[CP2K-user] dimension inconsistency of the overlap and MO coefficients

Vladimir Rybkin rybk... at gmail.com
Fri Oct 12 15:48:10 CEST 2018


Hi Xiaoming,

I am not sure whether it could be done without modifying the code. I would 
rather try to get the MOs printed, say by using DIAGONALIZATION in SCF, 
which finds coefficients for all MOs, not only the occupied ones.\

Yours,

Vladimir

пятница, 12 октября 2018 г., 14:53:59 UTC+2 пользователь Xiaoming Wang 
написал:
>
> Hi Vladimir,
>
> I'm sorry I made a mistake. I mean could the overlap matrix be transformed 
> to cartesian coordinates? Because I only have the MO of LUMO printed in 
> cartesian coordinates.
>
> Best,
> Xiaoming 
>
> On Friday, October 12, 2018 at 8:48:45 AM UTC-4, Vladimir Rybkin wrote:
>>
>> Hi Xiaoming,
>>
>> overlap matrix is already in spherical Gaussians. The overlap is taken 
>> between basis functions (AO), not between MO(s). It is calculated before 
>> any MOs are obtained.
>>
>> Yours,
>>
>> Vladimir
>>
>> пятница, 12 октября 2018 г., 14:34:43 UTC+2 пользователь Xiaoming Wang 
>> написал:
>>>
>>> Hi Vladimir,
>>>
>>> Thanks for your confirmation. Yes, with Cartesian off, the dimensions 
>>> are consistent now. If cp2k does not print MO of vacant state, then is it 
>>> possible to transform the overlap matrix to spherical coordinates?
>>>
>>> Best,
>>> Xiaoming
>>>
>>> On Friday, October 12, 2018 at 8:18:30 AM UTC-4, Vladimir Rybkin wrote:
>>>>
>>>> Dear Xiaoming,
>>>>
>>>> thank you for the data. I don't see any inconsistency now. You get 52 
>>>> with Cartesian off and 54 with Cartesian on. Turning Cartesian off you can 
>>>> now multiply your C with your S. Isn't that what you want? Unfortunately, I 
>>>> can't comment on why orbital #5 is not printed. Perhaps, that is due to the 
>>>> fact that it is vacant.
>>>>
>>>> Yours,
>>>>
>>>> Vladimir
>>>>
>>>> пятница, 12 октября 2018 г., 13:47:35 UTC+2 пользователь Xiaoming Wang 
>>>> написал:
>>>>>
>>>>> Hi Vladimir,
>>>>>
>>>>> Thanks for you reply.
>>>>>
>>>>> My input of the print part is:
>>>>>
>>>>> ------------
>>>>>
>>>>>     &MO
>>>>>
>>>>>       EIGENVALUES
>>>>>
>>>>>       EIGENVECTORS
>>>>>
>>>>>       CARTESIAN
>>>>>
>>>>>       FILENAME mos
>>>>>
>>>>>       MO_INDEX_RANGE 4 5
>>>>>
>>>>>       OCCUPATION_NUMBERS
>>>>>
>>>>>       &EACH
>>>>>
>>>>>        QS_SCF 0
>>>>>
>>>>>       &END EACH
>>>>>
>>>>>      &END MO
>>>>>
>>>>> --------------
>>>>>
>>>>>
>>>>> With CARTESIAN on, I get
>>>>>
>>>>>
>>>>> ----------------
>>>>>
>>>>>  MO EIGENVALUES, MO OCCUPATION NUMBERS, AND CARTESIAN MO EIGENVECTORS
>>>>>
>>>>>
>>>>>                               4            5
>>>>>
>>>>>                           -0.260963    -0.034173
>>>>>
>>>>>
>>>>>                            2.000000     0.000000
>>>>>
>>>>>
>>>>>      1     1  O  2s        0.000000     0.236782
>>>>>
>>>>>      2     1  O  3s        0.000000    -0.090781
>>>>>
>>>>>      3     1  O  4s        0.000000    -0.240258
>>>>>
>>>>>      4     1  O  3px      -0.917807    -0.000000
>>>>>
>>>>>      5     1  O  3py      -0.000000    -0.000000
>>>>>
