nnp::ElementMap Class Reference

Contains element map. More...

#include <ElementMap.h>

Collaboration diagram for nnp::ElementMap:

Public Member Functions
std::string	operator[] (std::size_t const index) const
	Overload [] operator for index search. More...
std::size_t	operator[] (std::string const symbol) const
	Overload [] operator for symbol search. More...
std::size_t	size () const
	Get element map size. More...
std::string	getElementsString () const
	Get sorted list of elements in one string (space separated). More...
std::size_t	index (std::string const &symbol) const
	Get index of given element. More...
std::string	symbol (std::size_t const index) const
	Get element symbol for given element index. More...
std::size_t	atomicNumber (std::size_t index) const
	Get atomic number from element index. More...
std::size_t	registerElements (std::string const &elementLine)
	Extract all elements and store in element map. More...
void	deregisterElements ()
	Clear element map. More...
std::vector< std::string >	info () const
	Get map information as a vector of strings. More...

Static Public Member Functions
static std::string	symbolFromAtomicNumber (std::size_t const atomicNumber)
	Get element symbol from atomic number. More...
static std::size_t	atomicNumber (std::string const &symbol)
	Get atomic number from element string. More...

Static Private Member Functions
static bool	compareAtomicNumber (std::string const &symbol1, std::string const &symbol2)
	Check if arguments are sorted according to atomic number. More...

Private Attributes
std::map< std::string, std::size_t >	forwardMap
	Map of elements present and corresponding index number. More...
std::map< std::size_t, std::string >	reverseMap
	Reverse element map. More...

Static Private Attributes
static std::string const	knownElements []
	List of element symbols (e.g. "He" for Helium). More...

Detailed Description

Contains element map.

Definition at line 29 of file ElementMap.h.

Member Function Documentation

operator[]() [1/2]

std::string nnp::ElementMap::operator[] ( std::size_t const  index ) const

inline

Overload [] operator for index search.

Parameters

[in]

index

Element index.

Returns

Symbol of element in map.

Definition at line 130 of file ElementMap.h.

{
    return symbol(index);
}

References index(), and symbol().

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operator[]() [2/2]

std::size_t nnp::ElementMap::operator[] ( std::string const  symbol ) const

inline

Overload [] operator for symbol search.

Parameters

[in]

symbol

Element symbol.

Returns

Index of element in map.

Definition at line 135 of file ElementMap.h.

{
    return index(symbol);
}

References index(), and symbol().

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size()

std::size_t nnp::ElementMap::size ( ) const

inline

Get element map size.

Returns

Number of elements registered.

Definition at line 140 of file ElementMap.h.

{
    return forwardMap.size();
}

References forwardMap.

Referenced by nnp::Structure::addAtom(), nnp::SymFnc::addCacheIndex(), nnp::SymFncBaseCompAngWeighted::getCacheIdentifiers(), nnp::SymFncCompRadWeighted::getCacheIdentifiers(), nnp::SymFncExpAngnWeighted::getCacheIdentifiers(), nnp::SymFncExpRadWeighted::getCacheIdentifiers(), getElementsString(), nnp::InterfaceLammps::initialize(), nnp::Structure::reset(), nnp::Structure::setElementMap(), LAMMPS_NS::PairHDNNPExternal::settings(), nnp::Mode::setupElectrostatics(), nnp::Mode::setupElementMap(), nnp::Mode::setupElements(), nnp::Mode::setupNeuralNetwork(), nnp::Element::setupSymmetryFunctionMemory(), nnp::SymFnc::SymFnc(), and nnp::Structure::writeToFilePoscar().

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getElementsString()

string ElementMap::getElementsString

(

)

const

Get sorted list of elements in one string (space separated).

Returns

Element string.

Definition at line 56 of file ElementMap.cpp.

{
    string elements = "";
 
    if (size() == 0) return elements;
    elements += symbol(0);
    if (size() == 1) return elements;
    for (size_t i = 1; i < size(); ++i)
    {
        elements += strpr(" %s", symbol(i).c_str());
    }
 
    return elements;
}

References size(), nnp::strpr(), and symbol().

Referenced by nnp::Structure::writeToFilePoscar().

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index()

size_t ElementMap::index

(

std::string const &

symbol

)

const

Get index of given element.

