Re: colvars: How to implement a collective variable of vector type?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 13 2018 - 09:07:18 CDT

Hi Haochuan,

1. The "atom" class only has a single field "grad" for the gradients of a
scalar variable. There is no general mechanism for storing gradients of
vector variables (I'm working on that very slowly and sporadically). I
would recommend allocating inside your new class several STL vectors of 3D
vectors (cvm::rvector), and storing their pointers in a container of your
choosing. This is what is done for the quaternion variable, in the
cvm::rotation class. This will be easier to port to the new general
mechanism that will some time see the light of day.

The implicit gradients flag tells the rest of the code about this
limitation, which affects for example computing the gradients of the
rotational fit. If your new variable is rotationally invariant (like e.g.
the angle between 3 COMs), you won't have to worry about that.

2. Yes, the applied force should have the same type as the variable. In
apply_force(), you should have a loop that projects a vector force onto the
atomic gradients that you are maintaining (step 1).

Giacomo

On Tue, Mar 13, 2018 at 4:12 AM, yjcoshc <yjcoshc_at_gmail.com> wrote:

> Hi Giacomo,
>
> Thanks for your reply! My collective variable is a 3D vector like
> (k0,k1,k2) and I know how to calculate (dk0/dri,dk1/dri,dk2/dri) where ri
> is the Cartesian coordinate of i-th COM. Now I encounter some other
> problems:
>
> 1. What is implicit gradients? It looks all vector or quaternion based
> colvars use enable(f_cvc_implicit_gradient) and have empty
> calc_gradients(). How do I choose which features in features_cvc enum to
> be enabled? Should I use some additional member variable to store the
> gradients other than atom_group->grad?
>
> 2. What is the type of the force in apply_force(colvarvalue const &force) ?
> Is the force a 3D vector like (f0,f1,f2) or just any type defined in the
> Type enum?
> Haochuan chen
>
>
> 在 2018年03月12日 20:13, Giacomo Fiorin 写道:
>
> Hi Haochuan, yes, that's because not finding the keyword "groupN" is
> considered an error, and it normally would be.
>
> You could either:
> (1) Add a keyword to set the number of groups in the configuration (
> numGroups?).
> (2) Use the lower-level parsing function colvarparse::key_lookup() to
> test whether the keyword "groupN" is used before attempting to parse it.
> You probably don't need to call key_lookup() with more than two arguments,
> if you only use it to test the availability of the keyword.
>
> Regarding using scriptedFunction in Tcl, yes, a vector is represented by a
> Tcl list.
>
> Giacomo
>
> On Mon, Mar 12, 2018 at 6:01 AM, yjcoshc <yjcoshc_at_gmail.com> wrote:
>
>> Hi Giacomo,
>>
>> Is there any way to parse unlimited atom groups (group1,...,groupN)? I
>> decide to write a loop checking groupN by cvc::parse_group and break the
>> loop when cvc::parse_group return NULL, but cvc::parse_group seems raising
>> an error when groupN is not defined.
>>
>> Haochuan Chen
>>
>> 在 2018年03月11日 20:05, Giacomo Fiorin 写道:
>>
>> Hi Haochuan, you need to derive a new class from the colvar::cvc, whose
>> structure is described here.
>> http://colvars.github.io/doxygen/html/classcolvar_1_1cvc.html#details
>> The rest of the webpage shows you also the current inheritance structure
>> (what classes are derived from what).
>>
>> Among the variables that have vector values, a good example to take a
>> look at could be distance_pairs. Presumably you only need to wrap your C++
>> code in the correct functions, and add the calls that read coordinates or
>> send forces.
>>
>> See also:
>> http://colvars.github.io/doxygen/html/index.html
>> for documentation on the other classes.
>>
>> Giacomo
>>
>> On Sat, Mar 10, 2018 at 4:27 AM, yjcoshc <yjcoshc_at_gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I want to implement a vector collective variable in NAMD through the
>>> colvars module. It can calculate the least square fitted plane among
>>> multiple atomgroups and return the normal vector of the plane. The example
>>> pathCV script in colvartools folder seems scalar type only. Any suggestion
>>> of implementing a vector type one? I have finished a sample C++ code to
>>> calculate this. How do I incorporate it in colvars?
>>>
>>> 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
>>
>>
>>
>
>
> --
> 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
>
>
>

-- 
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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