Introduction

Glossary

• atom, point: a vector in real (typically, 3D) space defining the location and the metadata associated with this location. This gives us information about an individual small object in space.

  

• structure, cell, box: a set of points enclosed into a parallelogram and representing a snapshot of atoms in media (molecular, solid, liquid, etc.). A box is a way to describe how multiple atoms share the same space. This can simply be a list of coordinates, for example. Related classes: miniff.kernel.Cell, miniff.kernel.CellImages.

  

• potential, interaction, spring: a protocol (a function) taking atomic coordinates of two or three atoms (optionally, matching a set of conditions) and producing a single floating-point number. For example, potentials may describe how strongly atoms interact with each other.

  

• atomic environment: a single point picked in a structure. Atomic environment is a very abstract way of telling which interactions are important and how atoms are grouped by these interactions.

  

• partial energy, atomic energy, potential energy: a sum of all interaction values the chosen atom participates in. The potential energy value may be subject to double-counting issues when a single potential is shared between many atoms. Related classes: miniff.potentials.LocalPotential, miniff.ml.NNPotential.

  

• machine learning (ML) potential: a variant of the partial energy where the sum is replaced by a more complex process involving machine learning techniques.

  

• (total) energy: a sum of all atomic energies defining the cumulative energy accumulated in the structure and originating from attractions and repulsions of individual atoms. Predicting total energy from structures is the primary purpose of this package.

  

• (total) energy landscape: total energy as a function of one or more parameters of a structure. It is simply a way to look at the total energy as a scalar function of many variables.

  

• (total) energy minimum: a structure and the corresponding total energy minimum of the potential landscape. Finding potential energy minimum is one of the primary purposes of the total energy description.

  

• charge: a scalar belonging to atomic metadata with the properties of partial energy. Charges are used to treat long-range potentials which cannot be described by atomic environments. Charges are not necessary physical (Coulomb) charges: they may also be electronegativities or any other scalar property of an atom.

• force, stress: negative gradients of the total energy with respect to coordinates describing structures. Forces indicate the direction in a multidimensional space where the total energy becomes smaller.

  

• descriptors: a special sort of potential energy intended to describe atomic environments. Descriptors are typically defined by local environments. Unlike potentials, descriptor functions usually have a simple smooth form.