[Wien] Help Structgen Problems and Questions about MPI and ScaLAPACK

Peter Blaha pblaha at theochem.tuwien.ac.at
Thu Oct 4 17:34:21 CEST 2012 

It is a R (rhombohedral) lattice. Did you read the hint given in Structgen ???

The positions must be converted to the rhombohedral setting. See UG (struct file)
and use    hex2rhomb   for conversion.

Am 04.10.2012 16:44, schrieb Joshua Davis:
> Dear all wien2k users
>
> I have two problems I have questions on. The first is about the Structgen program.  For me it has seems to mess up with layered type of compounds.
> When looking at compounds like LiCoO2 it seems to put the atoms too close together.  When I input the positions I do not leave any values out so it should have enough Sig Figs to
> calculate the proper positions.
>
> The LiCoO2.struct file is:
>
> blebleble
>
> R   LATTICE,NONEQUIV.ATOMS:  5166_R-3m
> MODE OF CALC=RELA unit=bohr
>    5.336587  5.336587 26.244517 90.000000 90.000000120.000000
> ATOM  -1: X=0.00000000 Y=0.00000000 Z=0.00000000
>            MULT= 1          ISPLIT= 8
> Li1+       NPT=  781  R0=0.00010000 RMT=    2.0000   Z:  3.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                       0.0000000 1.0000000 0.0000000
>                       0.0000000 0.0000000 1.0000000
> ATOM  -2: X=0.83333334 Y=0.66666667 Z=0.16666667
>            MULT=12          ISPLIT= 8
> ATOM  -2:X= 0.16666666 Y=0.33333333 Z=0.83333333
> ATOM  -2:X= 0.66666667 Y=0.16666667 Z=0.83333334
> ATOM  -2:X= 0.33333333 Y=0.83333333 Z=0.16666666
> ATOM  -2:X= 0.83333334 Y=0.16666667 Z=0.66666667
> ATOM  -2:X= 0.16666666 Y=0.83333333 Z=0.33333333
> ATOM  -2:X= 0.16666667 Y=0.83333334 Z=0.66666667
> ATOM  -2:X= 0.83333333 Y=0.16666666 Z=0.33333333
> ATOM  -2:X= 0.16666667 Y=0.66666667 Z=0.83333334
> ATOM  -2:X= 0.83333333 Y=0.33333333 Z=0.16666666
> ATOM  -2:X= 0.66666667 Y=0.83333334 Z=0.16666667
> ATOM  -2:X= 0.33333333 Y=0.16666666 Z=0.83333333
> Li1+       NPT=  781  R0=0.00010000 RMT=    2.0000   Z:  3.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                       0.0000000 1.0000000 0.0000000
>                       0.0000000 0.0000000 1.0000000
> ATOM  -3: X=0.00000000 Y=0.00000000 Z=0.00000000
>            MULT= 1          ISPLIT= 8
> Co3+       NPT=  781  R0=0.00005000 RMT=    2.0000   Z: 27.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                       0.0000000 1.0000000 0.0000000
>                       0.0000000 0.0000000 1.0000000
> ATOM  -4: X=0.83333334 Y=0.66666667 Z=0.16666667
>            MULT=12          ISPLIT= 8
> ATOM  -4:X= 0.16666666 Y=0.33333333 Z=0.83333333
> ATOM  -4:X= 0.66666667 Y=0.16666667 Z=0.83333334
> ATOM  -4:X= 0.33333333 Y=0.83333333 Z=0.16666666
> ATOM  -4:X= 0.83333334 Y=0.16666667 Z=0.66666667
> ATOM  -4:X= 0.16666666 Y=0.83333333 Z=0.33333333
> ATOM  -4:X= 0.16666667 Y=0.83333334 Z=0.66666667
> ATOM  -4:X= 0.83333333 Y=0.16666666 Z=0.33333333
> ATOM  -4:X= 0.16666667 Y=0.66666667 Z=0.83333334
> ATOM  -4:X= 0.83333333 Y=0.33333333 Z=0.16666666
> ATOM  -4:X= 0.66666667 Y=0.83333334 Z=0.16666667
> ATOM  -4:X= 0.33333333 Y=0.16666666 Z=0.83333333
> Co3+       NPT=  781  R0=0.00005000 RMT=    2.0000   Z: 27.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                       0.0000000 1.0000000 0.0000000
>                       0.0000000 0.0000000 1.0000000
> ATOM  -5: X=0.74863333 Y=0.49726667 Z=0.25136667
>            MULT=12          ISPLIT= 8
> ATOM  -5:X= 0.25136667 Y=0.50273333 Z=0.74863333
> ATOM  -5:X= 0.49726667 Y=0.25136667 Z=0.74863333
> ATOM  -5:X= 0.50273333 Y=0.74863333 Z=0.25136667
> ATOM  -5:X= 0.74863333 Y=0.25136667 Z=0.49726667
> ATOM  -5:X= 0.25136667 Y=0.74863333 Z=0.50273333
> ATOM  -5:X= 0.25136667 Y=0.74863333 Z=0.49726667
> ATOM  -5:X= 0.74863333 Y=0.25136667 Z=0.50273333
> ATOM  -5:X= 0.25136667 Y=0.49726667 Z=0.74863333
> ATOM  -5:X= 0.74863333 Y=0.50273333 Z=0.25136667
> ATOM  -5:X= 0.49726667 Y=0.74863333 Z=0.25136667
> ATOM  -5:X= 0.50273333 Y=0.25136667 Z=0.74863333
> O 2-       NPT=  781  R0=0.00010000 RMT=    2.0000   Z:  8.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                       0.0000000 1.0000000 0.0000000
>                       0.0000000 0.0000000 1.0000000
>     0      NUMBER OF SYMMETRY OPERATIONS
>
> If you look at it in xcrysden, there are lithium atoms, and oxygen atoms on top of each other (like mentioned before).  I have tried to replace the the present executetables with
> the precompiled executables one can download because I thought it may have compiled them wrong.  I have no problems with any other type of structures; layered structures are the
> only ones that seem to mess up.
> I have tower with 4 six-core Xeon processors, 48gb running Ubuntu 12.04. Wien2K 11.1 was compiled with gfortran 4.6.3 with the GotoBLAS library.  What can I do?
>
> The second question I have is, Do I need an MPI and ScaLAPACK libraries to fully utilize my hardware for calculations?  Or do I not need them because all of my hardware is on the
> same machine?  I am a bit confused by the information in the user guide.
>
> Help with both of the questions would be much appreciated.
>
> Josh Davis
>
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>

-- 

                                       P.Blaha
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Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
Email: blaha at theochem.tuwien.ac.at    WWW: http://info.tuwien.ac.at/theochem/
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