sc_MolecularCoor - Man Page

MolecularCoor (Ref< Molecule > &)
MolecularCoor (StateIn &)
MolecularCoor (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.
RefSCDimension dim_natom3 ()
Returns a smart reference to an SCDimension equal to the number of atoms in the molecule times 3.
Ref< Molecule > molecule () const
Returns the molecule.
virtual void print (std::ostream &=ExEnv::out0()) const =0
Print the coordinate.
virtual void print_simples (std::ostream &=ExEnv::out0()) const =0
virtual RefSCDimension dim ()=0
Returns a smart reference to an SCDimension equal to the number of coordinates (be they Cartesian, internal, or whatever) that are being optimized.
int to_cartesian (const RefSCVector &internal)
Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein.
virtual int to_cartesian (const Ref< Molecule > &mol, const RefSCVector &internal)=0
virtual int to_internal (RefSCVector &internal)=0
Fill in the vector “internal” with the current internal coordinates.
virtual int to_cartesian (RefSCVector &cartesian, RefSCVector &internal)=0
Convert the internal coordinate gradients in internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients tocartesian''.
virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)=0
Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and copy these internal coordinate gradients tointernal''.
virtual int to_cartesian (RefSymmSCMatrix &cartesian, RefSymmSCMatrix &internal)=0
Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''.
virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cartesian)=0
Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''.
virtual RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)=0
Calculate an approximate hessian and place the result in “hessian”.
virtual int nconstrained ()
Returns the number of constrained coordinates.
virtual Ref< NonlinearTransform > change_coordinates ()
When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it.
Ref< SCMatrixKit > matrixkit () 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.
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.

Ref< Molecule > molecule_
RefSCDimension dnatom3_
Ref< SCMatrixKit > matrixkit_
int debug_

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)

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 &)

The KeyVal constructor.

molecule

A Molecule object. There is no default.

debug

An integer which, if nonzero, will cause extra output.

matrixkit

A SCMatrixKit object. It is usually unnecessary to give this keyword.

natom3

An SCDimension object for the dimension of the vector of cartesian coordinates. It is usually unnecessary to give this keyword.

When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it. The default action is to not change anything and return an IdentityTransform.

Reimplemented in sc::SymmMolecularCoor.

Returns a smart reference to an SCDimension equal to the number of coordinates (be they Cartesian, internal, or whatever) that are being optimized.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

Calculate an approximate hessian and place the result in “hessian”. */ virtual void guess_hessian(RefSymmSCMatrix&hessian) = 0;

/** Given an Hessian, return the inverse of that hessian. For singular matrices this should return the generalized inverse.

Implemented in sc::CartMolecularCoor, sc::RedundMolecularCoor, and sc::SymmMolecularCoor.

Returns the number of constrained coordinates.

Reimplemented in sc::IntMolecularCoor.

Print the coordinate.

Reimplemented from sc::DescribedClass.

Implemented in sc::CartMolecularCoor, sc::IntMolecularCoor, and sc::SymmMolecularCoor.

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::SavableState.

Reimplemented in sc::RedundMolecularCoor, and sc::SymmMolecularCoor.

Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. This function does not change the vector “internal”.

Convert the internal coordinate gradients in internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients tocartesian''. Only the variable internal coordinate gradients are transformed.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''. Only the variable internal coordinate force constants are transformed.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

Fill in the vector “internal” with the current internal coordinates. Note that this member will update the values of the variable internal coordinates.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and copy these internal coordinate gradients tointernal''. Only the variable internal coordinate gradients are calculated.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. Only the variable internal coordinate force constants are calculated.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.