sc_ScaledTorsSimpleCo - Man Page
The ScaledTorsSimpleCo class describes an scaled torsion internal coordinate of a molecule.
Synopsis
#include <simple.h>
Inherits sc::SimpleCo.
Public Member Functions
ScaledTorsSimpleCo (const ScaledTorsSimpleCo &)
ScaledTorsSimpleCo (const char *refr, int, int, int, int)
This constructor takes a string containing a label, and four integers a, b, c, and d which give the indices of the atoms involved in the torsion angle abcd.
ScaledTorsSimpleCo (const Ref< KeyVal > &)
The KeyVal constructor.
const char * ctype () const
Always returns the string 'TORS'.
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.
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.
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.
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.
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.
IntCoor (const Ref< KeyVal > &)
The KeyVal constructor.
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
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.
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)
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 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 ScaledTorsSimpleCo class describes an scaled torsion internal coordinate of a molecule.
The scaled torsion is more stable that ordinary torsions (see the TorsSimpleCo class) in describing situations where one of the torsions plane's is given by three near linear atoms.
Designating the four atoms as $a$, $b$, $c$, and $d$ and their cartesian positions as $bar{r}_a$, $bar{r}_b$, $bar{r}_c$, and $bar{r}_d$, the value of the coordinate, $ au_s$, is given by
[ bar{u}_{ab} = ac{bar{r}_a - bar{r}_b}{ bar{r}_a - bar{r}_b }] [ bar{u}_{cb} = ac{bar{r}_c - bar{r}_b}{ bar{r}_c - bar{r}_b }] [ bar{u}_{cd} = ac{bar{r}_c - bar{r}_d}{ bar{r}_c - bar{r}_b }] [ bar{n}_{abc}= ac{bar{u}_{ab} imes bar{u}_{cb}}
{ bar{u}_{ab} imes bar{u}_{cb} }] [ bar{n}_{bcd}= ac{bar{u}_{cd} imes bar{u}_{cb}}
{ bar{u}_{cd} imes bar{u}_{cb} }] [ s = left
begin{array}{ll}
-1 & mbox{if $(bar{n}_{abc} imesbar{n}_{bcd})
cdot bar{u}_{cb} > 0$} \
1 & mbox{otherwise}
\nd{array}
right. ] [ au_s = s sqrt{left(1-(bar{u}_{ab} cdot bar{u}_{cb}right)^2)
left(1-(bar{u}_{cb} cdot bar{u}_{cd}right)^2)}
arccos ( - bar{n}_{abc} cdot bar{n}_{bcd} )]
Constructor & Destructor Documentation
sc::ScaledTorsSimpleCo::ScaledTorsSimpleCo (const char * refr, int , int , int , int )
This constructor takes a string containing a label, and four integers a, b, c, and d which give the indices of the atoms involved in the torsion angle abcd. Atom numbering begins at atom 1, not atom 0.
sc::ScaledTorsSimpleCo::ScaledTorsSimpleCo (const Ref< KeyVal > & )
The KeyVal constructor. This calls the SimpleCo keyval constructor with an integer argument of 4.
Member Function Documentation
const char * sc::ScaledTorsSimpleCo::ctype () const [virtual]
Always returns the string 'TORS'.
Implements sc::IntCoor.
double sc::ScaledTorsSimpleCo::preferred_value () const [virtual]
Returns the value of the angle abc in degrees.
Reimplemented from sc::IntCoor.
Author
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