information about an element More...

#include <elements.h>

Collaboration diagram for votca::tools::Elements:

[legend]

Public Member Functions
bool	isElement (std::string name)
	Determine if the name is a recognized element symbol or name.

double	getVdWChelpG (std::string name)

double	getVdWMK (std::string name)

Index	getNucCrg (std::string name)
	Return the Nuclear charges of each atom. H - 1, He - 2, Na - 3 etc...

Index	getEleNum (std::string name)

double	getMass (std::string name)
	Returns the mass of each atom in a.u.

double	getPolarizability (std::string name)
	Returns the atomic polarisability of atom.

double	getCovRad (std::string name, std::string unit)
	Returns the covalent Radii of the atom.

std::string	getEleName (Index elenum)

std::string	getEleShort (std::string elefull)

bool	isEleShort (std::string shortname)
	Is `eleshort` recognized an element symbol i.e. H, C, He, Ne etc.

bool	isEleFull (std::string fullname)
	Is `elefull` recognized as an element name i.e. Carbon, HYDROGEN, suphur.

bool	isMassAssociatedWithElement (double mass, double tolerance)

std::string	getEleShortClosestInMass (double mass, double tolerance)

std::string	getEleFull (std::string eleshort)

Private Member Functions
std::pair< std::string, double >	findShortNameOfElementClosestInMass (double mass)

void	FillMass ()

void	FillVdWChelpG ()

void	FillNucCrg ()

void	FillCovRad ()

void	FillEleNum ()

void	FillEleName ()

void	FillEleShort ()

void	FillEleFull ()

void	FillVdWMK ()

void	FillPolarizability ()

Private Attributes
bool	filled_VdWChelpG_ = false

bool	filled_VdWMK_ = false

bool	filled_NucCrg_ = false

bool	filled_CovRad_ = false

bool	filled_Mass_ = false

bool	filled_EleNum_ = false

bool	filled_EleName_ = false

bool	filled_ElPolarizability_ = false

bool	filled_EleShort_ = false

bool	filled_EleFull_ = false

std::map< std::string, double >	VdWChelpG_

std::map< std::string, double >	VdWMK_

std::map< std::string, Index >	NucCrg_

std::map< std::string, double >	CovRad_

std::map< std::string, double >	Mass_

std::map< std::string, Index >	EleNum_

std::map< Index, std::string >	EleName_

std::map< std::string, double >	ElPolarizability_

std::map< std::string, std::string >	EleShort_

std::map< std::string, std::string >	EleFull_

Detailed Description

information about an element

The Elements class stores properties of several elements in the periodic table includeing: mass, element name, element symbol, van der Waals radius, effective nuclear potential, element number as it appears in the periodic table.

Definition at line 42 of file elements.h.

Member Function Documentation

◆ FillCovRad()

void votca::tools::Elements::FillCovRad ( )

private

Definition at line 384 of file elements.cc.

◆ FillEleFull()

void votca::tools::Elements::FillEleFull ( )

private

Definition at line 688 of file elements.cc.

◆ FillEleName()

void votca::tools::Elements::FillEleName ( )

private

Definition at line 537 of file elements.cc.

◆ FillEleNum()

void votca::tools::Elements::FillEleNum ( )

private

Definition at line 462 of file elements.cc.

◆ FillEleShort()

void votca::tools::Elements::FillEleShort ( )

private

Definition at line 613 of file elements.cc.

◆ FillMass()

void votca::tools::Elements::FillMass ( )

private

Definition at line 209 of file elements.cc.

◆ FillNucCrg()

void votca::tools::Elements::FillNucCrg ( )

private

Definition at line 308 of file elements.cc.

◆ FillPolarizability()

void votca::tools::Elements::FillPolarizability ( )

private

Definition at line 785 of file elements.cc.

◆ FillVdWChelpG()

void votca::tools::Elements::FillVdWChelpG ( )

private

Definition at line 284 of file elements.cc.

◆ FillVdWMK()

void votca::tools::Elements::FillVdWMK ( )

private

Definition at line 763 of file elements.cc.

