[CP2K-user] dimension inconsistency of the overlap and MO coefficients
Vladimir Rybkin
rybk... at gmail.com
Fri Oct 12 14:04:18 UTC 2018
Dear Xiaoming,
you need to do the following:
1) use DIAGONALIZATION ins SCF
2) in SCF use ADDED_MOS #very large number
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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