Natural Electron Configuration vs Natural Population

Natural Electron Configuration vs Natural Population

Postby lyuben » Sun Jun 19, 2016 10:28 am

Hi all,

I have a problem understanding part of the output (comparing the Natural Electron Configuration and the Natural Population tables) for a particular molecule (SnCl_6)^2-.
What I would usually expect is that the numbers for the valence electron occupation from the "Natural Electron Configuration" table add to the number (or at least to close to it) for the valence orbitals in the Natural Population table. In this particular case the Natural Population for the Sn atom is a number close to 4. However, the sum of the valence electron occupation numbers from the Natural Electron Configuration for Sn add to only about 2. (see the tables below).
The question are whether such discrepancy is expected, what is causing it, and how it can be interpreted.

Code: Select all
                                   Natural Population
             Natural    ---------------------------------------------
  Atom No    Charge        Core      Valence    Rydberg      Total
 --------------------------------------------------------------------
   Sn  1    1.44540     38.48380     3.99933    6.07147    48.55460
   Cl  2   -0.57497      7.99991     7.63975    1.93531    17.57497
   Cl  3   -0.57497      9.99976     7.56784    0.00738    17.57497
   Cl  4   -0.57275      7.99991     7.63819    1.93465    17.57275
   Cl  5   -0.57275      9.99976     7.56550    0.00750    17.57275
   Cl  6   -0.57497      7.99991     7.63975    1.93531    17.57497
   Cl  7   -0.57497      9.99976     7.56784    0.00738    17.57497
 ====================================================================
 * Total * -2.00000     92.48280    49.61820   11.89900   154.00000

Code: Select all
    Atom No         Natural Electron Configuration
 ----------------------------------------------------------------------------
Sn 1 [core]5s( 1.04)5p( 0.96)4f( 0.01)5d( 0.03)6p( 0.03)
Cl 2 [core]3s( 1.93)3p( 5.64)3d( 0.01)
Cl 3 [core]3s( 1.93)3p( 5.64)3d( 0.01)
Cl 4 [core]3s( 1.93)3p( 5.64)3d( 0.01)
Cl 5 [core]3s( 1.93)3p( 5.64)3d( 0.01)
Cl 6 [core]3s( 1.93)3p( 5.64)3d( 0.01)
Cl 7 [core]3s( 1.93)3p( 5.64)3d( 0.01)


Best regards,
Lyuben
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Re: Natural Electron Configuration vs Natural Population

Postby ericg » Mon Jun 20, 2016 11:49 pm

There surely is an inconsistency here. I'm most concerned that significant Rydberg occupancies appear. Can you also post the NAO occupancies (the table at the top of the NPA output)? What basis set are you using?

Eric
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Re: Natural Electron Configuration vs Natural Population

Postby lyuben » Thu Jun 23, 2016 12:14 am

Sure, I attach the full output file (adf2013) as well. The calculation is using TZ2P basis set and hybrid PBE functional.
I also tried to reduce the charge of the system (to 0 and 2+) and I get the same results for Sn, unlike the rest of the series with SnCl3, SnCl4, and SnCl5 (for these the numbers in the Natural Electron Configuration and Natural Population fields are consistent).

