Re: colvars: make an extended CV periodic

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Apr 06 2018 - 13:05:07 CDT

+1!

On Fri, Apr 6, 2018 at 1:47 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Haochuan,
>
> This was not implemented, but it did seem to be a good suggestion.
>
> I have just committed the following change:
> https://github.com/Colvars/colvars/commit/431e52a11f34ccef1329396f91314c
> 6e56146a53
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Colvars_colvars_commit_431e52a11f34ccef1329396f91314c6e56146a53&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=sCG0xwB9Mh4SHYbNwCAso_CpfkkVSVBP6S4Q8E8UgqM&s=aAOxAFqFbg0K75ikvRt87f-naNz2ReSiM1RgkJAGSx4&e=>
>
> Now, scripted and custom function colvars accept the keywords *period* and
> *wrapAround*, to manually define them as periodic.
>
> Please test it and tell me if it works in your case.
>
> Best,
> Jerome
>
> On 6 April 2018 at 05:42, yjcoshc <yjcoshc_at_gmail.com> wrote:
>
>> Hello,
>>
>> I have defined a scripted function to calculate a collective variable
>> through the Colvars module. This function uses atan2 and have a period
>> ranged from -180.0 to 180.0. Now I enable the extended lagrangian dynamics,
>> but the extended CV looks not periodic. Is there any way to make the
>> extended CV periodic following the scripted function? (For example, wrap
>> the extended CV to 175 if it is -185)
>>
>> Thanks,
>>
>> Haochuan Chen
>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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