nnp::Element Class Reference

Contains element-specific data. More...

#include <Element.h>

Inheritance diagram for nnp::Element:

Collaboration diagram for nnp::Element:

Classes
struct	SFCacheList
	List of symmetry functions corresponding to one cache identifier. More...

Public Member Functions
	Element ()
	Default constructor. More...
	Element (std::size_t const index, ElementMap const &elementMap)
	Constructor using index. More...
virtual	~Element ()
	Destructor. More...
void	clearSymmetryFunctions ()
	Clear all symmetry functions and groups. More...
void	setAtomicEnergyOffset (double atomicEnergyOffset)
	Set atomicEnergyOffset. More...
void	setHardness (double hardness)
	Set hardness. More...
void	setQsigma (double qsigma)
	Set qsigma. More...
std::size_t	getIndex () const
	Get index. More...
std::size_t	getAtomicNumber () const
	Get atomicNumber. More...
double	getAtomicEnergyOffset () const
	Get atomicEnergyOffset. More...
double	getHardness () const
	Get hardness. More...
double	getQsigma () const
	Get qsigma. More...
std::string	getSymbol () const
	Get symbol. More...
void	addSymmetryFunction (std::string const &parameters, std::size_t const &lineNumber)
	Add one symmetry function. More...
void	changeLengthUnitSymmetryFunctions (double convLength)
	Change length unit for all symmetry functions. More...
void	sortSymmetryFunctions ()
	Sort all symmetry function. More...
std::vector< std::string >	infoSymmetryFunctionParameters () const
	Print symmetry function parameter value information. More...
std::vector< std::string >	infoSymmetryFunction (std::size_t index) const
	Print symmetry function parameter names and values. More...
std::vector< std::string >	infoSymmetryFunctionScaling () const
	Print symmetry function scaling information. More...
void	setupSymmetryFunctionGroups ()
	Set up symmetry function groups. More...
void	setupSymmetryFunctionMemory ()
	Extract relevant symmetry function combinations for derivative memory. More...
std::vector< std::string >	infoSymmetryFunctionGroups () const
	Print symmetry function group info. More...
void	setCutoffFunction (CutoffFunction::CutoffType const cutoffType, double const cutoffAlpha)
	Set cutoff function for all symmetry functions. More...
void	setScalingNone () const
	Set no scaling of symmetry function. More...
void	setScaling (SymFnc::ScalingType scalingType, std::vector< std::string > const &statisticsLine, double minS, double maxS) const
	Set scaling of all symmetry functions. More...
std::size_t	numSymmetryFunctions () const
	Get number of symmetry functions. More...
std::size_t	getMinNeighbors () const
	Get maximum of required minimum number of neighbors for all symmetry functions for this element. More...
double	getMinCutoffRadius () const
	Get minimum cutoff radius of all symmetry functions. More...
double	getMaxCutoffRadius () const
	Get maximum cutoff radius of all symmetry functions. More...
void	getCutoffRadii (std::vector< double > &cutoffs) const
	Get all different cutoff radii belonging to this element. More...
std::vector< std::size_t > const &	getSymmetryFunctionNumTable () const
	Get number of relevant symmetry functions per element. More...
std::vector< std::vector< std::size_t > > const &	getSymmetryFunctionTable () const
	Get symmetry function element relevance table. More...
void	calculateSymmetryFunctions (Atom &atom, bool const derivatives) const
	Calculate symmetry functions. More...
void	calculateSymmetryFunctionGroups (Atom &atom, bool const derivatives) const
	Calculate symmetry functions via groups. More...
std::size_t	updateSymmetryFunctionStatistics (Atom const &atom)
	Update symmetry function statistics. More...
SymFnc const &	getSymmetryFunction (std::size_t index) const
	Get symmetry function instance. More...
void	setCacheIndices (std::vector< std::vector< SFCacheList > > cacheLists)
	Set cache indices for all symmetry functions of this element. More...
std::vector< std::size_t >	getCacheSizes () const
	Get cache sizes for each neighbor atom element. More...

Public Attributes
std::map< std::string, NeuralNetwork >	neuralNetworks
	Neural networks for this element. More...
SymFncStatistics	statistics
	Symmetry function statistics. More...

