Symmetry function base class. More...

#include <SymFnc.h>

Inheritance diagram for nnp::SymFnc:

Collaboration diagram for nnp::SymFnc:

[legend]

Public Types
enum	ScalingType { ST_NONE , ST_SCALE , ST_CENTER , ST_SCALECENTER , ST_SCALESIGMA }
	List of available scaling types. More...

Public Member Functions
virtual	~SymFnc ()
	Virtual destructor. More...

virtual bool	operator== (SymFnc const &rhs) const =0
	Overload == operator. More...

virtual bool	operator< (SymFnc const &rhs) const =0
	Overload < operator. More...

bool	operator!= (SymFnc const &rhs) const
	Overload != operator. More...

bool	operator> (SymFnc const &rhs) const
	Overload > operator. More...

bool	operator<= (SymFnc const &rhs) const
	Overload <= operator. More...

bool	operator>= (SymFnc const &rhs) const
	Overload >= operator. More...

virtual void	setParameters (std::string const &parameterString)=0
	Set parameters. More...

virtual void	changeLengthUnit (double convLength)=0
	Change length unit. More...

virtual std::string	getSettingsLine () const =0
	Get settings file line from currently set parameters. More...

virtual void	calculate (Atom &atom, bool const derivatives) const =0
	Calculate symmetry function for one atom. More...

virtual std::string	parameterLine () const =0
	Give symmetry function parameters in one line. More...

virtual std::vector< std::string >	parameterInfo () const
	Get description with parameter names and values. More...

void	setScalingType (ScalingType scalingType, std::string statisticsLine, double Smin, double Smax)
	Set symmetry function scaling type. More...

double	scale (double value) const
	Apply symmetry function scaling and/or centering. More...

double	unscale (double value) const
	Undo symmetry function scaling and/or centering. More...

std::size_t	getType () const
	Get private type member variable. More...

std::size_t	getIndex () const
	Get private index member variable. More...

std::size_t	getLineNumber () const
	Get private lineNumber member variable. More...

std::size_t	getEc () const
	Get private ec member variable. More...

std::size_t	getMinNeighbors () const
	Get private minNeighbors member variable. More...

double	getRc () const
	Get private rc member variable. More...

double	getGmin () const
	Get private Gmin member variable. More...

double	getGmax () const
	Get private Gmax member variable. More...

double	getScalingFactor () const
	Get private scalingFactor member variable. More...

double	getConvLength () const
	Get private convLength member variable. More...

std::set< std::string >	getParameters () const
	Get private parameters member variable. More...

std::vector< std::size_t >	getIndexPerElement () const
	Get private indexPerElement member variable. More...

void	setIndex (std::size_t index)
	Set private index member variable. More...

void	setIndexPerElement (std::size_t elementIndex, std::size_t index)
	Set private indexPerElement member variable. More...

void	setLineNumber (std::size_t lineNumber)
	Set line number. More...

std::string	scalingLine () const
	Get string with scaling information. More...

virtual double	calculateRadialPart (double distance) const =0
	Calculate (partial) symmetry function value for one given distance. More...

virtual double	calculateAngularPart (double angle) const =0
	Calculate (partial) symmetry function value for one given angle. More...

virtual bool	checkRelevantElement (std::size_t index) const =0
	Check whether symmetry function is relevant for given element. More...

virtual std::vector< std::string >	getCacheIdentifiers () const
	Get unique cache identifiers. More...

void	addCacheIndex (std::size_t element, std::size_t cacheIndex, std::string cacheIdentifier)
	Add one cache index for given neighbor element and check identifier. More...

std::vector< std::vector< std::size_t > >	getCacheIndices () const
	Getter for cacheIndices. More...

Protected Types
typedef std::map< std::string, std::pair< std::string, std::string > >	PrintFormat

typedef std::vector< std::string >	PrintOrder

Protected Member Functions
	SymFnc (std::size_t type, ElementMap const &)
	Constructor, initializes type. More...

std::string	getPrintFormat () const
	Generate format string for symmetry function parameter printing. More...

Static Protected Member Functions
static PrintFormat const	initializePrintFormat ()
	Initialize static print format map for all possible parameters. More...

static PrintOrder const	initializePrintOrder ()
	Initialize static print order vector for all possible parameters. More...

Protected Attributes
std::size_t	type
	Symmetry function type. More...

ElementMap	elementMap
	Copy of element map. More...

std::size_t	index
	Symmetry function index (per element). More...

std::size_t	lineNumber
	Line number. More...

std::size_t	ec
	Element index of center atom. More...

std::size_t	minNeighbors
	Minimum number of neighbors required. More...

double	Smin
	Minimum for scaling range. More...

double	Smax
	Maximum for scaling range. More...

double	Gmin
	Minimum unscaled symmetry function value. More...

double	Gmax
	Maximum unscaled symmetry function value. More...

double	Gmean
	Mean unscaled symmetry function value. More...

double	Gsigma
	Sigma of unscaled symmetry function values. More...

double	rc
	Cutoff radius \(r_c\). More...

double	scalingFactor
	Scaling factor. More...

double	convLength
	Data set normalization length conversion factor. More...

