[Wien] ERROR: negative position

Laurence Marks L-marks at northwestern.edu
Fri Aug 10 12:59:23 CEST 2012 

A comment. In many cases "x patchsymm" will find errors like this.

---------------------------
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 1-847-491-3996
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
 On Aug 10, 2012 5:08 AM, "Kateryna Foyevtsova" <
foyevtsova at th.physik.uni-frankfurt.de> wrote:

> Thanks!
>
> eventually, converting the structure to .cif file using Vesta and then
> back with cif2struct plus running sgroup fixed the problem.
>
> Was the error message due to the old way of listing structural data
> being incompatible with wien2k expectations?
>
> What does it mean: "negative position in rstruc"?
>
> Bests,
> Kateryna
>
>
> On 10/08/12 11:56, Fecher, Gerhard wrote:
> > Check beta
> > check position of ATOM   3
> >
> > are these correct ?
> >
> > Ciao
> > Gerhard
> >
> > DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> > "I think the problem, to be quite honest with you,
> > is that you have never actually known what the question is."
> >
> > ====================================
> > Dr. Gerhard H. Fecher
> > Institut of Inorganic and Analytical Chemistry
> > Johannes Gutenberg - University
> > 55099 Mainz
> > ________________________________________
> > Von: wien-bounces at zeus.theochem.tuwien.ac.at [
> wien-bounces at zeus.theochem.tuwien.ac.at]&quot; im Auftrag von
> &quot;Kateryna Foyevtsova [foyevtsova at th.physik.uni-frankfurt.de]
> > Gesendet: Freitag, 10. August 2012 10:33
> > An: A Mailing list for WIEN2k users
> > Betreff: Re: [Wien] ERROR: negative position
> >
> > Dear Gavin,
> >
> > I am also getting this message
> >
> > ERROR: negative position in rstruc. Please report
> >
> > for the structure I append below.
> >
> > Could you give a hint what is the problem and what should I fix to get
> > rid of it? I am using version 12.1.
> >
> > Thanks!
> >
> > Kateryna Foyevtsova
> >
> >
> > blebleble
> > CXZ LATTICE,NONEQUIV.ATOMS:  6 12 C2/m
> > MODE OF CALC=RELA unit=bohr
> >  10.299379 11.320134 17.839048 90.000000 89.999999127.340625
> > ATOM   1: X=0.00000000 Y=0.00000000 Z=0.50000000
> >           MULT= 1          ISPLIT= 8
> > Na1        NPT=  781  R0=0.00010000 RMT=    2.0900   Z: 11.0
> > LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
> >                      0.0000000 1.0000000 0.0000000
> >                      0.0000000 0.0000000 1.0000000
> > ATOM   2: X=0.50000002 Y=0.50000002 Z=0.66666667
> >           MULT= 2          ISPLIT= 8
> >        2: X=0.49999998 Y=0.49999998 Z=0.33333333
> > Na2        NPT=  781  R0=0.00010000 RMT=    2.0900   Z: 11.0
> > LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
> >                      0.0000000 1.0000000 0.0000000
> >                      0.0000000 0.0000000 1.0000000
> > ATOM   3: X=0.50000002 Y=0.50000002 Z=0.00000000
> >           MULT= 1          ISPLIT= 8
> > Na3        NPT=  781  R0=0.00010000 RMT=    2.0900   Z: 11.0
> > LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
> >                      0.0000000 1.0000000 0.0000000
> >                      0.0000000 0.0000000 1.0000000
> > ATOM   4: X=0.00000000 Y=0.00000000 Z=0.83333333
> >           MULT= 2          ISPLIT= 8
> >        4: X=0.00000000 Y=0.00000000 Z=0.16666667
> > Ir1        NPT=  781  R0=0.00000500 RMT=    2.0500   Z: 77.0
> > LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
> >                      0.0000000 1.0000000 0.0000000
> >                      0.0000000 0.0000000 1.0000000
> > ATOM   5: X=0.97333334 Y=0.21000000 Z=0.33333334
> >           MULT= 4          ISPLIT= 8
