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Structure containing the options and parameters of the simulation.

Examples

julia> opt = Options()

julia> opt = Options(nsteps=2000)

Structure that contains a two-dimensional point, subtype of FieldVector from StaticArrays.

Structure that contains a three-dimensional point, subtype of FieldVector from StaticArrays.

Structure containing the system initial coordinates and box sides.

Example

julia> sys = System(n=100,sides=[100,100])

dim(T::DataType)

Returns the dimension associated to a Point2D (2) or Point3D (3).

forces!(x::Vector{T},f::Vector{T},opt::Options) where T

Subroutine that computes the force. It modifies the input f vector.

image(x,sides)

Move coordinates to minimum periodic image.

init_velocities(sys::System{T},opt::Options) where T

Initialize velocities with random distribution.

kinetic(v)

Function that computes the kinetic energy given a velocity vector v.

mc(sys::System{T},opt=Options=Options()) where T

Peforms a Monte-Carlos simulation.

md(sys::System{T},opt::Options) where T

Performs a simple MD simulation.

md_berendsen(sys::System{T},opt::Options) where T

Performs a MD simulation with a Berendsen bath.

md_isokinetic(sys::System{T},opt::Options) where T

Performs a MD simulation with an isokinetic bath.

md_langevin(sys::System{T},opt::Options) where T

Performs a MD simulation with a Langevin bath.

minimize!(sys::System{T},opt::Options)

Minimizes the potential energy of sys.x0. Modifies sys.x0.

Example

julia> sys = System(n=100,sides=[100,100])

julia> minimize!(sys,Options(tol=1e-3))
Energy before minimization: 38322.72337856496
Energy after minimization: -74.15646912098042

potential(x::Vector{T},sys::System{T},opt::Options) where T

Function that computes the potential energy given a vector of positions, x.

printxyz(time,x,sys,traj_file_buffer)

Subroutine that writes the current coordinates (or velocities) to output files, previously opened in respective buffers.

printxyz(time,x,v,sys,traj_file_buffer,vel_file_buffer)

Subroutine that writes the current coordinates and velocities to output files, previously opened in respective buffers.

printxyz(x,sys,file::String)

Prints one set of coordinates (or velocities), given in x to file file. Overwrites the file.

radial_distribution(
    sys::System{T},
    trajfile::String;
    dmax::Float64=10.,
    nbins::Int=100
) where T

Computes the g(r). If T=Point3D the system will be read as three-dimensional.

random_rotate(v)

Randomly rotate vector v, which might be a Point2D or a Point3D

readxyz(file; first=1, last=-1)

Function that reads a xyz file.

remove_drift!(v)

Removes possible drift from velocities.

velocity_distribution(
  sys::System{T},
  velfile::String;
  vmax::Float64=2.,
  nbins::Int=100
) where T

Computes the distribution of velocities. If T=Point3D the system will be read as three-dimensional.