Periodic boundary conditions and distances computations¶

The PBC module offers utilities for distance computations using periodic boundary conditions.

Minimal images¶

These functions take a vector and wrap it inside a cell, by finding the minimal vector fitting inside the cell.

minimal_image(vect, cell::UnitCell)¶: Wraps the vect vector inside the cell unit cell. vect can be a Vector (i.e. a 1D array), or a view from an Array3D. This function returns the wrapped vector.

minimal_image!(vect, cell::UnitCell)¶: Wraps vect inside of cell, and stores the result in vect.

minimal_image!(A::Matrix, cell::UnitCell): If A is a 3xN Array, wraps each one of the columns in the cell. The result is stored in A. If A is not a 3xN array, this throws an error.

Distances¶

Distances are computed using periodic boundary conditions, by wrapping the \(\vec r_i - \vec r_j\) vector in the cell before computing its norm.

Within one Frame¶

This set of functions computes distances within one frame.

distance(ref::Frame, i::Integer, j::Integer)¶: Computes the distance between particles i and j in the frame.

distance_array(ref::Frame[, result])¶: Computes all the distances between particles in frame. The result array can be passed as a pre-allocated storage for the \(N\times N\) distances matrix. result[i, j] will be the distance between the particle i and the particle j.

distance3d(ref::Frame, i::Integer, j::Integer)¶: Computes the \(\vec r_i - \vec r_j\) vector and wraps it in the cell. This function returns a 3D vector.

Between two Frames¶

This set of functions computes distances within two frames, either computing the how much a single particle moved between two frames or the distance between the position of a particle i in a reference frame and a particle j in a specific configuration frame.

distance(ref::Frame, conf::Frame, i::Integer, j::Integer): Computes the distance between the position of the particle i in ref, and the position of the particle j in conf

distance(ref::Frame, conf::Frame, i::Integer): Computes the distance between the position of the same particle i in ref and conf.

distance3d(ref::Frame, conf::Frame, i::Integer): Wraps the ref[i] - conf[i] vector in the ref unit cell.

distance3d(ref::Frame, conf::Frame, i::Integer, j::Integer): Wraps the ref[i] - conf[i] vector in the ref unit cell.