[CP2K-user] [CP2K:21987] Re: input files for geomtery optimization + normal mode calculations, DFT/B3LYP/6-31G(d, p))
Marcella Iannuzzi
marci.akira at gmail.com
Sun Nov 23 09:18:25 UTC 2025
Hi Derek
- The default options in GEO_OPT are in general good enough
- Any wfn optimisation method is ok for GEO_OPT, as long as the forces
are correct, i.e. sufficiently tight SCF converge
- QS uses grids defined by the simulation cell
- WAVELET or MT
- No, copy the last coordinates into a new xyz and pass it to the TOPOLOGY
section. The wfn RESTART can be used
Regards
Marcella
On Saturday, November 22, 2025 at 12:51:02 PM UTC+1 Darek wrote:
> 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?
>
> - the next issue relates to the PIOSSON section. Should I add "PERIODIC
> none" in this section? Then, what is the most recommended PIOSSON_SOLVER
> for a non-periodic system (a single molecule)?
>
> - is there a possibility to reuse the SCF results from the first step
> (geometry optimization) in the second step (normal mode analysis)? These
> calculations are related to each other by copying the optimized coordinates
> from the xyz file generated in the first step to the input file of
> vibrational analysis. Maybe there exists a better way to connect them?
>
> środa, 19 listopada 2025 o 11:03:16 UTC+1 Marcella Iannuzzi napisał(a):
>
>> 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
>>
>>
>>
>> On Monday, November 17, 2025 at 9:22:17 AM UTC+1 Darek wrote:
>>
>>> 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 <(737)%20607-1546>
>>> -0.2570119375
>>> S -8.5585608658 -1.6464676835 <(646)%20467-6835> 0.
>>> 3682299649 <(368)%20229-9649>
>>> O -1.7225075170 -2.4392359635 0.7342302791
>>> <(734)%20230-2791>
>>> O 5.6622419631 <(662)%20241-9631> 1.3122457843
>>> <(312)%20245-7843> 1.1113174377
>>> O 0.9652905974 -3.1942561175 -0.3363487203
>>> <(336)%20348-7203>
>>> O 2.1658590079 -2.3323000791 1.3665937632
>>> O -4.9053238253 0.1673494117 -2.0463926347
>>> O -4.4544493435 2.7626511207 0.2379754834
>>> N 6.3545677018 <(354)%20567-7018> -0.4587005407
>>> <(458)%20700-5407> -0.2173058006 <(217)%20305-8006>
>>> N -0.4169350061 <(416)%20935-0061> -0.9115933817
>>> -0.5569211969
>>> N 9.4893184194 1.4033386030 <(403)%20338-6030>
>>> -0.1592059976
>>> N -3.5658274844 -0.0051180853 -0.2025982838
>>> <(202)%20598-2838>
>>> N -5.6885165154 2.1721371832 0.5259183181
>>> <(525)%20918-3181>
>>> 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 <(214)%20313-5270>
>>> -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
>>> <(860)%20554-4139>
>>> C 5.7629413554 <(762)%20941-3554> -1.4298637284
>>> -1.1360479512
>>> C 9.1719475958 1.2144171484 <(214)%20417-1484> 1.2655995449
>>> C 4.2744882080 -1.4762775994 -0.7213993948
>>> C -1.5663836612 <(566)%20383-6612> -1.5577557543
>>> <(557)%20755-7543> -0.0680720881
>>> C 4.0716025858 -0.1943625484 0.0315586064
>>> C 5.4238465941 0.3368927791 0.4035861552 <(403)%20586-1552>
>>> C 0.8933804250 -0.8577504747 <(857)%20750-4747>
>>> -0.0585808185
>>> C 1.5674965874 <(567)%20496-5874> 0.3257798306 0.0133754186
>>> C 0.9014451990 1.6520119865 -0.3441922521
>>> C 2.9759425706 0.5127570608 0.3634760559 <(363)%20476-0559>
>>> C 1.4231751897 -2.1709072151 0.4227074326
>>> C -4.7170438553 0.3479662498 <(347)%20966-2498> -0.
>>> 8559959974 <(855)%20995-9974>
>>> 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 <(323)%20365-6666>
>>> -2.2436882539
>>> H -2.8751271072 -1.0778735441 -1.8043237475
>>> <(804)%20323-7475>
>>> H 9.0589202460 -0.9618997498 1.4505744426
>>> <(450)%20574-4426>
>>> H 7.6084764024 <(608)%20476-4024> -0.1201450754
>>> 2.0277323384
>>> H 8.4138713866 0.9747068173 -1.9356106950
>>> H 7.4570829920 1.8630843159 -0.7155959013
>>> <(715)%20595-9013>
>>> H 6.2534029772 <(253)%20402-9772> -2.4044071516
>>> <(404)%20407-1516> -1.0347403146
>>> H 5.8815186564 -1.1032004513 -2.1801586531
>>> H 8.5304379131 2.0138676841 1.6714600705
>>> H 10.0909812875 1.1704579948 1.8605596531
>>> <(860)%20559-6531>
>>> H 4.1026327029 -2.3209826434 <(320)%20982-6434>
>>> -0.0425246521
>>> H 3.5956582393 -1.6006612694 <(600)%20661-2694> -
>>> 1.5729579051 <(572)%20957-9051>
>>> H 9.8046010548 2.3522733933 <(352)%20273-3933> -0.
>>> 3518809070 <(351)%20880-9070>
>>> H 1.2572463082 <(257)%20246-3082> 2.4200491362 0.3506538043
>>> <(350)%20653-8043>
>>> H 1.2241001402 1.9694008035 -1.3440223345
>>> H 3.1977496713 1.4412646320 <(441)%20264-6320> 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
>>> <(562)%20328-3595>
>>> 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
>>>
>>
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