Narrow angular symmetry function with compact support (type 21) More...

#include <SymFncCompAngn.h>

Inheritance diagram for nnp::SymFncCompAngn:

Collaboration diagram for nnp::SymFncCompAngn:

Public Member Functions
	SymFncCompAngn (ElementMap const &elementMap)
	Constructor, sets type = 21. More...

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

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

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

Public Member Functions inherited from nnp::SymFncBaseCompAng
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...

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

Protected Member Functions inherited from nnp::SymFncBaseCompAng
	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...

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...

Protected Attributes inherited from nnp::SymFncBaseCompAng
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...

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

Narrow angular symmetry function with compact support (type 21)

\[ G^{21}_i = \sum_{\substack{j,k\neq i \\ j < k}} C(r_{ij}, r_l, r_c) C(r_{ik}, r_l, r_c) C(r_{jk}, r_l, r_c) C(\theta_{ijk}, \theta_l, \theta_r), \]

where \(C(x, x_\text{low}, x_\text{high})\) is a function with compact support \(\left[x_\text{low}, x_\text{high}\right]\).

Parameter string:

<element-central> 21 <element-neighbor1> <element-neighbor2> <rlow> <rcutoff> <left> <right> <subtype>

nnp::SymFncBaseComp::subtype

std::string subtype

Subtype string (specifies e.g. polynom type).

Definition: SymFncBaseComp.h:68

where

<element-central> ..... element symbol of central atom
<element-neighbor1> ... element symbol of neighbor atom 1
<element-neighbor2> ... element symbol of neighbor atom 2
<rlow> ................ low radius boundary \(r_{l}\)
<rcutoff> ............. high radius boundary \(r_{c}\)
<left> ................ left angle boundary \(\theta_l\)
<right> ............... right angle boundary \(\theta_r\)
<subtype> ............. compact function specifier

See the description of SymFncBaseComp::setCompactFunction() for possible values of the <subtype> argument.

Note: If <subtype> specifies an asymmetric version of a polynomial core function the asymmetry only applies to the radial parts, i.e. "p2a" sets a "p2a" radial compact function and a "p2" angular compact function.

Definition at line 65 of file SymFncCompAngn.h.

Constructor & Destructor Documentation

◆ SymFncCompAngn()

SymFncCompAngn::SymFncCompAngn ( ElementMap const & elementMap )

Constructor, sets type = 21.

Definition at line 31 of file SymFncCompAngn.cpp.

                                             :
    SymFncBaseCompAng(21, elementMap)
{
}

Member Function Documentation

◆ operator==()

bool SymFncCompAngn::operator== ( SymFnc const & rhs ) const

virtual

Overload == operator.

Implements nnp::SymFnc.

Definition at line 37 of file SymFncCompAngn.cpp.

{
    if (ec   != rhs.getEc()  ) return false;
    if (type != rhs.getType()) return false;
    SymFncCompAngn const& c = dynamic_cast<SymFncCompAngn const&>(rhs);
    if (subtype     != c.getSubtype()) return false;
    if (e1          != c.e1          ) return false;
    if (e2          != c.e2          ) return false;
    if (rc          != c.rc          ) return false;
    if (rl          != c.rl          ) return false;
    if (angleLeft   != c.angleLeft   ) return false;
    if (angleRight  != c.angleRight  ) return false;
    return true;
}

References nnp::SymFncBaseCompAng::angleLeft, nnp::SymFncBaseCompAng::angleRight, nnp::SymFncBaseCompAng::e1, nnp::SymFncBaseCompAng::e2, nnp::SymFnc::ec, nnp::SymFnc::getEc(), nnp::SymFncBaseComp::getSubtype(), nnp::SymFnc::getType(), nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::SymFncBaseComp::subtype, and nnp::SymFnc::type.

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◆ operator<()

bool SymFncCompAngn::operator< ( SymFnc const & rhs ) const

virtual

Overload < operator.

Implements nnp::SymFnc.

Definition at line 52 of file SymFncCompAngn.cpp.

