ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

Reasonable values of the threshhold and spring constant for some common bonds are below.
Bond threshhold_length springconstant
O-H 1.40 5
C-O 1.79 5
C-H 1.59 7
C=O 1.58 10
Pt sublimation 0.94 2
Cu sublimation 0.97 2
7.15.8 The FixInternals class
ASE Manual, Release 3.6.1.2828
This class allows to fix an arbitrary number of bond lengths, angles and dihedral angles. The defined constraints are
satisfied self consistently. To define the constraints one needs to specify the atoms object on which the constraint
works (needed for atomic masses), a list of bond, angle and dihedral constraints. Those constraint definitions
are always list objects containing the value to be set and a list of atomic indices. The epsilon value specifies the
accuracy to which the constraints are fullfilled.
class constraints.FixInternals(atoms, bonds=[bond1, bond2], angles=[angle1], dihedrals=[dihedral1,
dihedral2], epsilon=1.e-7)
Example of use:
>>> bond1 = [1.20, [1, 2]]
>>> angle_indices1 = [2, 3, 4]
>>> dihedral_indices1 = [2, 3, 4, 5]
>>> angle1 = [atoms.get_angle(angle_indices1), angle_indices1]
>>> dihedral1 = [atoms.get_dihedral(dihedral_indices1), \
dihedral_indices1]
>>> c = FixInternals(atoms, bonds=[bonds1], angles=[angles1], \
dihedrals=[dihedral1])
>>> atoms.set_onstraint(c)
This example defines a bond an angle and a dihedral angle constraint to be fixed at the same time.
7.15.9 Combining constraints
It is possible to supply several constraints on an atoms object. For example one may wish to keep the distance
between two nitrogen atoms fixed while relaxing it on a fixed ruthenium surface:
>>> pos = [[0.00000, 0.00000, 9.17625],
... [0.00000, 0.00000, 10.27625],
... [1.37715, 0.79510, 5.00000],
... [0.00000, 3.18039, 5.00000],
... [0.00000, 0.00000, 7.17625],
... [1.37715, 2.38529, 7.17625]]
>>> unitcell = [5.5086, 4.7706, 15.27625]
>>> atoms = Atoms(positions=pos,
... symbols=’N2Ru4’,
... cell=unitcell,
... pbc=[True,True,False])
>>> fa = FixAtoms(mask=[a.symbol == ’Ru’ for a in atoms])
>>> fb = FixBondLength(0, 1)
>>> atoms.set_constraint([fa, fb])
When applying more than one constraint they are passed as a list in the set_constraint() method, and they
will be applied one after the other.
Important: If wanting to fix the length of more than one bond in the simulation, do not supply a list of
FixBondLength instances; instead, use a single instance of FixBondLengths.
7.15. Constraints 141