>>>>>      6     1  O  3pz       0.000000    -0.238095
>>>>>
>>>>>      7     1  O  4px       0.020934    -0.000000
>>>>>
>>>>>      8     1  O  4py       0.000000    -0.000000
>>>>>
>>>>>      9     1  O  4pz      -0.000000     0.013849
>>>>>
>>>>>     10     1  O  5px      -0.003042     0.000000
>>>>>
>>>>>     11     1  O  5py       0.000000     0.000000
>>>>>
>>>>>     12     1  O  5pz      -0.000000     0.099980
>>>>>
>>>>>     13     1  O  3dx2     -0.000000     0.000099
>>>>>
>>>>>     14     1  O  3dxy     -0.000000    -0.000000
>>>>>
>>>>>     15     1  O  3dxz     -0.005256    -0.000000
>>>>>
>>>>>     16     1  O  3dy2     -0.000000     0.000744
>>>>>
>>>>>     17     1  O  3dyz      0.000000    -0.000000
>>>>>
>>>>>     18     1  O  3dz2      0.000000    -0.000844
>>>>>
>>>>>     19     1  O  4dx2     -0.000000     0.000357
>>>>>
>>>>>     20     1  O  4dxy      0.000000    -0.000000
>>>>>
>>>>>     21     1  O  4dxz     -0.022359     0.000000
>>>>>
>>>>>     22     1  O  4dy2      0.000000     0.004105
>>>>>
>>>>>     23     1  O  4dyz     -0.000000     0.000000
>>>>>
>>>>>     24     1  O  4dz2      0.000000    -0.004463
>>>>>
>>>>>     25     1  O  5s       -0.000000    -0.011663
>>>>>
>>>>>     26     1  O  5px       0.024750    -0.000000
>>>>>
>>>>>     27     1  O  5py      -0.000000     0.000000
>>>>>
>>>>>     28     1  O  5pz       0.000000    -0.077018
>>>>>
>>>>>
>>>>>     29     2  H  1s        0.000000    -0.116793
>>>>>
>>>>>     30     2  H  2s        0.000000    -0.003374
>>>>>
>>>>>     31     2  H  3s       -0.000000     0.197029
>>>>>
>>>>>     32     2  H  2px       0.011575    -0.000000
>>>>>
>>>>>     33     2  H  2py       0.000000     0.008716
>>>>>
>>>>>     34     2  H  2pz      -0.000000    -0.004748
>>>>>
>>>>>     35     2  H  3px       0.028901    -0.000000
>>>>>
>>>>>     36     2  H  3py       0.000000     0.013894
>>>>>
>>>>>     37     2  H  3pz      -0.000000    -0.010138
>>>>>
>>>>>     38     2  H  4s       -0.000000     0.421270
>>>>>
>>>>>     39     2  H  4px       0.026994     0.000000
>>>>>
>>>>>     40     2  H  4py       0.000000     0.041403
>>>>>
>>>>>     41     2  H  4pz      -0.000000    -0.044975
>>>>>
>>>>>
>>>>>     42     3  H  1s        0.000000    -0.116793
>>>>>
>>>>>     43     3  H  2s       -0.000000    -0.003374
>>>>>
>>>>>     44     3  H  3s        0.000000     0.197029
>>>>>
>>>>>     45     3  H  2px       0.011575    -0.000000
>>>>>
>>>>>     46     3  H  2py       0.000000    -0.008716
>>>>>
>>>>>     47     3  H  2pz      -0.000000    -0.004748
>>>>>
>>>>>     48     3  H  3px       0.028901    -0.000000
>>>>>
>>>>>     49     3  H  3py      -0.000000    -0.013894
>>>>>
>>>>>     50     3  H  3pz      -0.000000    -0.010138
>>>>>
>>>>>     51     3  H  4s        0.000000     0.421270
>>>>>
>>>>>     52     3  H  4px       0.026994     0.000000
>>>>>
>>>>>     53     3  H  4py       0.000000    -0.041403
>>>>>
>>>>>     54     3  H  4pz       0.000000    -0.044975
>>>>>
>>>>>
>>>>>
>>>>>   Fermi energy:                -0.260963
>>>>>
>>>>>
>>>>>   HOMO-LUMO gap:                0.226790 =   6.17 eV
