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NAME

       sc::Molecule -

       The Molecule class contains information about molecules.

SYNOPSIS

       #include <molecule.h>

       Inherits sc::SavableState.

   Public Member Functions
       Molecule (const Molecule &)
       Molecule (StateIn &)
       Molecule (const Ref< KeyVal > &input)
           The Molecule KeyVal constructor is used to generate a Molecule
           object from the input.
       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 iuniqth unique atom.
       int nequivalent (int iuniq) const
           Returns the number of atoms equivalent to iuniq.
       int equivalent (int iuniq, int j) const
           Returns the jth 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 molecules 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.

   Protected Member Functions
       void init_symmetry_info (double tol=0.5)
       void clear_symmetry_info ()
       void clear ()
       void throw_if_atom_duplicated (int begin=0, double tol=1e-3)

   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_
       int q_Z_
       bool include_q_
       bool include_qq_
       std::vector< int > q_atoms_
       std::vector< int > non_q_atoms_

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 which can be overridden with unit=angstrom.
       The atom_labels array can be omitted. The atoms and geometry arrays are
       required.

       As a special case, an atom can be given with the symbol Q or the name
       charge. Such centers are treated as point charges and not given basis
       functions. The values of the charges must be specified with a charge
       vector in the Molecule input. Since the charge vector assign charges to
       all centers, including atoms, it is easiest to place all point charge
       centers first in the geometry, and then give a charge vector with a
       number of elements equal to the number of point charges. The following
       example shows a water molecule interacting with a point charge having
       value 0.1:

       molecule<Molecule>: (
           unit=angstrom
           charge = [ 0.1 ]
           { atom_labels atoms           geometry            } = {
                 Q1         Q   [ 0.0         0 10.0         ]
                 O1         O   [ 0.000000000 0  0.369372944 ]
                 H1         H   [ 0.783975899 0 -0.184686472 ]
                 H2         H   [-0.783975899 0 -0.184686472 ]
            }
           )
         )

       This feature is designed for doing QM/MM calculations, so, by default,
       methods will not include interactions between the Q centers when
       computing the energy or the gradient. To include these interactions,
       set include_qq=1.

       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 $C_{2v}$ 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.

Constructor & Destructor Documentation

   sc::Molecule::Molecule (const Ref< KeyVal > & input)
       The Molecule KeyVal constructor is used to generate a Molecule object
       from the input. Several examples are given in the Molecule class
       overview. The full list of keywords that are accepted is below.

       KeywordTypeDefaultDescription

       include_qbooleanfalseSome of the atoms can be specified as Q and given
       a customizable charge. Such atoms are a point charge that do not have
       basis functions. If this option is true, then the Q atoms are included
       when computing the nuclear charge and the electric field due to the
       nuclear charge.

       include_qqbooleanfalseSome of the atoms can be specified as Q and given
       a customizable charge. Such atoms are a point charge that do not have
       basis functions. If this option is true, then the Q atoms are included
       when computing the nuclear repulsion energy and its derivatives.

       atominfoAtomInfolibrary valuesThis gives information about each atom,
       such as the symbol, name, and various atomic radii.

       symmetrystringC1The Schoenflies symbol of the point group. This is case
       insensitive. It should be a subgroup of D2h . If it is auto, then the
       appropriate subgroup of D2h  will be found.

       symmetry_tolerancedouble1.0e-4When a molecule has symmetry, some atoms
       may be related by symmetry operations. The distance between given atoms
       and atoms generated by symmetry operations is compared to this
       threshold to determine if they are the same. If they are the same, then
       the coordinates are cleaned up to make them exactly symmetry
       equivalent. If the given molecule was produced by a optimization that
       started in C1 symmetry, but produced a roughly symmetric structure and
       you would like to begin using symmetry, then this may need to be
       increased a bit to properly symmetrize the molecule.

       symmetry_framedouble[3][3][[1 0 0][0 1 0][0 0 1]]The symmetry frame.
       Ignored for symmetry = auto.

       origindouble[3][0 0 0]The origin of the symmetry frame. Ignored for
       symmetry = auto.

       redundant_atomsbooleanfalseIf true, do not generate symmetry equivalent
       atoms; they are already given in the input. It should not be necessary
       to specify this option, since, by default, if a symmetry operation
       duplicates an atom, the generated atom will not be added to the list of
       atoms. Ignored for symmetry = auto.

       pdb_filestringundefinedThis gives the name of a PDB file, from which
       the nuclear coordinates will be read. If this is given, the following
       options will be ignored.

       unitstringbohrThis gives the name of the units used for the geometry.
       See the Units class for information about the known units. This
       replaces deprecated keywords that are still recognized: angstrom and
       angstroms. This is ignored if pdb_file is given.

       geometrydouble[][3]noneThis gives the Cartesian coordinates of the
       molecule. This is ignored if pdb_file is given.

       atomsstring[]noneThis gives the Cartesian coordinates of the molecule.
       This is ignored if pdb_file is given.

       ghostboolean[]noneIf true, the atom will be given zero charge. It will
       still have basis functions, however. This is used to estimate basis set
       superposition error. This is ignored if pdb_file is given.

       chargedouble[]Z for each atomAllows specification of the charge for
       each atom. This is ignored if pdb_file is given.

       atom_labelsstring[]noneThis gives a user defined atom label for each
       atom. This is ignored if pdb_file is given.

       massdouble[]Taken from AtomInfo given by the atominfo keyword. This
       gives a user defined mass for each atom. This is ignored if pdb_file is
       given.

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.

   SCVector3 sc::Molecule::center_of_mass () const
       Returns a SCVector3 containing the cartesian coordinates of the center
       of mass for the molecule.

   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::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 sc::Molecule::nuclear_repulsion_1der (int center, double xyz[3])
       Compute the nuclear repulsion energy first derivative with respect to
       the given center.

   void sc::Molecule::principal_moments_of_inertia (double * evals, double **
       evecs = 0) const
       Compute the principal moments of inertia and, possibly, the principal
       axes.

   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::set_include_q (bool iq) [inline]
       If include_q is true, then include the ’Q’ atoms in the charge and
       efield routines.

   void sc::Molecule::set_include_qq (bool iqq) [inline]
       If include_qq is true, include the coupling between pairs of ’Q’ atoms
       when computing nuclear repulsion energy and gradients.

   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.

Author

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