Introduction to structural properties

Before we get started, we will introduce a few concepts that underlie the concept and the usage of chemiscope. Chemiscope is designed to help navigating structure-property maps, i.e. 2D or 3D representations of a set of atomic scale entities that reflect how structure influences materials properties.

Chemiscope can work with two kinds of entities: full structures, or atom-centred environments. A structure consists in a set of atoms, possibly representing the periodic repeat unit of an infinite structure. An environment consists in a set of atoms that surround a central atom. In both cases, these entities are fully defined by the position and nature of the atoms present in the structure, or in the neighborhood of the environment center.

For each structure or environment, one may have computed properties, e.g. the cohesive energy of a molecule, or the NMR chemical shielding of a nucleus, or structural representations, i.e. functions of the spatial arrangement of the atoms that incorporate some fundamental symmetries to achieve a description of the structure that is as complete as possible, yet concise. Examples of such representations are for instance atom density representationis or Behler-Parrinello symmetry functions. These representations are usually high-dimensional vectors, hard to visualize and interpret. For this reason, one usually applies a dimensionality reduction algorithm, such as PCA, sketch-map, PCovR, etc. The interpretation of the resulting descriptor will differ depending on both the descriptor used to represent the structures or environments and the dimensionality reduction algorithm applied.

Chemiscope simplifies visualizing the correlations between structural representations and properties associated with structures and environments, by representing in an interactive fashion these atomic-scale entities as points on a map, and by associating these points with an explicit, 3D visualization of the structure of the material or molecule.

Illustration of the process used to create structural properties from a molecule.

Chemiscope is completly agnostic with respect to how properties and structural representations are generated, and do not provide any facilities to generate them. In the rest of this document, we will refer to properties describing the structure of an environment or structure as structural properties and other associated properties associated (such as energy, density, …) as physical properties.