Re: Questions on implementing new collective variable in colvars.

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Jun 14 2017 - 07:26:16 CDT

Cartesian coordinates are a vector components with 3N scalar elements (x y
z for each atom), so if the component name is "c" the Lepton variable names
will be c1, c2, ..., c3N.

I don't have more examples of custom functions, but if you have a specific
request I can suggest the syntax to use.

Jerome

On 14 June 2017 at 03:36, yjcoshc <yjcoshc_at_gmail.com> wrote:

> Hi,
>
> I decided to call C in the TCL script. The new Lepton expression seems
> worth trying. I read the documents but still I am not sure how to use it
> with Cartesian coordinates. Are there more examples of custom functions?
>
> Thank you for your reply,
>
> yjcoshc
>
> 在 2017年06月13日 23:32, Jérôme Hénin 写道:
>
> Hi,
>
> There are many possible strategies.
>
> 1) writing a new C++ derived class of "colvarcomp".
>
> 2) writing a separate C code and calling it through a Tcl scripted
> variable (may or may not give a significant performance improvement).
>
> 3) Depending on your specific variable, you might get good results with
> the new expression parser that uses the Lepton library.
> Check out the latest colvars and NAMD codes, and see "custom functions" in
> the documentation.
>
> Jerome
>
> On 12 June 2017 at 23:48, yjcoshc <yjcoshc_at_gmail.com> wrote:
>
>> Hi,
>>
>> Is that means if I write a new CV then I should modify the colvarcomp.h
>> and recomplie the whole NAMD?
>>
>> Can the colvars module load external .so file and calculate the CV?
>>
>> Thanks,
>>
>> 在 2017年06月13日 11:38, Axel Kohlmeyer 写道:
>>
>>
>>
>> On Mon, Jun 12, 2017 at 11:14 PM, yjcoshc <yjcoshc_at_gmail.com> wrote:
>>
>>> Hello everyone,
>>>
>>> Someone has asked me to write a new collective variable using the
>>> colvars module in NAMD. Is there a C++ interface in colvars? I know how to
>>> implement it in TCL but I am not familiar with TCL and C++ may be faster.
>>>
>>
>> ​colvars is implemented in C++. please see ​http://colvars.github.io/
>>
>> axel.
>>
>>
>>
>>>
>>> Thanks,
>>>
>>> yjcoshc
>>>
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>>
>
>

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