ScalingType	scalingType
	Symmetry function scaling type used by this symmetry function. More...

std::set< std::string >	parameters
	Set with symmetry function parameter IDs (lookup for printing). More...

std::vector< std::size_t >	indexPerElement
	Per-element index for derivative memory in Atom::Neighbor::dGdr arrays. More...

std::vector< std::vector< std::size_t > >	cacheIndices
	Cache indices for each element. More...

Static Protected Attributes
static std::size_t const	sfinfoWidth = 12
	Width of the SFINFO parameter description field (see parameterInfo()). More...

static PrintFormat const	printFormat = initializePrintFormat()
	Map of parameter format strings and empty strings. More...

static PrintOrder const	printOrder = initializePrintOrder()
	Vector of parameters in order of printing. More...

Detailed Description

Symmetry function base class.

Actual symmetry functions derive from this class. Provides common functionality, e.g. scaling behavior.

Definition at line 39 of file SymFnc.h.

Member Typedef Documentation

◆ PrintFormat

typedef std::map<std::string, std::pair<std::string, std::string> > nnp::SymFnc::PrintFormat

protected

Definition at line 265 of file SymFnc.h.

◆ PrintOrder

typedef std::vector<std::string> nnp::SymFnc::PrintOrder

protected

Definition at line 266 of file SymFnc.h.

Member Enumeration Documentation

◆ ScalingType

enum nnp::SymFnc::ScalingType

List of available scaling types.

Enumerator
ST_NONE	\(G_\text{scaled} = G\)
ST_SCALE	\(G_\text{scaled} = S_\text{min} + \left(S_\text{max} - S_\text{min}\right) \cdot \frac{G - G_\text{min}} {G_\text{max} - G_\text{min}} \)
ST_CENTER	\(G_\text{scaled} = G - \left<G\right>\)
ST_SCALECENTER	\(G_\text{scaled} = S_\text{min} + \left(S_\text{max} - S_\text{min}\right) \cdot \frac{G - \left<G\right>} {G_\text{max} - G_\text{min}} \)
ST_SCALESIGMA	\(G_\text{scaled} = S_\text{min} + \left(S_\text{max} - S_\text{min}\right) \cdot \frac{G - \left<G\right>}{\sigma_G} \)

Definition at line 43 of file SymFnc.h.

    {
        ST_NONE,
        ST_SCALE,
        ST_CENTER,
        ST_SCALECENTER,
        ST_SCALESIGMA
    };

Constructor & Destructor Documentation

◆ ~SymFnc()

virtual nnp::SymFnc::~SymFnc ( )

inlinevirtual

Virtual destructor.

Definition at line 69 of file SymFnc.h.

69{};

◆ SymFnc()

SymFnc::SymFnc	(	std::size_t	type,
		ElementMap const &
	)

protected

Constructor, initializes type.

Definition at line 135 of file SymFnc.cpp.

                                                        :
    type         (type      ),
    elementMap   (elementMap),
    index        (0         ),
    ec           (0         ),
    minNeighbors (0         ),
    Smin         (0.0       ),
    Smax         (0.0       ),
    Gmin         (0.0       ),
    Gmax         (0.0       ),
    Gmean        (0.0       ),
    Gsigma       (0.0       ),
    rc           (0.0       ),
    scalingFactor(1.0       ),
    convLength   (1.0       ),
    scalingType  (ST_NONE   )
{
    // Add standard parameter IDs to set.
    parameters.insert("index");
    parameters.insert("ec");
    parameters.insert("type");
    parameters.insert("rc");
    parameters.insert("lineNumber");
 
    // Initialize per-element index vector, use max to indicate
    // "uninitialized" state.
    indexPerElement.resize(elementMap.size(), numeric_limits<size_t>::max());
 
#ifndef N2P2_NO_SF_CACHE
    // Initialize cache indices vector.
    cacheIndices.resize(elementMap.size(), vector<size_t>());
#endif
}

References cacheIndices, elementMap, indexPerElement, parameters, and nnp::ElementMap::size().

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Member Function Documentation

◆ operator==()

virtual bool nnp::SymFnc::operator== ( SymFnc const & rhs ) const

pure virtual

Overload == operator.

Implemented in nnp::SymFncCompAngn, nnp::SymFncCompAngnWeighted, nnp::SymFncCompAngw, nnp::SymFncCompAngwWeighted, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngn, nnp::SymFncExpAngnWeighted, nnp::SymFncExpAngw, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ operator<()

virtual bool nnp::SymFnc::operator< ( SymFnc const & rhs ) const

pure virtual

Overload < operator.

Implemented in nnp::SymFncCompAngn, nnp::SymFncCompAngnWeighted, nnp::SymFncCompAngw, nnp::SymFncCompAngwWeighted, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngn, nnp::SymFncExpAngnWeighted, nnp::SymFncExpAngw, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ operator!=()

bool nnp::SymFnc::operator!= ( SymFnc const & rhs ) const

inline

Overload != operator.

Definition at line 335 of file SymFnc.h.

{
    return !((*this) == rhs);
}

◆ operator>()

bool nnp::SymFnc::operator> ( SymFnc const & rhs ) const

inline

Overload > operator.

Definition at line 340 of file SymFnc.h.

{
    return rhs < (*this);
}

◆ operator<=()

bool nnp::SymFnc::operator<= ( SymFnc const & rhs ) const

inline

Overload <= operator.

Definition at line 345 of file SymFnc.h.

