sc_MolecularEnergy(3)

NAME

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

SYNOPSIS

#include <energy.h>

Inherits sc::Function.

Inherited by sc::SumMolecularEnergy, sc::TaylorMolecularEnergy, and sc::Wavefunction.

Public Member Functions

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

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. virtual void set_hessian (RefSymmSCMatrix &)
void x_to_molecule ()
void molecule_to_x ()

Protected Attributes

Ref< PointGroup > initial_pg_
int print_molecule_when_changed_

Additional Inherited Members

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

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

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.