Protected Attributes
ElementMap	elementMap
	Copy of element map. More...
std::size_t	index
	Global index of this element. More...
std::size_t	atomicNumber
	Atomic number of this element. More...
double	atomicEnergyOffset
	Offset energy for every atom of this element. More...
double	hardness
	Atomic hardness for global charge equilibration. More...
double	qsigma
	Gaussian width of charge distribution. More...
std::string	symbol
	Element symbol. More...
std::vector< std::size_t >	symmetryFunctionNumTable
	Number of relevant symmetry functions for each neighbor element. More...
std::vector< std::vector< std::size_t > >	symmetryFunctionTable
	List of symmetry function indices relevant for each neighbor element. More...
std::vector< std::vector< SFCacheList > >	cacheLists
	Symmetry function cache lists. More...
std::vector< SymFnc * >	symmetryFunctions
	Vector of pointers to symmetry functions. More...
std::vector< SymGrp * >	symmetryFunctionGroups
	Vector of pointers to symmetry function groups. More...

Detailed Description

Contains element-specific data.

Definition at line 38 of file Element.h.

Constructor & Destructor Documentation

Element() [1/2]

nnp::Element::Element ( )

inline

Default constructor.

Definition at line 57 of file Element.h.

{}

Element() [2/2]

nnp::Element::Element	(	std::size_t const	index,
		ElementMap const &	elementMap
	)

Constructor using index.

~Element()

Element::~Element ( )

virtual

Destructor.

Necessary because of symmetryFunctions vector of pointers.

Definition at line 67 of file Element.cpp.

{
    clearSymmetryFunctions();
}

References clearSymmetryFunctions().

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Member Function Documentation

clearSymmetryFunctions()

void Element::clearSymmetryFunctions

(

)

Clear all symmetry functions and groups.

Definition at line 72 of file Element.cpp.

{
    for (auto& s : symmetryFunctions) delete s;
    symmetryFunctions.clear();
    for (auto& s : symmetryFunctionGroups) delete s;
    symmetryFunctionGroups.clear();
 
    return;
}

References symmetryFunctionGroups, and symmetryFunctions.

Referenced by ~Element().

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setAtomicEnergyOffset()

void nnp::Element::setAtomicEnergyOffset ( double  atomicEnergyOffset )

inline

Set atomicEnergyOffset.

Definition at line 284 of file Element.h.

{
    this->atomicEnergyOffset = atomicEnergyOffset;
 
    return;
}

References atomicEnergyOffset.

setHardness()

void nnp::Element::setHardness ( double  hardness )

inline

Set hardness.

Definition at line 291 of file Element.h.

{
    this->hardness = hardness;
 
    return;
}

References hardness.

setQsigma()

void nnp::Element::setQsigma ( double  qsigma )

inline

Set qsigma.

Definition at line 298 of file Element.h.

{
    this->qsigma = qsigma;
 
    return;
}

References qsigma.

getIndex()

size_t nnp::Element::getIndex ( ) const

inline

Get index.

Definition at line 305 of file Element.h.

{
    return index;
}

References index.

Referenced by nnp::Mode::calculateSymmetryFunctionGroups(), and nnp::Mode::calculateSymmetryFunctions().

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getAtomicNumber()

size_t nnp::Element::getAtomicNumber ( ) const

inline

Get atomicNumber.

Definition at line 310 of file Element.h.

{
    return atomicNumber;
}

References atomicNumber.

Referenced by nnp::SetupAnalysis::writeSymmetryFunctionShape().

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getAtomicEnergyOffset()

double nnp::Element::getAtomicEnergyOffset ( ) const

inline

Get atomicEnergyOffset.

Definition at line 315 of file Element.h.

{
    return atomicEnergyOffset;
}

References atomicEnergyOffset.

Referenced by nnp::InterfaceLammps::getAtomicEnergy().

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getHardness()

double nnp::Element::getHardness ( ) const

inline

Get hardness.

Definition at line 320 of file Element.h.

{
    return hardness;
}

References hardness.

getQsigma()

double nnp::Element::getQsigma ( ) const

inline

Get qsigma.

Definition at line 325 of file Element.h.

{
    return qsigma;
}

References qsigma.

getSymbol()

std::string nnp::Element::getSymbol ( ) const

inline

Get symbol.

Definition at line 330 of file Element.h.

{
    return symbol;
}

References symbol.

Referenced by nnp::Mode::setupNeuralNetwork(), and nnp::Mode::setupSymmetryFunctionCache().

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addSymmetryFunction()

void Element::addSymmetryFunction	(	std::string const &	parameters,
		std::size_t const &	lineNumber
	)

Add one symmetry function.

