| CI | Coverage | License |
|---|---|---|
|
|
|
This package offers tools to create and manipulate atomic ensamble for molecular simulations.
- Parsing XYZ data
- Manipulation of atomic/geometric structure
- Properties such as center of mass, nuclear repulsion, nuclear dipoles and moments of inertia.
Read a string and convert into a vector of Atom objects
julia> water = Molecules.parse_string("""
O 1.2091536548 1.7664118189 -0.0171613972
H 2.1984800075 1.7977100627 0.0121161719
H 0.9197881882 2.4580185570 0.6297938830
""")
julia> water[1]
Oxygen Z = 8 M = 15.9990
Center: 1.2091536548 1.7664118189 -0.0171613972
Masses are taken from standard values, you can input the desired mass values as an extra column after the element symbol.
One can also create a Molecule object, where some information about the number of electrons, charge, and multiplicty are deduced.
julia> water = Molecule("""
O 1.2091536548 1.7664118189 -0.0171613972
H 2.1984800075 1.7977100627 0.0121161719
H 0.9197881882 2.4580185570 0.6297938830
""")
Molecule:
O 1.209153654800 1.766411818900 -0.017161397200
H 2.198480007500 1.797710062700 0.012116171900
H 0.919788188200 2.458018557000 0.629793883000
Charge: 0 Multiplicity: 1
Nuclear repulsion: 8.8880641743
julia> Molecules.nuclear_dipole(water)
3-element Vector{Float64}:
12.7914974341
18.3870231709
0.5046188773
julia> Molecules.center_of_mass(water)
3-element Vector{Float64}:
1.2483188267782848
1.8068607904101412
0.020676111103880096
Checkout our issue section for a list of desired features and milestone.