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

#include <chemistry/molecule/energy.h>

Inheritance diagram for sc::MolecularEnergy:

Public Member Functions
	MolecularEnergy (const MolecularEnergy &)

	MolecularEnergy (const Ref< KeyVal > &)
	The KeyVal constructor. More...

	MolecularEnergy (StateIn &)

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...

void	set_checkpoint ()
	Set up checkpointing.

void	set_checkpoint_file (const char *)

void	set_checkpoint_freq (int freq)

bool	if_to_checkpoint () const
	Check if need to checkpoint.

const char *	checkpoint_file () const

int	checkpoint_freq () const

MolecularEnergy &	operator= (const MolecularEnergy &)

virtual double	energy ()
	A wrapper around value();.

virtual Ref< Molecule >	molecule () const

virtual RefSCDimension	moldim () const

void	guess_hessian (RefSymmSCMatrix &)
	Compute a quick, approximate hessian.

RefSymmSCMatrix	inverse_hessian (RefSymmSCMatrix &)

int	gradient_implemented () const
	Reports whether gradient is implemented either analytically or using MolecularGradient object. More...

int	hessian_implemented () const
	Reports whether hessian is implemented either analytically or using MolecularHessian object. More...

void	set_desired_gradient_accuracy (double acc)
	These functions overload their Function counterparts. More...

void	set_desired_hessian_accuracy (double acc)

void	set_molhess (const Ref< MolecularHessian > &molhess)
	Use this function to provide MolecularHessian object that will be used to compute hessian. More...

const Ref< MolecularHessian > &	molhess () const

RefSymmSCMatrix	hessian ()
	Will throw if hessian_implemented() returns 0.

void	set_molgrad (const Ref< MolecularGradient > &molgrad)
	Use this function to provide MolecularGradient object that will be used to compute gradient. More...

const Ref< MolecularGradient > &	molgrad () const

RefSCVector	gradient ()
	Will throw if gradient_implemented() returns 0.

void	set_x (const RefSCVector &)
	Set and retrieve the coordinate values.

RefSCVector	get_cartesian_x ()
	Return the cartesian coordinates.

RefSCVector	get_cartesian_gradient ()
	Return the cartesian gradient.

RefSymmSCMatrix	get_cartesian_hessian ()
	Return the cartesian hessian.

Ref< MolecularCoor >	molecularcoor ()

virtual void	symmetry_changed ()
	Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.

Ref< NonlinearTransform >	change_coordinates ()
	An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system. More...

virtual void	purge ()
	This function purges any caches of data in MolecularEnergy. More...

const RefSCVector &	electric_field () const
	returns the electric field vector

void	print_natom_3 (const RefSCVector &, const char *t=0, std::ostream &o=ExEnv::out0()) const
	Nicely print n x 3 data that are stored in a vector.

void	print_natom_3 (double *, const char t=0, std::ostream &o=ExEnv::out0()) const

void	print_natom_3 (double , const char t=0, std::ostream &o=ExEnv::out0()) const

virtual void	print (std::ostream &=ExEnv::out0()) const
	Print information about the object.

Public Member Functions inherited from sc::Function
int	gradient_needed () const

int	do_gradient (int)

virtual double	actual_gradient_accuracy () const

virtual double	desired_gradient_accuracy () const

AccResultRefSCVector &	gradient_result ()

int	hessian_needed () const

int	do_hessian (int)

virtual double	actual_hessian_accuracy () const

virtual double	desired_hessian_accuracy () const

AccResultRefSymmSCMatrix &	hessian_result ()

virtual bool	desired_value_accuracy_set_to_default () const

virtual bool	desired_gradient_accuracy_set_to_default () const

virtual bool	desired_hessian_accuracy_set_to_default () const

virtual int	value_implemented () const

RefSCVector	get_x () const

const RefSCVector &	get_x_no_copy () const

void	print_desired_accuracy (std::ostream &=ExEnv::out0()) const
	similar to print(), but only prins desired accuracies

virtual bool	throw_if_tolerance_exceeded () const
	Overridden Compute member.

	Function ()

	Function (StateIn &)

	Function (const Function &)

	Function (const Ref< KeyVal > &, double funcacc=DBL_EPSILON, double gradacc=DBL_EPSILON, double hessacc=DBL_EPSILON)
	The keyval constructor reads the following keywords: More...

virtual	~Function ()

Function &	operator= (const Function &)

Ref< SCMatrixKit >	matrixkit () const
	Return the SCMatrixKit used to construct vectors and matrices.

