MPQC  3.0.0-alpha
sc::AtomInfo Class Reference

The AtomInfo class provides information about atoms. More...

#include <chemistry/molecule/atominfo.h>

Inheritance diagram for sc::AtomInfo:
sc::SavableState sc::DescribedClass sc::RefCount

Public Member Functions

 AtomInfo (const Ref< KeyVal > &)
 The AtomInfo KeyVal constructor is used to generate a AtomInfo object from the input. More...
 
 AtomInfo (StateIn &)
 
void save_data_state (StateOut &s)
 Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More...
 
double vdw_radius (int Z) const
 These return various measures of the atom's radius.
 
double bragg_radius (int Z) const
 
double atomic_radius (int Z) const
 
double maxprob_radius (int Z) const
 
double ip (int Z) const
 Returns the atomization potential for atomic number Z.
 
double vdw_radius_scale () const
 Return the scale factor for the VdW radii.
 
double bragg_radius_scale () const
 Return the scale factor for the Bragg radii.
 
double atomic_radius_scale () const
 Return the scale factor for the atomic radii.
 
double maxprob_radius_scale () const
 Return the scale factor for the maximum probability radii.
 
double rgb (int Z, int color) const
 These return information about the color of the atom for visualization programs.
 
double red (int Z) const
 
double green (int Z) const
 
double blue (int Z) const
 
double mass (int Z) const
 This returns the mass of the most abundant isotope.
 
std::string name (int Z) const
 This returns the full name of the element.
 
std::string symbol (int Z) const
 This returns the symbol for the element.
 
int string_to_Z (const std::string &, int allow_exceptions=1)
 This converts a name or symbol to the atomic number.
 
void print (std::ostream &os=ExEnv::out0()) const
 prints out the contents of AtomInfo to ostream os
 
- 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...
 

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 &)
 

Detailed Description

The AtomInfo class provides information about atoms.

The information is kept in a file named atominfo.kv in the SC library directory. That information can be overridden by the user.

Constructor & Destructor Documentation

◆ AtomInfo()

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

The AtomInfo KeyVal constructor is used to generate a AtomInfo object from the input.

Default values will be read in from the atominfo.kv file in library directory. These can be overridden by specifying the keyword below. The library file is also read using a KeyVal constructor syntax, so consult that file for an example.

KeywordTypeDefault

Description

mass:unitstringamu

The unit to be used for masses. See the Units class for more information about units.

mass:symboldoublelibrary value

The mass associated with the given atomic symbol.

vdw_radius:unitstringbohr

The unit to be used for van der Waals radii. See the Units class for more information about units.

vdw_radius:scaling_factordouble1.0

The scaling factor to be used for all van der Waals radii, including library values.

vdw_radius:symboldoublelibrary value

The van der Waals radius associated with the given atomic symbol.

atomic_radius:unitstringbohr

The unit to be used for atomic radii. See the Units class for more information about units.

atomic_radius:scaling_factordouble1.0

The scaling factor to be used for all atomic radii, including library values.

atomic_radius:symboldoublelibrary value

The atomic radius associated with the given atomic symbol.

bragg_radius:unitstringbohr

The unit to be used for Bragg radii. See the Units class for more information about units.

bragg_radius:scaling_factordouble1.0

The scaling factor to be used for all Bragg radii, including library values.

bragg_radius:symboldoublelibrary value

The Bragg radius associated with the given atomic symbol.

maxprob_radius:unitstringbohr

The unit to be used for maximum probability radii. See the Units class for more information about units.

maxprob_radius:scaling_factordouble1.0

The scaling factor to be used for all maximum probability radii, including library values.

maxprob_radius:symboldoublelibrary value

The maximum probability radius associated with the given atomic symbol.

ip:unitstringHartree

The unit to be used for ionization potentials. See the Units class for more information about units.

ip:symboldoublelibrary value

The ionization potential for the given atom.

rgb:symboldouble[3]library value

A vector with the red, green, and blue values used to color each atom. Each element is between 0 (off) and 1 (on).

Member Function Documentation

◆ save_data_state()

void sc::AtomInfo::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.


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

Generated at Sun Jan 26 2020 23:24:03 for MPQC 3.0.0-alpha using the documentation package Doxygen 1.8.16.