Code: Select all
   1   Sn  1  s      Cor( 1s)     2.00000   -1089.52251
   2   Sn  1  s      Cor( 2s)     2.00000    -164.56135
   3   Sn  1  s      Cor( 3s)     2.00000     -29.17110
   4   Sn  1  s      Cor( 4s)     1.99992      -6.36577
   5   Sn  1  s      Val( 5s)     1.04140       0.16201
   6   Sn  1  s      Ryd( 6s)     0.00245      13.43112
   7   Sn  1  s      Ryd( 7s)     0.00001       3.19828
   8   Sn  1  s      Ryd( 8s)     0.00000      60.75623
   9   Sn  1  s      Ryd( 9s)     0.00000    1075.37114
  10   Sn  1  s      Ryd(10s)     0.00000    4286.17195
  11   Sn  1  s      Ryd(12s)     0.00000   38133.41032
  12   Sn  1  s      Ryd(11s)     0.00000   15474.85636
  13   Sn  1  px     Cor( 2p)     2.00000     -54.62475
  14   Sn  1  px     Cor( 3p)     2.00000    -239.83303
  15   Sn  1  px     Cor( 4p)     1.99999      -5.23813
  16   Sn  1  px     Val( 5p)     0.47930       0.16962
  17   Sn  1  px     Ryd( 6p)     0.01027       1.37328
  18   Sn  1  px     Ryd( 7p)     0.00028       1.43310
  19   Sn  1  px     Ryd( 8p)     0.00000       5.95406
  20   Sn  1  px     Ryd( 9p)     0.00000     298.30061
  21   Sn  1  px     Ryd(10p)     0.00000     794.40091
  22   Sn  1  px     Ryd(11p)     0.00000    1700.46368
  23   Sn  1  py     Cor( 2p)     2.00000     -50.28535
  24   Sn  1  py     Val( 3p)     2.00000      12.81531
  25   Sn  1  py     Cor( 4p)     1.99999      -2.87489
  26   Sn  1  py     Cor( 5p)     0.47930       0.47453
  27   Sn  1  py     Ryd( 6p)     0.01027       1.48958
  28   Sn  1  py     Ryd( 7p)     0.00028       1.49990
  29   Sn  1  py     Ryd( 8p)     0.00000       7.01870
  30   Sn  1  py     Ryd( 9p)     0.00000     274.82134
  31   Sn  1  py     Ryd(10p)     0.00000     784.89243
  32   Sn  1  py     Ryd(11p)     0.00000    2735.15869
  33   Sn  1  pz     Cor( 2p)     2.00000     -52.45502
  34   Sn  1  pz     Cor( 3p)     2.00000    -113.50883
  35   Sn  1  pz     Cor( 4p)     1.99999      -4.05641
  36   Sn  1  pz     Val( 5p)     0.47863       0.32298
  37   Sn  1  pz     Ryd( 6p)     0.01045       1.42834
  38   Sn  1  pz     Ryd( 7p)     0.00028       1.46591
  39   Sn  1  pz     Ryd( 8p)     0.00000       6.48805
  40   Sn  1  pz     Ryd( 9p)     0.00000     286.55708
  41   Sn  1  pz     Ryd(10p)     0.00000     789.64534
  42   Sn  1  pz     Ryd(11p)     0.00000    2217.81134
  43   Sn  1  dxy    Cor( 3d)     2.00000     -16.19864
  44   Sn  1  dxy    Cor( 4d)     1.99985      -0.40054
  45   Sn  1  dxy    Ryd( 5d)     0.00808       1.33340
  46   Sn  1  dxy    Ryd( 6d)     0.00014       3.73142
  47   Sn  1  dxy    Ryd( 7d)     0.00000       7.19735
  48   Sn  1  dxy    Ryd( 8d)     0.00000      77.23629
  49   Sn  1  dxy    Ryd( 9d)     0.00000      59.52341
  50   Sn  1  dxz    Ryd( 3d)     2.00000      18.24065
  51   Sn  1  dxz    Ryd( 4d)     1.99997       1.91843
  52   Sn  1  dxz    Cor( 5d)     0.00484       1.74588
  53   Sn  1  dxz    Cor( 6d)     0.00011       1.81282
  54   Sn  1  dxz    Ryd( 7d)     0.00000       8.80598
  55   Sn  1  dxz    Ryd( 8d)     0.00000     106.52903
  56   Sn  1  dxz    Ryd( 9d)     0.00000     134.62864
  57   Sn  1  dyz    Cor( 3d)     2.00000     -50.63837
  58   Sn  1  dyz    Ryd( 4d)     1.99997      -2.72720
  59   Sn  1  dyz    Ryd( 5d)     0.00484       0.24870
  60   Sn  1  dyz    Ryd( 6d)     0.00011       0.91994
  61   Sn  1  dyz    Ryd( 7d)     0.00000       2.99765
  62   Sn  1  dyz    Ryd( 8d)     0.00000      45.76248
  63   Sn  1  dyz    Cor( 9d)     0.00000     -15.32312
  64   Sn  1  dx2y2  Cor( 3d)     2.00000     -16.19888
  65   Sn  1  dx2y2  Cor( 4d)     1.99997      -0.40443
  66   Sn  1  dx2y2  Ryd( 5d)     0.00482       0.99637
  67   Sn  1  dx2y2  Ryd( 6d)     0.00011       1.36617
  68   Sn  1  dx2y2  Ryd( 7d)     0.00000       5.89762
  69   Sn  1  dx2y2  Ryd( 8d)     0.00000      76.14062
  70   Sn  1  dx2y2  Ryd( 9d)     0.00000      59.65337
  71   Sn  1  dz2    Cor( 3d)     2.00000     -16.19858
  72   Sn  1  dz2    Cor( 4d)     1.99985      -0.40050
  73   Sn  1  dz2    Ryd( 5d)     0.00807       1.33818
  74   Sn  1  dz2    Ryd( 6d)     0.00015       3.74520
  75   Sn  1  dz2    Ryd( 7d)     0.00000       7.20558
  76   Sn  1  dz2    Ryd( 8d)     0.00000      77.24065
  77   Sn  1  dz2    Ryd( 9d)     0.00000      59.52302
  78   Sn  1  f(0)   Ryd( 4f)     0.00249       1.50942
  79   Sn  1  f(c1)  Ryd( 4f)     0.00166       1.84737
  80   Sn  1  f(s1)  Ryd( 4f)     0.00166       0.88491
  81   Sn  1  f(c2)  Ryd( 4f)     0.00000       1.19851
  82   Sn  1  f(s2)  Ryd( 4f)     0.00115       1.28084
  83   Sn  1  f(c3)  Ryd( 4f)     0.00198       2.00317
  84   Sn  1  f(s3)  Ryd( 4f)     0.00198       0.84003
Attachments
nbo_SnCl62-.out.gz
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lyuben
 
