MPQC  3.0.0-alpha
sc::SymmMolecularCoor Class Reference

The SymmMolecularCoor class derives from IntMolecularCoor. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::SymmMolecularCoor:
sc::IntMolecularCoor sc::MolecularCoor sc::SavableState sc::DescribedClass sc::RefCount

Public Member Functions

 SymmMolecularCoor (Ref< Molecule > &mol)
 
 SymmMolecularCoor (StateIn &)
 
 SymmMolecularCoor (const Ref< KeyVal > &)
 The KeyVal constructor. More...
 
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 form_coordinates (int keep_variable=0)
 Actually form the variable and constant internal coordinates from simple internal coordinates.
 
void guess_hessian (RefSymmSCMatrix &hessian)
 Form the approximate hessian.
 
RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
 Invert the hessian.
 
Ref< NonlinearTransformchange_coordinates ()
 This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates.
 
void print (std::ostream &=ExEnv::out0()) const
 Print the coordinate.
 
- Public Member Functions inherited from sc::IntMolecularCoor
 IntMolecularCoor (StateIn &)
 
 IntMolecularCoor (Ref< Molecule > &mol)
 
 IntMolecularCoor (const Ref< KeyVal > &)
 The KeyVal constructor. More...
 
virtual int all_to_cartesian (const Ref< Molecule > &, RefSCVector &internal)
 Like to_cartesians(), except all internal coordinates are considered, not just the variable ones.
 
virtual int all_to_internal (const Ref< Molecule > &, RefSCVector &internal)
 Like to_internal(), except all internal coordinates are considered, not just the variable ones.
 
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_simples (std::ostream &=ExEnv::out0()) const
 
virtual void print_variable (std::ostream &=ExEnv::out0()) const
 
virtual void print_constant (std::ostream &=ExEnv::out0()) const
 
int nconstrained ()
 Returns the number of constrained coordinates.
 
- 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...
 
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

void init ()
 This is called by the constructors of classes derived from IntMolecularCoor. More...
 
- Protected Member Functions inherited from sc::IntMolecularCoor
void form_K_matrix (RefSCDimension &dredundant, RefSCDimension &dfixed, RefSCMatrix &K, int *&is_totally_symmetric)
 
virtual void new_coords ()
 Allocates memory for the SetIntCoor's used to store the simple and internal coordinates.
 
virtual void read_keyval (const Ref< KeyVal > &)
 Reads the KeyVal input.
 
- 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

int change_coordinates_
 
int transform_hessian_
 
double max_kappa2_
 
- Protected Attributes inherited from sc::IntMolecularCoor
Ref< IntCoorGengenerator_
 
RefSCDimension dim_
 
RefSCDimension dvc_
 
Ref< SetIntCoorvariable_
 
Ref< SetIntCoorconstant_
 
Ref< SetIntCoorfixed_
 
Ref< SetIntCoorwatched_
 
Ref< IntCoorfollowed_
 
Ref< SetIntCoorbonds_
 
Ref< SetIntCoorbends_
 
Ref< SetIntCoortors_
 
Ref< SetIntCoorouts_
 
Ref< SetIntCoorextras_
 
Ref< SetIntCoorall_
 
int update_bmat_
 
int only_totally_symmetric_
 
double symmetry_tolerance_
 
double simple_tolerance_
 
double coordinate_tolerance_
 
double cartesian_tolerance_
 
double scale_bonds_
 
double scale_bends_
 
double scale_tors_
 
double scale_outs_
 
int nextra_bonds_
 
int * extra_bonds_
 
int given_fixed_values_
 
int decouple_bonds_
 
int decouple_bends_
 
int max_update_steps_
 
double max_update_disp_
 
int form_print_simples_
 
int form_print_variable_
 
int form_print_constant_
 
int form_print_molecule_
 
- 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 SymmMolecularCoor class derives from IntMolecularCoor.

It provides a unique set of totally symmetric internal coordinates. Giving an MolecularEnergy object a coor is usually the best way to optimize a molecular structure. However, for some classes of molecules SymmMolecularCoor doesn't work very well. For example, enediyne can cause problems. In these cases, cartesian coordinates (obtained by not giving the MolecularEnergy object the coor keyword) might be better or you can manually specify the coordinates that the SymmMolecularCoor object uses with the variable keyword (see the IntMolecularCoor class description).

Constructor & Destructor Documentation

◆ SymmMolecularCoor()

sc::SymmMolecularCoor::SymmMolecularCoor ( const Ref< KeyVal > &  )

The KeyVal constructor.

change_coordinates

If true, the quality of the internal coordinates will be checked periodically and if they are beginning to become linearly dependent a new set of internal coordinates will be computed. The default is false.

max_kappa2

A measure of the quality of the internal coordinates. Values of the 2-norm condition, $\kappa_2$, larger than max_kappa2 are considered linearly dependent. The default is 10.0.

transform_hessian

If true, the hessian will be transformed every time the internal coordinates are formed. The default is true.

Member Function Documentation

◆ init()

void sc::SymmMolecularCoor::init ( )
protectedvirtual

This is called by the constructors of classes derived from IntMolecularCoor.

It initialized the lists of simple internal coordinates, and then calls the form_coordinates() member.

Reimplemented from sc::IntMolecularCoor.

◆ save_data_state()

void sc::SymmMolecularCoor::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::IntMolecularCoor.


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

Generated at Sun Jan 26 2020 23:24:13 for MPQC 3.0.0-alpha using the documentation package Doxygen 1.8.16.