Terminology and Abbreviations

atomic basis set

An atomic (electronic) basis set describes the electrons on an isolated atom. Strictly speaking labels like “6-31G*” and “aug-cc-pVDZ” refer to atomic basis sets. Use of labels like “6-31G*” to label molecular basis sets is justifiable because there is often a straightforward mapping from the atomic basis set to the molecular basis set (see molecular basis set for more information).

chemical system

We use the term “chemical system” to refer to chemistry objects being simulated. A chemical system includes the set of atoms and the fields the atoms are embedded in. It’s the model of the experiment.

fragment

A distinction applied to a set of nuclei, a molecule, or a chemical system which establishes that the set of nuclei, molecule, or chemical system is a subset of another set of nuclei, molecule, or chemical system, respectively.

level of theory

In quantum chemistry a level of theory is the specification of an approximation to the Schroedinger equation. This requires specifying the approximate equations (e.g., Hartree-Fock, density functional theory, or coupled cluster) and the basis set in which the equations will be solved.

molecular basis set

An electronic basis set meant to describe a set of electrons interacting with multiple nuclei. The molecular basis set is usually just the union of the atomic basis set on each atom.

physics model

We use the term “physics model” to generalize the idea of a level of theory (which has quantum chemistry connotations) to whatever set of equations, parameters, and basis sets are being used to compute properties of the chemical system.

Abbreviations

API

Stands for application programming interface. This is the interface a program exposes so that it can be called by other software.

DFT

Stands for density-functional theory. DFT is usually differentiated from wavefunction-based theories.

DSL

Stands for domain-specific language. A DSL is a series of objects, and operations on those objects, which facilitates expressing ideas from a specific domain. For example, a quantum chemistry DSL should make it easy to build and construct quantum mechanical models of chemistry. Notably DSLs are used to express intent, they usually do not actually carry out the computation themselves.

MBE

The “many-body expansion”. The MBE is a mathematical identity which allows one to exactly express the property of a chemical system in terms of the properties of its subsystems.

ONIOM

Stands for “Our own N-layered Integrated molecular Orbital and Molecular mechanics”. The ONIOM method is a generalization of QM/MM, to an arbitrary number of methods.

QM/MM

Stands for “Quantum Mechanics/Molecular Mechanics”. QM/MM is a technique where part of a target system is modeled with quantum mechanics and the rest is modeled with molecular mechanics.

SAPT

Stands for symmetry adapted perturbation theory. SAPT is a technique for decomposing intermolecular interactions into their energetic components.

UI

Stands for user interface. This is how end users interact with a software component. The UI may be the same or different from the API (how other software interacts with the component).