[adf-list] Adflist Digest,Vol 35,问题6

Alexei Yakovlev. yakovlev在scm.com
3月22日星期三10:10:06 CET 2017

Dear Jinxiao Zhang,

Exactly in the case like yours, the π-π stacking dimer, you may want to 
use the MBH approach. The main difference with the partial Hessian 
approach is in the the Hessian matrix elements between the rigid part 
and the rest of the system. In the partial Hessian approach these 
elements are all zero while in the MBH they are computed explicitly. The 
difference usually translates to more accurate frequencies for modes 
that have a significant contribution from bonds that connect the rigid 
parts of your system with the rest.

As a matter of test I'd suggest you to calculate frequencies for a small 
system using all three approaches (full Hessian, MBH, and the partial 
Hessian) and compare the frequencies.

Kind regards,

Alexei


On 22/03/2017 09:26, 张金潇 wrote:
> Dear list:
> Thank you so much for your reply. But I think want I want is not MBH, I tried and it didn't work. I also tried the MBH examples in the manual. The selected region is just a rigid part in MBH, it can still move and contribute to frequencies, the frequencies of the rigid part are nonzero.
> Here is the problem, I want to calculate a π-π stacking dimer system, and freeze one molecule of the dimer. The frozen part should not allow to move and the frequencies should be zero. So what should I do to freeze one molecule of the dimer system and therefore the frozen part does not contribute to the total frequencies?
>
> Best regards.
>
> Jinxiao Zhang
>
>> -----原始福彩3d字迷-----
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>> 发送时间: 2017-03-21 19:00:01 (星期二)
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>> 主题: ADFlist Digest, Vol 35, Issue 6
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>> Today's Topics:
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>>     1. Freeze partial atoms in frequency calculation (张金潇)
>>     2. Re: Freeze partial atoms in frequency calculation (Fedor Goumans)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 20 Mar 2017 22:42:33 +0800 (GMT+08:00)
>> From: 张金潇 <jxzh at mail.ustc.edu.cn>
>> To: adflist at scm.com
>> Subject: [ADF-LIST] Freeze partial atoms in frequency calculation
>> Message-ID:
>> 	<44137491.74768.15aec2b6c41.Coremail.jxzh at mail.ustc.edu.cn>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear list;
>>
>>      I am doing frequency calculation with ADF-GUI and I want to freeze some atoms of the molecule and study the frequencies of the rest atoms.
>>
>>      I tried to freeze the atoms on ADF-GUI like this: Model------Geometry Constraints and Scan------freeze selected atoms,but I failed and I could still find the nonzero frequencies of the frozen atoms which I hope to be zero. Also, I tried Regions and Fragments, it didn’t work. I could not find anything about it in the manual, either.
>>
>>      So how can I freeze selected atoms and get the frequencies of the rest atoms?
>>
>>      Best regard!
>>     
>>
>>      Jinxiao Zhang
>>
>> Department of Chemical Physics
>>
>> University of Science and Technology of China
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>> Message: 2
>> Date: Mon, 20 Mar 2017 16:01:34 +0100
>> From: Fedor Goumans <goumans at scm.com>
>> To: adflist at scm.com
>> Subject: Re: [ADF-LIST] Freeze partial atoms in frequency calculation
>> Message-ID: <9efc9129-fb92-c409-dbf0-52c8b77fe2a5 at scm.com>
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>>
>> Dear Jinxiao Zhang,
>>
>> I think what you are looking for is the 'Partial Hessian' option, which
>> you can find in the Details => Frequencies panel.
>> You select the atoms you would want to calculate the Frequencies for and
>> click (+) next the 'Partial Hessian for'
>> (Or first add all and deselect the ones you don't want).
>>
>> Alternatively, you can use regions and freeze blocks with the Mobile
>> Block Hessian - this will give a better conditioned Hessian and should
>> give better frequencies than the Partial Hessian option.
>>
>> See more info here:
>> //www.tofoba.com/doc/ADF/Input/Frequencies.html#mobile-block-hessian-mbh
>>
>> Hope this helps.
>>
>> Best wishes,
>> Fedor
>>
>> On 3/20/2017 3:42 PM, 张金潇 wrote:
>>> Dear list;
>>>
>>> I am doing frequency calculation with ADF-GUI and I want to freeze
>>> some atoms of the molecule and study the frequencies of the rest atoms.
>>>
>>>   I tried to freeze the atoms on ADF-GUI like this: Model------Geometry
>>> Constraints and Scan------freeze selected atoms,but I failed and I
>>> could still find the nonzero frequencies of the frozen atoms which I
>>> hope to be zero. Also, I tried Regions and Fragments, it didn’t work.
>>> I could not find anything about it in the manual, either.
>>>
>>> So how can I freeze selected atoms and get the frequencies of the rest
>>> atoms?
>>>
>>> Best regard!
>>>
>>> Jinxiao Zhang
>>>
>>> Department of Chemical Physics
>>>
>>> University of Science and Technology of China
>>>
>>>
>>>
>>> _______________________________________________
>>> ADFlist mailing list
>>> ADFlist at scm.com
>>> //lists.tofoba.com/mailman/listinfo/adflist
>>
>> -- 
>> Dr. T. P. M. (Fedor) Goumans
>> Business Developer
>>  化学软件 & Materials
>> Vrije Universiteit, FEW, Theoretical Chemistry
>> De Boelelaan 1083
>> 1081 HV Amsterdam, The Netherlands
>> T +31 20 598 7625
>> //www.scm.com
>> //twitter.com/SCM_Amsterdam
>> //www.linkedin.com/company/software-for-chemistry-&-materials
>>
>>    
>>
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