{
    return !((*this) > rhs);
}

◆ operator>=()

bool nnp::SymFnc::operator>= ( SymFnc const & rhs ) const

inline

Overload >= operator.

Definition at line 350 of file SymFnc.h.

{
    return !((*this) < rhs);
}

◆ setParameters()

virtual void nnp::SymFnc::setParameters ( std::string const & parameterString )

pure virtual

Set parameters.

Parameters

[in] parameterString String containing all parameters for this symmetry function.

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ changeLengthUnit()

virtual void nnp::SymFnc::changeLengthUnit ( double convLength )

pure virtual

Change length unit.

Parameters

[in] convLength Multiplicative length unit conversion factor.

Note: This will permanently change all symmetry function parameters with dimension length. For convenience, some member functions for printing (getSettingsLine(), parameterLine(), calculateRadialPart() and calculateAngularPart()) will temporarily undo this change. In contrast, the member getter functions, e.g. getRc(), will return the internally stored values.

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ getSettingsLine()

virtual std::string nnp::SymFnc::getSettingsLine ( ) const

pure virtual

Get settings file line from currently set parameters.

Returns: Settings file string ("symfunction_short ...").

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ calculate()

virtual void nnp::SymFnc::calculate	(	Atom &	atom,
		bool const	derivatives
	)		const

pure virtual

Calculate symmetry function for one atom.

Parameters

[in,out]	atom	Atom for which the symmetry function is caluclated.
[in]	derivatives	If also symmetry function derivatives will be calculated and saved.

Implemented in nnp::SymFncCompAngn, nnp::SymFncCompAngnWeighted, nnp::SymFncCompAngw, nnp::SymFncCompAngwWeighted, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngn, nnp::SymFncExpAngnWeighted, nnp::SymFncExpAngw, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ parameterLine()

virtual std::string nnp::SymFnc::parameterLine ( ) const

pure virtual

Give symmetry function parameters in one line.

Returns: String containing symmetry function parameter values.

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

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

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◆ parameterInfo()

vector< string > SymFnc::parameterInfo ( ) const

virtual

Get description with parameter names and values.

Returns: Vector of parameter description strings.

Reimplemented in nnp::SymFncBaseComp, nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseCutoff, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

Definition at line 32 of file SymFnc.cpp.

{
    vector<string> v;
    string s;
    size_t w = sfinfoWidth;
 
    s = "lineNumber";
    v.push_back(strpr((pad(s, w) + "%zu"   ).c_str(), lineNumber + 1));
    s = "index";
    v.push_back(strpr((pad(s, w) + "%zu"   ).c_str(), index + 1));
    s = "type";
    v.push_back(strpr((pad(s, w) + "%zu"   ).c_str(), type));
    s = "ec";
    v.push_back(strpr((pad(s, w) + "%s"    ).c_str(), elementMap[ec].c_str()));
    s = "rc";
    v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), rc / convLength));
 
    return v;
}

References convLength, ec, elementMap, index, lineNumber, nnp::pad(), rc, sfinfoWidth, nnp::strpr(), and type.

Referenced by nnp::SymFncBaseComp::parameterInfo(), and nnp::SymFncBaseCutoff::parameterInfo().

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◆ setScalingType()

void SymFnc::setScalingType	(	ScalingType	scalingType,
		std::string	statisticsLine,
		double	Smin,
		double	Smax
	)

Set symmetry function scaling type.

Parameters

[in]	scalingType	Desired symmetry function scaling type.
[in]	statisticsLine	String containing symmetry function statistics ("min max mean sigma").
[in]	Smin	Minimum for scaling range \(S_\text{min}\).
[in]	Smax	Maximum for scaling range \(S_\text{max}\).

Definition at line 52 of file SymFnc.cpp.

{
    this->scalingType = scalingType;
 
    vector<string> s = split(reduce(statisticsLine));
    if (((size_t)atoi(s.at(0).c_str()) != ec + 1) &&
        ((size_t)atoi(s.at(1).c_str()) != index + 1))
    {
        throw runtime_error("ERROR: Inconsistent scaling statistics.\n");
    }
    Gmin       = atof(s.at(2).c_str());
    Gmax       = atof(s.at(3).c_str());
    Gmean      = atof(s.at(4).c_str());
    // Older versions may not supply sigma.
    if (s.size() > 5)
    {
        Gsigma = atof(s.at(5).c_str());
    }
    this->Smin = Smin;
    this->Smax = Smax;
 
    if(scalingType == ST_NONE)
    {
        scalingFactor = 1.0;
    }
    else if (scalingType == ST_SCALE)
    {
        scalingFactor = (Smax - Smin) / (Gmax - Gmin);
    }
    else if (scalingType == ST_CENTER)
    {
        scalingFactor = 1.0;
    }
    else if (scalingType == ST_SCALECENTER)
    {
        scalingFactor = (Smax - Smin) / (Gmax - Gmin);
    }
    else if (scalingType == ST_SCALESIGMA)
    {
        scalingFactor = (Smax - Smin) / Gsigma;
    }
 
    return;
}

References ec, Gmax, Gmean, Gmin, Gsigma, index, nnp::reduce(), scalingFactor, scalingType, Smax, Smin, nnp::split(), ST_CENTER, ST_NONE, ST_SCALE, ST_SCALECENTER, and ST_SCALESIGMA.

