Domain

class Domain

A Domain represents the spatial boundaries and constraints imposed upon the positions of the particles.

The origin is always located at the center of the domain.

By default, periodicity in each dimension is enabled when the side lengths are set.

A cuboid-shaped domain may have unique side lengths but the angles between the edges of the domain are fixed at ninety degrees. In two-dimensions, the cuboid reduces to a rectangle. The cuboid domain may be faster and cells are specific to cuboid domain.

A triclinic-shaped domain is similar to cuboid-shaped except that the angles between the boundaries may different from ninety degrees. In two-dimensions, this reduces to a parallelogram.

The triclinic periodic cell is defined by a vector for each dimension. This implementation is only valid for the following two- or three-dimensions.

For the first (i.e., “x”):

\( \vec{l_x} = {l_x, 0, 0} \)

For the second (i.e., “y”):

\( \vec{l_y} = {xy, l_y, 0} \)

For the third (i.e., “z”):

\( \vec{l_z} = {xz, yz, l_z} \)

Thus, the angle, \(\alpha\), between the “x” and “y” vectors is given by

\( |l_x| |l_y| \cos\alpha = \vec{l_x} \cdot \vec{l_y}\).

On the inner workings of Monte Carlo codes https://doi.org/10.1080/08927022.2013.819102

Public Functions

Domain(const argtype &args = argtype())

args:

  • side_length[i]: set the side length of the i-th dimension. The “[i]” is to be substituted for an integer 0, 1, 2, …

  • cubic_box_length: side length of cubic perioidic boundary conditions.

  • periodic[i]: set if the i-th dimension is periodic (default: true).

  • xy: set the tilt along the x-y direction (default: 0).

  • xz: set the tilt along the x-z direction (default: 0).

  • yz: set the tilt along the y-z direction (default: 0).

  • init_cells[i]: build cell list with given minimum length between cells. The “[i]” is to be substituted for an integer 0, 1, 2, … If only one cell, the “[i]” is optional.

  • cell_group[i]: only compute cells for those in given group index for cell of corresponding “i” (default: 0).

const Position &side_lengths() const

Get the side lengths.

double side_length(const int dimension) const

Get the side length.

void set_side_lengths(const Position &side_lengths)

Set the side lengths.

void set_side_length(const int dimension, const double length)

Set the side length.

void add_side_length(const double length)

Add a side length (and dimensionality) to the domain.

Domain &set_cubic(const double box_length)

Set the cubic box length. Return self for chain setting.

bool is_cubic() const

Return true if all side lengths are equal.

double xy() const

Return the xy tilt factor. By default it is zero.

double xz() const

Return the xz tilt factor.

double yz() const

Return the yz tilt factor.

void disable(const int dimension)

Disable periodicity in a given dimension.

bool periodic(const int dimension) const

Return true if given dimension is periodic.

int dimension() const

Return the dimensionality.

double volume() const

Return the volume.

Position shift(const Position &position) const

Return the shift necessary to wrap the position. This is an unoptimized version.

const Position &shift_opt(const Position &position)

Same as above, but optimized to use pre-initialized private data.

void wrap(Position *position) const

Wrap the input position. This is an unoptimized version.

Position random_position(Random *random) const

Return random position within boundaries.

void random_position(Position *position, Random *random) const

Optimized verison of the above, which allows update of existing position.

double min_side_length() const

Return the minimum side length.

double max_side_length() const

Return the maximum side length.

void init_cells(const double min_length, const int group_index = 0)

Initialize the cells according to the minimum side length.

Parameters
  • group_index: A group index corresponds to a group defined in configuration. If this index is set to 0 (default) use all particles and sites.

int num_cells() const

Return the number of cell lists.

const std::vector<Cells> &cells() const

Return the cells.

const Cells &cells(const int index) const

Return the cells by index.

void add_to_cell_list(const int cell_index, const Select &select, const int particle_cell)

Add selection to cells.

void update_cell_list(const int cell_index, const Select &select, const int cell_new, const int cell_old)

Update selection in cells.

void remove_from_cell_list(const int cell_index, const Select &select, const int cell)

Remove selection from cells.

int cell_id(const Position &position, const Cells &cells)

Return the unique cell number for the position.

bool is_cell_enabled() const

Return true if cell list is enabled.

void unwrap(const int dim, const int num_wrap, Position *shift) const

Return the shift for number of wraps, num_wrap, in a given dimension, dim.

std::string status_header() const

Return the header of the status for periodic output.

std::string status() const

Return the brief status for periodic output.