MPQC  3.0.0-alpha
sc::SimpleCo Class Referenceabstract

The SimpleCo abstract class describes a simple internal coordinate of a molecule. More...

#include <chemistry/molecule/simple.h>

Inheritance diagram for sc::SimpleCo:
sc::IntCoor sc::SavableState sc::DescribedClass sc::RefCount sc::BendSimpleCo sc::LinIPSimpleCo sc::LinOPSimpleCo sc::OutSimpleCo sc::ScaledTorsSimpleCo sc::StreSimpleCo sc::TorsSimpleCo

Public Member Functions

 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. More...
 
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 double preferred_value () const
 Returns the value of the coordinate in more familiar units.
 
virtual const char * ctype () const =0
 Returns a string representation of the type of coordinate this is.
 
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 MPQC__NOEXCEPT
 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.
 
Ref< DescribedClassref ()
 Return this object wrapped up in a Ref smart pointer. More...
 
- Public Member Functions inherited from sc::RefCount
size_t identifier () const
 Return the unique identifier for this object that can be compared for different objects of different types. More...
 
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...
 

Protected Attributes

int natoms_
 
int * atoms
 
- Protected Attributes inherited from sc::IntCoor
char * label_
 
double value_
 

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 &)
 
- Static Protected Attributes inherited from sc::IntCoor
static double bohr_conv
 
static double radian_conv
 

Detailed Description

The SimpleCo abstract class describes a simple internal coordinate of a molecule.

The number atoms involved can be 2, 3 or 4 and is determined by the specialization of SimpleCo.

There are three ways to specify the atoms involved in the internal coordinate. The first way is a shorthand notation, just a vector of a label followed by the atom numbers (starting at 1) is given. For example, a stretch between two atoms, 1 and 2, is given, in the ParsedKeyVal format, as

  stretch<StreSimpleCo>: [ R12 1 2 ]

The other two ways to specify the atoms are more general. With them, it is possible to give parameters for the IntCoor base class (and thus give the value of the coordinate). In the first of these input formats, a vector associated with the keyword atoms gives the atom numbers. The following specification for stretch is equivalent to that above:

  stretch<StreSimpleCo>:( label = R12 atoms = [ 1 2 ] )

In the second, a vector, atom_labels, is given along with a Molecule object. The atom labels are looked up in the Molecule object to find the atom numbers. The following specification for stretch is equivalent to those above:

  molecule<Molecule>: (
    { atom_labels atoms   geometry      } = {
          H1         H   [ 1.0 0.0 0.0 ]
          H2         H   [-1.0 0.0 0.0 ] } )
  stretch<StreSimpleCo>:( label = R12
                          atom_labels = [ H1 H2 ]
                          molecule = $:molecule )

Constructor & Destructor Documentation

◆ SimpleCo()

sc::SimpleCo::SimpleCo ( int  ,
const char *  = 0 
)

This constructor takes an integer argument which is the number of atoms needed to describe the coordinate.

A second optional char* argument is a label for the coordinate. This argument is passed on to the IntCoor constructor.

Member Function Documentation

◆ calc_force_con()

virtual double sc::SimpleCo::calc_force_con ( Molecule )
pure virtual

Calculates an approximate force constant and returns it's value.

Specializations implement this using the method of Fischer and Almlöf, J. Phys. Chem., 1992, 96, pp. 9768-9774.

◆ calc_intco()

virtual double sc::SimpleCo::calc_intco ( Molecule ,
double *  = 0,
double  = 1 
)
pure virtual

Calculate the value of the coordinate based on what's in Molecule.

If given a double*, fill in that part of the B matrix. If the bmatrix is to be calculated, the third argument gives the coefficient.

◆ equivalent()

int sc::SimpleCo::equivalent ( Ref< IntCoor > &  )
virtual

Tests to see if two coordinates are equivalent to each other.

This is false if the atoms don't match.

Implements sc::IntCoor.

◆ save_data_state()

void sc::SimpleCo::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::IntCoor.


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

Generated at Sun Jan 26 2020 23:24:12 for MPQC 3.0.0-alpha using the documentation package Doxygen 1.8.16.