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sc::Molecule Class Reference The Molecule class contains information about molecules. More... #include <molecule.h> Inheritance diagram for sc::Molecule: [legend]Collaboration diagram for sc::Molecule: [legend]List of all members. Public Methods   Molecule ()   Molecule (const Molecule &)   Molecule (StateIn &)   Molecule (const Ref< KeyVal > &input)   The KeyVal constructor. virtual  ~Molecule () 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. More... 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. More... int  atom_label_to_index (const char *label) const   Returns the index of the atom with the given label. More... double *  charges () const   Returns a double* containing the nuclear charges of the atoms. More... 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). More... 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. More... 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. More... 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. More... 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. More... 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. More... 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. More... int  atom_to_unique_offset (int iatom) const   Converts an atom number to the offset of this atom in the list of generated atoms. More... int  n_core_electrons ()   Return the number of core electrons. int  max_z ()   Return the maximum atomic number. Ref< AtomInfo >  atominfo () const   Return the molecules AtomInfo object. 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. More... Protected Methods void  init_symmetry_info (double tol=0.5) void  clear_symmetry_info () void  clear () Protected Attributes 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_ Detailed Description The Molecule class contains information about molecules. It has a KeyVal constructor that can create a new molecule from either a PDB file or from a list of Cartesian coordinates. The following ParsedKeyVal input reads from the PDB file h2o.pdb: molecule<Molecule>: ( pdb_file = "h2o.pdb" ) The following input explicitly gives the atom coordinates, using the ParsedKeyVal table notation: molecule<Molecule>: ( unit=angstrom { atom_labels atoms geometry } = { O1 O [ 0.000000000 0 0.369372944 ] H1 H [ 0.783975899 0 -0.184686472 ] H2 H [-0.783975899 0 -0.184686472 ] } ) ) The default units are Bohr with can be overridden with unit=angstrom#. The atom_labels# array can be omitted. The atoms# and geometry# arrays are required. The Molecule class has a PointGroup member object, which also has a KeyVal constructor that is called when a Molecule is made. The following example constructs a molecule with symmetry: molecule<Molecule>: ( symmetry=c2v unit=angstrom { atoms geometry } = { O [0.000000000 0 0.369372944 ] H [0.783975899 0 -0.184686472 ] } ) ) Only the symmetry unique atoms need to be specified. Nonunique atoms can be given too, however, numerical errors in the geometry specification can result in the generation of extra atoms so be careful. Member Function Documentation int sc::Molecule::atom_at_position (  double *   , double    tol = 0.05 )  const   Takes an (x, y, z) postion and finds an atom within the given tolerance distance. If no atom is found -1 is returned. int sc::Molecule::atom_label_to_index (  const char *    label )  const   Returns the index of the atom with the given label. If the label cannot be found -1 is returned. int sc::Molecule::atom_to_unique (  int    iatom )  const [inline]   Converts an atom number to the number of its generating unique atom. The return value is in [0, nunique). int sc::Molecule::atom_to_unique_offset (  int    iatom )  const   Converts an atom number to the offset of this atom in the list of generated atoms. The unique atom itself is allows offset 0. double* sc::Molecule::charges (    )  const   Returns a double* containing the nuclear charges of the atoms. The caller is responsible for freeing the return value. void sc::Molecule::cleanup_molecule (  double    tol = 0.1 )    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. Ref<PointGroup> sc::Molecule::highest_point_group (  double    tol = 1.0e-8 )  const   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. int sc::Molecule::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. The direction vector must be a unit vector. void sc::Molecule::is_linear_planar (  int &    linear, int &    planar, double    tol = 1.0e-5 )  const   Sets linear to 1 if the molecular is linear, 0 otherwise. Sets planar to 1 if the molecular is planar, 0 otherwise. int sc::Molecule::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. The perpendicular vector must be a unit vector. const char* sc::Molecule::label (  int    atom )  const   Returns the label explicitly assigned to atom. If no label has been assigned, then null is returned. void sc::Molecule::save_data_state (  StateOut &    )  [virtual]   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. void sc::Molecule::symmetrize (  double    tol = 0.5 )    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. The documentation for this class was generated from the following file: molecule.h