Periodic Table of the Elements Using element data is a place holder when we lack information about a specific atom type. More...

#include <ElementsTable.hpp>

Public Member Functions
	ElementsTable ()
	Constructor.

	~ElementsTable ()
	Destructor.

void	Init ()
	Read in the data file.

void	SetReadDirectory (char *dir)
	Set the directory before calling Init()

void	SetEnvironmentVariable (char *var)
	Set the environment variable to use before calling Init()

void	ParseLine (const char *line)
	Specified by particular table classes (parses an individual data line)

unsigned int	GetNumberOfElements ()

unsigned int	GetSize ()

int	GetAtomicNum (const char *str)

int	GetAtomicNum (const char *str, int &iso)

int	GetAtomicNum (std::string name, int &iso)

const char *	GetSymbol (int atomicnum)

RealType	GetVdwRad (int atomicnum)

RealType	GetCovalentRad (int atomicnum)

RealType	GetMass (int atomicnum)

RealType	CorrectedBondRad (int atomicnum, int hyb=3)

RealType	CorrectedVdwRad (int atomicnum, int hyb=3)

int	GetMaxBonds (int atomicnum)

RealType	GetElectroNeg (int atomicnum)

RealType	GetAllredRochowElectroNeg (int atomicnum)

RealType	GetIonization (int atomicnum)

RealType	GetElectronAffinity (int atomicnum)

std::vector< RealType >	GetRGB (int atomicnum)

std::string	GetName (int atomicnum)

Protected Attributes
bool	init_
	whether the data been read already

std::string	filename_
	file to search for

std::string	dir_
	data directory for file if _envvar fails

std::string	subdir_
	subdirectory (if using environment variable)

std::string	envvar_
	environment variable to check first

std::vector< Element * >	elements_

const char *	dataptr_
	default data table if file is unreadable

Detailed Description

Periodic Table of the Elements Using element data is a place holder when we lack information about a specific atom type.

In particular, the Langevin algorithms must assume specific atomic radii to predict drag and random forces on those atoms. For force fields which do not specify Lennard-Jones radii, the element's van der Waals radius is used instead. The ElementsTable class (etab) is declared as external in ElementsTable.cpp. Source files that include the header file ElementsTable.hpp automatically have an extern definition to etab. The following code sample demonstrates the use of the ElementsTable class:

cout << "The symbol for element 6 is " << etab.GetSymbol(6) << endl;
cout << "The atomic number for Sulfur is " << etab.GetAtomicNum(16) <<
endl; cout << "The van der Waal radius for Nitrogen is " <<
etab.GetVdwRad(7);

Stored information in the OBElementTable includes elemental:

symbols
covalent radii
van der Waal radii
expected maximum bonding valence
molar mass (by IUPAC recommended atomic masses)
electronegativity
ionization potential
electron affinity
RGB colors for visualization programs
names (by IUPAC recommendation)

Definition at line 72 of file ElementsTable.hpp.

Constructor & Destructor Documentation

◆ ElementsTable()

OpenMD::ElementsTable::ElementsTable ( )

Constructor.

Definition at line 58 of file ElementsTable.cpp.

References dir_, envvar_, filename_, and init_.

◆ ~ElementsTable()

OpenMD::ElementsTable::~ElementsTable ( )

Destructor.

Definition at line 65 of file ElementsTable.cpp.

Member Function Documentation

◆ CorrectedBondRad()

RealType OpenMD::ElementsTable::CorrectedBondRad	(	int	atomicnum,
		int	hyb = 3 )

Returns: a "corrected" bonding radius based on the hybridization. Scales the covalent radius by 0.95 for sp2 and 0.90 for sp hybrids

Parameters

atomicnum	the atomic number of the element
hyb	the hybridization of the element

Definition at line 190 of file ElementsTable.cpp.

References Init(), and init_.

◆ CorrectedVdwRad()

RealType OpenMD::ElementsTable::CorrectedVdwRad	(	int	atomicnum,
		int	hyb = 3 )

Returns: a "corrected" vdW radius based on the hybridization. Scales the van der Waals radius by 0.95 for sp2 and 0.90 for sp hybrids

Parameters

atomicnum	the atomic number of the element
hyb	the hybridization of the element

Definition at line 207 of file ElementsTable.cpp.

References Init(), and init_.

◆ GetAllredRochowElectroNeg()

RealType OpenMD::ElementsTable::GetAllredRochowElectroNeg ( int atomicnum )

Returns: the Allred-Rochow electronegativity for this element

Parameters

atomicnum the atomic number of the element

Definition at line 125 of file ElementsTable.cpp.

