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

#include <chemistry/molecule/findisp.h>

Inheritance diagram for sc::FinDispMolecularHessian:

Public Member Functions
	FinDispMolecularHessian (const Ref< MolecularEnergy > &)

	FinDispMolecularHessian (const Ref< KeyVal > &)
	The FinDispMolecularHessian KeyVal constructor is used to generate a FinDispMolecularHessian object from the input. More...

	FinDispMolecularHessian (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...

RefSymmSCMatrix	cartesian_hessian ()
	This returns the cartesian hessian. More...

void	set_energy (const Ref< MolecularEnergy > &energy)
	Some MolecularHessian specializations require a molecular energy object. More...

MolecularEnergy *	energy () const
	This returns a MolecularEnergy object, if used by this specialization. More...

const Ref< Params > &	params () const

void	set_desired_accuracy (double acc)
	Sets the desired accuracy. More...

Public Member Functions inherited from sc::MolecularHessian
	MolecularHessian (const Ref< KeyVal > &)
	The MolecularHessian KeyVal constructor is used to generate a MolecularHessian derivative object from the input. More...

	MolecularHessian (StateIn &)

RefSCDimension	d3natom ()

Ref< SCMatrixKit >	matrixkit () const

virtual double	desired_accuracy () const
	Reports the desired accuracy. More...

bool	desired_accuracy_set_to_default () const

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.

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

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...

Protected Member Functions
void	init_pimpl (const Ref< MolecularEnergy > &e)
	initializes pimpl_, it should not be called until e is fully initalized, hence use this lazily

void	restart ()

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 &)

Additional Inherited Members
Static Public Member Functions inherited from sc::MolecularHessian
static RefSCMatrix	cartesian_to_symmetry (const Ref< Molecule > &m, Ref< PointGroup > pg=0, Ref< SCMatrixKit > kit=0)
	Find transformation matrix from cartesian to symmetry coordinates.

static void	write_cartesian_hessian (const char *filename, const Ref< Molecule > &m, const RefSymmSCMatrix &hess)
	Write the hessian in a simple text format.

static void	read_cartesian_hessian (const char *filename, const Ref< Molecule > &m, const RefSymmSCMatrix &hess)
	Read the hessian from a simple text format.

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 Attributes inherited from sc::MolecularHessian
Ref< Molecule >	mol_

RefSCDimension	d3natom_

Ref< SCMatrixKit >	matrixkit_

Detailed Description

Computes the molecular hessian by finite displacements of gradients (or, if not available, energies).

This will use the minimum number of displacements, each in the highest possible point group.

Constructor & Destructor Documentation

◆ FinDispMolecularHessian()

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

The FinDispMolecularHessian KeyVal constructor is used to generate a FinDispMolecularHessian object from the input.

It reads the keywords below.

Keyword	Type	Default	Description
`energy`	MolecularEnergy	none	This gives an object which will be used to compute the gradients (or energies) needed to form the hessian. If this is not specified, the object using FinDispMolecularHessian will, in some cases, fill it in appropriately. However, even in these cases, it may be desirable to specify this keyword. For example, this could be used in an optimization to compute frequencies using a lower level of theory.
`debug`	boolean	false	If true, print out debugging information.
`point_group`	PointGroup	none	The point group to use for generating the displacements.
`restart`	boolean	true	If true, and a checkpoint file exists, restart from that file.
`restart_file`	string	basename`.ckpt.hess`	The name of the file where checkpoint information is written to or read from.
`checkpoint`	boolean	false	If true, checkpoint intermediate data.
`only_totally_symmetric`	boolean	false	If true, only follow totally symmetric displacments. The hessian will not be complete, but it has enough information to use it in a geometry optimization.
`eliminate_quadratic_terms`	boolean	see notes	If `true`, then contributions to the hessian quadratic in the displacement will be eliminated (i.e. the leading-order errors will be quartic in the displacement). If implemented in terms of gradients, this requires that two displacements are done for each totally symmetric coordinate, rather than one. If implemented in terms of energies, this requires twice as many displacements as the standard algorithm for each force constant, regardless of its symmetry. If using gradients, the default setting is `true` (in such case setting this keyword to `false` will produces lower accuracy which will only be sufficient for geometry optimizations). If using energies, the default setting is `false`. Benchmark calculations should always set this to `true`.
`do_null_displacement`	boolean	true	Run the calculation at the given geometry as well.
`displacement`	double	1.0e-2	The size of the displacement in Bohr.
`gradient_accuracy`	double	`accuracy` `displacement`	The accuracy to which the gradients will be computed.
`energy_accuracy`	double	`accuracy` `displacement`^2	The accuracy to which the energies will be computed.
`use_energies`	boolean	false	Setting to true will force computation from energies.

Member Function Documentation

◆ cartesian_hessian()

RefSymmSCMatrix sc::FinDispMolecularHessian::cartesian_hessian ( )

virtual

This returns the cartesian hessian.

If it has not yet been computed, it will be computed by finite displacements.

Implements sc::MolecularHessian.

◆ energy()

MolecularEnergy* sc::FinDispMolecularHessian::energy ( ) const

inlinevirtual

This returns a MolecularEnergy object, if used by this specialization.

Otherwise null is returned.

Reimplemented from sc::MolecularHessian.

References sc::Ref< T >::pointer().

◆ save_data_state()

void sc::FinDispMolecularHessian::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::MolecularHessian.

◆ set_desired_accuracy()

void sc::FinDispMolecularHessian::set_desired_accuracy ( double acc )

virtual

Sets the desired accuracy.

Parameters

acc	the desired accuracy

Reimplemented from sc::MolecularHessian.

◆ set_energy()

void sc::FinDispMolecularHessian::set_energy ( const Ref< MolecularEnergy > & energy )

virtual

Some MolecularHessian specializations require a molecular energy object.

The default implementations of this ignores the argument.

Reimplemented from sc::MolecularHessian.

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

src/lib/chemistry/molecule/findisp.h

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FinDispMolecularHessian()

Member Function Documentation

◆ cartesian_hessian()

◆ energy()

◆ save_data_state()

◆ set_desired_accuracy()

◆ set_energy()