MPQC  2.3.1
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
sc::MolecularEnergy Class Reference

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

#include <energy.h>

Inheritance diagram for sc::MolecularEnergy:
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Collaboration diagram for sc::MolecularEnergy:
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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
 
MolecularEnergyoperator= (const MolecularEnergy &)
 
virtual double energy ()
 A wrapper around value();.
 
virtual Ref< Moleculemolecule () const
 
virtual RefSCDimension moldim () const
 
void guess_hessian (RefSymmSCMatrix &)
 Compute a quick, approximate hessian.
 
RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
 
RefSymmSCMatrix hessian ()
 If a molecule hessian object is given, it will be used to provide a hessian.
 
int hessian_implemented () const
 
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< MolecularCoormolecularcoor ()
 
virtual void symmetry_changed ()
 Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.
 
Ref< NonlinearTransformchange_coordinates ()
 An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system. More...
 
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
virtual RefSCVector gradient ()
 
int gradient_needed () const
 
int do_gradient (int)
 
virtual void set_desired_gradient_accuracy (double)
 
virtual double actual_gradient_accuracy () const
 
virtual double desired_gradient_accuracy () const
 
AccResultRefSCVectorgradient_result ()
 
int hessian_needed () const
 
int do_hessian (int)
 
virtual void set_desired_hessian_accuracy (double)
 
virtual double actual_hessian_accuracy () const
 
virtual double desired_hessian_accuracy () const
 
AccResultRefSymmSCMatrixhessian_result ()
 
virtual int value_implemented () const
 Information about the availability of values, gradients, and hessians.
 
virtual int gradient_implemented () const
 
RefSCVector get_x () const
 
const RefSCVectorget_x_no_copy () const
 
 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 ()
 
Functionoperator= (const Function &)
 
Ref< SCMatrixKitmatrixkit () 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...
 
AccResultdoublevalue_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
SavableStateoperator= (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 &)
 
DescribedClassoperator= (const DescribedClass &)
 
ClassDescclass_desc () const throw ()
 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.
 
- Public Member Functions inherited from sc::RefCount
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...
 
int managed () const
 Return 1 if the object is managed. Otherwise return 0.
 
- Public Member Functions inherited from sc::Identity
Identifier identifier ()
 Return the Identifier for this argument. 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 ()
 
- 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)
 
RefSCVectorget_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 &)
 
RefCountoperator= (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< PointGroupinitial_pg_
 
int print_molecule_when_changed_
 
- Protected Attributes inherited from sc::Function
Ref< SCMatrixKitmatrixkit_
 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_.
 

Additional Inherited Members

- Static Public Member Functions inherited from sc::SavableState
static void save_state (SavableState *s, StateOut &)
 
static SavableStaterestore_state (StateIn &si)
 Restores objects saved with save_state. More...
 
static SavableStatekey_restore_state (StateIn &si, const char *keyword)
 Like restore_state, but keyword is used to override values while restoring.
 
static SavableStatedir_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. If this MolecularEnergy specialization does not provide a hessian of its own, and a hessian is needed, then this keyword must be specified.

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.

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

◆ 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.

◆ 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::MBPT2, sc::MBPT2_R12, sc::SumMolecularEnergy, sc::HCoreWfn, sc::SCF, sc::PsiCCSD_T, sc::PsiCCSD, sc::Wavefunction, sc::HSOSSCF, sc::PsiSCF, sc::HSOSKS, sc::OneBodyWavefunction, sc::UKS, sc::CLSCF, sc::CLKS, sc::UnrestrictedSCF, sc::TaylorMolecularEnergy, sc::TCSCF, sc::ExtendedHuckelWfn, sc::OSSSCF, sc::PsiWavefunction, sc::UHF, sc::CLHF, sc::HSOSHF, sc::MP2BasisExtrap, sc::OSSHF, and sc::TCHF.

◆ 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.


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

Generated at Sun Jan 26 2020 23:33:07 for MPQC 2.3.1 using the documentation package Doxygen 1.8.16.