[CP2K-user] [CP2K:22282] Re: Axial ligand-related issues in XAFS calculations

[Eason Jane]

Dear  Nanchen
  Thank you for your guidance. I will look into adjusting it accordingly.
Best regards
Eason


在2026年6月11日星期四 UTC+8 16:44:31<Nan Dong> 写道：

>
> 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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