Chemical System Design
The purpose of this page is to collect notes pertaining to the design of the
ChemicalSystem class and its affiliated classes.
What is a Chemical System?
Many quantum chemistry codes talk about the “molecule” as being the input to the code; however, in chemistry, molecules are simply sets of atoms. Even with the general definition adopted in What is a Molecule? there are often additional parts to the system being studied – for example external fields – that are not captured by the “molecule” concept. We define the chemical system to be the entire system we are trying to model. This will almost always include a molecule.
Chemical System Design Considerations
- Molecule
Following usual quantum chemistry conventions we define the molecule as all the atoms in the system, whether they are covalently bonded or not. In this sense a molecule is just a set of atoms. The molecule should describe the properties of the nuclei and the electrons comprising it.
- Periodicity
Periodic molecules (in the Molecule sense of the word) require one to specify the molecule (again in the Molecule sense) which forms the unit cell’s contents, as well as the shape of the unit cell.
- Fields
Rather than explicitly model the environment a molecular system is embedded in, we often treat that environment via a field. Important examples include:
Electric field, from say point charges
Magnetic field, from say an NMR experiment
Polarizable continuum, from PCM
Out of Scope Considerations
The considerations in this section were considered in the design, but ultimately ignored or thought to be better addressed by another component.
- Model parameters
In many cases it is a fine-line between model parameters and the system being modeled. Generally speaking we prefer to treat model parameters separate from the chemical system when they can be clearly distinguished. Of note the AO basis set is considered separately.