MPQC 2.3.1
sc::RedundMolecularCoor Class Reference

The RedundMolecularCoor class provides a redundant set of simple internal coordinates. More...

#include <coor.h>

Inheritance diagram for sc::RedundMolecularCoor:
Collaboration diagram for sc::RedundMolecularCoor:

Public Member Functions

 RedundMolecularCoor (Ref< Molecule > &mol)
 RedundMolecularCoor (StateIn &)
 RedundMolecularCoor (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.
void form_coordinates (int keep_variable=0)
 Actually form the variable and constant internal coordinates from the simple internal coordinates.
void guess_hessian (RefSymmSCMatrix &hessian)
 Form the approximate hessian.
RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
 Invert the hessian.
Public Member Functions inherited from sc::IntMolecularCoor
 IntMolecularCoor (StateIn &)
 IntMolecularCoor (Ref< Molecule > &mol)
 IntMolecularCoor (const Ref< KeyVal > &)
 The KeyVal constructor.
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.
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''.
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''.
virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
 Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result to cartesian''.
virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
 Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result to internal''.
virtual void print (std::ostream &=ExEnv::out0()) const
 Print the coordinate.
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.
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.
virtual Ref< NonlinearTransformchange_coordinates ()
 When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it.
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.
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 &)
DescribedClassoperator= (const DescribedClass &)
ClassDescclass_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.

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.
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)
Protected Member Functions inherited from sc::IntMolecularCoor
void form_K_matrix (RefSCDimension &dredundant, RefSCDimension &dfixed, RefSCMatrix &K, int *&is_totally_symmetric)
virtual void init ()
 This is called by the constructors of classes derived from IntMolecularCoor.
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.
Protected Member Functions inherited from sc::RefCount
 RefCount (const RefCount &)
RefCountoperator= (const RefCount &)
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_

Detailed Description

The RedundMolecularCoor class provides a redundant set of simple internal coordinates.

Member Function Documentation

◆ form_coordinates()

void sc::RedundMolecularCoor::form_coordinates ( int keep_variable = 0)
virtual

Actually form the variable and constant internal coordinates from the simple internal coordinates.

Implements sc::IntMolecularCoor.

◆ inverse_hessian()

RefSymmSCMatrix sc::RedundMolecularCoor::inverse_hessian ( RefSymmSCMatrix & )
virtual

Invert the hessian.

Implements sc::MolecularCoor.

◆ save_data_state()

void sc::RedundMolecularCoor::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 Fri Jan 31 2025 00:00:00 for MPQC 2.3.1 using the documentation package Doxygen 1.14.0.