#ifndef MMTBX_TLS_DECOMPOSE_H #define MMTBX_TLS_DECOMPOSE_H #include // Basic data types #include #include #include // Allow arrays of the above #include #include #include namespace mmtbx { namespace tls { namespace decompose { namespace af = scitbx::af; typedef scitbx::matrix::eigensystem::real_symmetric Eig; typedef af::shared eigenvalues; typedef af::versa > eigenvectors; // Actual validation functions class decompose_tls_matrices { public: // Constructor decompose_tls_matrices(scitbx::sym_mat3 const& T, scitbx::sym_mat3 const& L, scitbx::mat3 const& S, bool l_and_s_in_degrees = true, bool verbose = false, double tol = 1.e-6, double eps = 1.e-8, std::string const& t_S_formula = "11", double t_S_value = 0.0); bool is_valid(); bool is_verbose(); std::string error(); // Tolerance of the physical parameters double precision_tolerance(); // Tolerance of the numerical parameters double floating_point_limit(); // -------------------- // Output variables (set throughout and grouped here for clarity) // -------------------- // RMS amplitudes of libration af::shared l_amplitudes; // Libration axes ... in the M basis scitbx::vec3 l1_M, l2_M, l3_M; // Points on libration axes ... in M basis scitbx::vec3 w1_M, w2_M, w3_M; // Amplitudes of screw motions (along librational axes) af::shared s_amplitudes; // RMS amplitudes of vibration af::shared v_amplitudes; // Vibration axes ... in the L basis scitbx::vec3 v1_L, v2_L, v3_L; // Vibration axes ... in the M basis scitbx::vec3 v1_M, v2_M, v3_M; // -------------------- // Coordinate transformation // -------------------- // Rotation matrix to transform between original and libration coordinate frames (M -> L) // R_ML * a_M = a_L scitbx::mat3 R_ML; scitbx::mat3 R_ML_t; // Rotation matrix to transform between original and vibrational coordinate frames // R_MV * a_M = a_V scitbx::mat3 R_MV; scitbx::mat3 R_MV_t; private: bool verbose_; // Response variables bool valid_; std::string error_; // Define analysis precision (for determining positive-definiteness, etc). double tol; // Define floating point boundary (for determining when something is zero) double eps; // Value for forcing t_S double t_S_value; // Select which formula to choose for finding t_S std::string t_S_formula; // printing static std::string spacer; // -------------------- // Decomposition functions // -------------------- void run(); void stepA(); void stepB(); void stepC(); void stepD(); // -------------------- // Input variables // -------------------- // Input matrices scitbx::sym_mat3 T_M; scitbx::sym_mat3 L_M; scitbx::mat3 S_M; // Origin -- only used for manipulating the output axes, does not affect decomposition // TODO NOT IMPLEMENTED TODO //scitbx::vec3 const origin; // Matrices at various stages during the decomposition and internal variables // -------------------- // Set at step A // -------------------- // Matrices in the basis of the libration matrix scitbx::sym_mat3 T_L; scitbx::sym_mat3 L_L; scitbx::mat3 S_L; // -------------------- // Set at step B // -------------------- // Store information about the position of the libration axes struct W { double wy_lx; double wz_lx; double wz_ly; double wx_ly; double wx_lz; double wy_lz; scitbx::vec3 w_lx, w_ly, w_lz; } w_15, w; // Translational components from offset of librational axes from origin scitbx::sym_mat3 D_WL; // Translational components in the L-basis // T_CL = T_L - D_WL scitbx::sym_mat3 T_CL; // -------------------- // Set at step C // -------------------- // Amount to subtract from the trace of the S-matrix double t_S; // S-matrix after subtraction of t_S // S_C = S_L - diag(t_S) scitbx::mat3 S_C; // Screw contributions to translation matrix scitbx::sym_mat3 C_L_t_S; // Vibrational component in the L-basis // V_L = T_CL - C_L_t_S scitbx::sym_mat3 V_L; // -------------------- // Set at step D // -------------------- // (Pure) Vibrations in the vibration basis scitbx::sym_mat3 V_V; // -------------------- // Eigen-analysis functions // -------------------- bool is_pd(scitbx::sym_mat3 const& matrix); // Quadratic equation coefficients for determinant of V-matrix from T+S matrices scitbx::vec3 as_bs_cs( double t, double Sxx, double Syy, double Szz, double T11, double T22, double T33, double T12, double T13, double T23 ); // -------------------- // Logic/zero functions // -------------------- // Dealing with small values bool is_zero(double value); bool is_positive(double value); bool is_negative(double value); double zero_filter(double value); // Set small values to zero void zero_small_values(scitbx::vec3& vector); void zero_small_values(scitbx::mat3& matrix); void zero_small_values(scitbx::sym_mat3& matrix); // -------------------- // Matrix Helper functions // -------------------- // Regular matrices double xx(scitbx::mat3 const& matrix); double xy(scitbx::mat3 const& matrix); double xz(scitbx::mat3 const& matrix); double yx(scitbx::mat3 const& matrix); double yy(scitbx::mat3 const& matrix); double yz(scitbx::mat3 const& matrix); double zx(scitbx::mat3 const& matrix); double zy(scitbx::mat3 const& matrix); double zz(scitbx::mat3 const& matrix); // Symmetric matrices double xx(scitbx::sym_mat3 const& matrix); double xy(scitbx::sym_mat3 const& matrix); double xz(scitbx::sym_mat3 const& matrix); double yx(scitbx::sym_mat3 const& matrix); double yy(scitbx::sym_mat3 const& matrix); double yz(scitbx::sym_mat3 const& matrix); double zx(scitbx::sym_mat3 const& matrix); double zy(scitbx::sym_mat3 const& matrix); double zz(scitbx::sym_mat3 const& matrix); // Print matrices void print(std::string const& label, double value); void print(std::string const& label, scitbx::mat3 const& matrix); void print(std::string const& label, scitbx::sym_mat3 const& matrix); void print(std::string const& label, scitbx::vec3 const& vector); void print(std::string const& label, af::shared const& vector); }; }}} // close mmtbx/tls/decompose #endif