ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
7.15.10 Making your own constraint class
A constraint class must have these two methods:
constraints.adjust_positions(oldpositions, newpositions)
Adjust the newpositions array inplace.
constraints.adjust_forces(positions, forces)
Adjust the forces array inplace.
A simple example:
import numpy as np
class MyConstraint:
"""Constrain an atom to move along a given direction only."""
def __init__(self, a, direction):
self.a = a
self.dir = direction / sqrt(np.dot(direction, direction))
def adjust_positions(self, oldpositions, newpositions):
step = newpositions[self.a] - oldpositions[self.a]
step = np.dot(step, self.dir)
newpositions[self.a] = oldpositions[self.a] + step * self.dir
def adjust_forces(self, positions, forces):
forces[self.a] = self.dir * np.dot(forces[self.a], self.dir)
7.15.11 The Filter class
Constraints can also be applied via filters, which acts as a wrapper around an atoms object. A typical use case will
look like this:
------- -------- ----------
| | | | | |
| Atoms |> atoms = Atoms(...)
>>> filter = Filter(atoms, ...)
>>> dyn = Dynamics(filter, ...)
This class hides some of the atoms in an Atoms object.
class constraints.Filter(atoms, indices=None, mask=None)
You must supply either the indices of the atoms that should be kept visible or a mask. The mask is a list of
booleans, one for each atom, being true if the atom should be kept visible.
Example of use:
>>> from ase import Atoms, Filter
>>> atoms=Atoms(positions=[[ 0 , 0 , 0],
... [ 0.773, 0.600, 0],
... [-0.773, 0.600, 0]],
... symbols=’OH2’)
>>> f1 = Filter(atoms, indices=[1, 2])
>>> f2 = Filter(atoms, mask=[0, 1, 1])
>>> f3 = Filter(atoms, mask=[a.Z == 1 for a in atoms])
>>> f1.get_positions()
[[ 0.773 0.6 0. ]
[-0.773 0.6 0. ]]
142 Chapter 7. Documentation for modules in ASE