A Wavefunction is a MolecularEnergy that utilizies a GaussianBasisSet. More...

#include <chemistry/qc/wfn/wfn.h>

Inheritance diagram for sc::Wavefunction:

Public Member Functions
	Wavefunction (StateIn &)

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

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...

double	density (const SCVector3 &)

double	density_gradient (const SCVector3 &, double *)

double	natural_orbital (const SCVector3 &r, int iorb)

double	natural_orbital_density (const SCVector3 &r, int orb, double *orbval=0)

double	orbital (const SCVector3 &r, int iorb, const RefSCMatrix &orbs)

void	orbitals (const SCVector3 &r, const RefSCMatrix &orbs, RefSCVector &values)

double	orbital_density (const SCVector3 &r, int iorb, const RefSCMatrix &orbs, double *orbval=0)

double	total_charge () const
	Returns the total charge of the system.

virtual int	nelectron ()=0
	Returns the number of electrons.

virtual double	magnetic_moment () const
	Computes the S (or J) magnetic moment of the target state(s), in units of $\hbar/2$ . More...

virtual RefSymmSCMatrix	density ()=0
	Returns the SO density.

virtual RefSymmSCMatrix	ao_density ()
	Returns the AO density.

virtual RefSCMatrix	natural_orbitals ()
	Returns the natural orbitals, in SO basis.

virtual RefDiagSCMatrix	natural_density ()
	Returns the natural density (a diagonal matrix).

int	spin_polarized ()
	Return 1 if the magnetic moment != 0.

int	dk () const
	Returns the level the of the Douglas-Kroll approximation.

virtual RefSymmSCMatrix	alpha_density ()
	Return alpha electron densities in the SO basis.

virtual RefSymmSCMatrix	beta_density ()
	Return beta electron densities in the SO basis.

virtual RefSymmSCMatrix	alpha_ao_density ()
	Return alpha electron densities in the AO basis.

virtual RefSymmSCMatrix	beta_ao_density ()
	Return beta electron densities in the AO basis.

virtual RefSCMatrix	nao (double *atom_charges=0)
	returns the ao to nao transformation matrix

virtual RefSymmSCMatrix	overlap ()
	Returns the SO overlap matrix.

virtual RefSymmSCMatrix	core_hamiltonian_for_basis (const Ref< GaussianBasisSet > &bas, const Ref< GaussianBasisSet > &pbas=0)
	Returns the SO core Hamiltonian in the given basis and momentum basis. More...

virtual RefSymmSCMatrix	core_hamiltonian ()
	Returns the SO core Hamiltonian.

RefSymmSCMatrix	core_hamiltonian_nr (const Ref< GaussianBasisSet > &bas)

virtual double	nuclear_repulsion_energy ()
	Returns the nuclear repulsion energy. More...

void	nuclear_repulsion_energy_gradient (double *g)
	Computes the nuclear repulsion gradient. More...

virtual void	nuclear_repulsion_energy_gradient (double **g)
	Computes the nuclear repulsion gradient. More...

RefSCDimension	ao_dimension ()
	Atomic orbital dimension.

RefSCDimension	so_dimension ()
	Symmetry adapted orbital dimension.

RefSCDimension	oso_dimension ()
	Orthogonalized symmetry adapted orbital dimension.

Ref< SCMatrixKit >	basis_matrixkit ()
	Matrix kit for AO, SO, orthogonalized SO, and MO dimensioned matrices.

Ref< Molecule >	molecule () const
	Returns the Molecule.

Ref< GaussianBasisSet >	basis () const
	Returns the basis set.

Ref< GaussianBasisSet >	momentum_basis () const
	Returns the basis used for p^2 in the DK correction.

Ref< GaussianBasisSet >	atom_basis () const
	Returns the basis set describing the nuclear charge distributions.

const double *	atom_basis_coef () const
	Returns the coefficients of the nuclear charge distribution basis functions.

Ref< Integral >	integral ()
	Returns the integral evaluator.

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

RefSCMatrix	so_to_orthog_so ()
	Returns a matrix which does the default transform from SO's to orthogonal SO's. More...

RefSCMatrix	so_to_orthog_so_inverse ()
	Returns the inverse of the transformation returned by so_to_orthog_so.

OverlapOrthog::OrthogMethod	orthog_method () const
	Returns the orthogonalization method.

virtual void	set_orthog_method (const OverlapOrthog::OrthogMethod &)
	(Re)Sets the orthogonalization method and makes this obsolete. More...

double	lindep_tol () const
	Returns the tolerance for linear dependencies.

void	set_lindep_tol (double)
	Re(Sets) the tolerance for linear dependencies.

void	obsolete ()
	Marks all results as being out of date. More...

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

void	writeorbitals ()
	output orbitals to some files to facilitate plotting, with the help of the WriteOrbital class.

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

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

	MolecularEnergy (StateIn &)

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 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 ()

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

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...

Static Public Member Functions
static void	orbitals (const Ref< OrbitalSpace > &orbs, const std::vector< SCVector3 > &r, std::vector< double > &values)

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)

Protected Member Functions
double	min_orthog_res ()

double	max_orthog_res ()

void	copy_orthog_info (const Ref< Wavefunction > &)

Protected Member Functions inherited from sc::MolecularEnergy
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	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
ResultRefSCMatrix	natural_orbitals_

ResultRefDiagSCMatrix	natural_density_

Ref< GaussianBasisSet >	gbs_

int	debug_

Protected Attributes inherited from sc::MolecularEnergy
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_

Detailed Description

A Wavefunction is a MolecularEnergy that utilizies a GaussianBasisSet.

