Simulation domain

Some modules require a domain to work, mainly when periodicity is involved. For instance as in the case of the Force Coupling Method triply periodic hydrodynamics module.

In these cases the Box class is used.

class Box

A structure containing a domain size. Can describe a domain that is periodic in any direction.

Box(real3 L): Constructor taking a box size in each direction. The resulting box is periodic by default except when L is infinite in some direction.

real3 apply_pbc(real3 position): Applies the minimum image convention (MIC) to the provided position in the directions in which the box is periodic (leaving the rest untouched). Returns $q^\alpha= q^\alpha - \text{floor}\left(q^\alpha/L^\alpha + 0.5\right)L^\alpha$ applied only to the periodic directions. Being $L^\alpha$ the box size in the direction $\alpha$ . Note that this functions works for finding the minimum distance between two particles as well as for finding the position of the provided image in the primary cell.

void setPeriodicity(bool x, bool y, bool z): Sets the periodicity of the box in each direction (note that the box can be finite yet non-periodic).

bool isPeriodicX(): Returns true if the box is periodic in the X direction, false otherwise.

bool isPeriodicY(): Returns true if the box is periodic in the Y direction, false otherwise.

bool isPeriodicZ(): Returns true if the box is periodic in the Z direction, false otherwise.

real3 boxSize: A public member that holds the box size in each direction.

Example

#include<uammd.cuh>
using namespace uammd;
int main(){
  real lx, ly, lz;
  lx = ly = lz = 32.0;
  //A Box requires the size of the domain in each direction, which can be infinite
  Box box({lx, ly, lz});
  //Periodicity can be set independently for each direction. 1 meaning periodic and 0 aperiodic
  box.setPeriodicity(1,1,0);
  //The unit cell goes from -L/2 to L/2 in each direction.
  //Let's store in a variable a position just outside the unit cell.
  real3 position_outside_box = {0.5*lx+1, 0, 0};
  //Given that we have set the box as periodic in X, the position will be folded to the other side of the domain
  real3 position_in_box = box.apply_pbc(position_outside_box);
  //position_in_box holds {-lx*0.5+1,0,0}
  return 0;
}