calculate_potential(potential::AbstractPotential, cluster::AbstractCluster, indices)

Calculates energy from given potential. Needs to be implemented for each potential.

Arguments

• potential::AbstractPairPotential : potential
• cluster::AbstractCluster : molecule cluster
• indices : indices for atoms that represent potential

fit_potential!(solver, mpp::MoleculePairPotential, fdata::FitData)
fit_potential!(mpp::MoleculePairPotential, fdata::FitData)

Fits potential using given solver. If solver is not given use default solvers, which is LinearRegression().

Arguments

• solver : ScikitLearn solver
• mpp::MoleculePairPotential : potential
• fdata::FitData : data used in fitting

generate_initial_structure(args, kwargs)

Used to generate initial structures for MD runs

get_molecules(data::Dict)

Returns molecules from data file. This is usability function that is meant to simplify things.

get_potential!(potential, terms)

Function that sets potential term after potential has been fitted. That is this function transforms fitted term to potential terms. Needs to be implemented for each potential.

Arguments

• potential : used potential
• terms : terms from fitting method

give_as_potential(T, data)

Returns MoleculePairPotential{T} from given data that must have "c1_molecule" and "c2_molecule" fields

min_distance(points, c1::AbstractCluster, c2::AbstractCluster)

Minimum without needing fitted potential.

min_distance(mpp::MoleculePairPotential, points)

Gives minimum distance of molecules in mpp on given points. Used to help plotting.

plot_potential(points::AbstractVector, mpp::MoleculePairPotential; emax=100u"cm^-1")

Plots given potential on given points.

plot_potential(pes::Dict; mpp::MoleculePairPotential; emax=100u"cm^-1", marker=:circle)

Plots calculated potential values and fitted potential in same figure. pes is expected to be produced by PotentialCalculation or PotentialDB.

plot_potential(pes::Dict; emax=100u"cm^-1")

Plots calculated potential values. Input is expected to be produced by PotentialCalculation or PotentialDB.

potential_variables(mpp::MoleculePairPotential, points)

Used to transform cluster data to fittable form.

Arguments

• mpp::MoleculePairPotential : potential to be fitted
• points : array for clusters

Returns

Array holding an array for each potential term in mpp.topology that can the be used for fitting.

save_with_residue_data(fname, sys, res_name, indx_range)

Save structure sys in a CP2K QM/MM format to pdb file.

Background, CP2K needs QM- and MM-parts to have different residue names. This function add residue name res_name to atoms with index in indx_range and residue name "LIG" to all other atoms. The result is then saved to file fname - you should use pdb suffix.

scan_potential(args...; kwargs...)

Plot potentail and visualize structure.

Arguments

• data::Dict - Data generated by PotentialCalculation or PotentialDB
• mpp::MoleculePairPotential - (optional) fitted potential.

Keywords

• scale_radius=0.7 - Parameter for Van der Waals radius.
• emax=100u"cm^-1" - Maximum energy in plots. Defines also energy unit.
• extra_box_size=4 - How much extra space is in molecule visualization box.
• marker=:circle - Marker for calculated potential values.

set_atomic_symbol!(sys::FlexibleSystem, s, i::Int)

Changes atomic symbol of atom i. You can use this to edit the symbols so that it is possible to distinquish atoms to different groups in CP2K.

setweight_e_less!(data::FitData, w, emax)

Sets weigth when energy is more than given one.

Arguments

• data::FitData : data where weigth is adjusted
• w : new weigth
• emax : maximum energy

setweight_e_more!(data::FitData, w, emin)

Sets weigth when energy is more than given one.

Arguments

• data::FitData : data where weigth is adjusted
• w : new weigth
• emin : energy

visualize_points(points; stdout=devnull, stderr=devnull, command="vmd")

Visualize using external program.

rmsd(points, energy, mpp::MoleculePairPotential; emax=0u"cm^-1")

Calculates root mean square error for potential mpp.

Atributes

• points : points where potential is tested
• energy : referece energy for given points
• mpp::MoleculePairPotential : potential
• emax=0u"cm^-1" : cut points where energy is smaller than this

AbstractClusterPotential <: AbstractPotential

Potentials between groups of atoms

AbstractPairPotential  <: AbstractPotential

Potential that depends only on distance between two atoms

ClusterPotentialTopology{T} <: AbstractClusterPotentialTopology{T}

Container that maps a cluster potential to respective atoms.

Fields

• potential::T:
• indices::Vector{Vector{Int}}: Stores information of atoms between which the potentilal exist

FitData

Structure to help potential parameters fitting.

Fields

• variables : variables
• E : energy
• w : weights

Creation

FitData(mpp, points, energy)
FitData(mpp, data::Dict...)

• data::Dict : Dict that is returned by load_data_file

GeneralAngle <: AbstractClusterPotential

General potential with customizable powers for both radial polynomials and cosθ.

Fields

• constants::Array{Float64,2} : constants
• ppowers::Vector{Int} : powers for radial polynomials
• cpowers::Vector{Int} : powers for cosθ

To create potential use:

GeneralAngle(ppowers::AbstractVector{Int}, cpowers::AbstractVector{Int})

GeneralPowers

General potential with customizable powers.

Fields

• constants::Vector{Float64} : potential constants
• powers::Vector{Int} : powers for radius

LennardJones <: AbstractPairPotential

Holds constants for Lennard-Jones potential E = C12/R^12 - C6/R^6

MoleculePairPotential{T<:AbstractPairPotential} <: AbstractClusterPotential

Structure to hold potential information between two molecules

PairPotentialTopology{T} <: AbstractPairPotentialTopology{T}

Container that maps a pair potential to respective atoms.

Fields

• indices::Vector{Tuple{Int, Int}}: Stores information of atom pair(s) between which the potentilal exist
• potential::T: Potential structure

(p::PairPotentialTopology)(c1::AbstractCluster, c2::AbstractCluster)

Returns potential for given cluster pair. Index for atom 2 is expected to be in cluster c2.

(p::PairPotentialTopology)(c::AbstractCluster)

Returns potential for given cluster.

(p::PairPotentialTopology)(r)

Returns potential for given distance.