Parameters

[in]	parameters	String containing settings for symmetry function.
[in]	lineNumber	Line number of symmetry function in settings file.

Definition at line 82 of file Element.cpp.

{
    vector<string> args = split(reduce(parameters));
    size_t         type = (size_t)atoi(args.at(1).c_str());
 
    if (type == 2)
    {
        symmetryFunctions.push_back(new SymFncExpRad(elementMap));
    }
    else if (type == 3)
    {
        symmetryFunctions.push_back(new SymFncExpAngn(elementMap));
    }
    else if (type == 9)
    {
        symmetryFunctions.push_back(new SymFncExpAngw(elementMap));
    }
    else if (type == 12)
    {
        symmetryFunctions.push_back(new SymFncExpRadWeighted(elementMap));
    }
    else if (type == 13)
    {
        symmetryFunctions.push_back(new SymFncExpAngnWeighted(elementMap));
    }
    else if (type == 20)
    {
        symmetryFunctions.push_back(new SymFncCompRad(elementMap));
    }
    else if (type == 21)
    {
        symmetryFunctions.push_back(new SymFncCompAngn(elementMap));
    }
    else if (type == 22)
    {
        symmetryFunctions.push_back(new SymFncCompAngw(elementMap));
    }
    else if (type == 23)
    {
        symmetryFunctions.push_back(new SymFncCompRadWeighted(elementMap));
    }
    else if (type == 24)
    {
        symmetryFunctions.push_back(new SymFncCompAngnWeighted(elementMap));
    }
    else if (type == 25)
    {
        symmetryFunctions.push_back(new SymFncCompAngwWeighted(elementMap));
    }
    else
    {
        throw runtime_error("ERROR: Unknown symmetry function type.\n");
    }
 
    symmetryFunctions.back()->setParameters(parameters);
    symmetryFunctions.back()->setLineNumber(lineNumber);
 
    return;
}

References elementMap, nnp::reduce(), nnp::split(), and symmetryFunctions.

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changeLengthUnitSymmetryFunctions()

void Element::changeLengthUnitSymmetryFunctions

(

double

convLength

)

Change length unit for all symmetry functions.

Parameters

[in]

convLength

Length unit conversion factor.

Definition at line 143 of file Element.cpp.

{
    for (vector<SymFnc*>::iterator it = symmetryFunctions.begin();
         it != symmetryFunctions.end(); ++it)
    {
        (*it)->changeLengthUnit(convLength);
    }
 
    return;
}

References symmetryFunctions.

sortSymmetryFunctions()

void Element::sortSymmetryFunctions

(

)

Sort all symmetry function.

Definition at line 154 of file Element.cpp.

{
    sort(symmetryFunctions.begin(),
         symmetryFunctions.end(),
         comparePointerTargets<SymFnc>);
 
    for (size_t i = 0; i < symmetryFunctions.size(); ++i)
    {
        symmetryFunctions.at(i)->setIndex(i);
    }
 
    return;
}

References symmetryFunctions.

infoSymmetryFunctionParameters()

vector< string > Element::infoSymmetryFunctionParameters

(

)

const

Print symmetry function parameter value information.

Definition at line 168 of file Element.cpp.

{
    vector<string> v;
 
    for (vector<SymFnc*>::const_iterator
         sf = symmetryFunctions.begin(); sf != symmetryFunctions.end(); ++sf)
    {
        v.push_back((*sf)->parameterLine());
    }
 
    return v;
}

References symmetryFunctions.

infoSymmetryFunction()

std::vector< std::string > nnp::Element::infoSymmetryFunction ( std::size_t  index ) const

inline

Print symmetry function parameter names and values.

Definition at line 348 of file Element.h.

{
    return symmetryFunctions.at(index)->parameterInfo();
}

References index, and symmetryFunctions.

Referenced by nnp::SetupAnalysis::writeSymmetryFunctionShape().

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infoSymmetryFunctionScaling()

vector< string > Element::infoSymmetryFunctionScaling

(

)

const

Print symmetry function scaling information.

Definition at line 181 of file Element.cpp.

{
    vector<string> v;
 
    for (vector<SymFnc*>::const_iterator
         sf = symmetryFunctions.begin(); sf != symmetryFunctions.end(); ++sf)
    {
        v.push_back((*sf)->scalingLine());
    }
 
    return v;
}

References symmetryFunctions.

setupSymmetryFunctionGroups()

void Element::setupSymmetryFunctionGroups

(

)

Set up symmetry function groups.