>>>>> ---------------------------------------
>>>>>
>>>>> However, with CARTESIAN OFF, I get only the orbital #4:
>>>>>
>>>>> ----------------------------------------
>>>>>
>>>>>  MO EIGENVALUES, MO OCCUPATION NUMBERS, AND SPHERICAL MO EIGENVECTORS
>>>>>
>>>>>
>>>>>                               4
>>>>>
>>>>>                           -0.260963
>>>>>
>>>>>
>>>>>                            2.000000
>>>>>
>>>>>
>>>>>      1     1  O  2s        0.000000
>>>>>
>>>>>      2     1  O  3s        0.000000
>>>>>
>>>>>      3     1  O  4s        0.000000
>>>>>
>>>>>      4     1  O  3py      -0.000000
>>>>>
>>>>>      5     1  O  3pz       0.000000
>>>>>
>>>>>      6     1  O  3px      -0.917807
>>>>>
>>>>>      7     1  O  4py       0.000000
>>>>>
>>>>>      8     1  O  4pz      -0.000000
>>>>>
>>>>>      9     1  O  4px       0.020934
>>>>>
>>>>>     10     1  O  5py       0.000000
>>>>>
>>>>>     11     1  O  5pz      -0.000000
>>>>>
>>>>>     12     1  O  5px      -0.003042
>>>>>
>>>>>     13     1  O  3d-2     -0.000000
>>>>>
>>>>>     14     1  O  3d-1      0.000000
>>>>>
>>>>>     15     1  O  3d0       0.000000
>>>>>
>>>>>     16     1  O  3d+1     -0.005256
>>>>>
>>>>>     17     1  O  3d+2     -0.000000
>>>>>
>>>>>     18     1  O  4d-2      0.000000
>>>>>
>>>>>     19     1  O  4d-1     -0.000000
>>>>>
>>>>>     20     1  O  4d0       0.000000
>>>>>
>>>>>     21     1  O  4d+1     -0.022359
>>>>>
>>>>>     22     1  O  4d+2     -0.000000
>>>>>
>>>>>     23     1  O  5s       -0.000000
>>>>>
>>>>>     24     1  O  5py      -0.000000
>>>>>
>>>>>     25     1  O  5pz       0.000000
>>>>>
>>>>>     26     1  O  5px       0.024750
>>>>>
>>>>>
>>>>>     27     2  H  1s        0.000000
>>>>>
>>>>>     28     2  H  2s        0.000000
>>>>>
>>>>>     29     2  H  3s       -0.000000
>>>>>
>>>>>     30     2  H  2py       0.000000
>>>>>
>>>>>     31     2  H  2pz      -0.000000
>>>>>
>>>>>     32     2  H  2px       0.011575
>>>>>
>>>>>     33     2  H  3py       0.000000
>>>>>
>>>>>     34     2  H  3pz      -0.000000
>>>>>
>>>>>     35     2  H  3px       0.028901
>>>>>
>>>>>     36     2  H  4s       -0.000000
>>>>>
>>>>>     37     2  H  4py       0.000000
>>>>>
>>>>>     38     2  H  4pz      -0.000000
>>>>>
>>>>>     39     2  H  4px       0.026994
>>>>>
>>>>>
>>>>>     40     3  H  1s        0.000000
>>>>>
>>>>>     41     3  H  2s       -0.000000
>>>>>
>>>>>     42     3  H  3s        0.000000
>>>>>
>>>>>     43     3  H  2py       0.000000
>>>>>
>>>>>     44     3  H  2pz      -0.000000
>>>>>
>>>>>     45     3  H  2px       0.011575
>>>>>
>>>>>     46     3  H  3py      -0.000000
>>>>>
>>>>>     47     3  H  3pz      -0.000000
>>>>>
>>>>>     48     3  H  3px       0.028901
>>>>>
>>>>>     49     3  H  4s        0.000000
>>>>>
>>>>>     50     3  H  4py       0.000000
>>>>>
>>>>>     51     3  H  4pz       0.000000
>>>>>
>>>>>     52     3  H  4px       0.026994
>>>>>
>>>>>
>>>>>
>>>>>   Fermi energy:                -0.260963
>>>>>
>>>>> -----------------------------
>>>>>
>>>>>
>>>>> Why the MO #5 is not printed in spherical coordinate?