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◆ scale()

double SymFnc::scale ( double value ) const

Apply symmetry function scaling and/or centering.

Parameters

[in] value Raw symmetry function value.

Returns: Scaled symmetry function value.

Definition at line 169 of file SymFnc.cpp.

{
    if (scalingType == ST_NONE)
    {
        return value;
    }
    else if (scalingType == ST_SCALE)
    {
        return Smin + scalingFactor * (value - Gmin);
    }
    else if (scalingType == ST_CENTER)
    {
        return value - Gmean;
    }
    else if (scalingType == ST_SCALECENTER)
    {
        return Smin + scalingFactor * (value - Gmean);
    }
    else if (scalingType == ST_SCALESIGMA)
    {
        return Smin + scalingFactor * (value - Gmean);
    }
    else
    {
        return 0.0;
    }
}

References Gmean, Gmin, scalingFactor, scalingType, Smin, ST_CENTER, ST_NONE, ST_SCALE, ST_SCALECENTER, and ST_SCALESIGMA.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngw::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRad::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncExpAngn::calculate(), nnp::SymFncExpAngnWeighted::calculate(), nnp::SymFncExpAngw::calculate(), nnp::SymFncExpRad::calculate(), and nnp::SymFncExpRadWeighted::calculate().

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◆ unscale()

double SymFnc::unscale ( double value ) const

Undo symmetry function scaling and/or centering.

Parameters

[in] value Scaled symmetry function value.

Returns: Raw symmetry function value.

Definition at line 197 of file SymFnc.cpp.

{
    if (scalingType == ST_NONE)
    {
        return value;
    }
    else if (scalingType == ST_SCALE)
    {
        return (value - Smin) / scalingFactor + Gmin;
    }
    else if (scalingType == ST_CENTER)
    {
        return value + Gmean;
    }
    else if (scalingType == ST_SCALECENTER)
    {
        return (value - Smin) / scalingFactor + Gmean;
    }
    else if (scalingType == ST_SCALESIGMA)
    {
        return (value - Smin) / scalingFactor + Gmean;
    }
    else
    {
        return 0.0;
    }
}

References Gmean, Gmin, scalingFactor, scalingType, Smin, ST_CENTER, ST_NONE, ST_SCALE, ST_SCALECENTER, and ST_SCALESIGMA.

◆ getType()

std::size_t nnp::SymFnc::getType ( ) const

inline

Get private type member variable.

Definition at line 355 of file SymFnc.h.

355{ return type; }

References type.

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◆ getIndex()

std::size_t nnp::SymFnc::getIndex ( ) const

inline

Get private index member variable.

Definition at line 357 of file SymFnc.h.

357{ return index; }

References index.

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

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◆ getLineNumber()

std::size_t nnp::SymFnc::getLineNumber ( ) const

inline

Get private lineNumber member variable.

Definition at line 358 of file SymFnc.h.

358{ return lineNumber; }

References lineNumber.

◆ getEc()

std::size_t nnp::SymFnc::getEc ( ) const

inline

Get private ec member variable.

Definition at line 356 of file SymFnc.h.

356{ return ec; }

References ec.

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◆ getMinNeighbors()

std::size_t nnp::SymFnc::getMinNeighbors ( ) const

inline

Get private minNeighbors member variable.

Definition at line 359 of file SymFnc.h.

359{ return minNeighbors; }

References minNeighbors.

◆ getRc()

double nnp::SymFnc::getRc ( ) const

inline

Get private rc member variable.

Definition at line 360 of file SymFnc.h.

360{ return rc; }

References rc.

Referenced by nnp::SymGrpCompAngn::addMember(), nnp::SymGrpCompAngnWeighted::addMember(), nnp::SymGrpCompAngw::addMember(), nnp::SymGrpCompAngwWeighted::addMember(), nnp::SymGrpCompRad::addMember(), nnp::SymGrpCompRadWeighted::addMember(), nnp::SymGrpExpAngn::addMember(), nnp::SymGrpExpAngnWeighted::addMember(), nnp::SymGrpExpAngw::addMember(), nnp::SymGrpExpRad::addMember(), and nnp::SymGrpExpRadWeighted::addMember().

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◆ getGmin()

double nnp::SymFnc::getGmin ( ) const

inline

Get private Gmin member variable.

Definition at line 361 of file SymFnc.h.

361{ return Gmin; }

References Gmin.

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

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◆ getGmax()

double nnp::SymFnc::getGmax ( ) const

inline

Get private Gmax member variable.

Definition at line 362 of file SymFnc.h.

362{ return Gmax; }

References Gmax.

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

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◆ getScalingFactor()

double nnp::SymFnc::getScalingFactor ( ) const

inline

Get private scalingFactor member variable.

Definition at line 363 of file SymFnc.h.

363{ return scalingFactor; }

References scalingFactor.

◆ getConvLength()

double nnp::SymFnc::getConvLength ( ) const

inline

Get private convLength member variable.

Definition at line 364 of file SymFnc.h.

364{ return convLength; }

References convLength.