{
    if      (ec   < rhs.getEc()  ) return true;
    else if (ec   > rhs.getEc()  ) return false;
    if      (type < rhs.getType()) return true;
    else if (type > rhs.getType()) return false;
    SymFncCompAngn const& c = dynamic_cast<SymFncCompAngn const&>(rhs);
    if      (subtype     < c.getSubtype()) return true;
    else if (subtype     > c.getSubtype()) return false;
    if      (e1          < c.e1          ) return true;
    else if (e1          > c.e1          ) return false;
    if      (e2          < c.e2          ) return true;
    else if (e2          > c.e2          ) return false;
    if      (rc          < c.rc          ) return true;
    else if (rc          > c.rc          ) return false;
    if      (rl          < c.rl          ) return true;
    else if (rl          > c.rl          ) return false;
    if      (angleLeft   < c.angleLeft   ) return true;
    else if (angleLeft   > c.angleLeft   ) return false;
    if      (angleRight  < c.angleRight  ) return true;
    else if (angleRight  > c.angleRight  ) return false;
    return false;
}

References nnp::SymFncBaseCompAng::angleLeft, nnp::SymFncBaseCompAng::angleRight, nnp::SymFncBaseCompAng::e1, nnp::SymFncBaseCompAng::e2, nnp::SymFnc::ec, nnp::SymFnc::getEc(), nnp::SymFncBaseComp::getSubtype(), nnp::SymFnc::getType(), nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::SymFncBaseComp::subtype, and nnp::SymFnc::type.

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◆ calculate()

void SymFncCompAngn::calculate	(	Atom &	atom,
		bool const	derivatives
	)		const

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.

Implements nnp::SymFnc.

Definition at line 76 of file SymFncCompAngn.cpp.

{
    double r2l = 0.0;
    if (rl > 0.0) r2l = rl * rl;
    double r2c = rc * rc;
    double result = 0.0;
 
    size_t numNeighbors = atom.numNeighbors;
    // Prevent problematic condition in loop test below (j < numNeighbors - 1).
    if (numNeighbors == 0) numNeighbors = 1;
 
    for (size_t j = 0; j < numNeighbors - 1; j++)
    {
        Atom::Neighbor& nj = atom.neighbors[j];
        size_t const nej = nj.element;
        double const rij = nj.d;
        if ((e1 == nej || e2 == nej) && rij < rc && rij > rl)
        {
            double radij;
            double dradij;
#ifndef N2P2_NO_SF_CACHE
            if (cacheIndices[nej].size() == 0) cr.fdf(rij, radij, dradij);
            else
            {
                double& crad = nj.cache[cacheIndices[nej][0]];
                double& cdrad = nj.cache[cacheIndices[nej][1]];
                if (crad < 0) cr.fdf(rij, crad, cdrad);
                radij = crad;
                dradij = cdrad;
            }
#else
            cr.fdf(rij, radij, dradij);
#endif
            for (size_t k = j + 1; k < numNeighbors; k++)
            {
                Atom::Neighbor& nk = atom.neighbors[k];
                size_t const nek = nk.element;
                if ((e1 == nej && e2 == nek) ||
                    (e2 == nej && e1 == nek))
                {
                    double const rik = nk.d;
                    if (rik < rc && rik > rl)
                    {
                        // Energy calculation.
                        Vec3D drij = nj.dr;
                        Vec3D drik = nk.dr;
                        Vec3D drjk = nk.dr - nj.dr;
                        double rjk = drjk.norm2();
                        if (rjk >= r2c || rjk <= r2l) continue;
                        rjk = sqrt(rjk);
 
                        double radik;
                        double dradik;
#ifndef N2P2_NO_SF_CACHE
                        if (cacheIndices[nek].size() == 0)
                        {
                            cr.fdf(rik, radik, dradik);
                        }
                        else
                        {
                            double& crad = nk.cache[cacheIndices[nek][0]];
                            double& cdrad = nk.cache[cacheIndices[nek][1]];
                            if (crad < 0) cr.fdf(rik, crad, cdrad);
                            radik = crad;
                            dradik = cdrad;
                        }
#else
                        cr.fdf(rik, radik, dradik);
#endif
                        double radjk;
                        double dradjk;
                        cr.fdf(rjk, radjk, dradjk);
 
                        double costijk = drij * drik;
                        double rinvijik = 1.0 / rij / rik;
                        costijk *= rinvijik;
 
                        // By definition, our polynomial is zero at 0 and 180 deg.
                        // Therefore, skip the whole rest which might yield some NaN
                        if (costijk <= -1.0 || costijk >= 1.0) continue;
 
                        // Regroup later: Get acos(cos)
                        double const acostijk = acos(costijk);
                        // Only go on if we are within our compact support
                        if (acostijk < angleLeftRadians ||
                            acostijk > angleRightRadians) continue;
                        double ang  = 0.0;
                        double dang = 0.0;
                        ca.fdf(acostijk, ang, dang);
 
                        double const rad  = radij * radik * radjk; // product of cutoff fcts
                        result += rad * ang;
 
                        // Force calculation.
                        if (!derivatives) continue;
 
                        double const dacostijk = -1.0
                                               / sqrt(1.0 - costijk * costijk);
                        dang *= dacostijk;
                        double const rinvij = rinvijik * rik;
                        double const rinvik = rinvijik * rij;
                        double const rinvjk = 1.0 / rjk;
                        double phiijik = rinvij * (rinvik - rinvij*costijk);
                        double phiikij = rinvik * (rinvij - rinvik*costijk);
                        double psiijik = rinvijik; // careful: sign flip w.r.t. notes due to nj.dGd...
                        phiijik *= dang;
                        phiikij *= dang;
                        psiijik *= dang;
 
                        // Cutoff function might be a divide by zero, but we screen that case before
                        double const chiij =  rinvij * dradij *  radik *  radjk;
                        double const chiik =  rinvik *  radij * dradik *  radjk;
                        double const chijk = -rinvjk *  radij *  radik * dradjk;
 
                        // rijs/rij due to the shifted radial part of the Gaussian                        
                        double const p1 = rad * phiijik +  ang * chiij;
                        double const p2 = rad * phiikij +  ang * chiik;
                        double const p3 = rad * psiijik +  ang * chijk;
                        drij *= p1 * scalingFactor;
                        drik *= p2 * scalingFactor;
                        drjk *= p3 * scalingFactor;
 
                        // Save force contributions in Atom storage.
                        atom.dGdr[index] += drij + drik;
#ifndef N2P2_FULL_SFD_MEMORY
                        nj.dGdr[indexPerElement[nej]] -= drij + drjk;
                        nk.dGdr[indexPerElement[nek]] -= drik - drjk;
#else
                        nj.dGdr[index] -= drij + drjk;
                        nk.dGdr[index] -= drik - drjk;
#endif
                    } // rik <= rc
                } // elem
            } // k
        } // rij <= rc
    } // j
 
    atom.G[index] = scale(result);
 
    return;
}

References nnp::SymFncBaseCompAng::angleLeftRadians, nnp::SymFncBaseCompAng::angleRightRadians, nnp::SymFncBaseCompAng::ca, nnp::Atom::Neighbor::cache, nnp::SymFnc::cacheIndices, nnp::SymFncBaseComp::cr, nnp::Atom::Neighbor::d, nnp::Atom::Neighbor::dGdr, nnp::Atom::dGdr, nnp::Atom::Neighbor::dr, nnp::SymFncBaseCompAng::e1, nnp::SymFncBaseCompAng::e2, nnp::Atom::Neighbor::element, nnp::CompactFunction::fdf(), nnp::Atom::G, nnp::SymFnc::index, nnp::SymFnc::indexPerElement, nnp::Atom::neighbors, nnp::Vec3D::norm2(), nnp::Atom::numNeighbors, nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::SymFnc::scale(), and nnp::SymFnc::scalingFactor.

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SymFncCompAngn()

Member Function Documentation

◆ operator==()

◆ operator<()

◆ calculate()