Public Member Functions

IntMolecularCoor (StateIn &)
IntMolecularCoor (Ref< Molecule > &mol)
IntMolecularCoor (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. virtual void form_coordinates (int keep_variable=0)=0
Actually form the variable and constant internal coordinates from the simple internal coordinates. 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 tocartesian''. virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)
Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and copy these internal coordinate gradients tointernal''. virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''. virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. 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. 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. int to_cartesian (const RefSCVector &internal)
Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. virtual void guess_hessian (RefSymmSCMatrix &hessian)=0
Calculate an approximate hessian and place the result in ``hessian''. virtual RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)=0
Given an Hessian, return the inverse of that hessian. 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.

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. 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 &)
RefCount & operator= (const RefCount &)

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. 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)

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 $(i-1)imes 2 + 1$ and $iimes 2$ specify the atoms which are bound in extra bond $i$. 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 $B$ 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.

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::SymmMolecularCoor, and sc::RedundMolecularCoor.

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.

int sc::IntMolecularCoor::nconstrained () [virtual]

Returns the number of constrained coordinates.

Reimplemented from sc::MolecularCoor.

virtual void sc::IntMolecularCoor::print (std::ostream & = ExEnv::out0()) const [virtual]

Print the coordinate.

Implements sc::MolecularCoor.

Reimplemented in sc::SymmMolecularCoor.

virtual void sc::IntMolecularCoor::print_simples (std::ostream & = ExEnv::out0()) const [virtual]

Implements sc::MolecularCoor.

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::SavableState.

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

virtual int sc::IntMolecularCoor::to_cartesian (const Ref< Molecule > &, const RefSCVector & internal) [virtual]

Implements sc::MolecularCoor.

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 tocartesian''. 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 tocartesian''. 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 tointernal''. 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 tointernal''. Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.