Definition at line 194 of file Element.cpp.

{
    for (vector<SymFnc*>::const_iterator
         sf = symmetryFunctions.begin(); sf != symmetryFunctions.end(); ++sf)
    {
        bool createNewGroup = true;
        for (vector<SymGrp*>::const_iterator
             sfg = symmetryFunctionGroups.begin();
             sfg != symmetryFunctionGroups.end(); ++sfg)
        {
            if ((*sfg)->addMember((*sf)))
            {
                createNewGroup = false;
                break;
            }
        }
        if (createNewGroup)
        {
            if ((*sf)->getType() == 2)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpExpRad(elementMap));
            }
            else if ((*sf)->getType() == 3)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpExpAngn(elementMap));
            }
            else if ((*sf)->getType() == 9)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpExpAngw(elementMap));
            }
            else if ((*sf)->getType() == 12)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpExpRadWeighted(elementMap));
            }
            else if ((*sf)->getType() == 13)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpExpAngnWeighted(elementMap));
            }
            else if ((*sf)->getType() == 20)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpCompRad(elementMap));
            }
            else if ((*sf)->getType() == 21)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpCompAngn(elementMap));
            }
            else if ((*sf)->getType() == 22)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpCompAngw(elementMap));
            }
            else if ((*sf)->getType() == 23)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpCompRadWeighted(elementMap));
            }
            else if ((*sf)->getType() == 24)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpCompAngnWeighted(elementMap));
            }
            else if ((*sf)->getType() == 25)
            {
                symmetryFunctionGroups.push_back((SymGrp*)
                    new SymGrpCompAngwWeighted(elementMap));
            }
            else
            {
                throw runtime_error("ERROR: Unknown symmetry function group"
                                    " type.\n");
            }
            symmetryFunctionGroups.back()->addMember(*sf);
        }
    }
 
    sort(symmetryFunctionGroups.begin(),
         symmetryFunctionGroups.end(),
         comparePointerTargets<SymGrp>);
 
    for (size_t i = 0; i < symmetryFunctionGroups.size(); ++i)
    {
        symmetryFunctionGroups.at(i)->sortMembers();
        symmetryFunctionGroups.at(i)->setIndex(i);
    }
 
    return;
}

References elementMap, symmetryFunctionGroups, and symmetryFunctions.

setupSymmetryFunctionMemory()

void Element::setupSymmetryFunctionMemory

(

)

Extract relevant symmetry function combinations for derivative memory.

Definition at line 289 of file Element.cpp.

{
    symmetryFunctionTable.clear();
    symmetryFunctionTable.resize(elementMap.size());
    for (auto const& s : symmetryFunctions)
    {
        for (size_t i = 0; i < elementMap.size(); ++i)
        {
            if (s->checkRelevantElement(i))
            {
                s->setIndexPerElement(i, symmetryFunctionTable.at(i).size());
                symmetryFunctionTable.at(i).push_back(s->getIndex());
            }
        }
    }
    symmetryFunctionNumTable.clear();
    for (size_t i = 0; i < elementMap.size(); ++i)
    {
        symmetryFunctionNumTable.push_back(symmetryFunctionTable.at(i).size());
    }
 
    return;
}

References elementMap, nnp::ElementMap::size(), symmetryFunctionNumTable, symmetryFunctions, and symmetryFunctionTable.

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infoSymmetryFunctionGroups()

vector< string > Element::infoSymmetryFunctionGroups

(

)

const

Print symmetry function group info.

Definition at line 313 of file Element.cpp.

{
    vector<string> v;
 
    for (vector<SymGrp*>::const_iterator
         it = symmetryFunctionGroups.begin();
         it != symmetryFunctionGroups.end(); ++it)
    {
        vector<string> lines = (*it)->parameterLines();
        v.insert(v.end(), lines.begin(), lines.end());
    }
 
    return v;
}

References symmetryFunctionGroups.

setCutoffFunction()

void Element::setCutoffFunction	(	CutoffFunction::CutoffType const	cutoffType,
		double const	cutoffAlpha
	)

Set cutoff function for all symmetry functions.

Parameters

[in]	cutoffType	Type of cutoff function.
[in]	cutoffAlpha	Cutoff parameter for all functions.

Definition at line 328 of file Element.cpp.