Referenced by nnp::SymGrpCompAngn::addMember(), nnp::SymGrpCompAngnWeighted::addMember(), nnp::SymGrpCompAngw::addMember(), nnp::SymGrpCompAngwWeighted::addMember(), nnp::SymGrpCompRad::addMember(), nnp::SymGrpCompRadWeighted::addMember(), nnp::SymGrpExpAngn::addMember(), nnp::SymGrpExpAngnWeighted::addMember(), nnp::SymGrpExpAngw::addMember(), nnp::SymGrpExpRad::addMember(), and nnp::SymGrpExpRadWeighted::addMember().

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◆ getParameters()

std::set< std::string > nnp::SymFnc::getParameters ( ) const

inline

Get private parameters member variable.

Definition at line 378 of file SymFnc.h.

{
    return parameters;
}

References parameters.

◆ getIndexPerElement()

std::vector< std::size_t > nnp::SymFnc::getIndexPerElement ( ) const

inline

Get private indexPerElement member variable.

Definition at line 383 of file SymFnc.h.

{
    return indexPerElement;
}

References indexPerElement.

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

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◆ setIndex()

void nnp::SymFnc::setIndex ( std::size_t index )

inline

Set private index member variable.

Parameters

[in] index Symmetry function index.

Definition at line 366 of file SymFnc.h.

{
    this->index = index;
    return;
}

References index.

◆ setIndexPerElement()

void nnp::SymFnc::setIndexPerElement	(	std::size_t	elementIndex,
		std::size_t	index
	)

inline

Set private indexPerElement member variable.

Parameters

[in]	elementIndex	Element index.
[in]	index	Symmetry function index.

Definition at line 388 of file SymFnc.h.

{
    indexPerElement.at(elementIndex) = index;
    return;
}

References index, and indexPerElement.

◆ setLineNumber()

void nnp::SymFnc::setLineNumber ( std::size_t lineNumber )

inline

Set line number.

Parameters

[in] lineNumber Line number in settings file.

Definition at line 372 of file SymFnc.h.

{
    this->lineNumber = lineNumber;
    return;
}

References lineNumber.

◆ scalingLine()

string SymFnc::scalingLine ( ) const

Get string with scaling information.

Returns: Scaling information string.

Definition at line 225 of file SymFnc.cpp.

{
    return strpr("%4zu %9.2E %9.2E %9.2E %9.2E %9.2E %5.2f %5.2f %d\n",
                 index + 1,
                 Gmin,
                 Gmax,
                 Gmean,
                 Gsigma,
                 scalingFactor,
                 Smin,
                 Smax,
                 scalingType);
}

References Gmax, Gmean, Gmin, Gsigma, index, scalingFactor, scalingType, Smax, Smin, and nnp::strpr().

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◆ calculateRadialPart()

virtual double nnp::SymFnc::calculateRadialPart ( double distance ) const

pure virtual

Calculate (partial) symmetry function value for one given distance.

Parameters

[in] distance Distance between two atoms.

Returns: Symmetry function value.

Note: This function is not used for actual calculations but only for plotting symmetry functions. Derived classes should implement a meaningful symmetry function value for visualization.

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

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

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◆ calculateAngularPart()

virtual double nnp::SymFnc::calculateAngularPart ( double angle ) const

pure virtual

Calculate (partial) symmetry function value for one given angle.

Parameters

[in] angle Angle between triplet of atoms (in radians).

Returns: Symmetry function value.

Note: This function is not used for actual calculations but only for plotting symmetry functions. Derived classes should implement a meaningful symmetry function value for visualization.

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

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

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◆ checkRelevantElement()

virtual bool nnp::SymFnc::checkRelevantElement ( std::size_t index ) const

pure virtual

Check whether symmetry function is relevant for given element.

Parameters

[in] index Index of given element.

Returns: True if symmetry function is sensitive to given element, false otherwise.

Implemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

◆ getCacheIdentifiers()

vector< string > SymFnc::getCacheIdentifiers ( ) const

virtual

Get unique cache identifiers.

Returns: Vector of string identifying the type of cache this symmetry function requires.

Reimplemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncBaseExpAng, nnp::SymFncCompRad, nnp::SymFncCompRadWeighted, nnp::SymFncExpAngnWeighted, nnp::SymFncExpRad, and nnp::SymFncExpRadWeighted.

Definition at line 101 of file SymFnc.cpp.

{
    return vector<string>();
}

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

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◆ addCacheIndex()

void SymFnc::addCacheIndex	(	std::size_t	element,
		std::size_t	cacheIndex,
		std::string	cacheIdentifier
	)

Add one cache index for given neighbor element and check identifier.

Parameters

[in]	element	Index of neighbor atom element.
[in]	cacheIndex	Cache index in Atom::Neighbor.
[in]	cacheIdentifier	Cache identifier for checking.

Definition at line 106 of file SymFnc.cpp.

{
    // Check if provided cache identifier is identical to the originally
    // supplied one.
    vector<vector<string>> identifiersPerElement(elementMap.size());
    for (string id : getCacheIdentifiers())
    {
        size_t ne = atoi(split(id)[0].c_str());
        identifiersPerElement.at(ne).push_back(id);
    }
    size_t current = cacheIndices.at(element).size();
    if (identifiersPerElement.at(element).at(current) != cacheIdentifier)
    {
        throw runtime_error(strpr("ERROR: Cache identifiers do no match:\n"
                                  "%s\n"
                                  "    !=\n"
                                  "%s\n",
                                  identifiersPerElement.at(element)
                                  .at(current).c_str(),
                                  cacheIdentifier.c_str()));
    }
    cacheIndices.at(element).push_back(cacheIndex);
 
    return;
}

References cacheIndices, elementMap, getCacheIdentifiers(), nnp::ElementMap::size(), nnp::split(), and nnp::strpr().

