Re: colvars: make an extended CV periodic

From: yjcoshc_at_gmail.com
Date: Fri Apr 06 2018 - 21:21:12 CDT

Hi Jerome,

Thanks for adding this feature! I have tested it but got a dependency
error. This is the error log (in debug mode):

colvars:   DEPS: colvar arg enabling "scalar"
colvars:   DEPS: feature "scalar" in colvar arg enabled, ref_count = 1.
colvars:   DEPS: disabling feature "linear" in colvar arg
colvars:   DEPS: disabling feature "homogeneous" in colvar arg
colvars:   Looking for the keyword "period" and its value.
colvars:   Keyword value = "360.0".
colvars:   Looking for the keyword "period" and its value.
colvars:   Keyword "period" not found.
colvars:   # period = 360
colvars:   DEPS: colvar arg enabling "periodic"
colvars:   periodic requires self homogeneous
colvars:   DEPS: colvar arg enabling "homogeneous"
colvars:   Static feature "homogeneous" may not be enabled as a
dependency in colvar arg.
colvars:   ...required by "periodic" in colvar arg
colvars: Error: Failed dependency in colvar arg.
FATAL ERROR: Error in the collective variables module: exiting.

It looks the colvar is not "homogeneous". Any ideas?

Thanks again,

Haochuan Chen

在 2018年04月07日 01:47, Jérôme Hénin 写道:
> 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/431e52a11f34ccef1329396f91314c6e56146a53
>
> 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
> <mailto: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
>
>
>

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