Angular symmetry function (type 3) More...

#include <SymFncExpAngn.h>

Inheritance diagram for nnp::SymFncExpAngn:

Collaboration diagram for nnp::SymFncExpAngn:

Public Member Functions
	SymFncExpAngn (ElementMap const &elementMap)
	Constructor, sets type = 3. 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::SymFncBaseExpAng
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...

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...

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...

bool	getUseIntegerPow () const
	Get private useIntegerPow member variable. More...

std::size_t	getE1 () const
	Get private e1 member variable. More...

std::size_t	getE2 () const
	Get private e2 member variable. More...

int	getZetaInt () const
	Get private zetaInt member variable. More...

double	getLambda () const
	Get private lambda member variable. More...

double	getEta () const
	Get private eta member variable. More...

double	getZeta () const
	Get private zeta member variable. More...

double	getRs () const
	Get private rs member variable. More...

Public Member Functions inherited from nnp::SymFncBaseCutoff
virtual std::vector< std::string >	parameterInfo () const
	Get description with parameter names and values. More...

void	setCutoffFunction (CutoffFunction::CutoffType cutoffType, double cutoffAlpha)
	Set cutoff function type and parameter. More...

double	getCutoffAlpha () const
	Get private cutoffAlpha member variable. More...

std::string	getSubtype () const
	Get private subtype member variable. More...

CutoffFunction::CutoffType	getCutoffType () const
	Get private cutoffType 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::SymFncBaseExpAng
	SymFncBaseExpAng (std::size_t type, ElementMap const &)
	Constructor, initializes type. More...

Protected Member Functions inherited from nnp::SymFncBaseCutoff
	SymFncBaseCutoff (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::SymFncBaseExpAng
bool	useIntegerPow
	Whether to use integer version of power function (faster). More...

std::size_t	e1
	Element index of neighbor atom 1. More...

std::size_t	e2
	Element index of neighbor atom 2. More...

int	zetaInt
	Integer version of \(\zeta\). More...

double	lambda
	Cosine shift factor. More...

double	eta
	Width \(\eta\) of gaussian. More...

double	zeta
	Exponent \(\zeta\) of cosine term. More...

double	rs
	Shift \(r_s\) of gaussian. More...

Protected Attributes inherited from nnp::SymFncBaseCutoff
double	cutoffAlpha
	Cutoff parameter \(\alpha\). More...

std::string	subtype
	Subtype string (specifies cutoff type). More...

CutoffFunction	fc
	Cutoff function used by this symmetry function. More...

CutoffFunction::CutoffType	cutoffType
	Cutoff type used by this symmetry function. 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

Angular symmetry function (type 3)

\[ G^3_i = 2^{1-\zeta} \sum_{\substack{j,k\neq i \\ j < k}} \left( 1 + \lambda \cos \theta_{ijk} \right)^\zeta \mathrm{e}^{-\eta( (r_{ij}-r_s)^2 + (r_{ik}-r_s)^2 + (r_{jk}-r_s)^2 ) } f_c(r_{ij}) f_c(r_{ik}) f_c(r_{jk}) \]

Parameter string:

<element-central> 3 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff> <<rshift>>

nnp::SymFncBaseExpAng::lambda

double lambda

Cosine shift factor.

Definition: SymFncBaseExpAng.h:122

nnp::SymFncBaseExpAng::zeta

double zeta

Exponent of cosine term.

Definition: SymFncBaseExpAng.h:126

nnp::SymFncBaseExpAng::eta

double eta

Width of gaussian.

Definition: SymFncBaseExpAng.h:124

where

<element-central> ..... element symbol of central atom
<element-neighbor1> ... element symbol of neighbor atom 1
<element-neighbor2> ... element symbol of neighbor atom 2
<eta> ................. \(\eta\)
<lambda> .............. \(\lambda\)
<zeta> ................ \(\zeta\)
<rcutoff> ............. \(r_c\)
<<rshift>> ............ \(r_s\) (optional, default \(r_s = 0\))

Definition at line 54 of file SymFncExpAngn.h.

Constructor & Destructor Documentation

◆ SymFncExpAngn()

SymFncExpAngn::SymFncExpAngn ( ElementMap const & elementMap )

Constructor, sets type = 3.