Referenced by nnp::Element::setCacheIndices().

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◆ getCacheIndices()

std::vector< std::vector< std::size_t > > nnp::SymFnc::getCacheIndices ( ) const

inline

Getter for cacheIndices.

Definition at line 396 of file SymFnc.h.

{
    return cacheIndices;
}

References cacheIndices.

Referenced by nnp::SymGrpCompRadWeighted::calculate().

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◆ initializePrintFormat()

SymFnc::PrintFormat const SymFnc::initializePrintFormat ( )

staticprotected

Initialize static print format map for all possible parameters.

Definition at line 239 of file SymFnc.cpp.

{
    PrintFormat pf;
 
    pf["index"]       = make_pair("%4zu"  , string(4,  ' '));
    pf["ec"]          = make_pair("%2s"   , string(2,  ' '));
    pf["type"]        = make_pair("%2zu"  , string(2,  ' '));
    pf["subtype"]     = make_pair("%4s"   , string(4,  ' '));
    pf["e1"]          = make_pair("%2s"   , string(2,  ' '));
    pf["e2"]          = make_pair("%2s"   , string(2,  ' '));
    pf["eta"]         = make_pair("%9.3E" , string(9,  ' '));
    pf["rs/rl"]       = make_pair("%10.3E", string(10, ' '));
    pf["rc"]          = make_pair("%10.3E", string(10, ' '));
    pf["angleLeft"]   = make_pair("%6.1f" , string(6,  ' '));
    pf["angleRight"]  = make_pair("%6.1f" , string(6,  ' '));
    pf["lambda"]      = make_pair("%2.0f" , string(2,  ' '));
    pf["zeta"]        = make_pair("%4.1f" , string(4,  ' '));
    pf["alpha"]       = make_pair("%4.2f" , string(4,  ' '));
    pf["lineNumber"]  = make_pair("%5zu"  , string(5,  ' '));
 
    return pf;
}

◆ initializePrintOrder()

SymFnc::PrintOrder const SymFnc::initializePrintOrder ( )

staticprotected

Initialize static print order vector for all possible parameters.

Definition at line 262 of file SymFnc.cpp.

{
    vector<string> po;
 
    po.push_back("index"     );
    po.push_back("ec"        );
    po.push_back("type"      );
    po.push_back("subtype"   );
    po.push_back("e1"        );
    po.push_back("e2"        );
    po.push_back("eta"       );
    po.push_back("rs/rl"     );
    po.push_back("rc"        );
    po.push_back("angleLeft" );
    po.push_back("angleRight");
    po.push_back("lambda"    );
    po.push_back("zeta"      );
    po.push_back("alpha"     );
    po.push_back("lineNumber");
 
    return po;
}

◆ getPrintFormat()

string SymFnc::getPrintFormat ( ) const

protected

Generate format string for symmetry function parameter printing.

Returns: C-Style format string.

Definition at line 285 of file SymFnc.cpp.

{
    string s;
 
    for (PrintOrder::const_iterator it = printOrder.begin();
         it != printOrder.end(); ++it)
    {
        // If parameter is present add format string.
        if (parameters.find(*it) != parameters.end())
        {
            s += safeFind(printFormat, (*it)).first + ' ';
        }
        // Else add just enough empty spaces.
        else 
        {
            s += safeFind(printFormat, (*it)).second + ' ';
        }
    }
    // Remove extra space at the end.
    if (s.size () > 0)  s.resize (s.size () - 1);
    s += '\n';
 
    return s;
}

References parameters, printFormat, printOrder, and nnp::safeFind().

Referenced by nnp::SymFncBaseCompAng::parameterLine(), nnp::SymFncBaseCompAngWeighted::parameterLine(), nnp::SymFncBaseExpAng::parameterLine(), nnp::SymFncCompRad::parameterLine(), nnp::SymFncCompRadWeighted::parameterLine(), nnp::SymFncExpAngnWeighted::parameterLine(), nnp::SymFncExpRad::parameterLine(), and nnp::SymFncExpRadWeighted::parameterLine().

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Member Data Documentation

◆ type

std::size_t nnp::SymFnc::type

protected

Symmetry function type.

Definition at line 268 of file SymFnc.h.

◆ elementMap

ElementMap nnp::SymFnc::elementMap

protected

Copy of element map.

Definition at line 270 of file SymFnc.h.

