The AtomInfo class provides information about atoms. More...
#include <chemistry/molecule/atominfo.h>
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 | |
| SavableState & | operator= (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 &) | |
| DescribedClass & | operator= (const DescribedClass &) |
| ClassDesc * | class_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< DescribedClass > | ref () |
| 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 SavableState * | restore_state (StateIn &si) |
| Restores objects saved with save_state. More... | |
| 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. More... | |
| Protected Member Functions inherited from sc::RefCount | |
| RefCount (const RefCount &) | |
| RefCount & | operator= (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()
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.
| Keyword | Type | Default | Description |
mass:unit | string | amu | The unit to be used for masses. See the Units class for more information about units. |
mass:symbol | double | library value | The mass associated with the given atomic symbol. |
vdw_radius:unit | string | bohr | The unit to be used for van der Waals radii. See the Units class for more information about units. |
vdw_radius:scaling_factor | double | 1.0 | The scaling factor to be used for all van der Waals radii, including library values. |
vdw_radius:symbol | double | library value | The van der Waals radius associated with the given atomic symbol. |
atomic_radius:unit | string | bohr | The unit to be used for atomic radii. See the Units class for more information about units. |
atomic_radius:scaling_factor | double | 1.0 | The scaling factor to be used for all atomic radii, including library values. |
atomic_radius:symbol | double | library value | The atomic radius associated with the given atomic symbol. |
bragg_radius:unit | string | bohr | The unit to be used for Bragg radii. See the Units class for more information about units. |
bragg_radius:scaling_factor | double | 1.0 | The scaling factor to be used for all Bragg radii, including library values. |
bragg_radius:symbol | double | library value | The Bragg radius associated with the given atomic symbol. |
maxprob_radius:unit | string | bohr | The unit to be used for maximum probability radii. See the Units class for more information about units. |
maxprob_radius:scaling_factor | double | 1.0 | The scaling factor to be used for all maximum probability radii, including library values. |
maxprob_radius:symbol | double | library value | The maximum probability radius associated with the given atomic symbol. |
ip:unit | string | Hartree | The unit to be used for ionization potentials. See the Units class for more information about units. |
ip:symbol | double | library value | The ionization potential for the given atom. |
rgb:symbol | double[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()
|
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:
- src/lib/chemistry/molecule/atominfo.h