{
    for (vector<SymFnc*>::const_iterator
         it = symmetryFunctions.begin(); it != symmetryFunctions.end(); ++it)
    {
        SymFncBaseCutoff* sfcb = dynamic_cast<SymFncBaseCutoff*>(*it);
        if (sfcb != nullptr)
        {
            sfcb->setCutoffFunction(cutoffType, cutoffAlpha);
        }
    }
 
    return;
}

References nnp::SymFncBaseCutoff::setCutoffFunction(), and symmetryFunctions.

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setScalingNone()

void Element::setScalingNone

(

)

const

Set no scaling of symmetry function.

Still scaling factors need to be initialized.

Definition at line 344 of file Element.cpp.

{
    for (size_t i = 0; i < symmetryFunctions.size(); ++i)
    {
        string scalingLine = strpr("%d %d 0.0 0.0 0.0 0.0",
                                   symmetryFunctions.at(i)->getEc(),
                                   i + 1);
        symmetryFunctions.at(i)->setScalingType(SymFnc::ST_NONE,
                                                scalingLine,
                                                0.0,
                                                0.0);
    }
    for (size_t i = 0; i < symmetryFunctionGroups.size(); ++i)
    {
        symmetryFunctionGroups.at(i)->setScalingFactors();
    }
    
    return;
}

References nnp::SymFnc::ST_NONE, nnp::strpr(), symmetryFunctionGroups, and symmetryFunctions.

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setScaling()

void Element::setScaling	(	SymFnc::ScalingType	scalingType,
		std::vector< std::string > const &	statisticsLine,
		double	minS,
		double	maxS
	)		const

Set scaling of all symmetry functions.

Parameters

[in]	scalingType	Type of scaling, see SymFnc::ScalingType.
[in]	statisticsLine	Vector of strings containing statistics for all symmetry functions.
[in]	minS	Minimum for scaling range.
[in]	maxS	Maximum for scaling range.

Definition at line 364 of file Element.cpp.

{
    for (size_t i = 0; i < symmetryFunctions.size(); ++i)
    {
        symmetryFunctions.at(i)->setScalingType(scalingType,
                                                statisticsLine.at(i),
                                                Smin,
                                                Smax);
    }
    for (size_t i = 0; i < symmetryFunctionGroups.size(); ++i)
    {
        symmetryFunctionGroups.at(i)->setScalingFactors();
    }
 
    return;
}

References symmetryFunctionGroups, and symmetryFunctions.

numSymmetryFunctions()

size_t nnp::Element::numSymmetryFunctions ( ) const

inline

Get number of symmetry functions.

Returns

Number of symmetry functions.

Definition at line 353 of file Element.h.

{
    return symmetryFunctions.size();
}

References symmetryFunctions.

Referenced by nnp::Mode::calculateSymmetryFunctionGroups(), nnp::Mode::calculateSymmetryFunctions(), nnp::Mode::setupSymmetryFunctionCache(), and nnp::SetupAnalysis::writeSymmetryFunctionShape().

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getMinNeighbors()

size_t Element::getMinNeighbors

(

)

const

Get maximum of required minimum number of neighbors for all symmetry functions for this element.

Returns

Minimum number of neighbors required.

Definition at line 384 of file Element.cpp.

{
    size_t minNeighbors = 0;
 
    for (vector<SymFnc*>::const_iterator
         it = symmetryFunctions.begin(); it != symmetryFunctions.end(); ++it)
    {
        minNeighbors = max((*it)->getMinNeighbors(), minNeighbors);
    }
 
    return minNeighbors;
}

References symmetryFunctions.

getMinCutoffRadius()

double Element::getMinCutoffRadius

(

)

const

Get minimum cutoff radius of all symmetry functions.

Returns

Minimum cutoff radius.

Definition at line 397 of file Element.cpp.

{
    double minCutoffRadius = numeric_limits<double>::max();
 
    // MPB: Hack to work with negative radii
    //      Exploit the fact that all allowed symmetry functions are either
    //      defined for a domain > 0 or have to be symmetric around 0.
 
    for (vector<SymFnc*>::const_iterator
         it = symmetryFunctions.begin(); it != symmetryFunctions.end(); ++it)
    {
        minCutoffRadius = min((*it)->getRc(), minCutoffRadius);
    }
 
    return minCutoffRadius;
}

References symmetryFunctions.

getMaxCutoffRadius()

double Element::getMaxCutoffRadius

(

)

const

Get maximum cutoff radius of all symmetry functions.

Returns

Maximum cutoff radius.