RefSCDimension	dimension () const
	Return the SCDimension of the problem.

virtual double	value ()
	Return the value of the function.

int	value_needed () const
	Returns nonzero if the current value is not up-to-date.

int	do_value (int)
	If passed a nonzero number, compute the value the next time compute() is called. More...

AccResultdouble &	value_result ()

virtual void	set_desired_value_accuracy (double)
	Set the accuracy to which the value is to be computed.

virtual double	actual_value_accuracy () const
	Return the accuracy with which the value has been computed.

virtual double	desired_value_accuracy () const
	Return the accuracy with which the value is to be computed.

Public Member Functions inherited from sc::SavableState
SavableState &	operator= (const SavableState &)

void	save_state (StateOut &)
	Save the state of the object as specified by the StateOut object. More...

void	save_object_state (StateOut &)
	This can be used for saving state when the exact type of the object is known for both the save and the restore. More...

virtual void	save_vbase_state (StateOut &)
	Save the virtual bases for the object. More...

Public Member Functions inherited from sc::DescribedClass
	DescribedClass (const DescribedClass &)

DescribedClass &	operator= (const DescribedClass &)

ClassDesc *	class_desc () const MPQC__NOEXCEPT
	This returns the unique pointer to the ClassDesc corresponding to the given type_info object. More...

const char *	class_name () const
	Return the name of the object's exact type.

int	class_version () const
	Return the version of the class.

Ref< DescribedClass >	ref ()
	Return this object wrapped up in a Ref smart pointer. More...

Public Member Functions inherited from sc::RefCount
size_t	identifier () const
	Return the unique identifier for this object that can be compared for different objects of different types. More...

int	lock_ptr () const
	Lock this object.

int	unlock_ptr () const
	Unlock this object.

void	use_locks (bool inVal)
	start and stop using locks on this object

refcount_t	nreference () const
	Return the reference count.

refcount_t	reference ()
	Increment the reference count and return the new count.

refcount_t	dereference ()
	Decrement the reference count and return the new count.

int	managed () const

void	unmanage ()
	Turn off the reference counting mechanism for this object. More...

Public Member Functions inherited from sc::Compute
virtual void	obsolete ()
	Marks all results as being out of date. More...

Protected Member Functions
void	failure (const char *)

virtual void	set_energy (double)
	This is just a wrapper around set_value().

virtual void	set_gradient (RefSCVector &)
	These are passed gradients and hessian in cartesian coordinates. More...

virtual void	set_hessian (RefSymmSCMatrix &)

void	x_to_molecule ()

void	molecule_to_x ()

virtual bool	nonzero_efield_supported () const
	overload this in classes that support computations in nonzero electric field the default is to not support external electric fields.

virtual bool	analytic_gradient_implemented () const
	must overload this in a derived class if analytic gradient can be computed More...

virtual bool	analytic_hessian_implemented () const
	must overload this in a derived class if analytic hessian can be computed More...

Protected Member Functions inherited from sc::Function
virtual void	set_value (double)

virtual void	set_matrixkit (const Ref< SCMatrixKit > &)
	Set the SCMatrixKit that should be used to construct the requisite vectors and matrices.

virtual void	set_dimension (const RefSCDimension &)

virtual void	set_actual_value_accuracy (double)

virtual void	set_actual_gradient_accuracy (double)

virtual void	set_actual_hessian_accuracy (double)

RefSCVector &	get_x_reference ()
	Get read/write access to the coordinates for modification.

void	do_change_coordinates (const Ref< NonlinearTransform > &)
	Change the coordinate system and apply the given transform to intermediates matrices and vectors.

Protected Member Functions inherited from sc::SavableState
	SavableState (const SavableState &)

	SavableState (StateIn &)
	Each derived class StateIn CTOR handles the restore corresponding to calling save_object_state, save_vbase_state, and save_data_state listed above. More...

Protected Member Functions inherited from sc::RefCount
	RefCount (const RefCount &)

RefCount &	operator= (const RefCount &)

Protected Member Functions inherited from sc::Compute
virtual void	compute ()=0
	Recompute at least the results that have compute true and are not already computed. More...

Protected Attributes
Ref< PointGroup >	initial_pg_

int	print_molecule_when_changed_

Protected Attributes inherited from sc::Function
Ref< SCMatrixKit >	matrixkit_
	Used to construct new matrices.

