"autosym failed..."
Clicked A Few Times
11:59:07 PM PST - Wed, Dec 26th 2012
Hello folks. I have a geometry that I know to be O_h and one that I know to be I_h but when I put the coordinates in and attempt to use autosym it either finds no symmetry (the "WARNING: autosym failed!" error) or finds a much lower symmetry than the cluster possesses.

Are there ways of getting this to be more successful?

Thanks for any help.

Forum Vet
10:10:48 AM PST - Thu, Dec 27th 2012
Tolerances
You should try with a looser tolerance on the autosym, in case the coordinates are not pure Oh or Ih:

    autosym [real tol default 1d-2]

(see http://nwchemgit.github.io/index.php/Release61:Geometry) . If this doesn't work, please post a geometry that fails so we can take a look at it.

Clicked A Few Times
2:17:31 PM PST - Thu, Dec 27th 2012
For the Oh cluster, I put the full Cartesian coordinates in after "symmetry Oh" and it works fine. For the ico however, I put in the following coordinates (that have been "symmetrized" in gaussview to be Ih") with the line:
geometry bridge6 noautoz autosym 1d-0
and get only D3d symmetry:
Pd                 0.00000000   -0.00000000   -0.00000000

Pd                 0.00000000    0.00000000    2.74998368

Pd                -1.44575089    1.98990705    1.22983112

Pd                -2.33927505   -0.76007757    1.22983112

Pd                 0.00000098   -2.45965967    1.22983112

Pd                 2.33927505   -0.76007757    1.22983112

Pd                 1.44575247    1.98990589    1.22983112

Pd                 0.00000159    2.45966153   -1.22982739

Pd                -2.33927664    0.76007872   -1.22982739

Pd                -1.44575149   -1.98990891   -1.22982739

Pd                 1.44575149   -1.98990891   -1.22982739

Pd                 2.33927762    0.76007571   -1.22982739

Pd                -0.00000000    0.00000000   -2.74998368

Pd                 0.00000000    0.00000000    5.49998140

Pd                -2.89150915    3.97982425    2.45966852

Pd                -4.67856204   -1.52015902    2.45966852

Pd                 0.00000196   -4.91933189    2.45966852

Pd                 4.67856204   -1.52015902    2.45966852

Pd                 2.89151232    3.97982195    2.45966852

Pd                 0.00000317    4.91933561   -2.45966107

Pd                -4.67856521    1.52016132   -2.45966107

Pd                -2.89151036   -3.97982798   -2.45966107

Pd                 2.89151036   -3.97982798   -2.45966107

Pd                 4.67856717    1.52015529   -2.45966107

Pd                -0.00000000    0.00000000   -5.49998140

Pd                -1.44575767    1.98991471    3.97982701

Pd                -2.33928504   -0.76007979    3.97982701

Pd                 0.00000000   -2.45966986    3.97982701

Pd                 2.33928504   -0.76007979    3.97982701

Pd                 1.44575767    1.98991471    3.97982701

Pd                -3.78503869    1.22983726    2.45967095

Pd                -0.00000346    3.97982633    2.45967095

Pd                -1.44575383    4.44958365    0.00000130

Pd                -3.78503967    2.74999518    0.00000679

Pd                -2.33928406   -3.21974779    2.45966929

Pd                -4.67856803   -0.00000203    0.00000027

Pd                -3.78504019   -2.74999446    0.00000135

Pd                 2.33928476   -3.21974660    2.45967018

Pd                -1.44575798   -4.44958230    0.00000513

Pd                 1.44575725   -4.44958254    0.00000126

Pd                 3.78504065    1.22983457    2.45966929

Pd                 3.78504091   -2.74999348    0.00000126

Pd                 4.67856803    0.00000100    0.00000513

Pd                 1.44575896    4.44958198    0.00000027

Pd                 3.78504190    2.74999212    0.00000135

Pd                -2.33928245    3.21975026   -2.45966759

Pd                 2.33928761    3.21974934   -2.45966389

Pd                 0.00000172    2.45966825   -3.97982800

Pd                -3.78504322   -1.22983746   -2.45966389

Pd                -2.33928405    0.76007765   -3.97982800

Pd                 0.00000288   -3.97982902   -2.45966659

Pd                -1.44575639   -1.98991835   -3.97982565

Pd                 3.78504144   -1.22983754   -2.45966659

Pd                 1.44575930   -1.98991696   -3.97982529

Pd                 2.33928811    0.76007745   -3.97982565

Also, the structure is rotated in the .out file relative to the input coordinates; is there a preferred orientation that would give me a better shot of it "seeing" the higher order symmetries?

Thanks for your help.