Definition at line 414 of file Element.cpp.

{
    double maxCutoffRadius = 0.0;
 
    for (vector<SymFnc*>::const_iterator
         it = symmetryFunctions.begin(); it != symmetryFunctions.end(); ++it)
    {
        maxCutoffRadius = max((*it)->getRc(), maxCutoffRadius);
    }
 
    return maxCutoffRadius;
}

References symmetryFunctions.

getCutoffRadii()

void Element::getCutoffRadii

(

std::vector< double > &

cutoffs

)

const

Get all different cutoff radii belonging to this element.

Parameters

[in]

cutoffs

Vector to append the result.

Definition at line 427 of file Element.cpp.

{
    for (auto const& sf : symmetryFunctions)
    {
        double rc = sf->getRc();
        if (!vectorContains(cutoffs,rc)) cutoffs.push_back(rc);
    }
}

References symmetryFunctions, and nnp::vectorContains().

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getSymmetryFunctionNumTable()

std::vector< std::size_t > const & nnp::Element::getSymmetryFunctionNumTable ( ) const

inline

Get number of relevant symmetry functions per element.

Returns

symmetryFunctionNumTable

Definition at line 336 of file Element.h.

{
    return symmetryFunctionNumTable;
}

References symmetryFunctionNumTable.

Referenced by nnp::Mode::calculateSymmetryFunctionGroups(), and nnp::Mode::calculateSymmetryFunctions().

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getSymmetryFunctionTable()

std::vector< std::vector< std::size_t > > const & nnp::Element::getSymmetryFunctionTable ( ) const

inline

Get symmetry function element relevance table.

Returns

symmetryFunctionTable

Definition at line 342 of file Element.h.

{
    return symmetryFunctionTable;
}

References symmetryFunctionTable.

calculateSymmetryFunctions()

void Element::calculateSymmetryFunctions	(	Atom &	atom,
		bool const	derivatives
	)		const

Calculate symmetry functions.

Parameters

[in]	atom	Atom whose symmetry functions are calculated.
[in]	derivatives	If symmetry function derivatives will be calculated.

Definition at line 436 of file Element.cpp.

{
    for (vector<SymFnc*>::const_iterator
         it = symmetryFunctions.begin();
         it != symmetryFunctions.end(); ++it)
    {
        (*it)->calculate(atom, derivatives);
    }
 
    return;
}

References symmetryFunctions.

Referenced by nnp::Mode::calculateSymmetryFunctions().

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calculateSymmetryFunctionGroups()

void Element::calculateSymmetryFunctionGroups	(	Atom &	atom,
		bool const	derivatives
	)		const

Calculate symmetry functions via groups.

Parameters

[in]	atom	Atom whose symmetry functions are calculated.
[in]	derivatives	If symmetry function derivatives will be calculated.

Definition at line 449 of file Element.cpp.

{
    for (vector<SymGrp*>::const_iterator
         it = symmetryFunctionGroups.begin();
         it != symmetryFunctionGroups.end(); ++it)
    {
        (*it)->calculate(atom, derivatives);
    }
 
    return;
}

References symmetryFunctionGroups.

Referenced by nnp::Mode::calculateSymmetryFunctionGroups().

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updateSymmetryFunctionStatistics()

size_t Element::updateSymmetryFunctionStatistics

(

Atom const &

atom

)

Update symmetry function statistics.

Parameters

[in]

atom

Atom with symmetry function values.

Returns

Number of extrapolation warnings encountered.

This function checks also for extrapolation warnings.

Definition at line 462 of file Element.cpp.

{
    size_t countExtrapolationWarnings = 0;
    double epsilon = 1000.0 * numeric_limits<double>::epsilon();
 
    if (atom.element != index)
    {
        throw runtime_error("ERROR: Atom has a different element index.\n");
    }
 
    if (atom.numSymmetryFunctions != symmetryFunctions.size())
    {
        throw runtime_error("ERROR: Number of symmetry functions"
                            " does not match.\n");
    }
 
    for (size_t i = 0; i < atom.G.size(); ++i)
    {
        double const Gmin = symmetryFunctions.at(i)->getGmin();
        double const Gmax = symmetryFunctions.at(i)->getGmax();
        double const value = symmetryFunctions.at(i)->unscale(atom.G.at(i));
        size_t const sfindex = symmetryFunctions.at(i)->getIndex();
        size_t const type = symmetryFunctions.at(i)->getType();
        if (statistics.collectStatistics)
        {
            statistics.addValue(sfindex, atom.G.at(i));
        }
 
