ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

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7.15 Constraints
ASE Manual, Release 3.6.1.2828
When performing minimizations or dynamics one may wish to keep some degrees of freedom in the system fixed.
One way of doing this is by attaching constraint object(s) directly to the atoms object.
Important: setting constraints will freeze the corresponding atom positions. Changing such atom positions can be
achieved:
• by directly setting the positions attribute (see example of setting Special attributes),
• alternatively, by removing the constraints first:
del atoms.constraints
or:
atoms.set_constraint()
and using the set_positions() method.
7.15.1 The FixAtoms class
This class is used for fixing some of the atoms.
class constraints.FixAtoms(indices=None, mask=None)
You must supply either the indices of the atoms that should be fixed or a mask. The mask is a list of booleans, one
for each atom, being true if the atoms should be kept fixed.
For example, to fix the positions of all the Cu atoms in a simulation with the indices keyword:
>>> c = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == ’Cu’])
>>> atoms.set_constraint(c)
or with the mask keyword:
>>> c = FixAtoms(mask=[atom.symbol == ’Cu’ for atom in atoms])
>>> atoms.set_constraint(c)
7.15.2 The FixBondLength class
This class is used to fix the distance between two atoms specified by their indices (a1 and a2)
class constraints.FixBondLength(a1, a2)
Example of use:
>>> c = FixBondLength(0, 1)
>>> atoms.set_constraint(c)
In this example the distance between the atoms with indices 0 and 1 will be fixed in all following dynamics and/or
minimizations performed on the atoms object.
This constraint is useful for finding minimum energy barriers for reactions where the path can be described well
by a single bond length (see the Dissociation tutorial).
Important: If fixing multiple bond lengths, use the FixBondLengths class below, particularly if the same atom is
fixed to multiple partners.
7.15. Constraints 139