Forum Vet
6:40:57 PM PST - Thu, Dec 27th 2012
Ih autosym
Did some checking in the code, autosym cannot detect the high symmetry Ih group (has not been coded for that for some reason). The only suggestion I have right now is to input the geometry with the unique atoms and Ih symmetry. NWChem can handle Ih symmetry, it simply cannot automatically detect it. You'll need to identify the unique atoms to generate the whole molecule.

Here is where I got with that:

geometry
symmetry Ih
Pd 0.00000000 0.00000000 0.00000000
Pd 0.00000000 0.00000000 2.74998368 -> generates the next 11 atoms
  1. Pd -1.44575089 1.98990705 1.22983112
  2. Pd -2.33927505 -0.76007757 1.22983112
  3. Pd 0.00000098 -2.45965967 1.22983112
  4. Pd 2.33927505 -0.76007757 1.22983112
  5. Pd 1.44575247 1.98990589 1.22983112
  6. Pd 0.00000159 2.45966153 -1.22982739
  7. Pd -2.33927664 0.76007872 -1.22982739
  8. Pd -1.44575149 -1.98990891 -1.22982739
  9. Pd 1.44575149 -1.98990891 -1.22982739
  10. Pd 2.33927762 0.76007571 -1.22982739
  11. Pd -0.00000000 0.00000000 -2.74998368
Pd 0.00000000 0.00000000 5.49998140 -> generates the next 11 atoms
  1. Pd -2.89150915 3.97982425 2.45966852
  2. Pd -4.67856204 -1.52015902 2.45966852
  3. Pd 0.00000196 -4.91933189 2.45966852
  4. Pd 4.67856204 -1.52015902 2.45966852
  5. Pd 2.89151232 3.97982195 2.45966852
  6. Pd 0.00000317 4.91933561 -2.45966107
  7. Pd -4.67856521 1.52016132 -2.45966107
  8. Pd -2.89151036 -3.97982798 -2.45966107
  9. Pd 2.89151036 -3.97982798 -2.45966107
  10. Pd 4.67856717 1.52015529 -2.45966107
  11. Pd -0.00000000 0.00000000 -5.49998140

-> Some of the atoms below I have tried and generate too many atoms. Whole system might need to be rotated.

  1. Pd -0.00000346 3.97982633 2.45967095
  2. Pd -1.44575767 1.98991471 3.97982701
  3. Pd -2.33928504 -0.76007979 3.97982701
  4. Pd 0.00000000 -2.45966986 3.97982701
  5. Pd 2.33928504 -0.76007979 3.97982701
  6. Pd 1.44575767 1.98991471 3.97982701
  7. Pd -3.78503869 1.22983726 2.45967095
  8. Pd -1.44575383 4.44958365 0.00000000
  9. Pd -3.78503967 2.74999518 0.00000679
  10. Pd -2.33928406 -3.21974779 2.45966929
  11. Pd -4.67856803 -0.00000203 0.00000027
  12. Pd -3.78504019 -2.74999446 0.00000135
  13. Pd 2.33928476 -3.21974660 2.45967018
  14. Pd -1.44575798 -4.44958230 0.00000513
  15. Pd 1.44575725 -4.44958254 0.00000126
  16. Pd 3.78504065 1.22983457 2.45966929
  17. Pd 3.78504091 -2.74999348 0.00000126
  18. Pd 4.67856803 0.00000000 0.00000000
  19. Pd 1.44575896 4.44958198 0.00000027
  20. Pd 3.78504190 2.74999212 0.00000135
  21. Pd -2.33928245 3.21975026 -2.45966759
  22. Pd 2.33928761 3.21974934 -2.45966389
  23. Pd 0.00000172 2.45966825 -3.97982800
  24. Pd -3.78504322 -1.22983746 -2.45966389
  25. Pd -2.33928405 0.76007765 -3.97982800
  26. Pd 0.00000288 -3.97982902 -2.45966659
  27. Pd -1.44575639 -1.98991835 -3.97982565
  28. Pd 3.78504144 -1.22983754 -2.45966659
  29. Pd 1.44575930 -1.98991696 -3.97982529
  30. Pd 2.33928811 0.76007745 -3.97982565
end

Clicked A Few Times
9:23:12 PM PST - Sun, Feb 17th 2013
Does anyone else have any good ideas about how to figure out which unique atoms will reconstruct the full 55 atom cluster with Ih symmetry? Chemcraft can only find it for Th symmetry (it doesn't have Ih for whatever reason).

Forum Vet
11:59:23 AM PST - Mon, Feb 18th 2013
Adam
The following geometry input should reproduce the pd55 cluster you reported

geometry noautoz
 pd    0.00000000     0.00000000     0.00000000
 pd    0.00000000     0.00000000     2.75        #         12x
 pd    0.00000000     4.67856803     0.0         #         30x
 pd    0.00000000     0.00000000     5.5         #         12x
 symmetry ih
end

Clicked A Few Times
8:17:09 PM PST - Mon, Feb 18th 2013
Thanks, that's very helpful.


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