nnp::SymFncExpRad Class Reference

Radial symmetry function (type 2) More...

#include <SymFncExpRad.h>

Inheritance diagram for nnp::SymFncExpRad:

Collaboration diagram for nnp::SymFncExpRad:

Public Member Functions
	SymFncExpRad (ElementMap const &elementMap)
	Constructor, sets type = 2.
virtual bool	operator== (SymFnc const &rhs) const
	Overload == operator.
virtual bool	operator< (SymFnc const &rhs) const
	Overload < operator.
virtual void	setParameters (std::string const &parameterString)
	Set symmetry function parameters.
virtual void	changeLengthUnit (double convLength)
	Change length unit.
virtual std::string	getSettingsLine () const
	Get settings file line from currently set parameters.
virtual void	calculate (Atom &atom, bool const derivatives) const
	Calculate symmetry function for one atom.
virtual std::string	parameterLine () const
	Give symmetry function parameters in one line.
virtual std::vector< std::string >	parameterInfo () const
	Get description with parameter names and values.
std::size_t	getE1 () const
	Get private e1 member variable.
double	getEta () const
	Get private eta member variable.
double	getRs () const
	Get private rs member variable.
virtual double	calculateRadialPart (double distance) const
	Calculate (partial) symmetry function value for one given distance.
virtual double	calculateAngularPart (double angle) const
	Calculate (partial) symmetry function value for one given angle.
virtual bool	checkRelevantElement (std::size_t index) const
	Check whether symmetry function is relevant for given element.
virtual std::vector< std::string >	getCacheIdentifiers () const
	Get unique cache identifiers.
Public Member Functions inherited from nnp::SymFncBaseCutoff
void	setCutoffFunction (CutoffFunction::CutoffType cutoffType, double cutoffAlpha)
	Set cutoff function type and parameter.
double	getCutoffAlpha () const
	Get private cutoffAlpha member variable.
std::string	getSubtype () const
	Get private subtype member variable.
CutoffFunction::CutoffType	getCutoffType () const
	Get private cutoffType member variable.
Public Member Functions inherited from nnp::SymFnc
virtual	~SymFnc ()
	Virtual destructor.
bool	operator!= (SymFnc const &rhs) const
	Overload != operator.
bool	operator> (SymFnc const &rhs) const
	Overload > operator.
bool	operator<= (SymFnc const &rhs) const
	Overload <= operator.
bool	operator>= (SymFnc const &rhs) const
	Overload >= operator.
void	setScalingType (ScalingType scalingType, std::string statisticsLine, double Smin, double Smax)
	Set symmetry function scaling type.
double	scale (double value) const
	Apply symmetry function scaling and/or centering.
double	unscale (double value) const
	Undo symmetry function scaling and/or centering.
std::size_t	getType () const
	Get private type member variable.
std::size_t	getIndex () const
	Get private index member variable.
std::size_t	getLineNumber () const
	Get private lineNumber member variable.
std::size_t	getEc () const
	Get private ec member variable.
std::size_t	getMinNeighbors () const
	Get private minNeighbors member variable.
double	getRc () const
	Get private rc member variable.
double	getGmin () const
	Get private Gmin member variable.
double	getGmax () const
	Get private Gmax member variable.
double	getScalingFactor () const
	Get private scalingFactor member variable.
double	getConvLength () const
	Get private convLength member variable.
std::set< std::string >	getParameters () const
	Get private parameters member variable.
std::vector< std::size_t >	getIndexPerElement () const
	Get private indexPerElement member variable.
void	setIndex (std::size_t index)
	Set private index member variable.
void	setIndexPerElement (std::size_t elementIndex, std::size_t index)
	Set private indexPerElement member variable.
void	setLineNumber (std::size_t lineNumber)
	Set line number.
std::string	scalingLine () const
	Get string with scaling information.
void	addCacheIndex (std::size_t element, std::size_t cacheIndex, std::string cacheIdentifier)
	Add one cache index for given neighbor element and check identifier.
std::vector< std::vector< std::size_t > >	getCacheIndices () const
	Getter for cacheIndices.

Private Attributes
std::size_t	e1
	Element index of neighbor atom.
double	eta
	Width \(\eta\) of gaussian.
double	rs
	Shift \(r_s\) of gaussian.

