of Materials Science and Engineering
> > Northwestern University
> > www.numis.northwestern.edu
> > MURI4D.numis.northwestern.edu
> > Co-Editor, Acta Cryst A
> > "Research is to see what everybody else has seen, and to
> think what
> > nobody else has thought"
> > Albert Szent-Gyorgi
> >
> > Dear Wien2k mailing list,
> >
> > I have a problem with crash in parallel lapw1. It crash with
> SECLIT -
> > Error in Cholesky output in stderr. Looking at tail of
> corresponding
> > case.output1_2 I see:
> >
> > Time for los (hamilt, cpu/wall) : 0.8
> 5.6
> > Time for alm (hns) : 4.2
> > Time for vector (hns) : 14.8
> > Time for vector2 (hns) : 14.0
> > Time for VxV (hns) : 211.3
> > Wall Time for VxV (hns) : 2.8
> > reading Afacts -1 0.000000000000000E+000
> > :seclit: estimate of singular value, factor: 0.6527E+00
> 0.1000E-14
> > :seclit: min(sproj(ne+1:2ne)) 0.3110E-02
> > WARNING: INFO (Cholesky) = 679
> >
> > I found some suggestions for Cholesky errors here:
> > http://www.mail-archive.com/wien%
> > 40zeus.theochem.tuwien.ac.at/msg02400.html
> > however I'm quite sure my struct is OK, RKmax is default 7
> (which
> > should
> > be reasonable for compound with Si Ti and O) and neither can
> I spot
> > any
> > problems in my in1 file.
> >
> > This happens in second scf cycle. I'm using a LDA potential
> and
> > everything was initialized to the default in init_lapw
> (except for
> > energy seperation between core/valence which was set to
> -10.2 because
> > some Si core electrons were leaking out of MT sphere, and
> reduced
> > number
> > of k-points).
> >
> > I'm attaching my struct and in1 files. Any ideas?
> >
> > Best regards
> > Pavel Ondračka
> >
> > _______________________________________________
> > Wien mailing list
> > Wien at zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > SEARCH the MAILING-LIST at:
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>
>
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>
>
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu
> Corrosion in 4D: MURI4D.numis.northwestern.edu
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
-------------- next part --------------
Atom 1 O | RMT Charge 0.735 Grad 1.218 | Step Charge 0.55232, 0.00000 Gradient 1.5577, -1.5577 O
Atom 2 O | RMT Charge 1.336 Grad 2.340 | Step Charge 0.45330, 0.00000 Gradient 0.7627, -0.4468 O
Atom 3 O | RMT Charge 0.828 Grad 1.128 | Step Charge 0.48398, 0.00000 Gradient 1.6836, -1.6836 O
Atom 4 O | RMT Charge 1.086 Grad 1.181 | Step Charge 0.52137, 0.00000 Gradient 1.5631, -1.5631 O
Atom 5 O | RMT Charge 0.906 Grad 1.169 | Step Charge 0.52678, 0.00000 Gradient 1.6410, -1.6410 O
Atom 6 O | RMT Charge 1.117 Grad 1.041 | Step Charge 0.42773, 0.00000 Gradient 1.8157, -1.8157 O
Atom 7 O | RMT Charge 1.081 Grad 1.223 | Step Charge 0.52750, 0.00000 Gradient 1.5603, -1.5603 O
Atom 8 O | RMT Charge 1.057 Grad 1.169 | Step Charge 0.54726, 0.00000 Gradient 1.8075, -1.8075 O
Atom 9 O | RMT Charge 1.000 Grad 1.064 | Step Charge 0.42564, 0.00000 Gradient 1.7500, -1.7500 O
Atom 10 O | RMT Charge 0.774 Grad 1.180 | Step Charge 0.51698, 0.00000 Gradient 1.6013, -1.6013 O
Atom 11 O | RMT Charge 0.951 Grad 1.117 | Step Charge 0.49267, 0.00000 Gradient 1.6756, -1.6756 O
Atom 12 O | RMT Charge 1.054 Grad 1.101 | Step Charge 0.44834, 0.00000 Gradient 1.8909, -1.8909 O
Atom 13 O | RMT Charge 1.349 Grad 2.329 | Step Charge 0.45115, 0.00000 Gradient 0.7842, -0.4496 O
Atom 14 O | RMT Charge 1.157 Grad 1.162 | Step Charge 0.46745, 0.00000 Gradient 1.7435, -1.7435 O