References GetAllredRochowElectroNeg(), Init(), and init_.

Referenced by GetAllredRochowElectroNeg().

◆ GetAtomicNum() [1/3]

int OpenMD::ElementsTable::GetAtomicNum ( const char * str )

Returns: the atomic number matching the element symbol passed or 0 if not defined.

Parameters

str	the element symbol

Definition at line 242 of file ElementsTable.cpp.

References GetAtomicNum().

Referenced by GetAtomicNum(), and GetAtomicNum().

◆ GetAtomicNum() [2/3]

int OpenMD::ElementsTable::GetAtomicNum	(	const char *	str,
		int &	iso )

Returns: the atomic number matching the element symbol passed or 0 if not defined. For 'D' or 'T' hydrogen isotopes, will return a value in the second argument

Parameters

str	the element symbol
iso	the isotope index for Deuterium or Tritium

Definition at line 247 of file ElementsTable.cpp.

References Init(), and init_.

◆ GetAtomicNum() [3/3]

int OpenMD::ElementsTable::GetAtomicNum	(	std::string	name,
		int &	iso )

Returns: the atomic number matching the element symbol passed or 0 if not defined.

Parameters

name	the element name
iso	the isotope index for Deuterium or Tritium

Definition at line 297 of file ElementsTable.cpp.

References GetAtomicNum().

◆ GetCovalentRad()

RealType OpenMD::ElementsTable::GetCovalentRad ( int atomicnum )

Returns: the covalent radius for this atomic number

Parameters

atomicnum the atomic number of the element

Definition at line 224 of file ElementsTable.cpp.

References GetCovalentRad(), Init(), and init_.

Referenced by GetCovalentRad().

◆ GetElectronAffinity()

RealType OpenMD::ElementsTable::GetElectronAffinity ( int atomicnum )

Returns: the electron affinity (in eV) for this element

Parameters

atomicnum the atomic number of the element

Definition at line 143 of file ElementsTable.cpp.

References GetElectronAffinity(), Init(), and init_.

Referenced by GetElectronAffinity().

◆ GetElectroNeg()

RealType OpenMD::ElementsTable::GetElectroNeg ( int atomicnum )

Returns: the Pauling electronegativity for this element

Parameters

atomicnum the atomic number of the element

Definition at line 116 of file ElementsTable.cpp.

References GetElectroNeg(), Init(), and init_.

Referenced by GetElectroNeg().

◆ GetIonization()

RealType OpenMD::ElementsTable::GetIonization ( int atomicnum )

Returns: the ionization potential (in eV) for this element

Parameters

atomicnum the atomic number of the element

Definition at line 134 of file ElementsTable.cpp.

References GetIonization(), Init(), and init_.

Referenced by GetIonization().

◆ GetMass()

RealType OpenMD::ElementsTable::GetMass ( int atomicnum )

Returns: the average atomic mass for this element.

Parameters

atomicnum the atomic number of the element

Definition at line 233 of file ElementsTable.cpp.

References GetMass(), Init(), and init_.

Referenced by GetMass().

◆ GetMaxBonds()

int OpenMD::ElementsTable::GetMaxBonds ( int atomicnum )

Returns: the maximum expected number of bonds to this element

Parameters

atomicnum the atomic number of the element

Definition at line 107 of file ElementsTable.cpp.

References GetMaxBonds(), Init(), and init_.

Referenced by GetMaxBonds().

◆ GetName()

std::string OpenMD::ElementsTable::GetName ( int atomicnum )

Returns: the name of this element

Parameters

atomicnum the atomic number of the element

Definition at line 172 of file ElementsTable.cpp.

References GetName(), Init(), and init_.

Referenced by GetName().

◆ GetNumberOfElements()

unsigned int OpenMD::ElementsTable::GetNumberOfElements ( )

Returns: the number of elements in the periodic table

Definition at line 92 of file ElementsTable.cpp.

References Init(), and init_.

◆ GetRGB()

std::vector< RealType > OpenMD::ElementsTable::GetRGB ( int atomicnum )

Returns: a vector with red, green, blue color values for this element

Parameters

atomicnum the atomic number of the element

Definition at line 152 of file ElementsTable.cpp.

References Init(), and init_.

◆ GetSize()

unsigned int OpenMD::ElementsTable::GetSize ( )

inline

Definition at line 100 of file ElementsTable.hpp.

◆ GetSymbol()

const char * OpenMD::ElementsTable::GetSymbol ( int atomicnum )

Returns: the element symbol matching the atomic number passed

Parameters

atomicnum the atomic number of the element

Definition at line 98 of file ElementsTable.cpp.

