Developers.Structures.Main

Data structures used in MolDynSim

The most important variables are the coordinates of the atoms. (Velocities, forces, etc, are treated similarly). They are stored in two different schemes with conversions where appropriate

• matrix structure to hold atomic coordinates, without explicit reference to molecules or species

  q(dim,atom)

• cell vector to hold coordinates, with explicit reference to molecules and species

  q{species}(dim,atom,mol)

Conversion function

• from cell to matrix

• from matrix to cell