Architecture of Chemist

Statement of Need summarizes what Chemist needs to do. The point of this page is to use these needs to motivate the architecture of Chemist.

Architecture Considerations

The Chemist library will include abstractions used to define a DSL for describing the inputs and outputs of computational chemistry routines. In designing Chemist we have grouped the needed abstractions into the following categories:

Chemical system.

It is natural to express the phenomena we want to describe using chemistry concepts (think nuclei, atoms, molecules, etc.). Hence many users will feel most comfortable specifying their problem in terms of these chemical concepts.

• This component is responsible for describing how the user wants to model the system. For example: Are the atoms being treated classically (i.e., a composite particle with an overall charge)? Is the molecule subjected to the Born-Oppenheimer approximation (i.e., do the electrons move about in the field of the nuclei)?

• Different representations should have different classes. The shear number of possible classes justifies the existence of a component.

Atomic orbital (AO) basis set.

Gaussian-based quantum chemistry relies on AO basis sets. This component provides the abstractions necessary to represent AO basis sets.

• A traditional AO basis set has many levels (primitive, contracted Gaussian, etc.) which in turn requires many classes, justifying the existence of a component.

• N.b. many methods which don’t use Gaussian basis sets still need chemical system objects, which is the motivation for decoupling this from the chemical system component.

Fragmenting

There are a variety of computational chemistry methods which rely on selecting or partitioning the chemical system and/or the basis set. The pieces of the chemical system are usually called fragments, which gives rise to the name of this component.

• While say a std::vector<ChemicalSystem> representation seems reasonable at first, there are performance implications with such a choice, particularly when there are a lot of fragments. We need specialized containers to hold the pieces performantly.

• Fragmenting gives rise to other considerations such as needing to cap severed bonds. Such considerations can be decoupled from the chemical system component.

Quantum mechanics.

Quantum chemistry is predicated on the fact that chemistry can be fully described by the equations of quantum mechanics. Since we want to get an answer from quantum mechanics, it’s best to phrase the question in terms of quantum mechanical objects such as operators and wavefunctions. and we thus also need a software representation of quantum mechanical concepts.

Classical mechanics.

Quantum is expensive some mix of QM and classical mechanics is likely to be inevitable for the foreseeable future. We need the ability to seamlessly transition between domains. (TODO: this is supposed to motivate force-field like classes)

Architecture Overview

Fig. 2 High-level architecture of the Chemist library indicating the major components and dependencies.

The overall architecture of Chemist is depicted in Fig. 2 and the individual components are summarized below.

Chemical system component

Main Discussion: Design of the Chemical System Component.

As summarized in Architecture Considerations, users of computational chemistry software typically come to the software with questions like:

• What is the energy of this system vs. this other system?

• What is the minimum energy geometry of this system?

• What does the Raman spectrum of this system look like?

• How strongly does this system interact with this other system?

The key point is these questions revolve around computing the properties of one or more “chemical systems.” The point of the chemical system component is to provide the user with the abstractions necessary to fully describe the system they want to compute properties of.

AO basis set component

Main Discussion: Design of the AO Basis Set Component.

TODO: Write me!!!

Fragmenting component

Main Discussion: Design of the Fragmenting Component.

Quantum chemistry is computationally expensive. There are a number of approximations (e.g., QM/MM, ONIOM, and methods based on the MBE) which seek to circumvent this expense by breaking the system into “fragments.” There are also methods such as SAPT and density embedding which require partitioning the chemical system. The point is we need the ability to decompose members of the chemical system component (and potentially other components as well).

The fragmenting component contains abstractions which facilitate working with subsets of chemical system objects. For example Fragmented<Nuclei> represents the relationship among a superset Nuclei object and subsets of that object. The fragmenting component also contains classes like Cap which arise because fragmenting can “break” covalent bonds.

Quantum mechanics component

Main Discussion: Design of the Quantum Mechanics (QM) Component.