Definition at line 30 of file SymFncExpAngn.cpp.

                                                         :
    SymFncBaseExpAng(3, elementMap)
{
}

Member Function Documentation

◆ operator==()

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

virtual

Overload == operator.

Implements nnp::SymFnc.

Definition at line 35 of file SymFncExpAngn.cpp.

{
    if (ec   != rhs.getEc()  ) return false;
    if (type != rhs.getType()) return false;
    SymFncExpAngn const& c = dynamic_cast<SymFncExpAngn const&>(rhs);
    if (cutoffType  != c.cutoffType ) return false;
    if (cutoffAlpha != c.cutoffAlpha) return false;
    if (rc          != c.rc         ) return false;
    if (eta         != c.eta        ) return false;
    if (zeta        != c.zeta       ) return false;
    if (lambda      != c.lambda     ) return false;
    if (e1          != c.e1         ) return false;
    if (e2          != c.e2         ) return false;
    return true;
}

References nnp::SymFncBaseCutoff::cutoffAlpha, nnp::SymFncBaseCutoff::cutoffType, nnp::SymFncBaseExpAng::e1, nnp::SymFncBaseExpAng::e2, nnp::SymFnc::ec, nnp::SymFncBaseExpAng::eta, nnp::SymFnc::getEc(), nnp::SymFnc::getType(), nnp::SymFncBaseExpAng::lambda, nnp::SymFnc::rc, nnp::SymFnc::type, and nnp::SymFncBaseExpAng::zeta.

Here is the call graph for this function:

◆ operator<()

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

virtual

Overload < operator.

Implements nnp::SymFnc.

Definition at line 51 of file SymFncExpAngn.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;
    SymFncExpAngn const& c = dynamic_cast<SymFncExpAngn const&>(rhs);
    if      (cutoffType  < c.cutoffType ) return true;
    else if (cutoffType  > c.cutoffType ) return false;
    if      (cutoffAlpha < c.cutoffAlpha) return true;
    else if (cutoffAlpha > c.cutoffAlpha) return false;
    if      (rc          < c.rc         ) return true;
    else if (rc          > c.rc         ) return false;
    if      (eta         < c.eta        ) return true;
    else if (eta         > c.eta        ) return false;
    if      (rs          < c.rs         ) return true;
    else if (rs          > c.rs         ) return false;
    if      (zeta        < c.zeta       ) return true;
    else if (zeta        > c.zeta       ) return false;
    if      (lambda      < c.lambda     ) return true;
    else if (lambda      > c.lambda     ) 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;
    return false;
}

References nnp::SymFncBaseCutoff::cutoffAlpha, nnp::SymFncBaseCutoff::cutoffType, nnp::SymFncBaseExpAng::e1, nnp::SymFncBaseExpAng::e2, nnp::SymFnc::ec, nnp::SymFncBaseExpAng::eta, nnp::SymFnc::getEc(), nnp::SymFnc::getType(), nnp::SymFncBaseExpAng::lambda, nnp::SymFnc::rc, nnp::SymFncBaseExpAng::rs, nnp::SymFnc::type, and nnp::SymFncBaseExpAng::zeta.

Here is the call graph for this function:

◆ calculate()

void SymFncExpAngn::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 79 of file SymFncExpAngn.cpp.

{
    double const pnorm  = pow(2.0, 1.0 - zeta);
    double const pzl    = zeta * lambda;
    double const rc2    = 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)
        {
            double const r2ij   = rij * rij;
 