RefSCVector	x_
	The variables.

RefSCDimension	dim_
	The dimension of x_.

AccResultdouble	value_
	The value of the function at x_.

AccResultRefSCVector	gradient_
	The gradient at x_.

AccResultRefSymmSCMatrix	hessian_
	The hessian at x_.

bool	desired_value_accuracy_set_to_default_

bool	desired_gradient_accuracy_set_to_default_

bool	desired_hessian_accuracy_set_to_default_

bool	throw_if_tolerance_exceeded_

Additional Inherited Members
Static Public Member Functions inherited from sc::SavableState
static void	save_state (SavableState *s, StateOut &)

static SavableState *	restore_state (StateIn &si)
	Restores objects saved with save_state. More...

static SavableState *	key_restore_state (StateIn &si, const char *keyword)
	Like restore_state, but keyword is used to override values while restoring.

static SavableState *	dir_restore_state (StateIn &si, const char objectname, const char keyword=0)

Detailed Description

The MolecularEnergy abstract class inherits from the Function class.

It computes the energy of the molecule as a function of the geometry. The coordinate system used can be either internal or cartesian.

Constructor & Destructor Documentation

◆ MolecularEnergy()

sc::MolecularEnergy::MolecularEnergy ( const Ref< KeyVal > & )

The KeyVal constructor.

molecule

A Molecule object. There is no default.

coor

A MolecularCoor object that describes the coordinates. If this is not given cartesian coordinates will be used. For convenience, two keywords needed by the MolecularCoor object are automatically provided: natom3 and matrixkit.

value_accuracy

Sets the accuracy to which values are computed. The default is 1.0e-6 atomic units.

gradient_accuracy

Sets the accuracy to which gradients are computed. The default is 1.0e-6 atomic units.

hessian_accuracy

Sets the accuracy to which hessians are computed. The default is 1.0e-4 atomic units.

hessian

Specifies a MolecularHessian object that is used to compute the hessian. This keyword may only need to be specified. if "exact" hessian is needed but this MolecularEnergy specialization does not provide a hessian of its own.

guess_hessian

Specifies a MolecularHessian object that is used to compute a guess hessian. Guess hessians are used to improve the rate of convergence of optimizations. If this keyword is not specified, and a MolecularCoor object is given by coor, then the guess hessian is obtained from the MolecularCoor object. If neither this nor coor are given, then Function::guess_hessian is used, which returns a unit matrix.

electric_field

This 3-element vector specifies the Cartesian components of an external uniform electric field, in a.u. The default value, [0 0 0], causes computations in absence of an electric field. Not all MolecularEnergy objects will support computations in presence of an electric field – use MolecularEnergy::nonzero_efield_supported() to query objects about this capability.

print_molecule_when_changed

If true, then whenever the molecule's coordinates are updated they will be printed. The default is true.

checkpoint

If true, then this object will be checkpointed during its evaluation. Not all implementations of MolecularEnergy support checkpointing. The default is false.

checkpoint_file

Specifies the name of the file into which this object will be checkpointed. Default is "<inpubasename>.ckpt", where "<inputbasename>" is the name of the input file without ".in".

checkpoint_freq

Specifies how often this object to be checkpointed. Only matters for objects which are computed iteratively. Default is 1.

Member Function Documentation

◆ analytic_gradient_implemented()

virtual bool sc::MolecularEnergy::analytic_gradient_implemented ( ) const

protectedvirtual

must overload this in a derived class if analytic gradient can be computed

Returns: true (analytic gradient is available) or false (analytic gradient is not available, default)

Reimplemented in sc::PsiUHF, sc::PsiHSOSHF, sc::PsiCLHF, sc::SumMolecularEnergy, sc::MBPT2, sc::PsiCCSD, sc::MBPT2_R12, sc::HSOSKS, sc::CLKS, sc::UKS, sc::TaylorMolecularEnergy, sc::UHF, sc::OSSHF, sc::TCHF, sc::CLHF, and sc::HSOSHF.

◆ analytic_hessian_implemented()

virtual bool sc::MolecularEnergy::analytic_hessian_implemented ( ) const

protectedvirtual

must overload this in a derived class if analytic hessian can be computed

Returns: true (analytic hessian is available) or false (analytic hessian is not available, default)

Reimplemented in sc::SumMolecularEnergy, and sc::TaylorMolecularEnergy.