> >        5: X=0.02666666 Y=0.79000000 Z=0.33333334
> >        5: X=0.02666666 Y=0.79000000 Z=0.66666666
> >        5: X=0.97333334 Y=0.21000000 Z=0.66666666
> > O 1        NPT=  781  R0=0.00010000 RMT=    1.8200   Z:  8.0
> > LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
> >                      0.0000000 1.0000000 0.0000000
> >                      0.0000000 0.0000000 1.0000000
> > ATOM   6: X=0.47333333 Y=0.21000000 Z=0.50000000
> >           MULT= 2          ISPLIT= 8
> >        6: X=0.52666667 Y=0.79000000 Z=0.50000000
> > O 2        NPT=  781  R0=0.00010000 RMT=    1.8200   Z:  8.0
> > LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
> >                      0.0000000 1.0000000 0.0000000
> >                      0.0000000 0.0000000 1.0000000
> >    4      NUMBER OF SYMMETRY OPERATIONS
> >  1 0 0 0.00000000
> >  0 1 0 0.00000000
> >  0 0 1 0.00000000
> >        1
> > -1 0 0 0.00000000
> >  0-1 0 0.00000000
> >  0 0 1 0.00000000
> >        2
> > -1 0 0 0.00000000
> >  0-1 0 0.00000000
> >  0 0-1 0.00000000
> >        3
> >  1 0 0 0.00000000
> >  0 1 0 0.00000000
> >  0 0-1 0.00000000
> >        4
> >
> >
> >
> >
> > On 09/08/12 14:58, Gavin Abo wrote:
> >> What version of Wien2k are you using (cat $WIENROOT/VERSION)?  Maybe you
> >> are not using the latest 12.1 with the fix in SRC_symmetry described at
> >> http://www.wien2k.at/reg_user/updates/.
> >>
> >> On 8/9/2012 2:05 AM, Mojtaba Zareii wrote:
> >>> Hi dear Prof. Blaha
> >>>
> >>> I want to simulate the LaNi4.5Sn0.5H2.5 compound.
> >>> To do this, first I created the Struct file (case.struct) for LaNi5
> >>> compound and then used supercell prog to substitute Ni by Sn
> >>> (sepercell 1*1*2).
> >>>  Then I wanted to put hydrogen atoms into the lattice structure
> >>> created from the previous stage. After putting H atoms at proper
> >>> coordinates, I followed the "initialize stage" to wien2k program find
> >>> proper space group. In this stage "x nn"   complains and creates new
> >>> struct files. Accepted them and repeated this, until "nn" does not
> >>> find any error.
> >>> But in next stage, for  X Symmetry stage an error stop the program to
> >>> be continued as follows:
> >>> "ERROR: negative position in rstruc. Please report
> >>> 0.004u 0.000s 0:00.00 0.0%   0+0k 0+0io 0pf+0w"
> >>>
> >>> I have before seen such error which is due to rounding errors some
> >>> positions e.g. 0.500000001 Or 0.2499999999 when I used supercell prog,
> >>> But I could not solve this problem for this compound (I did it for one
> >>> atomic position as follows:   I changed x=0.13600000 and Y=0.27200000
> >>> coordinates to X=0.135 and Y=0.27, but it did not solve the problem).
> >>>
> >>> Could you please help me to solve this problem?
> >>> I have sent the struct files for  LaNi4.5Sn0.5H2.5 and LaNi5 compounds
> >>> which are used during this simulation.
> >>>
> >>> Thank you
> >>> Your Kindness will be appreciated in Advance
> >>>
> >>>
> >>> _______________________________________________
> >>> Wien mailing list
> >>> Wien at zeus.theochem.tuwien.ac.at
> >>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >>
> >>
> >>
> >> _______________________________________________
> >> Wien mailing list
> >> Wien at zeus.theochem.tuwien.ac.at
> >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >
> > _______________________________________________
> > Wien mailing list
> > Wien at zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > _______________________________________________
> > Wien mailing list
> > Wien at zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120810/e42760f7/attachment-0001.htm>

More information about the Wien mailing list