Referenced by addCacheIndex(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncExpAngnWeighted::calculate(), nnp::SymFncExpRadWeighted::calculate(), nnp::SymFncBaseCompAngWeighted::getCacheIdentifiers(), nnp::SymFncCompRadWeighted::getCacheIdentifiers(), nnp::SymFncExpAngnWeighted::getCacheIdentifiers(), nnp::SymFncExpRadWeighted::getCacheIdentifiers(), nnp::SymFncBaseCompAng::getSettingsLine(), nnp::SymFncBaseCompAngWeighted::getSettingsLine(), nnp::SymFncBaseExpAng::getSettingsLine(), nnp::SymFncCompRad::getSettingsLine(), nnp::SymFncCompRadWeighted::getSettingsLine(), nnp::SymFncExpAngnWeighted::getSettingsLine(), nnp::SymFncExpRad::getSettingsLine(), nnp::SymFncExpRadWeighted::getSettingsLine(), parameterInfo(), nnp::SymFncBaseCompAng::parameterInfo(), nnp::SymFncBaseExpAng::parameterInfo(), nnp::SymFncCompRad::parameterInfo(), nnp::SymFncExpRad::parameterInfo(), nnp::SymFncBaseCompAng::parameterLine(), nnp::SymFncBaseCompAngWeighted::parameterLine(), nnp::SymFncBaseExpAng::parameterLine(), nnp::SymFncCompRad::parameterLine(), nnp::SymFncCompRadWeighted::parameterLine(), nnp::SymFncExpAngnWeighted::parameterLine(), nnp::SymFncExpRad::parameterLine(), nnp::SymFncExpRadWeighted::parameterLine(), nnp::SymFncBaseCompAng::setParameters(), nnp::SymFncBaseCompAngWeighted::setParameters(), nnp::SymFncBaseExpAng::setParameters(), nnp::SymFncCompRad::setParameters(), nnp::SymFncCompRadWeighted::setParameters(), nnp::SymFncExpAngnWeighted::setParameters(), nnp::SymFncExpRad::setParameters(), nnp::SymFncExpRadWeighted::setParameters(), and SymFnc().

◆ index

std::size_t nnp::SymFnc::index

protected

Symmetry function index (per element).

Definition at line 272 of file SymFnc.h.

◆ lineNumber

std::size_t nnp::SymFnc::lineNumber

protected

Line number.

Definition at line 274 of file SymFnc.h.

Referenced by getLineNumber(), parameterInfo(), nnp::SymFncBaseCompAng::parameterLine(), nnp::SymFncBaseCompAngWeighted::parameterLine(), nnp::SymFncBaseExpAng::parameterLine(), nnp::SymFncCompRad::parameterLine(), nnp::SymFncCompRadWeighted::parameterLine(), nnp::SymFncExpAngnWeighted::parameterLine(), nnp::SymFncExpRad::parameterLine(), nnp::SymFncExpRadWeighted::parameterLine(), and setLineNumber().

◆ ec

std::size_t nnp::SymFnc::ec

protected

Element index of center atom.

Definition at line 276 of file SymFnc.h.

◆ minNeighbors

std::size_t nnp::SymFnc::minNeighbors

protected

Minimum number of neighbors required.

Definition at line 278 of file SymFnc.h.

Referenced by getMinNeighbors(), nnp::SymFncBaseCompAng::SymFncBaseCompAng(), nnp::SymFncBaseCompAngWeighted::SymFncBaseCompAngWeighted(), nnp::SymFncBaseExpAng::SymFncBaseExpAng(), nnp::SymFncCompRad::SymFncCompRad(), nnp::SymFncCompRadWeighted::SymFncCompRadWeighted(), nnp::SymFncExpAngnWeighted::SymFncExpAngnWeighted(), nnp::SymFncExpRad::SymFncExpRad(), and nnp::SymFncExpRadWeighted::SymFncExpRadWeighted().

◆ Smin

double nnp::SymFnc::Smin

protected

Minimum for scaling range.

Definition at line 280 of file SymFnc.h.

Referenced by scale(), scalingLine(), setScalingType(), and unscale().

◆ Smax

double nnp::SymFnc::Smax

protected

Maximum for scaling range.

Definition at line 282 of file SymFnc.h.

Referenced by scalingLine(), and setScalingType().

◆ Gmin

double nnp::SymFnc::Gmin

protected

Minimum unscaled symmetry function value.

Definition at line 284 of file SymFnc.h.

Referenced by getGmin(), scale(), scalingLine(), setScalingType(), and unscale().

◆ Gmax

double nnp::SymFnc::Gmax

protected

Maximum unscaled symmetry function value.

Definition at line 286 of file SymFnc.h.

Referenced by getGmax(), scalingLine(), and setScalingType().

◆ Gmean

double nnp::SymFnc::Gmean

protected

Mean unscaled symmetry function value.

Definition at line 288 of file SymFnc.h.

Referenced by scale(), scalingLine(), setScalingType(), and unscale().

◆ Gsigma

double nnp::SymFnc::Gsigma

protected

Sigma of unscaled symmetry function values.

Definition at line 290 of file SymFnc.h.

Referenced by scalingLine(), and setScalingType().

◆ rc

double nnp::SymFnc::rc

protected

Cutoff radius \(r_c\).

Definition at line 292 of file SymFnc.h.

◆ scalingFactor

double nnp::SymFnc::scalingFactor

protected

Scaling factor.

Definition at line 294 of file SymFnc.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngw::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRad::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncExpAngn::calculate(), nnp::SymFncExpAngnWeighted::calculate(), nnp::SymFncExpAngw::calculate(), nnp::SymFncExpRad::calculate(), nnp::SymFncExpRadWeighted::calculate(), getScalingFactor(), scale(), scalingLine(), setScalingType(), and unscale().

◆ convLength

double nnp::SymFnc::convLength

protected

Data set normalization length conversion factor.

Definition at line 296 of file SymFnc.h.

◆ scalingType

ScalingType nnp::SymFnc::scalingType

protected

Symmetry function scaling type used by this symmetry function.

