Re: colvars: make an extended CV periodic

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sun Apr 08 2018 - 09:46:23 CDT

Sorry about that, indeed with the new option that dependency needed to be
changed. Please check out my latest commit.

Best,
Jerome

On 7 April 2018 at 04:21, <yjcoshc_at_gmail.com> wrote:

> 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/431e52a11f34ccef1329396f91314c
> 6e56146a53
>
> 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
>>
>>
>>
>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 12 2019 - 23:19:42 CST