>>>>>
>>>>>
>>>>> Best,
>>>>>
>>>>> Xiaoming
>>>>>
>>>>> On Friday, October 12, 2018 at 5:51:08 AM UTC-4, Vladimir Rybkin wrote:
>>>>>>
>>>>>> Hi Xiaoming,
>>>>>>
>>>>>> it is. I mean that by default it is not printed, only the basis is. 
>>>>>> So, please attach your input/output: this will help to stay on equal 
>>>>>> footing.
>>>>>>
>>>>>> Yours,
>>>>>>
>>>>>> Vladimir
>>>>>>
>>>>>> четверг, 11 октября 2018 г., 16:26:57 UTC+2 пользователь Xiaoming 
>>>>>> Wang написал:
>>>>>>>
>>>>>>> Hi Vladimir,
>>>>>>>
>>>>>>> Are you saying the option of printing MOs with eigenvector on is not 
>>>>>>> printing the MO coefficients?
>>>>>>>
>>>>>>> Best,
>>>>>>> Xiaoming
>>>>>>>
>>>>>>> On Thursday, October 11, 2018 at 9:36:49 AM UTC-4, Vladimir Rybkin 
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Dear Xiaoming,
>>>>>>>>
>>>>>>>> by default CP2K does not print MO coefficients. It prints the 
>>>>>>>> basis, which is Cartesian (e.i. 6 d orbitals instead of 5). So, 
>>>>>>>> input/output would be helpful.
>>>>>>>>
>>>>>>>> Yours,
>>>>>>>>
>>>>>>>> Vladimir
>>>>>>>>
>>>>>>>> четверг, 11 октября 2018 г., 15:24:16 UTC+2 пользователь Xiaoming 
>>>>>>>> Wang написал:
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I just missed one thing. The MOs could also be printed with 
>>>>>>>>> spherical coordinates. Then, it should be consistent.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Xiaoming
>>>>>>>>>
>>>>>>>>> On Thursday, October 11, 2018 at 9:21:56 AM UTC-4, Xiaoming Wang 
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Vladimir,
>>>>>>>>>>
>>>>>>>>>> Thanks for your reply. I'm wondering why the eigenvectors and 
>>>>>>>>>> overlap are not using the same basis (or with same basis but different 
>>>>>>>>>> coordinates).
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> Xiaoming
>>>>>>>>>>
>>>>>>>>>> On Thursday, October 11, 2018 at 4:28:32 AM UTC-4, Vladimir 
>>>>>>>>>> Rybkin wrote:
>>>>>>>>>>>
>>>>>>>>>>> Dear Xiaoming,
>>>>>>>>>>>
>>>>>>>>>>> the 6 d orbitals correspond to the six components in the 
>>>>>>>>>>> Cartesian coordinates, whereas 5 d orbitals are the same expressed is 
>>>>>>>>>>> spherical coordinates. The coordinate transformation is involved in 
>>>>>>>>>>> between. 
>>>>>>>>>>>
>>>>>>>>>>> Yours,
>>>>>>>>>>>
>>>>>>>>>>> Vladimir
>>>>>>>>>>>
>>>>>>>>>>> среда, 10 октября 2018 г., 16:16:56 UTC+2 пользователь Xiaoming 
>>>>>>>>>>> Wang написал:
>>>>>>>>>>>>
>>>>>>>>>>>> Hello,
>>>>>>>>>>>>
>>>>>>>>>>>> I'd like to check the equation C^T S C = 1, where C is MO 
>>>>>>>>>>>> coefficient and S the overlap matrix. 
>>>>>>>>>>>> However, for my test calculation, C is 54*1 while S is 52*52. I 
>>>>>>>>>>>> checked the basis details, for the
>>>>>>>>>>>> MO coefficient, there are 6 d orbitals 
>>>>>>>>>>>> (dx2,dxy,dxz,dy2,dyz,dz2), while for the overlap matrix,
>>>>>>>>>>>> only 5 d orbitals (d-2,d-1,d0,d+1,d+2) are printed. Why is like 
>>>>>>>>>>>> that? Am I missing something?
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> Xiaoming 
>>>>>>>>>>>>
>>>>>>>>>>>
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