Help entries

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.

simulate_gui(; n=100, sides=(100.0, 100.0), kind=:md)

Opens a graphical interface to interactively run and visualize, in 2D, the simulations described in the tutorial: microcanonical MD (:md), MD with an isokinetic bath (:md_isokinetic), a Berendsen bath (:md_berendsen), a Langevin bath (:md_langevin), and Monte Carlo (:mc).

The interface shows the motion of the particles together with live plots of the potential, kinetic and total energies, and of the temperature (average kinetic energy per particle), and exposes all the relevant System and Options parameters. Changing any parameter or the simulation type restarts the simulation with the new settings.

This function is implemented as a package extension and requires GLMakie to be loaded:

julia> using FundamentosDMC

julia> import GLMakie

julia> simulate_gui()

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.