Energy Expression

In general the forcefield plug-in should combine the forcefield parameters and the structure to create an energy expression in the general data structures that SEAMM provides. This may not be possible in all cases, in which case the plug-in should create the description for the simulation codes it is compatible with.

The advantage of using the structures in SEAMM for the energy expression is that any plug-in can use the energy expression to calculate the energy, forces, etc. for the system by translating the generic energy expression to the form needed by a specific simulation code as long as the simulation code is capable of handling the functional form of the forcefield.


We need to add metadata to say whether the plug-in can create the general SEAMM energy expression as well as any code-specific implementations, such as the AMBER parameter/topology file.

Assuming that the plug-in can create the generic SEAMM energy epxression, the class needs to provide a method energy_expression that creates the energy expression. See XXXX for the documentation of the energy expression within SEAMM.


We need to bite the bullet and document the energy expression class and perhaps data structure, though perhaps it is wiser to hide the implementation using the class to access the underlying data.

If we want to store energy expressions, or think that they might be too large for memory, perhaps we should explore on-disk storage such as MDF5 or SQLite.