Arithmetic operations on CVs

[em819]

Hi there,

I was wondering if it is at all possible in pysages to define new CVs through arithmetic operations on 2 or more "basic" CVs.
One example would be to define the difference of two distance-CVs, as is commonly done for chemical reactions and is possible with more mature packages like PLUMED.

I haven't found anything on that in the documentation, and the code also doesn't seem to suggest the existence of such a feature, but perhaps someone here knows more?

Best wishes,
Evgeny

[p-zubieta]

Hi em819,

We do not have an interface to do so in the same way that PLUMED does. The main reason being that it's relatively straight forward to write in pysages (we do it internally for some projects all the time). Say you want the difference between distances from atoms 0--1 and 1--2. One could write:

from pysages.colvars import Distance
from pysages.colvars.coordinates import distance
from pysages.colvars.core import FourPointCV

class DistancesDifference(FourPointCV):
    def __init__(self, indices):
        super().__init__(indices)

    @property
    def function(self):
        return lambda p1, p2, p3, p4: distance(p1, p2) - distance(p3, p4)

Then, when declaring the CV to be passed to the sampling method, one can write:

cvs = (
    DistancesDifference([0, 1, 1, 2]),
)

That being said, I think it would also be relatively easy for us to add an interface similar to PLUMED's.

[em819]

I understand, thank you for the clarification. I will then "hardcode" the difference-CV in the meantime as you suggest.