Find Potential Energy Minimum

Here we show how to find the minimum energy (acc. to a force field) position of a molecule in a crystal.

Example

For example, we wish to find the minimum energy (acc. to the UFF) position of a xenon adsorbate in SBMOF-1.

xtal = Crystal("SBMOF-1.cif")
molecule  = Molecule("Xe")
ljff = LJForceField("UFF")

# grid search to find min energy position.
#  gives good starting guess for optimization algorithm to fine tune.
resolution = 1.0 # resolution of grid points in Å
minimized_molecule, min_E = find_energy_minimum_gridsearch(xtal, molecule, ljff, resolution=resolution)
# minimized_molecule: xenon at its min energy position
# min_E: associated minimum energy of xenon (kJ/mol)

# fine tune the minimum energy position according to the grid search.
minimized_molecule, min_E = find_energy_minimum(xtal, minimized_molecule, ljff)
# output
Computing energy grid of Xe in SBMOF-1.cif
	Regular grid (in fractional space) of 13 by 7 by 24 points superimposed over the unit cell.
(Molecule species: Xe
Center of mass (fractional coords): Frac([0.01749943805846959; 0.9372916114895011; 0.011192272400742498;;])
Atoms:

	atom = Xe, xf = [0.017, 0.937, 0.011], -37.69376112588296)

detailed docs

PorousMaterials.find_energy_minimum — Function

minimized_molecule, min_energy  = find_energy_minimum(xtal, molecule, ljff) # molecule set at initial guess

find the minimum energy position, and associated minimum energy, of a molecule in a crystal. n.b. if molecule has more than one atom, it will not minimize over the orientation (rotations). the optimizer needs an initial estimate of the minimum energy position. pass molecule with good initial position. if you don't have a good initial position, use find_energy_minimum_gridsearch.

Arguments

xtal::Crystal: the crystal
molecule::Molecule: the molecule, whose position we seek to tune until we reach a local minimum. must start at a good initial position close to the minimum.
ljff::LJForceField: the force field used to calculate crystal-molecule interaction energies

Returns

minimized_molecule::Molecule{Frac}: the molecule at its minimum energy position
min_energy::Float64: the associated minimum molecule-crystal interaciton energy (kJ/mol)

source

PorousMaterials.find_energy_minimum_gridsearch — Function

xf₀ = find_energy_minimum_gridsearch(xtal, molecule, ljff; resolution=(50, 50, 50))

perform an energy_grid calculation and, via a grid search, find the minimum energy position of a molecule.

Arguments

xtal::Crystal: The crystal being investigated
molecule::Molecule{Cart}: The molecule used to probe energy surface
ljff::LJForceField: The force field used to calculate interaction energies
resolution::Union{Float64, Tuple{Int, Int, Int}}=1.0: maximum distance between grid points, in Å, or a tuple specifying the number of grid points in each dimension.

Returns

minimized_molecule::Molecule{Frac}: the molecule at its minimum energy position
min_energy::Float64: the associated minimum molecule-crystal interaciton energy (kJ/mol)

source