Atoms missing from the geometry.


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Unfortunately, on the system I'm using (NCSA Ember SGI Altix UV, NCSA-provided build of 6.0), it doesn't make any difference:
    1 Li1                  3.0000     1.75250000     0.00000000    19.95682000
    2 Li2                  3.0000     0.00000000     2.47841000    19.95682000
    3 Li3                  3.0000     1.75250000     2.47841000    22.43505791
    4 Li4                  3.0000     0.00000000     0.00000000    22.43505791
    5 Li5                  3.0000     1.75250000     0.00000000    24.91369495
    6 Li6                  3.0000     0.00000000     2.47841000    24.91369495
    7 Li7                  3.0000     5.25750000     0.00000000    19.95682000
    8 Li8                  3.0000     3.50500000     2.47841000    19.95682000
    9 Li9                  3.0000     5.25750000     2.47841000    22.43505791
   10 Li10                 3.0000     3.50500000     0.00000000    22.43505791
   11 Li11                 3.0000     5.25750000     0.00000000    24.91369495
   12 Li12                 3.0000     3.50500000     2.47841000    24.91369495
   13 H                    1.0000     1.75250000     3.68291726    25.94386600


Let me try it with something besides H and I'll let you know if that impacts it at all.