            // Calculate cutoff function and derivative.
            double pfcij;
            double pdfcij;
#ifndef N2P2_NO_SF_CACHE
            if (cacheIndices[nej].size() == 0) fc.fdf(rij, pfcij, pdfcij);
            else
            {
                double& cfc = nj.cache[cacheIndices[nej][0]];
                double& cdfc = nj.cache[cacheIndices[nej][1]];
                if (cfc < 0) fc.fdf(rij, cfc, cdfc);
                pfcij = cfc;
                pdfcij = cdfc;
            }
#else
            fc.fdf(rij, pfcij, pdfcij);
#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)
                    {
                        Vec3D drjk = nk.dr - nj.dr;
                        double rjk = drjk.norm2();;
                        if (rjk < rc2)
                        {
                            // Energy calculation.
                            double pfcik;
                            double pdfcik;
#ifndef N2P2_NO_SF_CACHE
                            if (cacheIndices[nej].size() == 0)
                            {
                                fc.fdf(rik, pfcik, pdfcik);
                            }
                            else
                            {
                                double& cfc = nk.cache[cacheIndices[nek][0]];
                                double& cdfc = nk.cache[cacheIndices[nek][1]];
                                if (cfc < 0) fc.fdf(rik, cfc, cdfc);
                                pfcik = cfc;
                                pdfcik = cdfc;
                            }
#else
                            fc.fdf(rik, pfcik, pdfcik);
#endif
                            rjk = sqrt(rjk);
                            double pfcjk;
                            double pdfcjk;
                            fc.fdf(rjk, pfcjk, pdfcjk);
 
                            Vec3D drij = nj.dr;
                            Vec3D drik = nk.dr;
                            double costijk = drij * drik;;
                            double rinvijik = 1.0 / rij / rik;
                            costijk *= rinvijik;
 
                            double const pfc = pfcij * pfcik * pfcjk;
                            double const r2ik = rik * rik;
                            double const rijs = rij - rs;
                            double const riks = rik - rs;
                            double const rjks = rjk - rs;
                            double const pexp = exp(-eta * (rijs * rijs +
                                                            riks * riks +
                                                            rjks * rjks));
                            double const plambda = 1.0 + lambda * costijk;
                            double       fg = pexp;
                            if (plambda <= 0.0) fg = 0.0;
                            else
                            {
                                if (useIntegerPow)
                                {
                                    fg *= pow_int(plambda, zetaInt - 1);
                                }
                                else
                                {
                                    fg *= pow(plambda, zeta - 1.0);
                                }
                            }
                            result += fg * plambda * pfc;
 
                            // Force calculation.
                            if (!derivatives) continue;
                            fg       *= pnorm;
                            rinvijik *= pzl;
                            costijk  *= pzl;
                            double const p2etapl = 2.0 * eta * plambda;
                            double const p1 = fg * (pfc * (rinvijik - costijk
                                            / r2ij - p2etapl * rijs / rij)
                                            + pfcik * pfcjk * pdfcij * plambda
                                            / rij);
                            double const p2 = fg * (pfc * (rinvijik - costijk
                                            / r2ik - p2etapl * riks / rik)
                                            + pfcij * pfcjk * pdfcik * plambda
                                            / rik);
                            double const p3 = fg * (pfc * (rinvijik + p2etapl
                                            * rjks / rjk) - pfcij * pfcik
                                            * pdfcjk * plambda / rjk);
                            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
                        } // rjk <= rc
                    } // rik <= rc
                } // elem
            } // k
        } // rij <= rc
    } // j
    result *= pnorm;
 
    atom.G[index] = scale(result);
 
    return;
}

References nnp::Atom::Neighbor::cache, nnp::SymFnc::cacheIndices, nnp::Atom::Neighbor::d, nnp::Atom::Neighbor::dGdr, nnp::Atom::dGdr, nnp::Atom::Neighbor::dr, nnp::SymFncBaseExpAng::e1, nnp::SymFncBaseExpAng::e2, nnp::Atom::Neighbor::element, nnp::SymFncBaseExpAng::eta, nnp::SymFncBaseCutoff::fc, nnp::CutoffFunction::fdf(), nnp::Atom::G, nnp::SymFnc::index, nnp::SymFnc::indexPerElement, nnp::SymFncBaseExpAng::lambda, nnp::Atom::neighbors, nnp::Vec3D::norm2(), nnp::Atom::numNeighbors, nnp::pow_int(), nnp::SymFnc::rc, nnp::SymFncBaseExpAng::rs, nnp::SymFnc::scale(), nnp::SymFnc::scalingFactor, nnp::SymFncBaseExpAng::useIntegerPow, nnp::SymFncBaseExpAng::zeta, and nnp::SymFncBaseExpAng::zetaInt.

Here is the call graph for this function:

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SymFncExpAngn()

Member Function Documentation

◆ operator==()

◆ operator<()

◆ calculate()