[CP2K-user] [CP2K:21985] Re: input files for geomtery optimization + normal mode calculations, DFT/B3LYP/6-31G(d, p))
Darek
darek.boczar at gmail.com
Sat Nov 22 09:52:25 UTC 2025
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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