        // Avoid "fake" EWs at the boundaries.
        if (value + epsilon < Gmin || value - epsilon > Gmax)
        {
            countExtrapolationWarnings++;
            if (statistics.collectExtrapolationWarnings)
            {
                statistics.addExtrapolationWarning(sfindex,
                                                   type,
                                                   value,
                                                   Gmin,
                                                   Gmax,
                                                   symbol,
                                                   atom.indexStructure,
                                                   atom.tag);
            }
            if (statistics.writeExtrapolationWarnings)
            {
                cerr << strpr("### NNP EXTRAPOLATION WARNING ### "
                              "STRUCTURE: %6zu ATOM: %9" PRId64 " ELEMENT: "
                              "%2s SYMFUNC: %4zu TYPE: %2zu VALUE: %10.3E "
                              "MIN: %10.3E MAX: %10.3E\n",
                              atom.indexStructure,
                              atom.tag,
                              symbol.c_str(),
                              sfindex + 1,
                              type,
                              value,
                              Gmin,
                              Gmax);
            }
            if (statistics.stopOnExtrapolationWarnings)
            {
                throw out_of_range(
                        strpr("### NNP EXTRAPOLATION WARNING ### "
                              "STRUCTURE: %6zu ATOM: %9" PRId64 " ELEMENT: "
                              "%2s SYMFUNC: %4zu TYPE: %2zu VALUE: %10.3E "
                              "MIN: %10.3E MAX: %10.3E\n"
                              "ERROR: Symmetry function value out of range.\n",
                              atom.indexStructure,
                              atom.tag,
                              symbol.c_str(),
                              sfindex + 1,
                              type,
                              value,
                              Gmin,
                              Gmax));
            }
        }
    }
 
    return countExtrapolationWarnings;
}

References nnp::SymFncStatistics::addExtrapolationWarning(), nnp::SymFncStatistics::addValue(), nnp::SymFncStatistics::collectExtrapolationWarnings, nnp::SymFncStatistics::collectStatistics, nnp::Atom::element, nnp::Atom::G, index, nnp::Atom::indexStructure, nnp::Atom::numSymmetryFunctions, statistics, nnp::SymFncStatistics::stopOnExtrapolationWarnings, nnp::strpr(), symbol, symmetryFunctions, nnp::Atom::tag, and nnp::SymFncStatistics::writeExtrapolationWarnings.

Referenced by nnp::Mode::calculateSymmetryFunctionGroups(), and nnp::Mode::calculateSymmetryFunctions().

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getSymmetryFunction()

SymFnc const & nnp::Element::getSymmetryFunction ( std::size_t  index ) const

inline

Get symmetry function instance.

Parameters

[in]

index

Symmetry function index.

Returns

Symmetry function object.

Definition at line 358 of file Element.h.

{
    return *(symmetryFunctions.at(index));
}

References index, and symmetryFunctions.

Referenced by nnp::Mode::setupSymmetryFunctionCache(), and nnp::SetupAnalysis::writeSymmetryFunctionShape().

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setCacheIndices()

void Element::setCacheIndices

(

std::vector< std::vector< SFCacheList > >

cacheLists

)

Set cache indices for all symmetry functions of this element.

Parameters

[in]

cacheLists

List of cache identifier strings and corresponding SF indices for each neighbor element.

Definition at line 544 of file Element.cpp.

{
    this->cacheLists = cacheLists;
    for (size_t i = 0; i < cacheLists.size(); ++i)
    {
        for (size_t j = 0; j < cacheLists.at(i).size(); ++j)
        {
            SFCacheList const& c = cacheLists.at(i).at(j);
            for (size_t k = 0; k < c.indices.size(); ++k)
            {
                SymFnc*& sf = symmetryFunctions.at(c.indices.at(k));
                sf->addCacheIndex(c.element, j, c.identifier);
            }
        }
    }
 
    return;
}

References nnp::SymFnc::addCacheIndex(), cacheLists, nnp::Element::SFCacheList::element, nnp::Element::SFCacheList::identifier, nnp::Element::SFCacheList::indices, and symmetryFunctions.

Referenced by nnp::Mode::setupSymmetryFunctionCache().

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getCacheSizes()

vector< size_t > Element::getCacheSizes

(

)

const

Get cache sizes for each neighbor atom element.

