Developers.Variables.initial

Variable "initial" in MolDynSim

This variable characterizes the generation of initial geometries to be used in geometry optimization using MATLAB function mol_Optimize. It is a structured variable that should initially contain the following fields

field	description
handle	handle of function to be used for generation of initial coordinates.
...	further parameters may be required, depending on the choice of the function handle, see below

@ini.cuboid	random configuration inside a cuboid
box	Size of cuboid (vector of length n_dim)
overlap	Reject geometry if any distance goes below that value

@ini.fcc	face centered cubic lattice
lattice	Lattice constants (vector of length n_dim; identical entries)
n_cell	Number of elementary cells (vector of length n_dim)
substitution	substitute this many host particles with guest molecule (integer)

@ini.growth	Simulate cluster/crystal growth: read structure for n_mol-1 molecules and add one molecule randomly on surface of a sphere.
radius	Radius of that sphere
overlap	Reject geometry if any distance goes below that value
filename	filename (atom numbers appended automatically)
frame	index of frame (coming soon!)

@ini.hcp	hexagonal close packed lattice
lattice	Lattice constants (vector of length n_dim; identical entries)
n_cell	Number of elementary cells (vector of length n_dim)
substitution	substitute this many host particles with guest molecule (integer). Still to be checked!!!

@ini.read	read configuration from xyz data file
filename	filename (atom numbers appended automatically)
frame	index of frame (coming soon!)

@ini.rutile	rutile lattice
lattice	Lattice constants (vector of length n_dim)
n_cell	Number of elementary cells (vector of length n_dim)

@ini.spheroid	random configuration on the surface of a sphere
radius	Radius of that sphere
overlap	Reject geometry if any distance goes below that value