References GetSymbol(), Init(), and init_.

Referenced by GetSymbol().

◆ GetVdwRad()

RealType OpenMD::ElementsTable::GetVdwRad ( int atomicnum )

Returns: the van der Waals radius for this atomic number

Parameters

atomicnum the atomic number of the element

Definition at line 181 of file ElementsTable.cpp.

References GetVdwRad(), Init(), and init_.

Referenced by GetVdwRad().

◆ Init()

void OpenMD::ElementsTable::Init ( )

Read in the data file.

Definition at line 301 of file ElementsTable.cpp.

References OpenMD::ifstrstream::close(), envvar_, filename_, init_, OpenMD::ifstrstream::open(), ParseLine(), and subdir_.

Referenced by CorrectedBondRad(), CorrectedVdwRad(), GetAllredRochowElectroNeg(), GetAtomicNum(), GetCovalentRad(), GetElectronAffinity(), GetElectroNeg(), GetIonization(), GetMass(), GetMaxBonds(), GetName(), GetNumberOfElements(), GetRGB(), GetSymbol(), and GetVdwRad().

◆ ParseLine()

void OpenMD::ElementsTable::ParseLine ( const char * line )

Specified by particular table classes (parses an individual data line)

Parameters

line	the data line to parse

Definition at line 71 of file ElementsTable.cpp.

Referenced by Init().

◆ SetEnvironmentVariable()

void OpenMD::ElementsTable::SetEnvironmentVariable ( char * var )

inline

Set the environment variable to use before calling Init()

Definition at line 90 of file ElementsTable.hpp.

References envvar_.

◆ SetReadDirectory()

void OpenMD::ElementsTable::SetReadDirectory ( char * dir )

inline

Set the directory before calling Init()

Definition at line 86 of file ElementsTable.hpp.

References dir_.

Member Data Documentation

◆ dataptr_

const char* OpenMD::ElementsTable::dataptr_

protected

default data table if file is unreadable

Definition at line 200 of file ElementsTable.hpp.

◆ dir_

std::string OpenMD::ElementsTable::dir_

protected

data directory for file if _envvar fails

Definition at line 196 of file ElementsTable.hpp.

Referenced by ElementsTable(), and SetReadDirectory().

◆ elements_

std::vector<Element*> OpenMD::ElementsTable::elements_

protected

Definition at line 199 of file ElementsTable.hpp.

◆ envvar_

std::string OpenMD::ElementsTable::envvar_

protected

environment variable to check first

Definition at line 198 of file ElementsTable.hpp.

Referenced by ElementsTable(), Init(), and SetEnvironmentVariable().

◆ filename_

std::string OpenMD::ElementsTable::filename_

protected

file to search for

Definition at line 195 of file ElementsTable.hpp.

Referenced by ElementsTable(), and Init().

◆ init_

bool OpenMD::ElementsTable::init_

protected

whether the data been read already

Definition at line 194 of file ElementsTable.hpp.

Referenced by CorrectedBondRad(), CorrectedVdwRad(), ElementsTable(), GetAllredRochowElectroNeg(), GetAtomicNum(), GetCovalentRad(), GetElectronAffinity(), GetElectroNeg(), GetIonization(), GetMass(), GetMaxBonds(), GetName(), GetNumberOfElements(), GetRGB(), GetSymbol(), GetVdwRad(), and Init().

◆ subdir_

std::string OpenMD::ElementsTable::subdir_

protected

subdirectory (if using environment variable)

Definition at line 197 of file ElementsTable.hpp.

Referenced by Init().

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

utils/ElementsTable.hpp
utils/ElementsTable.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ElementsTable()

◆ ~ElementsTable()

Member Function Documentation

◆ CorrectedBondRad()

◆ CorrectedVdwRad()

◆ GetAllredRochowElectroNeg()

◆ GetAtomicNum() [1/3]

◆ GetAtomicNum() [2/3]

◆ GetAtomicNum() [3/3]

◆ GetCovalentRad()

◆ GetElectronAffinity()

◆ GetElectroNeg()

◆ GetIonization()

◆ GetMass()

◆ GetMaxBonds()

◆ GetName()

◆ GetNumberOfElements()

◆ GetRGB()

◆ GetSize()

◆ GetSymbol()

◆ GetVdwRad()

◆ Init()

◆ ParseLine()

◆ SetEnvironmentVariable()

◆ SetReadDirectory()

Member Data Documentation

◆ dataptr_

◆ dir_

◆ elements_

◆ envvar_

◆ filename_

◆ init_

◆ subdir_