Returns

Vector with cache sizes.

Definition at line 563 of file Element.cpp.

{
    vector<size_t> cacheSizes;
    for (auto const& c : cacheLists)
    {
        cacheSizes.push_back(c.size());
    }
 
    return cacheSizes;
}

References cacheLists.

Referenced by nnp::Mode::calculateSymmetryFunctionGroups(), and nnp::Mode::calculateSymmetryFunctions().

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Member Data Documentation

neuralNetworks

std::map<std::string, NeuralNetwork> nnp::Element::neuralNetworks

Neural networks for this element.

Definition at line 247 of file Element.h.

Referenced by nnp::Mode::setupNeuralNetwork().

statistics

SymFncStatistics nnp::Element::statistics

Symmetry function statistics.

Definition at line 249 of file Element.h.

Referenced by updateSymmetryFunctionStatistics().

elementMap

ElementMap nnp::Element::elementMap

protected

Copy of element map.

Definition at line 253 of file Element.h.

Referenced by addSymmetryFunction(), setupSymmetryFunctionGroups(), and setupSymmetryFunctionMemory().

index

std::size_t nnp::Element::index

protected

Global index of this element.

Definition at line 255 of file Element.h.

Referenced by getIndex(), getSymmetryFunction(), infoSymmetryFunction(), and updateSymmetryFunctionStatistics().

atomicNumber

std::size_t nnp::Element::atomicNumber

protected

Atomic number of this element.

Definition at line 257 of file Element.h.

Referenced by getAtomicNumber().

atomicEnergyOffset

double nnp::Element::atomicEnergyOffset

protected

Offset energy for every atom of this element.

Definition at line 259 of file Element.h.

Referenced by getAtomicEnergyOffset(), and setAtomicEnergyOffset().

hardness

double nnp::Element::hardness

protected

Atomic hardness for global charge equilibration.

Definition at line 261 of file Element.h.

Referenced by getHardness(), and setHardness().

qsigma

double nnp::Element::qsigma

protected

Gaussian width of charge distribution.

Definition at line 263 of file Element.h.

Referenced by getQsigma(), and setQsigma().

symbol

std::string nnp::Element::symbol

protected

Element symbol.

Definition at line 265 of file Element.h.

Referenced by getSymbol(), and updateSymmetryFunctionStatistics().

symmetryFunctionNumTable

std::vector<std::size_t> nnp::Element::symmetryFunctionNumTable

protected

Number of relevant symmetry functions for each neighbor element.

Definition at line 267 of file Element.h.

Referenced by getSymmetryFunctionNumTable(), and setupSymmetryFunctionMemory().

symmetryFunctionTable

std::vector<std::vector<std::size_t> > nnp::Element::symmetryFunctionTable

protected

List of symmetry function indices relevant for each neighbor element.

Definition at line 269 of file Element.h.

Referenced by getSymmetryFunctionTable(), and setupSymmetryFunctionMemory().

cacheLists

std::vector<std::vector<SFCacheList> > nnp::Element::cacheLists

protected

Symmetry function cache lists.

Definition at line 272 of file Element.h.

Referenced by getCacheSizes(), and setCacheIndices().

symmetryFunctions

std::vector<SymFnc*> nnp::Element::symmetryFunctions

protected

Vector of pointers to symmetry functions.

Definition at line 275 of file Element.h.

Referenced by addSymmetryFunction(), calculateSymmetryFunctions(), changeLengthUnitSymmetryFunctions(), clearSymmetryFunctions(), getCutoffRadii(), getMaxCutoffRadius(), getMinCutoffRadius(), getMinNeighbors(), getSymmetryFunction(), infoSymmetryFunction(), infoSymmetryFunctionParameters(), infoSymmetryFunctionScaling(), numSymmetryFunctions(), setCacheIndices(), setCutoffFunction(), setScaling(), setScalingNone(), setupSymmetryFunctionGroups(), setupSymmetryFunctionMemory(), sortSymmetryFunctions(), and updateSymmetryFunctionStatistics().

symmetryFunctionGroups

std::vector<SymGrp*> nnp::Element::symmetryFunctionGroups

protected

Vector of pointers to symmetry function groups.

Definition at line 277 of file Element.h.

Referenced by calculateSymmetryFunctionGroups(), clearSymmetryFunctions(), infoSymmetryFunctionGroups(), setScaling(), setScalingNone(), and setupSymmetryFunctionGroups().

---

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

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