Constructor & Destructor Documentation

◆ Wavefunction()

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

The KeyVal constructor.

It accepts all keywords of MolecularEnergy and the following additional keywords:

basis

Specifies a GaussianBasisSet object. There is no default.

integrals

Specifies an Integral object that computes the two electron integrals. The default is a IntegralV3 object.

orthog_method

This is a string that specifies the orthogonalization method to be used. It can be one one canonical, gramschmidt, or symmetric. The default is symmetric.

lindep_tol

The tolerance used to detect linearly dependent basis functions. The precise meaning depends on the orthogonalization method. The default value is 1e-8.

print_nao

This specifies a boolean value. If true the natural atomic orbitals will be printed. Not all wavefunction will be able to do this. The default is false.

print_npa

This specifies a boolean value. If true the natural population analysis will be printed. Not all wavefunction will be able to do this. The default is true if print_nao is true, otherwise it is false.

debug

This integer can be used to produce output for debugging. The default is 0.

Member Function Documentation

◆ core_hamiltonian_for_basis()

virtual RefSymmSCMatrix sc::Wavefunction::core_hamiltonian_for_basis	(	const Ref< GaussianBasisSet > &	bas,
		const Ref< GaussianBasisSet > &	pbas = `0`
	)

virtual

Returns the SO core Hamiltonian in the given basis and momentum basis.

The momentum basis is not needed if no Douglas-Kroll correction is being performed.

◆ magnetic_moment()

virtual double sc::Wavefunction::magnetic_moment ( ) const

virtual

Computes the S (or J) magnetic moment of the target state(s), in units of $\hbar/2$ .

Can be evaluated from density and overlap, as;

(this->alpha_density() * this-> overlap()).trace() -

(this->beta_density() * this-> overlap()).trace()

but derived Wavefunction may have this value as user input.

Returns: the magnetic moment

Reimplemented in sc::LMP2, sc::PsiSCF, sc::PT2R12, sc::HCoreWfn, sc::MBPT2, sc::PsiCorrWavefunction, sc::HSOSSCF, sc::UnrestrictedSCF, sc::TCSCF, sc::SuperpositionOfAtomicDensities, sc::OSSSCF, sc::CLSCF, sc::ExtendedHuckelWfn, sc::SpinOrbitalPT2R12, sc::PsiRASCI, sc::CCR12, sc::ExternPT2R12, and sc::CI.

Referenced by spin_polarized().

◆ nuclear_repulsion_energy()

virtual double sc::Wavefunction::nuclear_repulsion_energy ( )

virtual

Returns the nuclear repulsion energy.

This must be used instead of Molecule::nuclear_repulsion_energy() since there may be contributions from diffuse atomic charges or an external electric field (

See also: MolecularEnergy::electric_field).

Reimplemented in sc::PsiWavefunction.

◆ nuclear_repulsion_energy_gradient() [1/2]

virtual void sc::Wavefunction::nuclear_repulsion_energy_gradient ( double ** g )

virtual

Computes the nuclear repulsion gradient.

This must be used instead of Molecule::nuclear_repulsion_1der() since there may be contributions from diffuse atomic charges. The gradient, g, is first zeroed. Its dimensions are g[natom][3].

◆ nuclear_repulsion_energy_gradient() [2/2]

void sc::Wavefunction::nuclear_repulsion_energy_gradient ( double * g )

Computes the nuclear repulsion gradient.

This must be used instead of Molecule::nuclear_repulsion_1der() since there may be contributions from diffuse atomic charges. The gradient, g, is zeroed and set to x_0, y_0, z_0, x_1, ... .

◆ obsolete()

void sc::Wavefunction::obsolete ( )

virtual

Marks all results as being out of date.

Any subsequent access to results will cause Compute::compute() to be called.

Reimplemented from sc::Compute.

◆ save_data_state()

void sc::Wavefunction::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::MolecularEnergy.

◆ set_orthog_method()

virtual void sc::Wavefunction::set_orthog_method ( const OverlapOrthog::OrthogMethod & )

virtual

(Re)Sets the orthogonalization method and makes this obsolete.

Must be virtual to allow proper obsoletion of the object.

◆ so_to_orthog_so()

RefSCMatrix sc::Wavefunction::so_to_orthog_so ( )

Returns a matrix which does the default transform from SO's to orthogonal SO's.

This could be either the symmetric or canonical orthogonalization matrix. The row dimension is SO and the column dimension is ortho SO. An operator $O$ in the ortho SO basis is given by $X O X^T$ where $X$ is the return value of this function.

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

src/lib/chemistry/qc/wfn/wfn.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Wavefunction()

Member Function Documentation

◆ core_hamiltonian_for_basis()

◆ magnetic_moment()

◆ nuclear_repulsion_energy()

◆ nuclear_repulsion_energy_gradient() [1/2]

◆ nuclear_repulsion_energy_gradient() [2/2]

◆ obsolete()

◆ save_data_state()

◆ set_orthog_method()

◆ so_to_orthog_so()