Dipole moment, Polarizability, Bond orders

This page in the AMS manual describes the calculation of the dipole moment, the polarizability, and bond orders.

Properties
   DipoleMoment Yes/No
   Polarizability Yes/No
   BondOrders Yes/No
End

Note that because these properties are tied to a particular point on the potential energy surface, they are found on the engine output files. Note also that the properties are not always calculated in every PES point that the AMS driver visits during a calculation. By default they are only calculated in special PES points, where the definition of special depends on the task AMS is performing: For a geometry optimization properties would for example only be calculated at the final, converged geometry. This behavior can often be modified by keywords special to the particular running task.

Charges, Dipole Moment, Polarizability

Properties
   Charges Yes/No
   DipoleMoment Yes/No
   DipoleGradients Yes/No
   Polarizability Yes/No
End
Properties
Charges
Type:Bool
Default value:No
Description:Requests the engine to calculate the atomic charges.
DipoleMoment
Type:Bool
Default value:No
Description:Requests the engine to calculate the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
DipoleGradients
Type:Bool
Default value:No
Description:Requests the engine to calculate the nuclear gradients of the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
Polarizability
Type:Bool
Default value:No
Description:Requests the engine to calculate the polarizability tensor of the system.

Bond orders & Molecule detection

Many engines can determine bond orders between atoms. For engines based on force fields, these might just be the bond orders used internally by the force field, while for quantum mechanical engines the bond orders are usually determined by analyzing the results of the quantum mechanical calculation, e.g. the electronic density. We refer users to the manuals of the respective engine for details.

Properties
   BondOrders Yes/No
End
Properties
BondOrders
Type:Bool
Default value:No
Description:Requests the engine to calculate bond orders. For MM engines these might just be the defined bond orders that go into the force-field, while for QM engines, this might trigger a bond order analysis based on the electronic structure.

Based on the bond orders, the AMS driver can analyze the atomic connectivity graph in order to determine which sets of atoms together constitute molecules. This allows for example to monitor the changes in molecular composition during a reactive molecular dynamics calculation. For molecular dynamics calculations this option is enabled by default. For other tasks the molecular analysis can explicitly be requested in the Properties block.

Properties
   Molecules Yes/No
End
Properties
Molecules
Type:Bool
Default value:No
Description:Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.

Details of the molecule detection are configured in a dedicated block:

Molecules
   AdsorptionSupportRegion string
   BondOrderCutoff float
End
Molecules
Type:Block
Description:Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
AdsorptionSupportRegion
Type:String
GUI name:Adsorption support region
Description:Select region that will represent a support for adsorption analysis. Adsorbed molecules will receive an ‘(ads)’ suffix after name of the element bonded to the support. Such elements will be listed separate from atoms of the same element not bonded to the support, for example, HOH(ads) for a water molecule bonded to a surface via one of its H atoms.
BondOrderCutoff
Type:Float
Default value:0.5
Description:Bond order cutoff for analysis of the molecular composition. Bonds with bond order smaller than this value are neglected when determining the molecular composition.