Building Molecules

Input structures are defined by AtomsBase, but internally calculations are done with a structure called Cluster. It is AtomsBase compatible and you can convert back and forth and use it where AtomsBase structures can be used. Atoms base is exported by PotentialCalculation, so there is no need to load it.

While you can create Cluster directly, it is recommended that you use AtomsBase to create structures. You can e.g. use AtomsIO to load data molecule or just create molecules by hand on the fly.

Example

using PotentialCalculation
using AtomsIO

# Load from file with AtomsIO
system = load_system("molecule.xyz")

# Convert to Cluster
csystem = Cluster(system)

# Convert back to AtomsBase standard structure
fsystem = FlexibleSystem(csystem)

# Create structure by hand
N2 = isolated_system( [Atom(:N, [1., 0., 0.].*u"Å"), Atom(:N, [0., 0., 0.].*u"Å")] )