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]" im Auftrag von > "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... 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