cp2k COMBINE_COLVAR/FUNCTION define exponential form function

Sun Tao taosun... at gmail.com
Sun Jan 22 21:34:53 CET 2017


I found that in the section XYZ_DIAG, there is a key word 
ABSOLUTE_POSITION, saying *If enabled, the absolute position of the atoms 
will be used. *
I think this will be the right option to me. Thanks very much for your 
reminding!

在 2017年1月20日星期五 UTC-6上午11:02:31,Marcella Iannuzzi写道:
>
> Hi, 
>
> yes, this would be an option. 
> Other possibilities are the DISTANCE_POINT_PLANE variable, or the 
> displacement variable, called XYZ_DIAG
> regards
> Marcella
>
>
>
> On Friday, January 20, 2017 at 4:56:09 PM UTC+1, Sun Tao wrote:
>>
>> Hi Marcella:
>>
>> Thanks for your response! Another question is how could I define a 
>> collective variable as the z-coordinate of a specific atom? In the COLVAR 
>> session I only found DISTANCE which defines the distance between 2 specific 
>> atoms and COORDINATION which defines the coordination number of a specific 
>> atom. I did not find anything like COORDINATES. Shall I fix the position of 
>> some atoms and use DISTANCE to define the z-coordinate? 
>>
>> Thanks ~
>>
>> Tao
>>
>>
>> Dear Tao,
>>>
>>> yes this is the right way, but please keep the same name of the variable 
>>> in the expression of the FUNCTION as the one you assign with the keyword 
>>> VARIABLES 
>>>
>>> regards
>>> Marcella
>>>
>>>
>>> On Friday, January 20, 2017 at 5:19:28 AM UTC+1, Sun Tao wrote:
>>>>
>>>> Dear All:
>>>>
>>>> I am trying to set up some collective variables in cp2k. I need to 
>>>> calculate the exponential-form value of a defined collective variable, 
>>>> which is the distance between certain 2 atoms, the form is as the following:
>>>>
>>>> f = 1/{1 + exp([distance(i, j) - 0.5]/1.5)}
>>>>
>>>> Shall I define the CV as the following?
>>>>
>>>>   &SUBSYS
>>>>     &COLVAR
>>>>        &COMBINE_COLVAR
>>>>           &COLVAR
>>>>              &DISTANCE
>>>>                 ATOMS 1 5
>>>>
>>>>              &END
>>>>           &END COLVAR
>>>>           FUNCTION 1/(1+exp((CV-0.5)/1.5))
>>>>           VARIABLES CV1 
>>>>           ERROR_LIMIT 1.0E-8
>>>>        &END
>>>>     &END
>>>>
>>>>    &END
>>>>
>>>>
>>>>
>>>> Or the correct form should be something else? Thanks ~
>>>>
>>>>
>>>> Tao
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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