◆ findShortNameOfElementClosestInMass()

std::pair< std::string, double > votca::tools::Elements::findShortNameOfElementClosestInMass ( double mass )

private

Finds the element closest in mass and returns the difference as well as the string of elements short name

Definition at line 192 of file elements.cc.

◆ getCovRad()

double votca::tools::Elements::getCovRad	(	std::string	name,
		std::string	unit
	)

Returns the covalent Radii of the atom.

Definition at line 109 of file elements.cc.

◆ getEleFull()

std::string votca::tools::Elements::getEleFull ( std::string eleshort )

Provided the element symbol returns the element name "Pb" = "LEAD", "Na" = "SODIUM", ....

Definition at line 137 of file elements.cc.

◆ getEleName()

std::string votca::tools::Elements::getEleName ( Index elenum )

Provided the element number returns the symbol for the element name (1) = "H", (2) = "He", ...

Definition at line 129 of file elements.cc.

◆ getEleNum()

Index votca::tools::Elements::getEleNum ( std::string name )

Similar to the Nuclear charges but returns in integer form represents the id of the atom in the periodic table, the id starts at 1

Definition at line 49 of file elements.cc.

◆ getEleShort()

std::string votca::tools::Elements::getEleShort ( std::string elefull )

Provided the full element name returns the element symbol "Hydrogen" = "H", "HELIUM" = "He",...

Definition at line 145 of file elements.cc.

◆ getEleShortClosestInMass()

std::string votca::tools::Elements::getEleShortClosestInMass	(	double	mass,
		double	tolerance
	)

Get the shortened element name given a mass similar in size to one of the elements. Provided the mass is within the specified tolerance of the match.

Definition at line 178 of file elements.cc.

◆ getMass()

double votca::tools::Elements::getMass ( std::string name )

Returns the mass of each atom in a.u.

Definition at line 62 of file elements.cc.

◆ getNucCrg()

Index votca::tools::Elements::getNucCrg ( std::string name )

Return the Nuclear charges of each atom. H - 1, He - 2, Na - 3 etc...

Definition at line 36 of file elements.cc.

◆ getPolarizability()

double votca::tools::Elements::getPolarizability ( std::string name )

Returns the atomic polarisability of atom.

Definition at line 97 of file elements.cc.

◆ getVdWChelpG()

double votca::tools::Elements::getVdWChelpG ( std::string name )

ChelpG is a method for calculating the electrostatic potential outside of a molecule. The VdWChelpG radius in this case is specific to each element and defines the radius outside of which the electrostatic potential is calculated. The electrostatic potential within the radius is not calculated. For more information see the reference paper CHELPG paper [Journal of Computational Chemistry 11, 361, 1990]

Definition at line 75 of file elements.cc.

◆ getVdWMK()

double votca::tools::Elements::getVdWMK ( std::string name )

Merz-Singh-Kollman MK method is a similar method for calculating the electrostatic potential outside of a molecule. Details of the method can be found here [Singh, U. Chandra (04/01/1984). "An approach to computing electrostatic charges for molecules". Journal of computational chemistry 5 (2), 129, 1984]. The VdWMK method will return the radii used to define where the electrostatic grid starts.

Definition at line 86 of file elements.cc.

◆ isEleFull()

bool votca::tools::Elements::isEleFull ( std::string fullname )

Is elefull recognized as an element name i.e. Carbon, HYDROGEN, suphur.

Definition at line 153 of file elements.cc.

◆ isElement()

bool votca::tools::Elements::isElement ( std::string name )

Determine if the name is a recognized element symbol or name.

Definition at line 32 of file elements.cc.

◆ isEleShort()

bool votca::tools::Elements::isEleShort ( std::string shortname )

Is eleshort recognized an element symbol i.e. H, C, He, Ne etc.

Definition at line 162 of file elements.cc.

◆ isMassAssociatedWithElement()

bool votca::tools::Elements::isMassAssociatedWithElement	(	double	mass,
		double	tolerance
	)

Definition at line 170 of file elements.cc.

Member Data Documentation

◆ CovRad_

std::map<std::string, double> votca::tools::Elements::CovRad_

private

Definition at line 123 of file elements.h.

