[CP2K-user] [CP2K:22281] Re: Axial ligand-related issues in XAFS calculations

[Nan Dong]

Hi Eason,

have you tried to make the x-axis (energy interval) as the same with your 
FDMNES png. I tried with one of your CP2K results attached here. you can 
see you should have this pre-peak. If you plot them together, it could be 
more clear. The pre-peak is not a "problem" or "something wrong". 
Another option, with the same spectrum data, but use different broadening 
methods, and adjust the sigma. 
BTW, for the exact energy, TDDFT cannot give a correct excitation energy, 
so the rigid shift is needed. but the relative peaks positions should be 
fine. 

Best,
Nanchen 

在2026年6月11日星期四 UTC+2 10:11:58<Eason Jane> 写道：

> Dear  Nanchen
>    After reading this  literature, I have conducted the following tests: 
> (1) increasing the GRID Fex to 500 and 1000; (2) modifying the RI_REGION to 
> 6.0; and (3) performing both modifications simultaneously. However, the 
> resulting spectra do not show significant differences from previous ones. 
> Subsequently, I attempted to change the functional (as shown in the 
> figure), but the issue of a significant peak appearing before the main peak 
> remains unresolved. Could you please advise on what steps I should take 
> next?
>   Thank you in advance for your time and help.
> Eason
>
> 在2026年6月9日星期二 UTC+8 14:48:41<Nan Dong> 写道：
>
>>
>> Hi Eason,
>>
>> the GRID of Fe seems still small, you could check this 
>> https://doi.org/10.1021/acs.jpclett.5c02836 
>> It simulated Fe L-edge, and tested functionals (HF portions), basis-sets, 
>> RI REGION, and also GRID (LEBEDEV, RADICAL) in SI. 
>> Some factors influenced the shape of spectrum a lot. 
>>
>> Best,
>> Nanchen 
>>
>>
>> 在2026年6月9日星期二 UTC+2 08:28:37<Eason Jane> 写道：
>>
>> Dear Marcella
>>   I have already tried (1) changing the GRID to CUTOFF 500 and REL_CUTOFF 
>> 60; (2) changing the GRID Fex parameters to 200, 300; (3) increasing the 
>> RI_REGION to 5.0. However, none of these adjustments resulted in any 
>> significant changes in the values.  
>>   Thank you in advance for your time and help.
>> Eason
>>
>> 在2026年6月8日星期一 UTC+8 15:05:12<Marcella Iannuzzi> 写道：
>>
>>
>> Hi
>>
>> Have you tried to modify some settings in XAS_TDP like the GRID, the 
>> RI_REGION, the RI basis set?
>>
>> Regards
>> Marcella
>>
>> On Monday, June 8, 2026 at 7:51:44 AM UTC+2 easo... at gmail.com wrote:
>>
>> Dear  Marcella
>>
>>   After performing the calculation using FDMNES, I observed a small peak 
>> before the main peak (the black line). However, the spectrum obtained from 
>> the CP2K calculation (the blue line) shows a huge peak in the same region. 
>> This makes me suspect that the data for this peak might be incorrect, and I 
>> am also concerned that my parameter settings may be improperly configured. 
>> Therefore, I am seeking some assistance.  
>>   Thank you in advance for your time and help.
>> Eason
>> 在2026年6月6日星期六 UTC+8 22:29:13<Marcella Iannuzzi> 写道：
>>
>> Hi Eason
>>
>> What is exactly the problem. 
>> The output seems OK
>> Regards
>> Marcella
>>
>> On Thursday, June 4, 2026 at 10:34:02 AM UTC+2 easo... at gmail.com wrote:
>>
>> Dear Community，
>>   I would like to ask a question regarding a recent calculation. After 
>> adding an O2 molecule as an axial ligand to an Fe-N4 structure, the 
>> calculated XAFS spectrum using CP2K shows an intense peak at ~6999 eV. 
>> Could anyone kindly provide some insights into why this happens? I have 
>> found that this specific feature appears whenever the Fe center is bonded 
>> to O or S atoms. 
>>   （ GLOBAL ： RUN_TYPE ENERGY    theoretical method：PBEh_ADMM with HFX of 
>> 45.000 % without RI-HFX    basis set and 
>> pseudopotential：DZVP-MOLOPT-SR-GTH     OT   GAPW     TD-DFT 
>>    Fex ： POTENTIAL ALL  BASIS_SET：def2-TZVP）
>>   Thank you in advance for your time and help.
>> Eason
>>
>>

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