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::SymFncBaseCutoff
	SymFncBaseCutoff (std::size_t type, ElementMap const &)
	Constructor, initializes type.
Protected Member Functions inherited from nnp::SymFnc
	SymFnc (std::size_t type, ElementMap const &)
	Constructor, initializes type.
std::string	getPrintFormat () const
	Generate format string for symmetry function parameter printing.
Static Protected Member Functions inherited from nnp::SymFnc
static PrintFormat const	initializePrintFormat ()
	Initialize static print format map for all possible parameters.
static PrintOrder const	initializePrintOrder ()
	Initialize static print order vector for all possible parameters.
Protected Attributes inherited from nnp::SymFncBaseCutoff
double	cutoffAlpha
	Cutoff parameter \(\alpha\).
std::string	subtype
	Subtype string (specifies cutoff type).
CutoffFunction	fc
	Cutoff function used by this symmetry function.
CutoffFunction::CutoffType	cutoffType
	Cutoff type used by this symmetry function.
Protected Attributes inherited from nnp::SymFnc
std::size_t	type
	Symmetry function type.
ElementMap	elementMap
	Copy of element map.
std::size_t	index
	Symmetry function index (per element).
std::size_t	lineNumber
	Line number.
std::size_t	ec
	Element index of center atom.
std::size_t	minNeighbors
	Minimum number of neighbors required.
double	Smin
	Minimum for scaling range.
double	Smax
	Maximum for scaling range.
double	Gmin
	Minimum unscaled symmetry function value.
double	Gmax
	Maximum unscaled symmetry function value.
double	Gmean
	Mean unscaled symmetry function value.
double	Gsigma
	Sigma of unscaled symmetry function values.
double	rc
	Cutoff radius \(r_c\).
double	scalingFactor
	Scaling factor.
double	convLength
	Data set normalization length conversion factor.
ScalingType	scalingType
	Symmetry function scaling type used by this symmetry function.
std::set< std::string >	parameters
	Set with symmetry function parameter IDs (lookup for printing).
std::vector< std::size_t >	indexPerElement
	Per-element index for derivative memory in Atom::Neighbor::dGdr arrays.
std::vector< std::vector< std::size_t > >	cacheIndices
	Cache indices for each element.
Static Protected Attributes inherited from nnp::SymFnc
static std::size_t const	sfinfoWidth = 12
	Width of the SFINFO parameter description field (see parameterInfo()).
static PrintFormat const	printFormat = initializePrintFormat()
	Map of parameter format strings and empty strings.
static PrintOrder const	printOrder = initializePrintOrder()
	Vector of parameters in order of printing.

Detailed Description

Radial symmetry function (type 2)

\[ G^2_i = \sum_{j \neq i} \mathrm{e}^{-\eta(r_{ij} - r_\mathrm{s})^2} f_c(r_{ij}) \]

Parameter string:

<element-central> 2 <element-neighbor> <eta> <rshift> <rcutoff>

where

• <element-central> .... element symbol of central atom
• <element-neighbor> ... element symbol of neighbor atom
• <eta> ................ \(\eta\)
• <rshift> ............. \(r_\mathrm{s}\)
• <rcutoff> ............ \(r_c\)

Definition at line 48 of file SymFncExpRad.h.

Constructor & Destructor Documentation

SymFncExpRad()

SymFncExpRad::SymFncExpRad

(

ElementMap const &

elementMap

)

Constructor, sets type = 2.

Definition at line 29 of file SymFncExpRad.cpp.

                                                       :
    SymFncBaseCutoff(2, elementMap),
    e1              (0  ),
    eta             (0.0),
    rs              (0.0)
{
    minNeighbors = 1;
    parameters.insert("e1");
    parameters.insert("eta");
    parameters.insert("rs/rl");
}

References e1, nnp::SymFnc::elementMap, eta, nnp::SymFnc::minNeighbors, nnp::SymFnc::parameters, rs, and nnp::SymFncBaseCutoff::SymFncBaseCutoff().

Referenced by operator<(), and operator==().

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Member Function Documentation

operator==()

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

virtual

Overload == operator.

Implements nnp::SymFnc.

Definition at line 41 of file SymFncExpRad.cpp.

{
    if (ec   != rhs.getEc()  ) return false;
    if (type != rhs.getType()) return false;
    SymFncExpRad const& c = dynamic_cast<SymFncExpRad 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 (rs          != c.rs         ) return false;
    if (e1          != c.e1         ) return false;
    return true;
}

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

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operator<()

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

virtual

Overload < operator.

Implements nnp::SymFnc.

Definition at line 55 of file SymFncExpRad.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;
    SymFncExpRad const& c = dynamic_cast<SymFncExpRad 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      (e1          < c.e1         ) return true;
    else if (e1          > c.e1         ) return false;
    return false;
}

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

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setParameters()

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

virtual

Set symmetry function parameters.

Parameters

[in]

parameterString

String containing radial symmetry function parameters.

