Classes

  • namespace bond Functions for bond-related analyses This namespace contains functions that are used for determining the hydrogen bonds, or lists of bonded atoms for write-outs to data files and visualization.
  • namespace cage Functions for topological network criteria cage types. This namespace contains structs and enums for cage types.
    • struct Cage This contains a cage, with the constituent rings.
  • namespace chill CHILL and CHILL+ structure classification. This namespace contains functions that are used in the CHILL/CHILL+ classification scheme, as well as a yodaCloud struct to hold all the information.
    • struct QlmAtom This is the local orientational bond order parameter $q_{lm}$ , of length $2l+1$ .
    • struct YlmAtom This contains a complex vector of length $2l+1$ .
  • namespace clump Clustering functions. This namespace contains functions that are used in the for clustering ice-like particles.
  • namespace gen Small generic functions that are shared by all namespaces.
  • namespace molSys Bare-bones structs used throughout the architecture. This namespace defines Point and PointCloud structs, alongwith other basic functions and enums.
    • struct Point This contains per-particle information.
    • struct PointCloud This contains a collection of points; contains information for a particular frame.
    • struct Result This contains the bond classifier of enum type bond_type, and the bond correlation factor.
  • namespace nneigh Functions for building neighbour lists. This namespace contains functions that build neighbour lists (using brute-force), saving either the atom IDs or atom indices (according to a PointCloud) in a row-ordered vector of vectors.
  • namespace primitive Functions for generating primitive rings. This namespace contains struct definitions and functions that are used for generating primitive (shortest-path) rings (directed cyclic graphs).
    • struct Graph This is a per-frame object, containing all the vertices for the particular frame, along with the vector of rings generated.
    • struct Vertex This is a collection of elements, for each point, required for graph traversal.
  • namespace rdf2 Defines RDF-specific functions.
  • namespace ring Topological network criteria functions. This namespace contains functions for the topological network criteria for bulk and confined systems both.
  • namespace sinp Functions for the d-SEAMS readers. This namespace contains functions that are used for reading in the formats supported by d-SEAMS. LAMMPS trajectory files and XYZ files are currently supported, though it is recommended to use LAMMPS trajectory files, since the simulation box size etc. are not normally present in XYZ files, and many analyses may fail without the correct box dimensions.
  • namespace sph Functions used for spherical harmonics.
  • namespace std STL namespace.