plucky (3) sc_MolecularEnergy.3.gz
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.
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
AccResultRefSCVector & gradient_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
AccResultRefSymmSCMatrix & hessian_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 RefSCVector & get_x_no_copy () const
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:
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.
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.
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.
virtual void save_vbase_state (StateOut &)
Save the virtual bases for the object.
Public Member Functions inherited from sc::DescribedClass
DescribedClass (const DescribedClass &)
DescribedClass & operator= (const DescribedClass &)
ClassDesc * class_desc () const throw ()
This returns the unique pointer to the ClassDesc corresponding to the given type_info
object.
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.
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.
Public Member Functions inherited from sc::Compute
virtual void obsolete ()
Marks all results as being out of date.
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 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.
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.
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_.
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.
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
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.
Reimplemented from sc::Function.
void sc::MolecularEnergy::guess_hessian (RefSymmSCMatrix &) [virtual]
Compute a quick, approximate hessian.
Reimplemented from sc::Function.
RefSymmSCMatrix sc::MolecularEnergy::hessian () [virtual]
If a molecule hessian object is given, it will be used to provide a hessian.
Reimplemented from sc::Function.
int sc::MolecularEnergy::hessian_implemented () const [virtual]
Reimplemented from sc::Function.
RefSymmSCMatrix sc::MolecularEnergy::inverse_hessian (RefSymmSCMatrix &) [virtual]
Reimplemented from sc::Function.
virtual Ref< Molecule > sc::MolecularEnergy::molecule () const [virtual]
Reimplemented in sc::Wavefunction.
virtual void sc::MolecularEnergy::print (std::ostream & = ExEnv::out0()) const [virtual]
Print information about the object.
Reimplemented from sc::Function.
Reimplemented in sc::TaylorMolecularEnergy, sc::Wavefunction, sc::CLKS, sc::HSOSKS,
sc::UKS, sc::MBPT2, sc::MBPT2_R12, sc::PsiWavefunction, sc::CLHF, sc::CLSCF, sc::HSOSHF,
sc::HSOSSCF, sc::OSSHF, sc::OSSSCF, sc::SCF, sc::TCHF, sc::TCSCF, sc::UHF,
sc::UnrestrictedSCF, and sc::OneBodyWavefunction.
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::SumMolecularEnergy, sc::TaylorMolecularEnergy, sc::UKS,
sc::MP2BasisExtrap, sc::PsiWavefunction, sc::PsiSCF, sc::PsiCCSD, sc::PsiCCSD_T,
sc::OSSHF, sc::OSSSCF, sc::SCF, sc::TCHF, sc::TCSCF, sc::UHF, sc::UnrestrictedSCF,
sc::OneBodyWavefunction, and sc::Wavefunction.
virtual void sc::MolecularEnergy::set_gradient (RefSCVector &) [protected], [virtual]
These are passed gradients and hessian in cartesian coordinates. The gradient and hessian
in internal coordinates are computed.
Reimplemented from sc::Function.
virtual void sc::MolecularEnergy::set_hessian (RefSymmSCMatrix &) [protected], [virtual]
Reimplemented from sc::Function.
void sc::MolecularEnergy::set_x (const RefSCVector &) [virtual]
Set and retrieve the coordinate values.
Reimplemented from sc::Function.
Reimplemented in sc::SumMolecularEnergy.
virtual void sc::MolecularEnergy::symmetry_changed () [virtual]
Call this if you have changed the molecular symmetry of the molecule contained by this
MolecularEnergy.
Reimplemented in sc::MBPT2, sc::CLSCF, sc::HSOSSCF, sc::OSSSCF, sc::SCF, sc::TCSCF,
sc::UnrestrictedSCF, sc::OneBodyWavefunction, and sc::Wavefunction.
Author
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