[Wien] Help Structgen Problems and Questions about MPI and ScaLAPACK
Gavin Abo
gsabo at crimson.ua.edu
Thu Oct 4 17:34:36 CEST 2012
You have Li1+ and Co3+ placed at the same atomic positions X=0.00000000
Y=0.00000000 Z=0.00000000 and 0.83333334 Y=0.66666667 Z=0.16666667.
On 10/4/2012 8:44 AM, Joshua Davis wrote:
> 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
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