Public Member Functions | Private Attributes | List of all members
opt::FB_FRAG Class Reference

#include <fb_frag.h>

Inheritance diagram for opt::FB_FRAG:

Public Member Functions

 ~FB_FRAG ()
void set_values (double *values_in)
void set_forces (double *forces_in)
double * get_values_pointer () const
double * get_forces_pointer () const
void add_dummy_coords (int ndummy)
void print_intcos (std::string psi_fp, FILE *qc_fp)
double ** H_guess ()
void displace (int fb_frag_index, double *dq)
- Public Member Functions inherited from opt::FRAG
 FRAG (int natom_in, double *Z_in, double **geom_in)
 FRAG (int natom_in)
 ~FRAG ()
int g_natom () const
void set_masses ()
void print_geom (std::string psi_fp, FILE *qc_fp, const int id, bool print_mass=false)
void print_geom_grad (std::string psi_fp, FILE *qc_fp, const int id, bool print_mass=false)
void print_simples (std::string psi_fp, FILE *qc_fp, int atom_offset=0) const
void print_coords (std::string psi_fp, FILE *qc_fp, int atom_offset=0) const
void print_combinations (std::string psi_fp, FILE *qc_fp) const
void print_intco_dat (std::string psi_fp, FILE *qc_fp, int atom_offset=0) const
std::string get_coord_definition (int coord_index, int atom_offset=0)
std::string get_simple_definition (int simple_index, int atom_offset=0)
INTCO_TYPE get_simple_type (int simple_index)
void update_connectivity_by_distances ()
void update_connectivity_by_bonds ()
void print_connectivity (std::string psi_fp, FILE *qc_fp, const int id, const int offset=0) const
int add_stre_by_connectivity ()
int add_bend_by_connectivity ()
int add_tors_by_connectivity ()
int add_cartesians ()
int form_trivial_coord_combinations ()
void add_trivial_coord_combination (int simple_id)
int form_delocalized_coord_combinations ()
int form_natural_coord_combinations ()
int add_simples_by_connectivity ()
int add_auxiliary_bonds ()
void connect (int i, int j)
double ** compute_B () const
void compute_B (double **B_in, int coord_offset, int atom_offset) const
void compute_G (double **, bool use_masses=false) const
void compute_derivative_B (GeomType g, int coord_index, double **Bprime, int atom_offset) const
void compute_derivative_B (int coord_index, double **Bprime, int atom_offset) const
double ** compute_derivative_B (int coord_index) const
void print_B (std::string psi_fp, FILE *qc_fp) const
void fix_tors_near_180 ()
void fix_oofp_near_180 ()
void fix_bend_axes ()
void unfix_bend_axes ()
int Ncoord () const
int g_simple_natom (const int coord_index) const
int g_simple_atom (const int coord_index, const int atom) const
double * g_Z () const
double * g_Z_pointer ()
void print_s (std::string psi_fp, FILE *qc_fp, GeomType geom) const
double * coord_values () const
double * coord_values (GeomType geom) const
double coord_value (int lookup) const
double coord_value (GeomType geom, int lookup) const
std::vector< int > validate_angles (double const *const dq, int atom_offset)
bool present (const SIMPLE_COORDINATE *one) const
int find (const SIMPLE_COORDINATE *one) const
void displace (double *dq, double *fq, int atom_offset=0)
bool displace_util (double *dq, bool focus_on_constraints)
double ** g_geom_pointer ()
double ** g_geom () const
GeomType g_geom_const_pointer () const
double ** g_grad ()
double ** g_grad_pointer ()
double * g_geom_array ()
double * g_grad_array ()
void set_geom_array (double *geom_array_in)
void set_geom (double **geom_in)
void set_grad (double **grad_in)
void print_geom (std::string psi_fp, FILE *qc_fp)
void print_geom_irc (std::string psi_fp, FILE *qc_fp)
double ** H_guess ()
double Lindh_rho (int A, int B, double RAB) const
double ** Lindh_guess ()
bool ** g_connectivity () const
const bool *const * g_connectivity_pointer () const
bool read_coord (std::vector< std::string > &tokens, int first_atom_offset)
double ** compute_constraints () const
int add_hbonds ()
void simple_add (SIMPLE_COORDINATE *i)
double g_mass (int i)
bool is_frozen () const
void freeze ()
void unfreeze ()
void freeze_coords ()
double * com (GeomType in_geom)
double * com ()
double ** inertia_tensor (GeomType in_geom)
double ** inertia_tensor ()
int principal_axes (GeomType geom, double **axes, double *evals)
int principal_axes (double **axes, double *evals)
bool coord_has_fixed_eq_val (int coord_index) const
double coord_fixed_eq_val (int coord_index) const
void add_combination_coord (vector< int > ids, vector< double > coeffs)
bool apply_frozen_constraints (std::string R_string, std::string B_string, std::string D_string, std::string C_string)
bool apply_fixed_constraints (std::string R_string, std::string B_string, std::string D_string)
void erase_combo_coord (int index)
bool is_noncart_present () const

Private Attributes

double * values
double * forces

Additional Inherited Members

- Protected Attributes inherited from opt::FRAG
int natom
 number of atoms in fragment More...
double * Z
 atomic numbers More...
double ** geom
 cartesian coordinates More...
double ** grad
 cartesian coordinates More...
double * mass
 nuclear masses More...
bool ** connectivity
 connectivity matrix More...
bool frozen
 whether to optimize More...
 simple or linear combinations of simple coordinates More...

Constructor & Destructor Documentation

opt::FB_FRAG::FB_FRAG ( )
opt::FB_FRAG::~FB_FRAG ( )

Member Function Documentation

void opt::FB_FRAG::add_dummy_coords ( int  ndummy)
void opt::FB_FRAG::displace ( int  fb_frag_index,
double *  dq 
double* opt::FB_FRAG::get_forces_pointer ( ) const
double* opt::FB_FRAG::get_values_pointer ( ) const
double ** opt::FB_FRAG::H_guess ( )
void opt::FB_FRAG::print_intcos ( std::string  psi_fp,
FILE *  qc_fp 
void opt::FB_FRAG::set_forces ( double *  forces_in)
void opt::FB_FRAG::set_values ( double *  values_in)

Member Data Documentation

double* opt::FB_FRAG::forces
double* opt::FB_FRAG::values

The documentation for this class was generated from the following files: