nnp::SymFncBaseCompAng Class Reference

Intermediate symmetry function class for angular SFs with compact support. More...

#include <SymFncBaseCompAng.h>

Inheritance diagram for nnp::SymFncBaseCompAng:

Collaboration diagram for nnp::SymFncBaseCompAng:

Public Member Functions
virtual void	setParameters (std::string const &parameterString)
	Set symmetry function parameters. More...
virtual void	changeLengthUnit (double convLength)
	Change length unit. More...
virtual std::string	getSettingsLine () const
	Get settings file line from currently set parameters. More...
void	getCompactAngle (double const x, double &fx, double &dfx) const
void	getCompactRadial (double const x, double &fx, double &dfx) const
virtual std::string	parameterLine () const
	Give symmetry function parameters in one line. More...
virtual std::vector< std::string >	parameterInfo () const
	Get description with parameter names and values. More...
std::size_t	getE1 () const
	Get private e1 member variable. More...
std::size_t	getE2 () const
	Get private e2 member variable. More...
double	getAngleLeft () const
	Get private angleLeft member variable. More...
double	getAngleRight () const
	Get private angleRight member variable. More...
virtual double	calculateRadialPart (double distance) const
	Calculate (partial) symmetry function value for one given distance. More...
virtual double	calculateAngularPart (double angle) const
	Calculate (partial) symmetry function value for one given angle. More...
virtual bool	checkRelevantElement (std::size_t index) const
	Check whether symmetry function is relevant for given element. More...
virtual std::vector< std::string >	getCacheIdentifiers () const
	Get unique cache identifiers. More...
Public Member Functions inherited from nnp::SymFncBaseComp
virtual std::vector< std::string >	parameterInfo () const
	Get description with parameter names and values. More...
void	setCompactFunction (std::string subtype)
	Set radial compact function. More...
std::string	getSubtype () const
	Get private subtype member variable. More...
double	getRl () const
	Get private rl member variable. More...
Public Member Functions inherited from nnp::SymFnc
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 Member Functions
	SymFncBaseCompAng (std::size_t type, ElementMap const &)
	Constructor, initializes type. More...
Protected Member Functions inherited from nnp::SymFncBaseComp
	SymFncBaseComp (std::size_t type, ElementMap const &)
	Constructor, initializes type. More...
Protected Member Functions inherited from nnp::SymFnc
	SymFnc (std::size_t type, ElementMap const &)
	Constructor, initializes type. More...
std::string	getPrintFormat () const
	Generate format string for symmetry function parameter printing. More...

Protected Attributes
std::size_t	e1
	Element index of neighbor atom 1. More...
std::size_t	e2
	Element index of neighbor atom 2. More...
double	angleLeft
	Left angle boundary. More...
double	angleRight
	Right angle boundary. More...
double	angleLeftRadians
	Left angle boundary in radians. More...
double	angleRightRadians
	Right angle boundary in radians. More...
CompactFunction	ca
	Compact function member for angular part. More...
Protected Attributes inherited from nnp::SymFncBaseComp
bool	asymmetric
	If asymmetric version of polynomials should be used. More...
double	rl
	Lower bound of compact function, \(r_{l}\). More...
std::string	subtype
	Subtype string (specifies e.g. polynom type). More...
CompactFunction	cr
	Compact function for radial part. More...
Protected Attributes inherited from nnp::SymFnc
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...

Additional Inherited Members
Public Types inherited from nnp::SymFnc
enum	ScalingType {   ST_NONE , ST_SCALE , ST_CENTER , ST_SCALECENTER ,   ST_SCALESIGMA }
	List of available scaling types. More...
Protected Types inherited from nnp::SymFnc
typedef std::map< std::string, std::pair< std::string, std::string > >	PrintFormat
typedef std::vector< std::string >	PrintOrder
Static Protected Member Functions inherited from nnp::SymFnc
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...
Static Protected Attributes inherited from nnp::SymFnc
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

Intermediate symmetry function class for angular SFs with compact support.

Definition at line 30 of file SymFncBaseCompAng.h.

Constructor & Destructor Documentation

SymFncBaseCompAng()

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

protected

Constructor, initializes type.

Definition at line 31 of file SymFncBaseCompAng.cpp.

                                                             :
    SymFncBaseComp(type, elementMap),
    e1               (0  ),
    e2               (0  ),
    angleLeft        (0.0),
    angleRight       (0.0),
    angleLeftRadians (0.0),
    angleRightRadians(0.0)
{
    minNeighbors = 2;
    parameters.insert("e1");
    parameters.insert("e2");
    parameters.insert("angleLeft");
    parameters.insert("angleRight");
}

References nnp::SymFnc::minNeighbors, and nnp::SymFnc::parameters.

Member Function Documentation

setParameters()

void SymFncBaseCompAng::setParameters ( std::string const &  parameterString )

virtual

Set symmetry function parameters.

Parameters

[in]

parameterString

String containing angular symmetry function parameters.

Implements nnp::SymFnc.

Definition at line 48 of file SymFncBaseCompAng.cpp.

{
    vector<string> splitLine = split(reduce(parameterString));
 
    if (type != (size_t)atoi(splitLine.at(1).c_str()))
    {
        throw runtime_error("ERROR: Incorrect symmetry function type.\n");
    }
 
    ec         = elementMap[splitLine.at(0)];
    e1         = elementMap[splitLine.at(2)];
    e2         = elementMap[splitLine.at(3)];
    rl         = atof(splitLine.at(4).c_str());
    rc         = atof(splitLine.at(5).c_str());
    angleLeft  = atof(splitLine.at(6).c_str());
    angleRight = atof(splitLine.at(7).c_str());
    subtype    = splitLine.at(8);
 
    if (e1 > e2)
    {
        size_t tmp = e1;
        e1         = e2;
        e2         = tmp;
    }
 
    // Radial part.
    if (rl > rc)
    {
        throw runtime_error("ERROR: Lower radial boundary >= upper "
                            "radial boundary.\n");
    }
    //if (rl < 0.0 && abs(rl + rc) > numeric_limits<double>::epsilon())
    //{
    //    throw runtime_error("ERROR: Radial function not symmetric "
    //                        "w.r.t. origin.\n");
    //}
   
    setCompactFunction(subtype);
    cr.setLeftRight(rl,rc);
 
    // Angular part.
    if (angleLeft >= angleRight)
    {
        throw runtime_error("ERROR: Left angle boundary right of or equal to "
                            "right angle boundary.\n");
    }
 
    double const center = (angleLeft + angleRight) / 2.0;
    if ( (angleLeft  <   0.0 && center != 0.0) ||
         (angleRight > 180.0 && center != 180.0) )
    {
        throw runtime_error("ERROR: Angle boundary out of [0,180] and "
                            "center of angular function /= 0 or /= 180.\n");
    }
    if (angleRight - angleLeft > 360.0)
    {
        throw runtime_error("ERROR: Periodic symmetry function cannot spread "
                            "over domain > 360 degrees\n");
    }
 
    ca.setCoreFunction(cr.getCoreFunctionType());
    angleLeftRadians = angleLeft * M_PI / 180.0;
    angleRightRadians = angleRight * M_PI / 180.0;
    ca.setLeftRight(angleLeftRadians, angleRightRadians);
 
    return;
}

References angleLeft, angleLeftRadians, angleRight, angleRightRadians, ca, nnp::SymFncBaseComp::cr, e1, e2, nnp::SymFnc::ec, nnp::SymFnc::elementMap, nnp::CompactFunction::getCoreFunctionType(), nnp::SymFnc::rc, nnp::reduce(), nnp::SymFncBaseComp::rl, nnp::SymFncBaseComp::setCompactFunction(), nnp::CompactFunction::setCoreFunction(), nnp::CompactFunction::setLeftRight(), nnp::split(), nnp::SymFncBaseComp::subtype, and nnp::SymFnc::type.

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changeLengthUnit()

void SymFncBaseCompAng::changeLengthUnit ( double  convLength )

virtual

Change length unit.

Parameters

[in]

convLength

Multiplicative length unit conversion factor.

Implements nnp::SymFnc.

Definition at line 116 of file SymFncBaseCompAng.cpp.

{
    this->convLength = convLength;
    rc *= convLength;
    rl *= convLength;
 
    cr.setLeftRight(rl,rc);
 
    return;
}

References nnp::SymFnc::convLength, nnp::SymFncBaseComp::cr, nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, and nnp::CompactFunction::setLeftRight().

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getSettingsLine()

string SymFncBaseCompAng::getSettingsLine ( ) const

virtual

Get settings file line from currently set parameters.

Returns

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

Implements nnp::SymFnc.

Definition at line 127 of file SymFncBaseCompAng.cpp.

{
    string s = strpr("symfunction_short %2s %2zu %2s %2s %16.8E %16.8E "
                     "%16.8E %16.8E %s\n",
                     elementMap[ec].c_str(),
                     type,
                     elementMap[e1].c_str(),
                     elementMap[e2].c_str(),
                     rl / convLength,
                     rc / convLength,
                     angleLeft,
                     angleRight,
                     subtype.c_str());
 
    return s;
}

References angleLeft, angleRight, nnp::SymFnc::convLength, e1, e2, nnp::SymFnc::ec, nnp::SymFnc::elementMap, nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::strpr(), nnp::SymFncBaseComp::subtype, and nnp::SymFnc::type.

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getCompactAngle()

void nnp::SymFncBaseCompAng::getCompactAngle ( double const  x, double &  fx, double &  dfx  ) const

inline

Definition at line 138 of file SymFncBaseCompAng.h.

{
    ca.fdf(x, fx, dfx);
    return;
}

References ca, and nnp::CompactFunction::fdf().

Referenced by nnp::SymGrpCompAngn::calculate(), and nnp::SymGrpCompAngw::calculate().

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getCompactRadial()

void nnp::SymFncBaseCompAng::getCompactRadial ( double const  x, double &  fx, double &  dfx  ) const

inline

Definition at line 146 of file SymFncBaseCompAng.h.

{
    cr.fdf(x, fx, dfx);
    return;
}

References nnp::SymFncBaseComp::cr, and nnp::CompactFunction::fdf().

Referenced by nnp::SymGrpCompAngn::calculate(), and nnp::SymGrpCompAngw::calculate().

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parameterLine()

string SymFncBaseCompAng::parameterLine ( ) const

virtual

Give symmetry function parameters in one line.

Returns

String containing symmetry function parameter values.

Implements nnp::SymFnc.

Definition at line 144 of file SymFncBaseCompAng.cpp.

{
    return strpr(getPrintFormat().c_str(),
                 index + 1,
                 elementMap[ec].c_str(),
                 type,
                 subtype.c_str(),
                 elementMap[e1].c_str(),
                 elementMap[e2].c_str(),
                 rl / convLength,
                 rc / convLength,
                 angleLeft,
                 angleRight,
                 lineNumber + 1);
}

References angleLeft, angleRight, nnp::SymFnc::convLength, e1, e2, nnp::SymFnc::ec, nnp::SymFnc::elementMap, nnp::SymFnc::getPrintFormat(), nnp::SymFnc::index, nnp::SymFnc::lineNumber, nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::strpr(), nnp::SymFncBaseComp::subtype, and nnp::SymFnc::type.

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parameterInfo()

vector< string > SymFncBaseCompAng::parameterInfo ( ) const

virtual

Get description with parameter names and values.

Returns

Vector of parameter description strings.

Reimplemented from nnp::SymFncBaseComp.

Definition at line 160 of file SymFncBaseCompAng.cpp.

{
    vector<string> v = SymFncBaseComp::parameterInfo();
    string s;
    size_t w = sfinfoWidth;
 
    s = "e1";
    v.push_back(strpr((pad(s, w) + "%s"    ).c_str(), elementMap[e1].c_str()));
    s = "e2";
    v.push_back(strpr((pad(s, w) + "%s"    ).c_str(), elementMap[e2].c_str()));
    s = "angleLeft";
    v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), angleLeft));
    s = "angleRight";
    v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), angleRight));
 
    return v;
}

References angleLeft, angleRight, e1, e2, nnp::SymFnc::elementMap, nnp::pad(), nnp::SymFncBaseComp::parameterInfo(), nnp::SymFnc::sfinfoWidth, and nnp::strpr().

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getE1()

std::size_t nnp::SymFncBaseCompAng::getE1 ( ) const

inline

Get private e1 member variable.

Definition at line 133 of file SymFncBaseCompAng.h.

{ return e1; }

References e1.

Referenced by nnp::SymGrpCompAngn::addMember(), and nnp::SymGrpCompAngw::addMember().

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getE2()

std::size_t nnp::SymFncBaseCompAng::getE2 ( ) const

inline

Get private e2 member variable.

Definition at line 134 of file SymFncBaseCompAng.h.

{ return e2; }

References e2.

Referenced by nnp::SymGrpCompAngn::addMember(), and nnp::SymGrpCompAngw::addMember().

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getAngleLeft()

double nnp::SymFncBaseCompAng::getAngleLeft ( ) const

inline

Get private angleLeft member variable.

Definition at line 135 of file SymFncBaseCompAng.h.

{ return angleLeft; }

References angleLeft.

getAngleRight()

double nnp::SymFncBaseCompAng::getAngleRight ( ) const

inline

Get private angleRight member variable.

Definition at line 136 of file SymFncBaseCompAng.h.

{ return angleRight; }

References angleRight.

calculateRadialPart()

double SymFncBaseCompAng::calculateRadialPart ( double  distance ) const

virtual

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

Parameters

[in]

distance

Distance between two atoms.

Returns

\(\left(e^{-\eta r^2} f_c(r)\right)^2\)

Implements nnp::SymFnc.

Definition at line 178 of file SymFncBaseCompAng.cpp.

{
    double const& r = distance * convLength;
 
    return cr.f(r);
}

References nnp::SymFnc::convLength, nnp::SymFncBaseComp::cr, and nnp::CompactFunction::f().

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calculateAngularPart()

double SymFncBaseCompAng::calculateAngularPart ( double  angle ) const

virtual

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

Parameters

[in]

angle

Angle between triplet of atoms (in radians).

Returns

\(1\)

Implements nnp::SymFnc.

Definition at line 185 of file SymFncBaseCompAng.cpp.

{
    return ca.f(angle);
}

References ca, and nnp::CompactFunction::f().

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checkRelevantElement()

bool SymFncBaseCompAng::checkRelevantElement ( std::size_t  index ) const

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.

Implements nnp::SymFnc.

Definition at line 190 of file SymFncBaseCompAng.cpp.

{
    if (index == e1 || index == e2) return true;
    else return false;
}

References e1, e2, and nnp::SymFnc::index.

getCacheIdentifiers()

vector< string > SymFncBaseCompAng::getCacheIdentifiers ( ) const

virtual

Get unique cache identifiers.

Returns

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

Reimplemented from nnp::SymFnc.

Definition at line 197 of file SymFncBaseCompAng.cpp.

{
    vector<string> v;
    string s("");
 
    s += subtype;
    s += " ";
    s += strpr("rl = %16.8E", rl / convLength);
    s += " ";
    s += strpr("rc = %16.8E", rc / convLength);
 
    v.push_back(strpr("%zu f ", e1) + s);
    v.push_back(strpr("%zu df ", e1) + s);
    if (e1 != e2) v.push_back(strpr("%zu f ", e2) + s);
    if (e1 != e2) v.push_back(strpr("%zu df ", e2) + s);
 
    return v;
}

References nnp::SymFnc::convLength, e1, e2, nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::strpr(), and nnp::SymFncBaseComp::subtype.

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Member Data Documentation

e1

std::size_t nnp::SymFncBaseCompAng::e1

protected

Element index of neighbor atom 1.

Definition at line 110 of file SymFncBaseCompAng.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngw::calculate(), checkRelevantElement(), getCacheIdentifiers(), getE1(), getSettingsLine(), nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngw::operator==(), parameterInfo(), parameterLine(), and setParameters().

e2

std::size_t nnp::SymFncBaseCompAng::e2

protected

Element index of neighbor atom 2.

Definition at line 112 of file SymFncBaseCompAng.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngw::calculate(), checkRelevantElement(), getCacheIdentifiers(), getE2(), getSettingsLine(), nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngw::operator==(), parameterInfo(), parameterLine(), and setParameters().

angleLeft

double nnp::SymFncBaseCompAng::angleLeft

protected

Left angle boundary.

Definition at line 114 of file SymFncBaseCompAng.h.

Referenced by getAngleLeft(), getSettingsLine(), nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngw::operator==(), parameterInfo(), parameterLine(), and setParameters().

angleRight

double nnp::SymFncBaseCompAng::angleRight

protected

Right angle boundary.

Definition at line 116 of file SymFncBaseCompAng.h.

Referenced by getAngleRight(), getSettingsLine(), nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngw::operator==(), parameterInfo(), parameterLine(), and setParameters().

angleLeftRadians

double nnp::SymFncBaseCompAng::angleLeftRadians

protected

Left angle boundary in radians.

Definition at line 118 of file SymFncBaseCompAng.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngw::calculate(), and setParameters().

angleRightRadians

double nnp::SymFncBaseCompAng::angleRightRadians

protected

Right angle boundary in radians.

Definition at line 120 of file SymFncBaseCompAng.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngw::calculate(), and setParameters().

ca

CompactFunction nnp::SymFncBaseCompAng::ca

protected

Compact function member for angular part.

Definition at line 122 of file SymFncBaseCompAng.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngw::calculate(), calculateAngularPart(), getCompactAngle(), and setParameters().

---

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

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