Definition at line 298 of file SymFnc.h.

Referenced by scale(), scalingLine(), setScalingType(), and unscale().

◆ parameters

std::set<std::string> nnp::SymFnc::parameters

protected

Set with symmetry function parameter IDs (lookup for printing).

Definition at line 300 of file SymFnc.h.

Referenced by getParameters(), getPrintFormat(), SymFnc(), nnp::SymFncBaseComp::SymFncBaseComp(), nnp::SymFncBaseCompAng::SymFncBaseCompAng(), nnp::SymFncBaseCompAngWeighted::SymFncBaseCompAngWeighted(), nnp::SymFncBaseCutoff::SymFncBaseCutoff(), nnp::SymFncBaseExpAng::SymFncBaseExpAng(), nnp::SymFncCompRad::SymFncCompRad(), nnp::SymFncExpAngnWeighted::SymFncExpAngnWeighted(), nnp::SymFncExpRad::SymFncExpRad(), and nnp::SymFncExpRadWeighted::SymFncExpRadWeighted().

◆ indexPerElement

std::vector<std::size_t> nnp::SymFnc::indexPerElement

protected

Per-element index for derivative memory in Atom::Neighbor::dGdr arrays.

Definition at line 302 of file SymFnc.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngw::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRad::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncExpAngn::calculate(), nnp::SymFncExpAngnWeighted::calculate(), nnp::SymFncExpAngw::calculate(), nnp::SymFncExpRad::calculate(), nnp::SymFncExpRadWeighted::calculate(), getIndexPerElement(), setIndexPerElement(), and SymFnc().

◆ cacheIndices

std::vector< std::vector<std::size_t> > nnp::SymFnc::cacheIndices

protected

Cache indices for each element.

Definition at line 306 of file SymFnc.h.

Referenced by addCacheIndex(), nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngw::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRad::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncExpAngn::calculate(), nnp::SymFncExpAngnWeighted::calculate(), nnp::SymFncExpAngw::calculate(), nnp::SymFncExpRad::calculate(), nnp::SymFncExpRadWeighted::calculate(), getCacheIndices(), and SymFnc().

◆ sfinfoWidth

size_t const SymFnc::sfinfoWidth = 12

staticprotected

Width of the SFINFO parameter description field (see parameterInfo()).

Definition at line 309 of file SymFnc.h.

Referenced by parameterInfo(), nnp::SymFncBaseComp::parameterInfo(), nnp::SymFncBaseCompAng::parameterInfo(), nnp::SymFncBaseCompAngWeighted::parameterInfo(), nnp::SymFncBaseCutoff::parameterInfo(), nnp::SymFncBaseExpAng::parameterInfo(), nnp::SymFncCompRad::parameterInfo(), nnp::SymFncExpAngnWeighted::parameterInfo(), nnp::SymFncExpRad::parameterInfo(), and nnp::SymFncExpRadWeighted::parameterInfo().

◆ printFormat

SymFnc::PrintFormat const SymFnc::printFormat = initializePrintFormat()

staticprotected

Map of parameter format strings and empty strings.

Definition at line 311 of file SymFnc.h.

Referenced by getPrintFormat().

◆ printOrder

SymFnc::PrintOrder const SymFnc::printOrder = initializePrintOrder()

staticprotected

Vector of parameters in order of printing.

Definition at line 313 of file SymFnc.h.

Referenced by getPrintFormat().

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

/home/runner/work/n2p2/n2p2/src/libnnp/SymFnc.h
/home/runner/work/n2p2/n2p2/src/libnnp/SymFnc.cpp

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ PrintFormat

◆ PrintOrder

Member Enumeration Documentation

◆ ScalingType

Constructor & Destructor Documentation

◆ ~SymFnc()

◆ SymFnc()

Member Function Documentation

◆ operator==()

◆ operator<()

◆ operator!=()

◆ operator>()

◆ operator<=()

◆ operator>=()

◆ setParameters()

◆ changeLengthUnit()

◆ getSettingsLine()

◆ calculate()

◆ parameterLine()

◆ parameterInfo()

◆ setScalingType()

◆ scale()

◆ unscale()

◆ getType()

◆ getIndex()

◆ getLineNumber()

◆ getEc()

◆ getMinNeighbors()

◆ getRc()

◆ getGmin()

◆ getGmax()

◆ getScalingFactor()

◆ getConvLength()

◆ getParameters()

◆ getIndexPerElement()

◆ setIndex()

◆ setIndexPerElement()

◆ setLineNumber()

◆ scalingLine()

◆ calculateRadialPart()

◆ calculateAngularPart()

◆ checkRelevantElement()

◆ getCacheIdentifiers()

◆ addCacheIndex()

◆ getCacheIndices()

◆ initializePrintFormat()

◆ initializePrintOrder()

◆ getPrintFormat()

Member Data Documentation

◆ type

◆ elementMap

◆ index

◆ lineNumber

◆ ec

◆ minNeighbors

◆ Smin

◆ Smax

◆ Gmin

◆ Gmax

◆ Gmean

◆ Gsigma

◆ rc

◆ scalingFactor

◆ convLength

◆ scalingType

◆ parameters

◆ indexPerElement

◆ cacheIndices

◆ sfinfoWidth

◆ printFormat

◆ printOrder