[CP2K-user] dimension inconsistency of the overlap and MO coefficients
Xiaoming Wang
wxia... at gmail.com
Fri Oct 12 12:53:59 UTC 2018
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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