Implements nnp::SymFnc.

Definition at line 77 of file SymFncExpRad.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)];
    eta  = atof(splitLine.at(3).c_str());
    rs   = atof(splitLine.at(4).c_str());
    rc   = atof(splitLine.at(5).c_str());
 
    fc.setCutoffRadius(rc);
    fc.setCutoffParameter(cutoffAlpha);
 
    return;
}

References nnp::SymFncBaseCutoff::cutoffAlpha, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFncBaseCutoff::fc, nnp::SymFnc::rc, nnp::reduce(), rs, nnp::split(), and nnp::SymFnc::type.

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changeLengthUnit()

void SymFncExpRad::changeLengthUnit ( double convLength )

virtual

Change length unit.

Parameters

[in]

convLength

Multiplicative length unit conversion factor.

Implements nnp::SymFnc.

Definition at line 98 of file SymFncExpRad.cpp.

{
    this->convLength = convLength;
    eta /= convLength * convLength;
    rs *= convLength;
    rc *= convLength;
 
    fc.setCutoffRadius(rc);
    fc.setCutoffParameter(cutoffAlpha);
 
    return;
}

References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, eta, nnp::SymFncBaseCutoff::fc, nnp::SymFnc::rc, and rs.

getSettingsLine()

string SymFncExpRad::getSettingsLine ( ) const

virtual

Get settings file line from currently set parameters.

Returns

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

Implements nnp::SymFnc.

Definition at line 111 of file SymFncExpRad.cpp.

{
    string s = strpr("symfunction_short %2s %2zu %2s %16.8E %16.8E %16.8E\n",
                     elementMap[ec].c_str(),
                     type,
                     elementMap[e1].c_str(),
                     eta * convLength * convLength,
                     rs / convLength,
                     rc / convLength);
 
    return s;
}

References nnp::SymFnc::convLength, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFnc::rc, rs, nnp::strpr(), and nnp::SymFnc::type.

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calculate()

void SymFncExpRad::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 124 of file SymFncExpRad.cpp.

{
    double result = 0.0;
#ifndef N2P2_NO_SF_CACHE
    bool unique = true;
    size_t c0 = 0;
    size_t c1 = 0;
    if (cacheIndices.at(e1).size() > 0)
    {
        unique = false;
        c0 = cacheIndices.at(e1).at(0);
        c1 = cacheIndices.at(e1).at(1);
    }
#endif
 
    for (size_t j = 0; j < atom.getStoredMinNumNeighbors(rc); ++j)
    {
        Atom::Neighbor& n = atom.neighbors[j];
        if (e1 == n.element && n.d < rc)
        {
            // Energy calculation.
            double const rij = n.d;
            double const pexp = exp(-eta * (rij - rs) * (rij - rs));
 
            // Calculate cutoff function and derivative.
            double pfc;
            double pdfc;
#ifndef N2P2_NO_SF_CACHE
            if (unique) fc.fdf(rij, pfc, pdfc);
            else
            {
                double& cfc = n.cache[c0];
                double& cdfc = n.cache[c1];
                if (cfc < 0) fc.fdf(rij, cfc, cdfc);
                pfc = cfc;
                pdfc = cdfc;
            }
#else
            fc.fdf(rij, pfc, pdfc);
#endif
            result += pexp * pfc;
            // Force calculation.
            if (!derivatives) continue;
            double const p1 = scalingFactor
                * (pdfc - 2.0 * eta * (rij - rs)
                * pfc) * pexp / rij;
            Vec3D dij = p1 * n.dr;
            // Save force contributions in Atom storage.
            atom.dGdr[index] += dij;
#ifndef N2P2_FULL_SFD_MEMORY
            n.dGdr[indexPerElement[e1]] -= dij;
#else
            n.dGdr[index] -= dij;
#endif
        }
    }
 
    atom.G[index] = scale(result);
 
    return;
}

References nnp::Atom::Neighbor::cache, nnp::SymFnc::cacheIndices, nnp::Atom::Neighbor::d, nnp::Atom::dGdr, nnp::Atom::Neighbor::dGdr, nnp::Atom::Neighbor::dr, e1, nnp::Atom::Neighbor::element, eta, nnp::SymFncBaseCutoff::fc, nnp::Atom::G, nnp::Atom::getStoredMinNumNeighbors(), nnp::SymFnc::index, nnp::SymFnc::indexPerElement, nnp::Atom::neighbors, nnp::SymFnc::rc, rs, nnp::SymFnc::scale(), and nnp::SymFnc::scalingFactor.