◆ EleFull_

std::map<std::string, std::string> votca::tools::Elements::EleFull_

private

Definition at line 131 of file elements.h.

◆ EleName_

std::map<Index, std::string> votca::tools::Elements::EleName_

private

Definition at line 126 of file elements.h.

◆ EleNum_

std::map<std::string, Index> votca::tools::Elements::EleNum_

private

Definition at line 125 of file elements.h.

◆ EleShort_

std::map<std::string, std::string> votca::tools::Elements::EleShort_

private

Definition at line 130 of file elements.h.

◆ ElPolarizability_

std::map<std::string, double> votca::tools::Elements::ElPolarizability_

private

Definition at line 128 of file elements.h.

◆ filled_CovRad_

bool votca::tools::Elements::filled_CovRad_ = false

private

Definition at line 112 of file elements.h.

◆ filled_EleFull_

bool votca::tools::Elements::filled_EleFull_ = false

private

Definition at line 118 of file elements.h.

◆ filled_EleName_

bool votca::tools::Elements::filled_EleName_ = false

private

Definition at line 115 of file elements.h.

◆ filled_EleNum_

bool votca::tools::Elements::filled_EleNum_ = false

private

Definition at line 114 of file elements.h.

◆ filled_EleShort_

bool votca::tools::Elements::filled_EleShort_ = false

private

Definition at line 117 of file elements.h.

◆ filled_ElPolarizability_

bool votca::tools::Elements::filled_ElPolarizability_ = false

private

Definition at line 116 of file elements.h.

◆ filled_Mass_

bool votca::tools::Elements::filled_Mass_ = false

private

Definition at line 113 of file elements.h.

◆ filled_NucCrg_

bool votca::tools::Elements::filled_NucCrg_ = false

private

Definition at line 111 of file elements.h.

◆ filled_VdWChelpG_

bool votca::tools::Elements::filled_VdWChelpG_ = false

private

Definition at line 109 of file elements.h.

◆ filled_VdWMK_

bool votca::tools::Elements::filled_VdWMK_ = false

private

Definition at line 110 of file elements.h.

◆ Mass_

std::map<std::string, double> votca::tools::Elements::Mass_

private

Definition at line 124 of file elements.h.

◆ NucCrg_

std::map<std::string, Index> votca::tools::Elements::NucCrg_

private

Definition at line 122 of file elements.h.

◆ VdWChelpG_

std::map<std::string, double> votca::tools::Elements::VdWChelpG_

private

Definition at line 120 of file elements.h.

◆ VdWMK_

std::map<std::string, double> votca::tools::Elements::VdWMK_

private

Definition at line 121 of file elements.h.

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

tools/include/votca/tools/elements.h
tools/src/libtools/elements.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Function Documentation

◆ FillCovRad()

◆ FillEleFull()

◆ FillEleName()

◆ FillEleNum()

◆ FillEleShort()

◆ FillMass()

◆ FillNucCrg()

◆ FillPolarizability()

◆ FillVdWChelpG()

◆ FillVdWMK()

◆ findShortNameOfElementClosestInMass()

◆ getCovRad()

◆ getEleFull()

◆ getEleName()

◆ getEleNum()

◆ getEleShort()

◆ getEleShortClosestInMass()

◆ getMass()

◆ getNucCrg()

◆ getPolarizability()

◆ getVdWChelpG()

◆ getVdWMK()

◆ isEleFull()

◆ isElement()

◆ isEleShort()

◆ isMassAssociatedWithElement()

Member Data Documentation

◆ CovRad_

◆ EleFull_

◆ EleName_

◆ EleNum_

◆ EleShort_

◆ ElPolarizability_

◆ filled_CovRad_

◆ filled_EleFull_

◆ filled_EleName_

◆ filled_EleNum_

◆ filled_EleShort_

◆ filled_ElPolarizability_

◆ filled_Mass_

◆ filled_NucCrg_

◆ filled_VdWChelpG_

◆ filled_VdWMK_

◆ Mass_

◆ NucCrg_

◆ VdWChelpG_

◆ VdWMK_