Parameters

[in]

symbol

Element symbol.

Returns

Element index.

Definition at line 71 of file ElementMap.cpp.

{
    return safeFind(forwardMap, symbol);
}

References forwardMap, nnp::safeFind(), and symbol().

Referenced by atomicNumber(), operator[](), and symbol().

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symbol()

string ElementMap::symbol

(

std::size_t const

index

)

const

Get element symbol for given element index.

Parameters

[in]

index

Element index.

Returns

Element symbol.

Definition at line 76 of file ElementMap.cpp.

{
    return safeFind(reverseMap, index);
}

References index(), reverseMap, and nnp::safeFind().

Referenced by atomicNumber(), getElementsString(), index(), and operator[]().

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atomicNumber() [1/2]

std::size_t nnp::ElementMap::atomicNumber ( std::size_t  index ) const

inline

Get atomic number from element index.

Parameters

[in]

index

Element index in map.

Returns

Atomic number (proton number Z) of element.

Definition at line 145 of file ElementMap.h.

{
    return atomicNumber(symbol(index));
}

References atomicNumber(), index(), and symbol().

Referenced by atomicNumber(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncExpAngnWeighted::calculate(), nnp::SymFncExpRadWeighted::calculate(), nnp::SymGrpCompAngnWeighted::calculate(), nnp::SymGrpCompAngwWeighted::calculate(), nnp::SymGrpCompRadWeighted::calculate(), nnp::SymGrpExpAngnWeighted::calculate(), nnp::SymGrpExpRadWeighted::calculate(), compareAtomicNumber(), nnp::InterfaceLammps::initialize(), main(), LAMMPS_NS::PairHDNNPExternal::settings(), nnp::Mode::setupElementMap(), symbolFromAtomicNumber(), nnp::Dataset::writeNeighborLists(), nnp::Dataset::writeSymmetryFunctionFile(), nnp::Dataset::writeSymmetryFunctionHistograms(), and nnp::Training::writeUpdaterStatus().

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registerElements()

size_t ElementMap::registerElements

(

std::string const &

elementLine

)

Extract all elements and store in element map.

Parameters

[in]

elementLine

String containing all elements, e.g. "Cd S Zn", separated by whitespaces.

Returns

Number of registered elements.

Sorts all elements according to their atomic number and populates forwardMap and reverseMap with the symbol and the corresponding index number.

Definition at line 36 of file ElementMap.cpp.

{
    vector<string> elements = split(reduce(elementLine));
 
    sort(elements.begin(), elements.end(), compareAtomicNumber);
 
    if (!forwardMap.empty())
    {
        throw runtime_error("ERROR: Element map not empty.\n");
    }
 
    for (size_t i = 0; i < elements.size(); i++)
    {
        forwardMap[elements[i]] = i;
        reverseMap[i] = elements[i];
    }
 
    return forwardMap.size();
}

References compareAtomicNumber(), forwardMap, nnp::reduce(), reverseMap, and nnp::split().

Referenced by main(), LAMMPS_NS::PairHDNNPExternal::settings(), and nnp::Mode::setupElementMap().

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deregisterElements()

void ElementMap::deregisterElements

(

)

Clear element map.

Definition at line 81 of file ElementMap.cpp.

{
    forwardMap.clear();
    reverseMap.clear();
 
    return;
}

References forwardMap, and reverseMap.

symbolFromAtomicNumber()

string ElementMap::symbolFromAtomicNumber ( std::size_t const  atomicNumber )

static

Get element symbol from atomic number.

Parameters

[in]

atomicNumber

Atomic number of element.

Returns

Element symbol.

Definition at line 106 of file ElementMap.cpp.

{
    size_t numKnownElements = sizeof(knownElements) / sizeof(*knownElements);
 
    if (atomicNumber >= numKnownElements)
    {
        throw runtime_error(strpr("ERROR: Only the first %zu elements are "
                                  "known to this library.\n",
                                  numKnownElements));
    }
    else if (atomicNumber == 0)
    {
        throw runtime_error("ERROR: Invalid atomic number.\n");
    }
 
    atomicNumber--;
    return knownElements[atomicNumber];
}

References atomicNumber(), knownElements, and nnp::strpr().

