sc::IntMolecularCoor Class Referenceabstract

    The IntMolecularCoor abstract class describes a molecule's coordinates

in terms of internal coordinates. More...

`#include <coor.h>`

Inheritance diagram for sc::IntMolecularCoor:
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Collaboration diagram for sc::IntMolecularCoor:
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## Public Member Functions

| IntMolecularCoor (StateIn &)
| IntMolecularCoor (Ref< Molecule > &mol)
| IntMolecularCoor (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...
virtual void | form_coordinates (int keep_variable=0)=0
| Actually form the variable and constant internal coordinates from the simple internal coordinates. 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. More...
virtual int | all_to_internal (const Ref< Molecule > &, RefSCVector &internal)
| Like to_internal(), except all internal coordinates are considered, not just the variable ones. More...
virtual RefSCDimension | dim ()
| These implement the virtual functions inherited from MolecularCoor. More...
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 to`cartesian''. More...
virtual int | to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
| Convert the Cartesian coordinate Hessian `cartesian'' to internal coordinates and copy the result to`internal''. More...
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. More...
RefSCDimension | dim_natom3 ()
| Returns a smart reference to an SCDimension equal to the number of atoms in the molecule times 3. More...
Ref< Molecule > | molecule () 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 void | guess_hessian (RefSymmSCMatrix &hessian)=0
| Calculate an approximate hessian and place the result in ``hessian''. More...
virtual RefSymmSCMatrix | inverse_hessian (RefSymmSCMatrix &)=0
| Given an Hessian, return the inverse of that hessian. More...
virtual Ref< NonlinearTransform > | change_coordinates ()
| When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it. More...
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. 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 &)
DescribedClass & | operator= (const DescribedClass &)
ClassDesc * | class_desc () const throw ()
| 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.
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. More...
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. More...

## Protected Member Functions

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. More...
virtual void | new_coords ()
| Allocates memory for the SetIntCoor's used to store the simple and internal coordinates. More...
virtual void | read_keyval (const Ref< KeyVal > &)
| Reads the KeyVal input.

## Protected Attributes

Ref< IntCoorGen > | generator_
RefSCDimension | dim_
RefSCDimension | dvc_
Ref< SetIntCoor > | variable_
Ref< SetIntCoor > | constant_
Ref< SetIntCoor > | fixed_
Ref< SetIntCoor > | watched_
Ref< IntCoor > | followed_
Ref< SetIntCoor > | bonds_
Ref< SetIntCoor > | bends_
Ref< SetIntCoor > | tors_
Ref< SetIntCoor > | outs_
Ref< SetIntCoor > | extras_
Ref< SetIntCoor > | all_
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< Molecule > | molecule_
RefSCDimension | dnatom3_
Ref< SCMatrixKit > | matrixkit_
int | debug_

## 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. More...
static SavableState * | key_restore_state (StateIn &si, const char *keyword)
| Like restore_state, but keyword is used to override values while restoring. More...
static SavableState * | dir_restore_state (StateIn &si, const char *objectname, const char *keyword=0)

## Detailed Description

    The IntMolecularCoor abstract class describes a molecule's coordinates

in terms of internal coordinates.

## Constructor & Destructor Documentation

sc::IntMolecularCoor::IntMolecularCoor | ( | const Ref< KeyVal > & |  | ) |

The KeyVal constructor.

`variable`

  Gives a SetIntCoor object that specifies the internal coordinates that can be varied. If this is not given, the variable coordinates will be generated.

`followed`

  Gives a IntCoor object that specifies a coordinate to used as the first coordinate in the variable coordinate list. The remaining coordinates will be automatically generated. The default is no followed coordinate. This option is usually used to set the initial search direction for a transition state optimization, where it is used in conjunction with the mode_following keyword read by the EFCOpt class.

`fixed`

  Gives a SetIntCoor object that specifies the internal coordinates that will be fixed. The default is no fixed coordinates.

`watched`

  Gives a SetIntCoor object that specifies internal coordinates that will be printed out whenever the coordinates are changed. The default is none.

`have_fixed_values`

  If true, then values for the fixed coordinates must be given in fixed and an attempt will be made to displace the initial geometry to the given fixed values. The default is false.