Atom 15 O | RMT Charge 1.179 Grad 1.606 | Step Charge 0.60882, 0.00000 Gradient 1.1521, -1.1521 O
Atom 16 O | RMT Charge 1.210 Grad 1.143 | Step Charge 0.45245, 0.00000 Gradient 1.7479, -1.7479 O
Atom 17 O | RMT Charge 0.885 Grad 1.204 | Step Charge 0.54605, 0.00000 Gradient 1.6256, -1.6256 O
Atom 18 O | RMT Charge 0.903 Grad 1.109 | Step Charge 0.47422, 0.00000 Gradient 1.7481, -1.7481 O
Atom 19 O | RMT Charge 0.817 Grad 1.198 | Step Charge 0.52499, 0.00000 Gradient 1.6177, -1.6177 O
Atom 20 O | RMT Charge 1.441 Grad 1.415 | Step Charge 0.66240, 0.00000 Gradient 1.4866, -1.4866 O
Atom 21 O | RMT Charge 1.150 Grad 1.345 | Step Charge 0.53438, 0.00000 Gradient 1.4273, -1.4273 O
Atom 22 O | RMT Charge 1.531 Grad 1.628 | Step Charge 0.69100, 0.00000 Gradient 1.3441, -1.3441 O
Atom 23 O | RMT Charge 0.954 Grad 1.041 | Step Charge 0.40371, 0.00000 Gradient 1.8236, -1.8236 O
Atom 24 O | RMT Charge 1.388 Grad 1.274 | Step Charge 0.65507, 0.00000 Gradient 1.5909, -1.5909 O
Atom 25 O | RMT Charge 1.130 Grad 1.023 | Step Charge 0.43678, 0.00000 Gradient 1.8395, -1.8395 O
Atom 26 O | RMT Charge 1.281 Grad 1.157 | Step Charge 0.59740, 0.00000 Gradient 1.6738, -1.6738 O
Atom 27 O | RMT Charge 1.011 Grad 1.218 | Step Charge 0.53229, 0.00000 Gradient 1.5540, -1.5540 O
Atom 28 O | RMT Charge 1.217 Grad 1.142 | Step Charge 0.48300, 0.00000 Gradient 1.7885, -1.7885 O
Atom 29 O | RMT Charge 1.546 Grad 1.449 | Step Charge 0.72929, 0.00000 Gradient 1.3156, -1.3156 O
Atom 30 O | RMT Charge 1.246 Grad 1.237 | Step Charge 0.59042, 0.00000 Gradient 1.7036, -1.7036 O
Atom 31 O | RMT Charge 1.536 Grad 1.457 | Step Charge 0.68169, 0.00000 Gradient 1.3292, -1.3292 O
Atom 32 O | RMT Charge 1.158 Grad 1.441 | Step Charge 0.24237, 0.00000 Gradient 1.3333, -1.3333 O
Atom 33 Ti | RMT Charge 1.244 Grad 1.148 | Step Charge 0.63236, 0.00000 Gradient 1.1334, -1.1334 Ti
Atom 34 Ti | RMT Charge 1.450 Grad 1.745 | Step Charge 0.76683, 0.00000 Gradient 0.9481, -0.4578 Ti
Atom 35 Ti | RMT Charge 1.060 Grad 0.933 | Step Charge 0.44866, 0.00000 Gradient 1.4654, -1.4654 Ti
Atom 36 Ti | RMT Charge 0.981 Grad 1.185 | Step Charge 0.48618, 0.00000 Gradient 1.0066, -1.0066 Ti
Atom 37 Ti | RMT Charge 0.943 Grad 0.871 | Step Charge 0.41829, 0.00000 Gradient 1.4024, -1.4024 Ti
Atom 38 Ti | RMT Charge 0.821 Grad 0.896 | Step Charge 0.39194, 0.00000 Gradient 1.5541, -1.5541 Ti
Atom 39 Ti | RMT Charge 0.758 Grad 0.822 | Step Charge 0.33285, 0.00000 Gradient 1.4409, -1.4409 Ti
Atom 40 Ti | RMT Charge 0.953 Grad 0.901 | Step Charge 0.42587, 0.00000 Gradient 1.3865, -1.3865 Ti
Atom 41 Ti | RMT Charge 1.005 Grad 0.951 | Step Charge 0.52805, 0.00000 Gradient 1.4239, -1.4239 Ti
Atom 42 Ti | RMT Charge 0.725 Grad 0.928 | Step Charge 0.43632, 0.00000 Gradient 1.3264, -1.3264 Ti
Atom 43 Ti | RMT Charge 0.651 Grad 0.860 | Step Charge 0.34429, 0.00000 Gradient 1.3672, -1.3672 Ti
Atom 44 Ti | RMT Charge 0.575 Grad 0.927 | Step Charge 0.38398, 0.00000 Gradient 1.2897, -1.2897 Ti
Atom 45 Ti | RMT Charge 1.299 Grad 1.580 | Step Charge 0.60694, 0.00000 Gradient 1.1682, -0.5965 Ti
Atom 46 Ti | RMT Charge 1.048 Grad 1.046 | Step Charge 0.47706, 0.00000 Gradient 1.3685, -1.3685 Ti
Atom 47 Ti | RMT Charge 0.980 Grad 0.862 | Step Charge 0.40059, 0.00000 Gradient 1.5274, -1.5274 Ti
Atom 48 Si | RMT Charge 1.352 Grad 1.237 | Step Charge 0.51048, 0.00000 Gradient 0.8886, 0.8044 Si
7.860u 0.170s 0:08.04 99.8% 0+0k 0+368io 0pf+0w
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