Classes
class	sc::Atom
	Atom represents an atom in a Molecule. More...

class	sc::AtomInfo
	The AtomInfo class provides information about atoms. More...

class	sc::IntCoor
	The IntCoor abstract class describes an internal coordinate of a molecule. More...

class	sc::SumIntCoor
	SumIntCoor is used to construct linear combinations of internal coordinates. More...

class	sc::SetIntCoor
	The SetIntCoor class describes a set of internal coordinates. More...

class	sc::IntCoorGen
	IntCoorGen generates a set of simple internal coordinates for a molecule. More...

class	sc::MolecularCoor
	The MolecularCoor abstract class describes the coordinate system used to describe a molecule. More...

class	sc::IntMolecularCoor
	The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates. More...

class	sc::SymmMolecularCoor
	The SymmMolecularCoor class derives from IntMolecularCoor. More...

class	sc::RedundMolecularCoor
	The RedundMolecularCoor class provides a redundant set of simple internal coordinates. More...

class	sc::CartMolecularCoor
	The CartMolecularCoor class implements Cartesian coordinates in a way suitable for use in geometry optimizations. More...

class	sc::MolecularHessian
	MolecularHessian is an abstract class that computes a molecule's second derivatives of the energy with respect to changes in the nuclear coordinates. More...

class	sc::ReadMolecularHessian
	ReadMolecularHessian is an implementation of MolecularHessian that reads the hessian from a file. More...

class	sc::GuessMolecularHessian
	GuessMolecularHessian is an implementation of MolecularHessian that estimates the hessian based on the internal coordinates. More...

class	sc::DiagMolecularHessian
	DiagMolecularHessian is an implementation of MolecularHessian that returns a hessian that is a diagonal matrix. More...

class	sc::MolecularGradient
	MolecularGradient is an abstract class that computes a molecule's first derivatives of the energy with respect to changes in the nuclear coordinates. More...

class	sc::MolecularEnergy
	The MolecularEnergy abstract class inherits from the Function class. More...

class	sc::SumMolecularEnergy
	linear combination of MolecularEnergy objects More...

class	sc::MolEnergyConvergence

class	sc::Displacements< Value >
	Maps displacements in terms of symmetrized coordinates to property values. More...

struct	sc::EGH
	energy + gradient + hessian More...

class	sc::FinDispMolecularHessian
	Computes the molecular hessian by finite displacements of gradients (or, if not available, energies). More...

class	sc::FinDispMolecularGradient
	Computes the molecular gradient by finite differences of energies. More...

class	sc::MolecularFormula
	The MolecularFormula class is used to calculate the molecular formula of a Molecule. More...

class	sc::MolecularFragment
	MolecularFragment is a Molecule that is a fragment of another Molecule object. More...

class	sc::Molecule
	The Molecule class contains information about molecules. More...

class	sc::MolecularFrequencies
	The MolecularFrequencies class is used to compute the molecular frequencies and thermodynamic information. More...

class	sc::MolFreqAnimate

class	sc::SimpleCo
	The SimpleCo abstract class describes a simple internal coordinate of a molecule. More...

class	sc::StreSimpleCo
	The StreSimpleCo class describes an stretch internal coordinate of a molecule. More...

class	sc::BendSimpleCo
	The BendSimpleCo class describes an bend internal coordinate of a molecule. More...

class	sc::TorsSimpleCo
	The TorsSimpleCo class describes an torsion internal coordinate of a molecule. More...

class	sc::ScaledTorsSimpleCo
	The ScaledTorsSimpleCo class describes an scaled torsion internal coordinate of a molecule. More...

class	sc::OutSimpleCo

class	sc::LinIPSimpleCo
	The LinIPSimpleCo class describes an in-plane component of a linear bend internal coordinate of a molecule. More...

class	sc::LinOPSimpleCo
	The LinOPSimpleCo class describes an out-of-plane component of a linear bend internal coordinate of a molecule. More...

class	sc::TaylorMolecularEnergy

Macros
#define	SimpleCo_DECLARE(classname)

