Developers.Variables.molecule

Variable "molecule{.}" in MolDynSim

This variable characterizes each molecular species to be used in all of the MolDynSim programs. Every entry of the cell vector is a structured variable that should initially contain the following fields :

Settable parameters

field	description
type	type of molecular species, used for labeling, e.g., 'water' (character string)
n_mol	number of molecules of this species (integer)
n_froz	Optional: The last n_froz molecules of this species can be frozen. (integer, between 0 and n_mol, default=0)
n_atom	number of atoms in each molecules of this species (integer)
atomtype	atom types, e.g., {'O' 'H' 'H'} (row cell(!) vector of strings indicating chemical elements)
mass	atomic masses (row vector of real numbers, length n_atom)
geometry	positions of all atoms inside a molecule (n_dim * n_atom matrix). Not required for monatomic species.

Internal variables

field	description
n_thaw	The first n_thaw molecules of this species are not frozen: n_mol-n_froz (integer, between 0 and n_mol, default=n_mol)
frozen	coordinates of all frozen atoms (3-dim arrays). Only if n_froz>0