MPQC 2.3.1
|
The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates. More...
#include <coor.h>
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
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. | |
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 RefSymmSCMatrix | inverse_hessian (RefSymmSCMatrix &)=0 |
Calculate an approximate hessian and place the result in `‘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) |
The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates.
The KeyVal constructor.
Gives a SetIntCoor object that specifies the internal coordinates that can be varied. If this is not given, the variable coordinates will be generated.
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.
Gives a SetIntCoor object that specifies the internal coordinates that will be fixed. The default is no fixed coordinates.
Gives a SetIntCoor object that specifies internal coordinates that will be printed out whenever the coordinates are changed. The default is none.
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.
This is only read if the generator keyword is not given. It is a vector of atom numbers, where elements
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.
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.
This is like decouple_bonds except it applies to the bend-like coordinates. The default is false.
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.
The maximum number of steps permitted to convert internal coordinate displacements to cartesian coordinate displacements. The default is 100.
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
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.
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.
The tolerance for conversion of internal coordinate displacements to cartesian displacements. The default is 1.0e-12.
Print the simple internal coordinates. The default is false.
Print the variable internal coordinates. The default is false.
Print the constant internal coordinates. The default is false.
Print the molecule when forming coordinates. The default is false.
Obsolete. The default value is 1.0.
Obsolete. The default value is 1.0.
Obsolete. The default value is 1.0.
Obsolete. The default value is 1.0.
Obsolete. The default is 1.0e-5.
Obsolete. The default is 1.0e-7.
|
virtual |
These implement the virtual functions inherited from MolecularCoor.
Implements sc::MolecularCoor.
|
pure virtual |
Actually form the variable and constant internal coordinates from the simple internal coordinates.
Implemented in sc::RedundMolecularCoor, and sc::SymmMolecularCoor.
|
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 in sc::SymmMolecularCoor.
|
virtual |
Returns the number of constrained coordinates.
Reimplemented from sc::MolecularCoor.
|
virtual |
Print the coordinate.
Implements sc::MolecularCoor.
Reimplemented in sc::SymmMolecularCoor.
References sc::ExEnv::out0().
|
virtual |
Implements sc::MolecularCoor.
|
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::RedundMolecularCoor, and sc::SymmMolecularCoor.
|
virtual |
Implements sc::MolecularCoor.
|
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 |
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 |
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 |
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 |
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.