cp2k COMBINE_COLVAR/FUNCTION define exponential form function

Sun Tao taosun... at gmail.com
Fri Jan 20 16:56:09 CET 2017


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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