`extra_bonds`

  This is only read if the generator keyword is not given. It is a vector of atom numbers, where elements and specify the atoms which are bound in extra bond . The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.

`generator`

  Specifies an IntCoorGen object that creates simple, redundant internal coordinates. If this keyword is not given, then a vector giving extra bonds to be added is read from extra_bonds and this is used to create an IntCoorGen object.

`decouple_bonds`

  Automatically generated internal coordinates are linear combinations of possibly any mix of simple internal coordinates. If decouple_bonds is true, an attempt will be made to form some of the internal coordinates from just stretch simple coordinates. The default is false.

`decouple_bends`

  This is like decouple_bonds except it applies to the bend-like coordinates. The default is false.

`max_update_disp`

  The maximum displacement to be used in the displacement to fixed internal coordinates values. Larger displacements will be broken into several smaller displacements and new coordinates will be formed for each of these displacments. This is only used when fixed and have_fixed_values are given. The default is 0.5.

`max_update_steps`

  The maximum number of steps permitted to convert internal coordinate displacements to cartesian coordinate displacements. The default is 100.

`update_bmat`

  Displacements in internal coordinates are converted to a cartesian displacements iteratively. If there are large changes in the cartesian coordinates during conversion, then recompute the matrix, which is using to do the conversion. The default is false.

`only_totally_symmetric`

  If a simple test reveals that an internal coordinate is not totally symmetric, then it will not be added to the internal coordinate list. The default is true.

`simple_tolerance`

  The internal coordinates are formed as linear combinations of simple, redundant internal coordinates. Coordinates with coefficients smaller then simple_tolerance will be omitted. The default is 1.0e-3.

`cartesian_tolerance`

  The tolerance for conversion of internal coordinate displacements to cartesian displacements. The default is 1.0e-12.

`form:print_simple`

  Print the simple internal coordinates. The default is false.

`form:print_variable`

  Print the variable internal coordinates. The default is false.

`form:print_constant`

  Print the constant internal coordinates. The default is false.

`form:print_molecule`

  Print the molecule when forming coordinates. The default is false.

`scale_bonds`

  Obsolete. The default value is 1.0.

`scale_bends`

  Obsolete. The default value is 1.0.

`scale_tors`

  Obsolete. The default value is 1.0.

`scale_outs`

  Obsolete. The default value is 1.0.

`symmetry_tolerance`

  Obsolete. The default is 1.0e-5.

`coordinate_tolerance`

  Obsolete. The default is 1.0e-7.

## Member Function Documentation

virtual int sc::IntMolecularCoor::all_to_cartesian | ( | const Ref< Molecule > & | ,
|  | RefSCVector & | internal
| ) |  |

virtual

Like to_cartesians(), except all internal coordinates are considered, not just the variable ones.

virtual int sc::IntMolecularCoor::all_to_internal | ( | const Ref< Molecule > & | ,
|  | RefSCVector & | internal
| ) |  |

virtual

Like to_internal(), except all internal coordinates are considered, not just the variable ones.

virtual RefSCDimension sc::IntMolecularCoor::dim | ( |  | ) |

virtual

These implement the virtual functions inherited from MolecularCoor.

Implements sc::MolecularCoor.

virtual void sc::IntMolecularCoor::form_coordinates | ( | int | keep_variable = `0` | ) |

pure virtual

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

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

virtual void sc::IntMolecularCoor::init | ( |  | ) |

protected virtual

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 in sc::SymmMolecularCoor.

virtual void sc::IntMolecularCoor::new_coords | ( |  | ) |

protected virtual

Allocates memory for the SetIntCoor's used to store the simple and internal coordinates.

void sc::IntMolecularCoor::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.

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

virtual int sc::IntMolecularCoor::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.

virtual int sc::IntMolecularCoor::to_cartesian | ( | RefSymmSCMatrix & | cartesian,
|  | RefSymmSCMatrix & | internal
| ) |  |

virtual

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

Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

virtual int sc::IntMolecularCoor::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.

virtual int sc::IntMolecularCoor::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.

virtual int sc::IntMolecularCoor::to_internal | ( | RefSymmSCMatrix & | internal,
|  | RefSymmSCMatrix & | cartesian
| ) |  |

virtual

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

Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.

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

- coor.h