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atomicNumber() [2/2]

size_t ElementMap::atomicNumber ( std::string const &  symbol )

static

Get atomic number from element string.

Parameters

[in]

symbol

Element symbol (e.g. "He" for Helium).

Returns

Atomic number (proton number Z) of element.

Definition at line 89 of file ElementMap.cpp.

{
    size_t numKnownElements = sizeof(knownElements) / sizeof(*knownElements);
 
    for (size_t i = 0; i < numKnownElements; i++)
    {
        if (knownElements[i] == symbol)
        {
            return i + 1;
        }
    }
 
    throw runtime_error("ERROR: Element \"" + symbol + "\" unknown.\n");
 
    return 0;
}

References knownElements, and symbol().

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info()

vector< string > ElementMap::info

(

)

const

Get map information as a vector of strings.

Returns

Lines with map information.

Definition at line 125 of file ElementMap.cpp.

{
    vector<string> v;
 
    v.push_back(strpr("********************************\n"));
    v.push_back(strpr("ELEMENT MAP                     \n"));
    v.push_back(strpr("********************************\n"));
    v.push_back(strpr("--------------------------------\n"));
    v.push_back(strpr("forwardMap                 [*] : %d\n", forwardMap.size()));
    v.push_back(strpr("--------------------------------\n"));
    for (map<string, size_t>::const_iterator it = forwardMap.begin();
         it != forwardMap.end(); ++it)
    {
        v.push_back(strpr("%29s  : %d\n", it->first.c_str(), it->second));
    }
    v.push_back(strpr("--------------------------------\n"));
    v.push_back(strpr("--------------------------------\n"));
    v.push_back(strpr("reverseMap                 [*] : %d\n", reverseMap.size()));
    v.push_back(strpr("--------------------------------\n"));
    for (map<size_t, string>::const_iterator it = reverseMap.begin();
         it != reverseMap.end(); ++it)
    {
        v.push_back(strpr("%29d  : %s\n", it->first, it->second.c_str()));
    }
    v.push_back(strpr("--------------------------------\n"));
    v.push_back(strpr("********************************\n"));
 
    return v;
}

References forwardMap, reverseMap, and nnp::strpr().

Referenced by nnp::Structure::info().

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compareAtomicNumber()

bool nnp::ElementMap::compareAtomicNumber ( std::string const &  symbol1, std::string const &  symbol2  )

inlinestaticprivate

Check if arguments are sorted according to atomic number.

Parameters

[in]	symbol1	Element symbol 1.
[in]	symbol2	Element symbol 2.

Returns

true if atomic number of element 1 is smaller than atomic number of element 2, false otherwise.

Used for sorting in registerElements().

Definition at line 150 of file ElementMap.h.

{
    return atomicNumber(symbol1) < atomicNumber(symbol2);
}

References atomicNumber().

Referenced by registerElements().

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Member Data Documentation

forwardMap

std::map<std::string, std::size_t> nnp::ElementMap::forwardMap

private

Map of elements present and corresponding index number.

Definition at line 107 of file ElementMap.h.

Referenced by deregisterElements(), index(), info(), registerElements(), and size().

reverseMap

std::map<std::size_t, std::string> nnp::ElementMap::reverseMap

private

Reverse element map.

Definition at line 109 of file ElementMap.h.

Referenced by deregisterElements(), info(), registerElements(), and symbol().

knownElements

string const ElementMap::knownElements

staticprivate

Initial value:

= {
"H" , "He", "Li", "Be", "B" , "C" , "N" , "O" , "F" , "Ne", "Na", "Mg", "Al",
"Si", "P" , "S" , "Cl", "Ar", "K" , "Ca", "Sc", "Ti", "V" , "Cr", "Mn", "Fe",
"Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y" ,
"Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te",
"I" , "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb",
"Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt",
"Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa",
"U" , "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No"
}

List of element symbols (e.g. "He" for Helium).

Definition at line 111 of file ElementMap.h.

Referenced by atomicNumber(), and symbolFromAtomicNumber().

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

• /home/runner/work/n2p2/n2p2/src/libnnp/ElementMap.h
• /home/runner/work/n2p2/n2p2/src/libnnp/ElementMap.cpp