Constrain angle metal/molecule in optimization geometry

[jalmeida]

Hello 

Please, I would like to optimize a system surface + molecule while maintaining the angle that the molecule makes with the surface. Is there a way to do it in QuantumATK?

I just found the class BondConstrain, but in that case I also have to constrain the bond length.

Best,
Joseane

[Anders Blom]

Not automatically or easily, no. If you want to keep the molecule rigid and in a particular orientation, maybe it is more efficient to scan various positions and record the total energy or forces, and run a manual minimization algorithm on that (like scipy.minimize). However, this requires that you program the geometry setup using a simple parameter like the surface-molecule distance, which is then the (only) parameter.you optimize.

[jalmeida]

Do you mean run the optimization in different angles? I would like to optimize the scattering region as usual but keeping a specific angle (the same from experiment).

 

[Anders Blom]

It's a tricky case since we don't have any angle constraint... It also depends on what we mean by angle, is it for the whole molecule, or a particular bond angle. Either way, I don't have a simple method to suggest.