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parameterLine()

string SymFncExpRad::parameterLine ( ) const

virtual

Give symmetry function parameters in one line.

Returns

String containing symmetry function parameter values.

Implements nnp::SymFnc.

Definition at line 186 of file SymFncExpRad.cpp.

{
    return strpr(getPrintFormat().c_str(),
                 index + 1,
                 elementMap[ec].c_str(),
                 type,
                 subtype.c_str(),
                 elementMap[e1].c_str(),
                 eta * convLength * convLength,
                 rs / convLength,
                 rc / convLength,
                 cutoffAlpha,
                 lineNumber + 1);
}

References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFnc::getPrintFormat(), nnp::SymFnc::index, nnp::SymFnc::lineNumber, nnp::SymFnc::rc, rs, nnp::strpr(), nnp::SymFncBaseCutoff::subtype, and nnp::SymFnc::type.

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parameterInfo()

vector< string > SymFncExpRad::parameterInfo ( ) const

virtual

Get description with parameter names and values.

Returns

Vector of parameter description strings.

Reimplemented from nnp::SymFncBaseCutoff.

Definition at line 201 of file SymFncExpRad.cpp.

{
    vector<string> v = SymFncBaseCutoff::parameterInfo();
    string s;
    size_t w = sfinfoWidth;
 
    s = "e1";
    v.push_back(strpr((pad(s, w) + "%s"    ).c_str(), elementMap[e1].c_str()));
    s = "eta";
    v.push_back(strpr((pad(s, w) + "%14.8E").c_str(),
                      eta * convLength * convLength));
    s = "rs";
    v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), rs / convLength));
 
    return v;
}

References nnp::SymFnc::convLength, e1, nnp::SymFnc::elementMap, eta, nnp::pad(), nnp::SymFncBaseCutoff::parameterInfo(), rs, nnp::SymFnc::sfinfoWidth, and nnp::strpr().

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getE1()

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

inline

Get private e1 member variable.

Definition at line 145 of file SymFncExpRad.h.

{ return e1; }

References e1.

Referenced by nnp::SymGrpExpRad::addMember().

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getEta()

double nnp::SymFncExpRad::getEta ( ) const

inline

Get private eta member variable.

Definition at line 146 of file SymFncExpRad.h.

{ return eta; }

References eta.

getRs()

double nnp::SymFncExpRad::getRs ( ) const

inline

Get private rs member variable.

Definition at line 147 of file SymFncExpRad.h.

{ return rs; }

References rs.

calculateRadialPart()

double SymFncExpRad::calculateRadialPart ( double distance ) const

virtual

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

Parameters

[in]

distance

Distance between two atoms.

Returns

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

Implements nnp::SymFnc.

Definition at line 218 of file SymFncExpRad.cpp.

{
    double const& r = distance * convLength;
 
    return exp(-eta * (r - rs) * (r - rs)) * fc.f(r);
}

References nnp::SymFnc::convLength, eta, nnp::SymFncBaseCutoff::fc, and rs.

calculateAngularPart()

double SymFncExpRad::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 225 of file SymFncExpRad.cpp.

{
    return 1.0;
}

checkRelevantElement()

bool SymFncExpRad::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 230 of file SymFncExpRad.cpp.

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

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

getCacheIdentifiers()

vector< string > SymFncExpRad::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 237 of file SymFncExpRad.cpp.

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

References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, e1, nnp::SymFnc::rc, nnp::strpr(), and nnp::SymFncBaseCutoff::subtype.

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Member Data Documentation

e1

std::size_t nnp::SymFncExpRad::e1

private

Element index of neighbor atom.

Definition at line 134 of file SymFncExpRad.h.

Referenced by calculate(), checkRelevantElement(), getCacheIdentifiers(), getE1(), getSettingsLine(), operator<(), operator==(), parameterInfo(), parameterLine(), setParameters(), and SymFncExpRad().

eta

double nnp::SymFncExpRad::eta

private

Width \(\eta\) of gaussian.

Definition at line 136 of file SymFncExpRad.h.

Referenced by calculate(), calculateRadialPart(), changeLengthUnit(), getEta(), getSettingsLine(), operator<(), operator==(), parameterInfo(), parameterLine(), setParameters(), and SymFncExpRad().

rs

double nnp::SymFncExpRad::rs

private

Shift \(r_s\) of gaussian.

Definition at line 138 of file SymFncExpRad.h.

Referenced by calculate(), calculateRadialPart(), changeLengthUnit(), getRs(), getSettingsLine(), operator<(), operator==(), parameterInfo(), parameterLine(), setParameters(), and SymFncExpRad().

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

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