MPQC  2.3.1
Public Member Functions | List of all members
sc::LinOPSimpleCo Class Reference

The LinOPSimpleCo class describes an out-of-plane component of a linear bend internal coordinate of a molecule. More...

#include <simple.h>

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Public Member Functions

 LinOPSimpleCo (const LinOPSimpleCo &)
 
 LinOPSimpleCo (const char *refr, int, int, int, const SCVector3 &u)
 This constructor takes a string containing a label, and three integers a, b, and c which give the indices of the atoms involved in the linear angle abc. More...
 
 LinOPSimpleCo (const Ref< KeyVal > &)
 The KeyVal constructor. More...
 
const char * ctype () const
 Always returns the string "LINIP".
 
double radians () const
 Returns the value of the angle abc in radians.
 
double degrees () const
 Returns the value of the angle abc in degrees.
 
double preferred_value () const
 Returns the value of the angle abc in degrees.
 
- Public Member Functions inherited from sc::SimpleCo
 SimpleCo (int, const char *=0)
 This constructor takes an integer argument which is the number of atoms needed to describe the coordinate. More...
 
 SimpleCo (const Ref< KeyVal > &, int natom)
 The KeyVal constructor requires the number of atoms.
 
int natoms () const
 Returns the number of atoms in the coordinate.
 
int operator[] (int i) const
 Returns the index of the i'th atom in the coordinate.
 
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...
 
 SimpleCo (StateIn &)
 
virtual int operator== (SimpleCo &)
 
int operator!= (SimpleCo &u)
 
double force_constant (Ref< Molecule > &)
 Returns an approximate force constant (a la Almlof).
 
void update_value (const Ref< Molecule > &)
 Recalculates the value of the coordinate based on the geometry in the Molecule.
 
void bmat (const Ref< Molecule > &, RefSCVector &bmat, double coef=1.0)
 Fill in a row of the B matrix.
 
virtual double calc_force_con (Molecule &)=0
 Calculates an approximate force constant and returns it's value.
 
virtual double calc_intco (Molecule &, double *=0, double=1)=0
 Calculate the value of the coordinate based on what's in Molecule. More...
 
void print_details (const Ref< Molecule > &, std::ostream &=ExEnv::out0()) const
 Print the coordinate.
 
int equivalent (Ref< IntCoor > &)
 Tests to see if two coordinates are equivalent to each other. More...
 
- Public Member Functions inherited from sc::IntCoor
 IntCoor (StateIn &)
 
 IntCoor (const IntCoor &)
 
 IntCoor (const char *label=0)
 This constructor takes a string containing a label for the internal coordinate. More...
 
 IntCoor (const Ref< KeyVal > &)
 The KeyVal constructor. More...
 
virtual const char * label () const
 Returns the string containing the label for the internal coordinate.
 
virtual double value () const
 Returns the value of the coordinate in atomic units or radians.
 
virtual void set_value (double)
 Sets the value of the coordinate in atomic units or radians.
 
virtual void print (std::ostream &o=ExEnv::out0()) const
 Print information about the coordinate.
 
- 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 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...
 

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)
 
- 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 inherited from sc::SimpleCo
int natoms_
 
int * atoms
 
- Protected Attributes inherited from sc::IntCoor
char * label_
 
double value_
 
- Static Protected Attributes inherited from sc::IntCoor
static double bohr_conv
 
static double radian_conv
 

Detailed Description

The LinOPSimpleCo class describes an out-of-plane component of a linear bend internal coordinate of a molecule.

The input is described in the documentation of its parent class SimpleCo. A vector, $\bar{u}$, given as the keyword u, that is not colinear with either $\bar{r}_a - \bar{r}_b$ or $\bar{r}_b - \bar{r}_c$ must be provided, where $\bar{r}_a$, $\bar{r}_b$, and $\bar{r}_c$ are the positions of the first, second, and third atoms, respectively.

Usually, LinOPSimpleCo is used with a corresponding LinIPSimpleCo, which is given exactly the same u.

Designating the three atoms as $a$, $b$, and $c$ and their cartesian positions as $\bar{r}_a$, $\bar{r}_b$, and $\bar{r}_c$, the value of the coordinate, $\theta_o$, is given by

\[ \bar{u}_{ab} = \frac{\bar{r}_a - \bar{r}_b}{\| \bar{r}_a - \bar{r}_b \|}\]

\[ \bar{u}_{cb} = \frac{\bar{r}_b - \bar{r}_c}{\| \bar{r}_c - \bar{r}_b \|}\]

\[ \bar{n} = \frac{\bar{u} \times \bar{u}_{ab}} {\| \bar{u} \times \bar{u}_{ab} \|}\]

\[ \theta_o = \pi - \arccos ( \bar{u}_{ab} \cdot \bar{n} ) - \arccos ( \bar{u}_{cb} \cdot \bar{n} )\]

Constructor & Destructor Documentation

◆ LinOPSimpleCo() [1/2]

sc::LinOPSimpleCo::LinOPSimpleCo ( const char *  refr,
int  ,
int  ,
int  ,
const SCVector3 u 
)

This constructor takes a string containing a label, and three integers a, b, and c which give the indices of the atoms involved in the linear angle abc.

The last argument, u, is a unit vector used to defined the direction perpendicular to the direction in which distortion is measured. Atom numbering begins at atom 1, not atom 0.

◆ LinOPSimpleCo() [2/2]

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

The KeyVal constructor.

This calls the SimpleCo keyval constructor with an integer argument of 3.


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

Generated at Sun Jan 26 2020 23:33:07 for MPQC 2.3.1 using the documentation package Doxygen 1.8.16.