nucleationParameters.h

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#ifndef INCLUDE_NUCLEATIONPARAMETERS_H_
#define INCLUDE_NUCLEATIONPARAMETERS_H_

template<int dim>
class nucleationParameters
{
public:
    unsigned int var_index;
    std::vector<double> semiaxes;
    std::vector<double> ellipsoid_rotation;
    std::vector<double> freeze_semiaxes;
    double no_nucleation_border_thickness;
    double hold_time;
    dealii::Tensor<2,dim,double> rotation_matrix;

    nucleationParameters(unsigned int _var_index,
        std::vector<double> _semiaxes,
        std::vector<double> _freeze_semiaxes,
        std::vector<double> _ellipsoid_rotation,
        double _hold_time,
        double _no_nucleation_border_thickness){

        var_index =_var_index;
        semiaxes = _semiaxes;
        freeze_semiaxes = _freeze_semiaxes;
        ellipsoid_rotation = _ellipsoid_rotation;
        hold_time = _hold_time;
        no_nucleation_border_thickness = _no_nucleation_border_thickness;

        set_rotation_matrix();
    };

    void set_rotation_matrix(){
        // Rotation conventions:
        // Rx refers to rotations about the x axis, Ry refers to rotations about the y axis, and Rz refers to rotations about the z axis.
        // A positive rotation angle about the z axis corresponds to a clockwise rotation of the particle in a 2D calculation.

        double degrees_to_rad = std::acos(0.0)/90.0;

        dealii::Tensor<2,dim,double> Rx, Ry, Rz;

        Rx[0][0] = 1.0;
        Rx[1][1] = std::cos(ellipsoid_rotation.at(0)*degrees_to_rad);

        Ry[0][0] = std::cos(ellipsoid_rotation.at(1)*degrees_to_rad);
        Ry[1][1] = 1.0;

        Rz[0][0] = std::cos(ellipsoid_rotation.at(2)*degrees_to_rad);
        Rz[1][0] = std::sin(ellipsoid_rotation.at(2)*degrees_to_rad);
        Rz[0][1] = -std::sin(ellipsoid_rotation.at(2)*degrees_to_rad);
        Rz[1][1] = std::cos(ellipsoid_rotation.at(2)*degrees_to_rad);

        if (dim == 3){
            Rx[1][2] = - std::sin(ellipsoid_rotation.at(0)*degrees_to_rad);
            Rx[2][1] = std::sin(ellipsoid_rotation.at(0)*degrees_to_rad);
            Rx[2][2] = std::cos(ellipsoid_rotation.at(0)*degrees_to_rad);

            Ry[0][2] = std::sin(ellipsoid_rotation.at(1)*degrees_to_rad);
            Ry[2][0] = -std::sin(ellipsoid_rotation.at(1)*degrees_to_rad);
            Ry[2][2] = std::cos(ellipsoid_rotation.at(1)*degrees_to_rad);

            Rz[2][2] = 1.0;
        }

        rotation_matrix = Rx*Ry*Rz; // Note: these are tensor multiplications

    };

};

#endif