[Pw_forum] Fwd: NaN in plotbands.x
Varadharajan Srinivasan
varadharajan.srinivasan at gmail.com
Thu May 22 16:26:59 CEST 2014
Dear Paolo,
Thanks for the advice. I compared the bands.dat.rap files from both runs
and also looked into plotbands.f90. The plain DFT run recognizes only one
high-symmetry point (first one) in the .rap file but detects the rest in
plotband.f90 through, I suppose, through the code lines below.
But the DFT+U file sets more points in the .rap to high-symmetry (in
particular the point 0.026578 -0.015345 0.588005 (in ibrav=5) which is
next in the list to 0.000000 0.000000 0.609387 which should be Z point).
This causes two high-symmetry (HS) points to be next to each other and not
differing by a G vector. This might be causing the NaN.
An easy fix was to by hand set to F the entry for the point 0.026578
-0.015345 0.588005 in the corresponding .rap file. This seemed to make the
plotband.x work without giving NaN. The resulting plot looks quite
reasonable too.
I didn't quite get what the codelet below is supposed to do. It seems to
turn a point into a HS point if the directions on either side are not
parallel.
The .rap files are attached.
Thanks,
Vardha.
DO n=1,nks
IF (n==1 .OR. n==nks) THEN
high_symmetry(n) = .true.
ELSE
k1(:) = k(:,n) - k(:,n-1)
k2(:) = k(:,n+1) - k(:,n)
ps = ( k1(1)*k2(1) + k1(2)*k2(2) + k1(3)*k2(3) ) / &
sqrt( k1(1)*k1(1) + k1(2)*k1(2) + k1(3)*k1(3) ) / &
sqrt( k2(1)*k2(1) + k2(2)*k2(2) + k2(3)*k2(3) )
high_symmetry(n) = (ABS(ps-1.d0) >1.0d-4).OR.high_symmetry(n)
!
! The gamma point is a high symmetry point
!
IF (k(1,n)**2+k(2,n)**2+k(3,n)**2 < 1.0d-9) high_symmetry(n)=.true.
ENDIF
ENDDO
On Tue, May 20, 2014 at 1:39 AM, Paolo Giannozzi
<paolo.giannozzi at uniud.it>wrote:
> On Mon, 2014-05-19 at 23:30 +0530, Varadharajan Srinivasan wrote:
>
> > The error I got was during the interactive run. And I had checked the
> > "bands.dat" file and found no NaNs in there. This is why I was
> > confused. I attach below the output of the interactive run. The line
> > in bold is the one that doesn't appear in the regular DFT run :
>
> if it appears, there is a reason. Follow what the code does
> (PP/src/plotband.f90 if I remember correctly), compare
> "bands.dat" and "bands.dat.rep" (if it exists) for the
> two cases.
>
> P.
>
> >
> > Input file > bands.dat
> > Reading 118 bands at 77 k-points
> > Range: -79.6540 17.5030eV Emin, Emax > 10.2125 14.2125
> > high-symmetry point: 0.0000-0.5831 0.4063 x coordinate 0.0000
> > high-symmetry point: 0.0000 0.0000 0.0000 x coordinate 0.7107
> > high-symmetry point: 0.0000 0.0000 0.6094 x coordinate 1.3201
> > high-symmetry point: 0.0266-0.0153 0.5880 x coordinate 1.3201
> > high-symmetry point: 0.5050-0.2916 0.2031 x coordinate 1.9933
> > high-symmetry point: 0.0000 0.0000 0.0000 x coordinate 2.6108
> > output file (xmgr) > bfobands.xmgr
> > lines nrap 1 1
> > lines nrap 2 3
> > lines nrap 3 0
> > lines nrap 4 1
> > lines nrap 5 1
> > bands in xmgr format written to file bfobands.xmgr
> >
> >
> >
> >
> > output file (ps) > bfobands.ps
> > Efermi > 12.2125
> > deltaE, reference E (for tics) 1 12.2125
> > n= 2 3
> > 1.320062 1.320062
> > 10.37700 10.37000
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.37700 10.37100
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.80900 10.79800
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.80900 10.80400
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.94000 10.92600
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.94000 10.93100
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.94300 10.95200
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 10.94400 10.95300
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 12.72700 12.73000
> > NaN NaN
> > n= 2 3
> > 1.320062 1.320062
> > 12.72800 12.73300
> > NaN NaN
> >
> >
> >
> >
> > On Mon, May 19, 2014 at 6:08 PM, Lorenzo Paulatto
> > <lorenzo.paulatto at impmc.upmc.fr> wrote:
> > Did you try to run plotbands interactively?
> >
> > i.e., just run plotbands.x and then answer the questions it
> > prints on screen?
> >
> > You can also try to open the output file of bands.x
> > (bands.dat) with a text editor and check if the NaN are there
> > already (it is a very simple file).
> >
> > Please let us know as it gos for more accurate help.
> >
> >
> >
> >
> > On 05/19/2014 02:19 PM, Varadharajan Srinivasan wrote:
> >
> > >
> > >
> > > ---------- Forwarded message ----------
> > > From: Varadharajan Srinivasan
> > > <varadharajan.srinivasan at gmail.com>
> > > Date: Mon, May 19, 2014 at 2:28 PM
> > > Subject: NaN in plotbands.x
> > > To: PWSCF Forum <pw_forum at pwscf.org>
> > >
> > >
> > > Dear all,
> > >
> > >
> > > I am trying to calculate bands for an oxide using
> > > plotbands.x after scf and bands calculation. I am doing this
> > > for regular DFT, DFT+U and a non-collinear calculation with
> > > regular DFT and with U and J. For the regular DFT cases the
> > > plotbands.x works just fine giving me a ps file. But for the
> > > DFT+U and DFT+U+J cases I keep getting NaNs in the output
> > > for the same k-paths. I've read that repeating k values
> > > twice can cause this but I've checked my input and this
> > > doesn't seem to be the case. However, plotbands for some
> > > reason adds an extra high-symmetry point at the same
> > > x-coordinate :
> > >
> > >
> > > Just DFT :
> > >
> > >
> > > high-symmetry point: 0.0000 0.0000 0.0000 x coordinate
> > > 0.7107
> > > high-symmetry point: 0.0000 0.0000 0.6094 x coordinate
> > > 1.3201
> > > high-symmetry point: 0.5050-0.2916 0.2031 x coordinate
> > > 2.0307
> > > high-symmetry point: 0.0000 0.0000 0.0000 x coordinate
> > > 2.6482
> > >
> > >
> > > DFT+U(+J) :
> > > high-symmetry point: 0.0000 0.0000 0.0000 x coordinate
> > > 0.7107
> > > high-symmetry point: 0.0000 0.0000 0.6094 x coordinate
> > > 1.3201
> > > high-symmetry point: 0.0266-0.0153 0.5880 x coordinate
> > > 1.3201
> > > high-symmetry point: 0.5050-0.2916 0.2031 x coordinate
> > > 1.9933
> > >
> > >
> > > I am attaching below my nscf, postprocessing and plotbands
> > > input files. Hope you can help.
> > >
> > >
> > > Thanks,
> > > Vardha.
> > >
> > >
> > >
> > >
> > >
> > >
> > > Dept. of Chemistry
> > > IISER Bhopal,
> > > India.
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > --
> > Dr. Lorenzo Paulatto
> > IdR @ IMPMC -- CNRS & Université Paris 6
> > +33 (0)1 44 275 084 / skype: paulatz
> > http://www-int.impmc.upmc.fr/~paulatto/
> > 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex
> 05
> >
> > _______________________________________________
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> >
> >
> > _______________________________________________
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>
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