◆ change_coordinates()

Ref<NonlinearTransform> sc::MolecularEnergy::change_coordinates ( )

virtual

An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system.

A return value of 0 means the coordinates were not changed. Otherwise, a transform object to the new coordinate system is return. The function object applies the transform to any objects it contains. This will obsolete the function data.

Reimplemented from sc::Function.

◆ gradient_implemented()

int sc::MolecularEnergy::gradient_implemented ( ) const

virtual

Reports whether gradient is implemented either analytically or using MolecularGradient object.

I don't see a need to reimplement this in a derived class

Returns: 0 (gradient cannot be computed) or 1 (gradient can be computed)

Reimplemented from sc::Function.

◆ hessian_implemented()

int sc::MolecularEnergy::hessian_implemented ( ) const

virtual

Reports whether hessian is implemented either analytically or using MolecularHessian object.

I don't see a need to reimplement this in a derived class

Returns: 0 (hessian cannot be computed) or 1 (hessian can be computed)

Reimplemented from sc::Function.

◆ purge()

virtual void sc::MolecularEnergy::purge ( )

virtual

This function purges any caches of data in MolecularEnergy.

It is useful with MolecularEnergy objects that keep state when obsolete() is called (for example, it makes sense for SCF to keep its old eigenvector and reuse it as a guess when geometry changes). The default implementation does nothing and must be overloaded in classes which need it

Reimplemented in sc::SumMolecularEnergy, sc::SCF, sc::MolcasPT2R12, and sc::ManyBodyWavefunction.

◆ save_data_state()

void sc::MolecularEnergy::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::Function.

Reimplemented in sc::CI, sc::PT2R12, sc::SpinOrbitalPT2R12, sc::PsiRASCI, sc::PsiSCF, sc::SumMolecularEnergy, sc::HCoreWfn, sc::SCF, sc::MBPT2, sc::PsiCC3, sc::PsiCC2, sc::CADFCLHF, sc::PsiRASSCF, sc::PsiCorrWavefunction, sc::PsiCCSD_T, sc::Wavefunction, sc::PsiCCSD, sc::PsiCC3_PT2R12, sc::PsiCC, sc::PsiCCSD_PT2R12T, sc::MBPT2_R12, sc::HSOSSCF, sc::PsiCCSD_PT2R12, sc::UnrestrictedSCF, sc::PsiWavefunction, sc::TCSCF, sc::PsiCC_PT2R12, sc::OSSSCF, sc::DFCLHF, sc::ExtendedHuckelWfn, sc::OneBodyWavefunction, sc::SuperpositionOfAtomicDensities, sc::HSOSKS, sc::TaylorMolecularEnergy, sc::ManyBodyWavefunction, sc::CLSCF, sc::UKS, sc::CLKS, sc::FockBuildCLHF, sc::UHF, sc::OSSHF, sc::TCHF, sc::CLHF, sc::HSOSHF, sc::MP2BasisExtrap, sc::LMP2, and sc::LCorr.

◆ set_desired_gradient_accuracy()

void sc::MolecularEnergy::set_desired_gradient_accuracy ( double acc )

virtual

These functions overload their Function counterparts.

If hessian/gradient objects are provided, these functions will convey desired accuracy to them.

Reimplemented from sc::Function.

◆ set_gradient()

virtual void sc::MolecularEnergy::set_gradient ( RefSCVector & )

protectedvirtual

These are passed gradients and hessian in cartesian coordinates.

The gradient and hessian in internal coordinates are computed.

Reimplemented from sc::Function.

◆ set_molgrad()

void sc::MolecularEnergy::set_molgrad ( const Ref< MolecularGradient > & molgrad )

Use this function to provide MolecularGradient object that will be used to compute gradient.

You can call this function with null pointer to restore the state to the original state.

◆ set_molhess()

void sc::MolecularEnergy::set_molhess ( const Ref< MolecularHessian > & molhess )

Use this function to provide MolecularHessian object that will be used to compute hessian.

You can call this function with null pointer to restore the state to the original state.

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

src/lib/chemistry/molecule/energy.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MolecularEnergy()

Member Function Documentation

◆ analytic_gradient_implemented()

◆ analytic_hessian_implemented()

◆ change_coordinates()

◆ gradient_implemented()

◆ hessian_implemented()

◆ purge()

◆ save_data_state()

◆ set_desired_gradient_accuracy()

◆ set_gradient()

◆ set_molgrad()

◆ set_molhess()