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Re: Natural Electron Configuration vs Natural Population

Postby ericg » Thu Jun 23, 2016 1:58 am

Some of the NAOs are clearly inappropriately assigned in your calculation as Cor, Val, or Ryd orbitals. I believe that this is an issue that we resolved a couple years ago and that more recent distributions of NBO6 would not reveal this problem. Unfortunately, an early 2013 version of NBO6 is currently distributed with ADF.

I recall that ADF passes information to NBO via a *.47 file (FILE47). Is it possible for you to locate this file and post it here? I'll use your FILE47 as input for the most recent version of NBO to determine whether the orbital types are still misassigned.

Eric
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Re: Natural Electron Configuration vs Natural Population

Postby lyuben » Thu Jun 23, 2016 6:03 am

Hi,

I believe that this is an issue that we resolved a couple years ago and that more recent distributions of NBO6 would not reveal this problem. Unfortunately, an early 2013 version of NBO6 is currently distributed with ADF.

if this is the case do you know if the numbers in rest of the series are to be trusted?

Is it possible for you to locate this file and post it here?

I have the file but it is a bit big. The gz archive is more than 2MB (not accepted by the forum engine as the limit is 2MB). The 7za archive is also not accepted because it has 7za extension (thought the size is 1.3 MB). And if I change the extension of the 7za archive with .gz I get "The file is too big, maximum allowed size is 256 KiB"
Do you have any other means to communicate that file?
lyuben
 
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Re: Natural Electron Configuration vs Natural Population

Postby ericg » Sun Jun 26, 2016 10:22 am

Sure. You can send the file directly to me at glendening@indstate.edu.

Thanks,

Eric
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Re: Natural Electron Configuration vs Natural Population

Postby ericg » Mon Jun 27, 2016 3:13 pm

It appears that ADF is passing a bogus Fock (or Kohn-Sham) matrix to NBO. Note that the occupancies of the NAOs reflect the approximate octahedral symmetry of this system, but that the energies of the NAOs do not.

The asymmetry in the NAOs is probably best observed in the px, py, and pz sets of Sn. There are three NAOs, one of each of these symmetries, that have occupancies of 0.479. The energies reported for these NAOs are 0.170 (px), 0.475 (py), and 0.323 (pz) a.u., whereas they should be identical. Likewise three-fold degeneracies that one would expect to find in the dxy, dyz, and dxz sets, and the two-fold in the dx2-y2 and dz2 sets are not apparent.

Cor, Val, and Ryd labels are assigned by sorting the NAOs by energy (if the Fock matrix is available). Note, then, the assignments for the dxz NAOs of Sn (NAOs 50-53). The two lowest energy NAOs (52, 53) are assigned Cor, although both NAOs are nearly vacant. NAOs 50 and 51 are both nearly doubly occupied but are assigned Ryd due to their higher energies.

The Fock matrix ($FOCK input in the FILE47 input to NBO6) must be fixed to make sense of these data. Alternatively, you can ignore the energy output in the NBO output (including the energies reported in the NAO and NBO summary tables, the NAO labels, and in the perturbative analysis). The NAOs and NBOs themselves are fine because their construction does not depend on the details of the Fock matrix.

I'd encourage you to contact the ADF team with your case here. They should be able to correct $FOCK in FILE47.

Eric
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Re: Natural Electron Configuration vs Natural Population

Postby lyuben » Thu Jun 30, 2016 10:27 pm

It appears that ADF is passing a bogus Fock (or Kohn-Sham) matrix to NBO. Note that the occupancies of the NAOs reflect the approximate octahedral symmetry of this system, but that the energies of the NAOs do not.


After discussing the problem with the ADF developers it seems the problem appears because ADF applies symmetry by default (when possible). That leads to KS matrix/matrices which is/are not expected by NBO.
The solution is to always disable the symmetry when second order perturbation analysis is requested in NBO
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