input files for geomtery optimization + normal mode calculations, DFT/B3LYP/6-31G(d,p))

[Darek -]

Dear CP2K community,

I would like to use CP2K software to reproduce the results obtained with GAUSSIAN.

I would like to (i) optimize the geometry and (ii) calculate the normal modes (perform a vibrational analysis) for the molecule C20H22N8O6S2, characterised with the following atomic coordinates:

    S    -0.9348288137    1.7376071546    -0.2570119375
    S    -8.5585608658    -1.6464676835    0.3682299649
    O    -1.7225075170    -2.4392359635    0.7342302791
    O    5.6622419631    1.3122457843    1.1113174377
    O    0.9652905974    -3.1942561175    -0.3363487203
    O    2.1658590079    -2.3323000791    1.3665937632
    O    -4.9053238253    0.1673494117    -2.0463926347
    O    -4.4544493435    2.7626511207    0.2379754834
    N    6.3545677018    -0.4587005407    -0.2173058006
    N    -0.4169350061    -0.9115933817    -0.5569211969
    N    9.4893184194    1.4033386030    -0.1592059976
    N    -3.5658274844    -0.0051180853    -0.2025982838
    N    -5.6885165154    2.1721371832    0.5259183181
    N    -8.1321722706    0.8440732729    0.7945817183
    N    -7.0363906121    -1.0486351883    -0.0393578921
    N    -10.2999029178    0.2054481393    1.4678591822
    C    7.7930165612    -0.2143135270    -0.1716658051
    C    -1.1573409766    0.1792764349    -1.1905621796
    C    -2.4777133786    -0.6180481502    -0.8958502950
    C    8.3918274207    -0.1136621170    1.2686455991
    C    8.2402637597    1.1016089745    -0.8605544139
    C    5.7629413554    -1.4298637284    -1.1360479512
    C    9.1719475958    1.2144171484    1.2655995449
    C    4.2744882080    -1.4762775994    -0.7213993948
    C    -1.5663836612    -1.5577557543    -0.0680720881
    C    4.0716025858    -0.1943625484    0.0315586064
    C    5.4238465941    0.3368927791    0.4035861552
    C    0.8933804250    -0.8577504747    -0.0585808185
    C    1.5674965874    0.3257798306    0.0133754186
    C    0.9014451990    1.6520119865    -0.3441922521
    C    2.9759425706    0.5127570608    0.3634760559
    C    1.4231751897    -2.1709072151    0.4227074326
    C    -4.7170438553    0.3479662498    -0.8559959974
    C    -5.7802339700    0.9914077791    0.0248863957
    C    -7.0237244808    0.2344333237    0.2587938635
    C    -9.0780969978    -0.0503761848    0.9219919910
    H    8.2557508097    -1.0585499776    -0.6901466240
    H    -0.9003302047    0.3233656666    -2.2436882539
    H    -2.8751271072    -1.0778735441    -1.8043237475
    H    9.0589202460    -0.9618997498    1.4505744426
    H    7.6084764024    -0.1201450754    2.0277323384
    H    8.4138713866    0.9747068173    -1.9356106950
    H    7.4570829920    1.8630843159    -0.7155959013
    H    6.2534029772    -2.4044071516    -1.0347403146
    H    5.8815186564    -1.1032004513    -2.1801586531
    H    8.5304379131    2.0138676841    1.6714600705
    H    10.0909812875    1.1704579948    1.8605596531
    H    4.1026327029    -2.3209826434    -0.0425246521
    H    3.5956582393    -1.6006612694    -1.5729579051
    H    9.8046010548    2.3522733933    -0.3518809070
    H    1.2572463082    2.4200491362    0.3506538043
    H    1.2241001402    1.9694008035    -1.3440223345
    H    3.1977496713    1.4412646320    0.8921322369
    H    -3.4461485491    0.2673126885    0.7641005027
    H    1.2586806877    -4.0116269657    0.1086545502
    H    -4.5381784035    3.6359508941    0.6535919460
    H    -10.5286245204    1.1873855850    1.5623283595
    H    -11.0747019402    -0.3991506813    1.2341985330

Could you help me in preparing the synatctically correct input files to accomplish this task?
CP2K software offers mamy default options and thus I am unsure which keywords must necessarily be included in the input files.
For instance, I am not sure whether I should include the &MOTION block in the input file to optimize the geomtery.
My intention is to perform the calculations using an all-electron potential (not pseudopotential) and obtain the normal modes saved in the MOLDEN format.

Hence, I would like to kindly ask for the support of an experienced CP2K user for the support in the preparation of working input files.

Thank you in advance,

Darek

[Marcella Iannuzzi]

Dear Derek, 

Have a look at the tutorials and materials available on line

For instance: https://manual.cp2k.org/trunk/methods/optimization/geometry.html

https://manual.cp2k.org/trunk/methods/dft/index.html

Regards

Marcella

[Darek]

Thank you for your answer.

I have known this websistes; nevertheless, I have still some unvertainties:

- the  RUN_TYPE should be obviously set to GEO_OPT. Hence, I wonder whether adding the &MOTION block with  &GEO_OPT sub-block is necessary if I prefer to rely on default parameters of CP2K?

- what would be a better approach to geometry optimization - to rely on traditional diagonalization or utilize orbital transformation (OT) methods, e.g. DIIS?

- the input file needs to contain information about the unit cell parameters. Meanwhile, I am interested in the analysis of a single molecule in a vacuum. Despite the fact that I sepcified PERIODOC as NONE, the program still urges me to speicfy the dimensions of a unit cell. Should I worry about it?