#define	SimpleCo_IMPL_eq(classname)

#define	SimpleCo_IMPL_StateIn(classname)

#define	SimpleCo_IMPL_save_data_state(classname)

#define	SimpleCo_IMPL(classname)

Typedefs
typedef StreSimpleCo	sc::Stre

typedef BendSimpleCo	sc::Bend

typedef TorsSimpleCo	sc::Tors

typedef ScaledTorsSimpleCo	sc::ScaledTors

typedef OutSimpleCo	sc::Out

typedef LinIPSimpleCo	sc::LinIP

typedef LinOPSimpleCo	sc::LinOP

Functions
void	sc::ToStateOut (const Atom &a, StateOut &so, int &count)
	writes Atom to sc::StateOut

void	sc::FromStateIn (Atom &a, StateIn &si, int &count)
	reads Atom from sc::StateIn

bool	sc::operator== (const Atom &a, const Atom &b)

bool	sc::operator!= (const Atom &a, const Atom &b)

template<>
void	sc::FromStateIn< EGH > (EGH &v, StateIn &s, int &count)

template<>
void	sc::ToStateOut< EGH > (const EGH &v, StateOut &so, int &count)

bool	sc::operator== (const Molecule &mol1, const Molecule &mol2)

Detailed Description

Provides Molecule class and related functionality.

Macro Definition Documentation

◆ SimpleCo_DECLARE

#define SimpleCo_DECLARE ( classname )

Value:

public:                                   \
    virtual classname& operator=(const classname&);               \
    SimpleCo& operator=(const SimpleCo&);                     \
    double calc_force_con(Molecule&);                         \
    double calc_intco(Molecule&, double* =0, double =1);              \
    classname(StateIn&);                              \
    void save_data_state(StateOut&)

◆ SimpleCo_IMPL

#define SimpleCo_IMPL ( classname )

Value:

SimpleCo_IMPL_eq(classname)     \
        SimpleCo_IMPL_StateIn(classname)    \
        SimpleCo_IMPL_save_data_state(classname)

◆ SimpleCo_IMPL_eq

#define SimpleCo_IMPL_eq ( classname )

Value:

SimpleCo& classname::operator=(const SimpleCo& c)                 \
{                                         \
  classname *cp = dynamic_cast<classname*>((SimpleCo*)&c);                \
  if(cp) {                                    \
      *this=*cp;                                  \
    }                                         \
  else {                                      \
      natoms_ = 0;                                \
      atoms = 0;                                  \
    }                                         \
                                          \
  return *this;                                   \
  }

◆ SimpleCo_IMPL_save_data_state

#define SimpleCo_IMPL_save_data_state ( classname )

Value:

void classname::save_data_state(StateOut&so)                      \
{                                         \
  SimpleCo::save_data_state(so);                          \
}

◆ SimpleCo_IMPL_StateIn

#define SimpleCo_IMPL_StateIn ( classname )

Value:

classname::classname(StateIn&si):                         \
  SimpleCo(si)                                    \
{                                         \
}

Function Documentation

◆ operator!=()

bool sc::operator!=	(	const Atom &	a,
		const Atom &	b
	)

inline

Returns: false if a and b are exactly identical

◆ operator==() [1/2]

bool sc::operator==	(	const Atom &	a,
		const Atom &	b
	)

Returns: true if a and b are exactly identical

◆ operator==() [2/2]

bool sc::operator==	(	const Molecule &	mol1,
		const Molecule &	mol2
	)

Returns: true is mol1 and mol2 are exactly identical (this includes symmetry, frame, atom ordering, and fragments)

Classes

Macros

Typedefs

Functions

Detailed Description

Macro Definition Documentation

◆ SimpleCo_DECLARE

◆ SimpleCo_IMPL

◆ SimpleCo_IMPL_eq

◆ SimpleCo_IMPL_save_data_state

◆ SimpleCo_IMPL_StateIn

Function Documentation

◆ operator!=()

◆ operator==() [1/2]

◆ operator==() [2/2]