MPQC  3.0.0-alpha
sc::CartMolecularCoor Class Reference

The CartMolecularCoor class implements Cartesian coordinates in a way suitable for use in geometry optimizations. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::CartMolecularCoor:
sc::MolecularCoor sc::SavableState sc::DescribedClass sc::RefCount

Public Member Functions

 CartMolecularCoor (Ref< Molecule > &mol)
 
 CartMolecularCoor (StateIn &)
 
 CartMolecularCoor (const Ref< KeyVal > &)
 The KeyVal constructor.
 
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...
 
virtual RefSCDimension dim ()
 These implement the virtual functions inherited from MolecularCoor.
 
virtual int to_cartesian (const Ref< Molecule > &, const RefSCVector &internal)
 
virtual int to_internal (RefSCVector &internal)
 Fill in the vector `‘internal’' with the current internal coordinates. More...
 
virtual int to_cartesian (RefSCVector &cartesian, RefSCVector &internal)
 Convert the internal coordinate gradients in `‘internal’' to Cartesian coordinates and copy these Cartesian coordinate gradients to `‘cartesian’'. More...
 
virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)
 Convert the Cartesian coordinate gradients in `‘cartesian’' to internal coordinates and copy these internal coordinate gradients to `‘internal’'. More...
 
virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
 Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''. More...
 
virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
 Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. More...
 
virtual void print (std::ostream &=ExEnv::out0()) const
 Print the coordinate.
 
virtual void print_simples (std::ostream &=ExEnv::out0()) const
 
void guess_hessian (RefSymmSCMatrix &hessian)
 Calculate an approximate hessian and place the result in `‘hessian’'.
 
RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
 Given an Hessian, return the inverse of that hessian. More...
 
- Public Member Functions inherited from sc::MolecularCoor
 MolecularCoor (Ref< Molecule > &)
 
 MolecularCoor (StateIn &)
 
 MolecularCoor (const Ref< KeyVal > &)
 The KeyVal constructor. More...
 
RefSCDimension dim_natom3 ()
 Returns a smart reference to an SCDimension equal to the number of atoms in the molecule times 3.
 
Ref< Moleculemolecule () const
 Returns the molecule.
 
int to_cartesian (const RefSCVector &internal)
 Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. More...
 
virtual int nconstrained ()
 Returns the number of constrained coordinates.
 
virtual Ref< NonlinearTransformchange_coordinates ()
 When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it. More...
 
Ref< SCMatrixKitmatrixkit () const
 
- 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 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< DescribedClassref ()
 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

virtual void init ()
 Initializes the dimensions.
 
- 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 Attributes

RefSCDimension dim_
 
- Protected Attributes inherited from sc::MolecularCoor
Ref< Moleculemolecule_
 
RefSCDimension dnatom3_
 
Ref< SCMatrixKitmatrixkit_
 
int debug_
 

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 CartMolecularCoor class implements Cartesian coordinates in a way suitable for use in geometry optimizations.

CartMolecularCoor is a SavableState has StateIn and KeyVal constructors. CartMolecularCoor is derived from MolecularCoor.

Member Function Documentation

◆ inverse_hessian()

RefSymmSCMatrix sc::CartMolecularCoor::inverse_hessian ( RefSymmSCMatrix )
virtual

Given an Hessian, return the inverse of that hessian.

For singular matrices this should return the generalized inverse.

Implements sc::MolecularCoor.

◆ save_data_state()

void sc::CartMolecularCoor::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::MolecularCoor.

◆ to_cartesian() [1/2]

virtual int sc::CartMolecularCoor::to_cartesian ( RefSCVector cartesian,
RefSCVector internal 
)
virtual

Convert the internal coordinate gradients in `‘internal’' to Cartesian coordinates and copy these Cartesian coordinate gradients to `‘cartesian’'.

Only the variable internal coordinate gradients are transformed.

Implements sc::MolecularCoor.

◆ to_cartesian() [2/2]

virtual int sc::CartMolecularCoor::to_cartesian ( RefSymmSCMatrix cartesian,
RefSymmSCMatrix internal 
)
virtual

Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''.

Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

◆ to_internal() [1/3]

virtual int sc::CartMolecularCoor::to_internal ( RefSCVector internal)
virtual

Fill in the vector `‘internal’' with the current internal coordinates.

Note that this member will update the values of the variable internal coordinates.

Implements sc::MolecularCoor.

◆ to_internal() [2/3]

virtual int sc::CartMolecularCoor::to_internal ( RefSCVector internal,
RefSCVector cartesian 
)
virtual

Convert the Cartesian coordinate gradients in `‘cartesian’' to internal coordinates and copy these internal coordinate gradients to `‘internal’'.

Only the variable internal coordinate gradients are calculated.

Implements sc::MolecularCoor.

◆ to_internal() [3/3]

virtual int sc::CartMolecularCoor::to_internal ( RefSymmSCMatrix internal,
RefSymmSCMatrix cartesian 
)
virtual

Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''.

Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.


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

Generated at Sun Jan 26 2020 23:24:03 for MPQC 3.0.0-alpha using the documentation package Doxygen 1.8.16.