Molecule (const Molecule &)

Molecule (StateIn &)

Molecule (const Ref< KeyVal > &input)

The KeyVal constructor. Molecule & operator= (const Molecule &)

void add_atom (int Z, double x, double y, double z, const char *=0, double mass=0.0, int have_charge=0, double charge=0.0)

Add an AtomicCenter to the Molecule. virtual void print (std::ostream &=ExEnv::out0()) const

Print information about the molecule. virtual void print_parsedkeyval (std::ostream &=ExEnv::out0(), int print_pg=1, int print_unit=1, int number_atoms=1) const

int natom () const

Returns the number of atoms in the molcule. int Z (int atom) const

double & r (int atom, int xyz)

const double & r (int atom, int xyz) const

double * r (int atom)

const double * r (int atom) const

double mass (int atom) const

const char * label (int atom) const

Returns the label explicitly assigned to atom. int atom_at_position (double *, double tol=0.05) const

Takes an (x, y, z) postion and finds an atom within the given tolerance distance. int atom_label_to_index (const char *label) const

Returns the index of the atom with the given label. double * charges () const

Returns a double* containing the nuclear charges of the atoms. double charge (int iatom) const

Return the charge of the atom. double nuclear_charge () const

Returns the total nuclear charge. void set_point_group (const Ref< PointGroup > &, double tol=1.0e-7)

Sets the PointGroup of the molecule. Ref< PointGroup > point_group () const

Returns the PointGroup of the molecule. Ref< PointGroup > highest_point_group (double tol=1.0e-8) const

Find this molecules true point group (limited to abelian groups). int is_axis (SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const

Return 1 if this given axis is a symmetry element for the molecule. int is_plane (SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const

Return 1 if the given plane is a symmetry element for the molecule. int has_inversion (SCVector3 &origin, double tol=1.0e-8) const

Return 1 if the molecule has an inversion center. int is_linear (double tolerance=1.0e-5) const

Returns 1 if the molecule is linear, 0 otherwise. int is_planar (double tolerance=1.0e-5) const

Returns 1 if the molecule is planar, 0 otherwise. void is_linear_planar (int &linear, int &planar, double tol=1.0e-5) const

Sets linear to 1 if the molecular is linear, 0 otherwise. SCVector3 center_of_mass () const

Returns a SCVector3 containing the cartesian coordinates of the center of mass for the molecule. double nuclear_repulsion_energy ()

Returns the nuclear repulsion energy for the molecule. void nuclear_repulsion_1der (int center, double xyz[3])

Compute the nuclear repulsion energy first derivative with respect to the given center. void nuclear_efield (const double *position, double *efield)

Compute the electric field due to the nuclei at the given point. void nuclear_charge_efield (const double *charges, const double *position, double *efield)

Compute the electric field due to the given charges at the positions of the nuclei at the given point. void symmetrize (double tol=0.5)

If the molecule contains only symmetry unique atoms, this function will generate the other, redundant atoms. void symmetrize (const Ref< PointGroup > &pg, double tol=0.5)

Set the point group and then symmetrize. void cleanup_molecule (double tol=0.1)

This will try to carefully correct symmetry errors in molecules. void translate (const double *r)

void move_to_com ()

void transform_to_principal_axes (int trans_frame=1)

void transform_to_symmetry_frame ()

void print_pdb (std::ostream &=ExEnv::out0(), char *title=0) const

void read_pdb (const char *filename)

void principal_moments_of_inertia (double *evals, double **evecs=0) const

Compute the principal moments of inertia and, possibly, the principal axes. int nunique () const

Return information about symmetry unique and equivalent atoms. int unique (int iuniq) const

Returns the overall number of the iuniq'th unique atom. int nequivalent (int iuniq) const

Returns the number of atoms equivalent to iuniq. int equivalent (int iuniq, int j) const

Returns the j'th atom equivalent to iuniq. int atom_to_unique (int iatom) const

Converts an atom number to the number of its generating unique atom. int atom_to_unique_offset (int iatom) const

Converts an atom number to the offset of this atom in the list of generated atoms. int n_core_electrons ()

Return the number of core electrons. int max_z ()

Return the maximum atomic number. Ref< AtomInfo > atominfo () const

Return the molecule's AtomInfo object. std::string atom_name (int iatom) const

Returns the element name of the atom. std::string atom_symbol (int iatom) const

Returns the element symbol of the atom. void set_include_q (bool iq)

If include_q is true, then include the 'Q' atoms in the charge and efield routines. bool include_q () const

Returns include_q. See set_include_q. void set_include_qq (bool iqq)

If include_qq is true, include the coupling between pairs of 'Q' atoms when computing nuclear repulsion energy and gradients. bool include_qq () const

Returns include_qq. See set_include_qq. int n_q_atom () const

Retrieve the number of 'Q' atoms. int q_atom (int i) const

Retrieve the 'Q' atoms. int n_non_q_atom () const

Retrieve the number of non-'Q' atoms. int non_q_atom (int i) const

Retrieve the of non-'Q' atoms. void save_data_state (StateOut &)

Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them.

void init_symmetry_info (double tol=0.5)

void clear_symmetry_info ()

void clear ()

int natoms_

Ref< AtomInfo > atominfo_

Ref< PointGroup > pg_

Ref< Units > geometry_units_

double ** r_

int * Z_

double * charges_

int nuniq_

int * nequiv_

int ** equiv_

int * atom_to_uniq_

double * mass_

char ** labels_

int q_Z_

bool include_q_

bool include_qq_

std::vector< int > q_atoms_

std::vector< int > non_q_atoms_

Takes an (x, y, z) postion and finds an atom within the given tolerance distance.

If no atom is found -1 is returned.

Returns the index of the atom with the given label.

If the label cannot be found -1 is returned.

Converts an atom number to the number of its generating unique atom.

The return value is in [0, nunique).

Converts an atom number to the offset of this atom in the list of generated atoms.

The unique atom itself is allows offset 0.

Returns a double* containing the nuclear charges of the atoms.

The caller is responsible for freeing the return value.

This will try to carefully correct symmetry errors in molecules.

If any atom is out of place by more then tol, abort will be called.

Find this molecules true point group (limited to abelian groups).

If the point group of this molecule is set to the highest point group, then the origin must first be set to the center of mass.

Return 1 if this given axis is a symmetry element for the molecule.

The direction vector must be a unit vector.

Sets linear to 1 if the molecular is linear, 0 otherwise.

Sets planar to 1 if the molecular is planar, 0 otherwise.

Return 1 if the given plane is a symmetry element for the molecule.

The perpendicular vector must be a unit vector.

Returns the label explicitly assigned to atom.

If no label has been assigned, then null is returned.

Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them.

This must be implemented by the derived class if the class has data.

Reimplemented from sc::SavableState.

If the molecule contains only symmetry unique atoms, this function will generate the other, redundant atoms.

The redundant atom will only be generated if there is no other atoms within a distance of tol. If the is another atom and it is not identical, then abort will be called.