nnp::SymFncCompRad Class Reference

Radial symmetry function with compact support (type 20) More...

#include <SymFncCompRad.h>

Inheritance diagram for nnp::SymFncCompRad:

Collaboration diagram for nnp::SymFncCompRad:

Public Member Functions
	SymFncCompRad (ElementMap const &elementMap)
	Constructor, sets type = 20.
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.
void	getCompactOnly (double const x, double &fx, double &dfx) const
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.
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::SymFncBaseComp
void	setCompactFunction (std::string subtype)
	Set radial compact function.
std::string	getSubtype () const
	Get private subtype member variable.
double	getRl () const
	Get private rl 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.

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::SymFncBaseComp
	SymFncBaseComp (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::SymFncBaseComp
bool	asymmetric
	If asymmetric version of polynomials should be used.
double	rl
	Lower bound of compact function, \(r_{l}\).
std::string	subtype
	Subtype string (specifies e.g. polynom type).
CompactFunction	cr
	Compact function for radial part.
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 with compact support (type 20)

\[ G^{20}_i = \sum_{\substack{j \neq i}} C(r_{ij}, r_l, r_c), \]

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> 20 <element-neighbor> <rlow> <rcutoff> <subtype>

where

• <element-central> .... element symbol of central atom
• <element-neighbor> ... element symbol of neighbor atom
• <rlow> ............... low radius boundary \(r_{l}\)
• <rcutoff> ............ high radius boundary \(r_{c}\)
• <subtype> ............ compact function specifier

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

Definition at line 55 of file SymFncCompRad.h.

Constructor & Destructor Documentation

SymFncCompRad()

SymFncCompRad::SymFncCompRad

(

ElementMap const &

elementMap

)

Constructor, sets type = 20.

Definition at line 31 of file SymFncCompRad.cpp.

                                                         :
    SymFncBaseComp(20, elementMap),
    e1(0)
{
    minNeighbors = 1;
    parameters.insert("e1");
}

References e1, nnp::SymFnc::elementMap, nnp::SymFnc::minNeighbors, nnp::SymFnc::parameters, and nnp::SymFncBaseComp::SymFncBaseComp().

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

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Member Function Documentation

operator==()

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

virtual

Overload == operator.

Implements nnp::SymFnc.

Definition at line 39 of file SymFncCompRad.cpp.

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

References e1, nnp::SymFnc::ec, nnp::SymFnc::getEc(), nnp::SymFncBaseComp::getSubtype(), nnp::SymFnc::getType(), nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::SymFncBaseComp::subtype, SymFncCompRad(), and nnp::SymFnc::type.

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operator<()

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

virtual

Overload < operator.

Implements nnp::SymFnc.

Definition at line 51 of file SymFncCompRad.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;
    SymFncCompRad const& c = dynamic_cast<SymFncCompRad 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      (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;
    return false;
}

References e1, nnp::SymFnc::ec, nnp::SymFnc::getEc(), nnp::SymFncBaseComp::getSubtype(), nnp::SymFnc::getType(), nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::SymFncBaseComp::subtype, SymFncCompRad(), and nnp::SymFnc::type.

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setParameters()

void SymFncCompRad::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 69 of file SymFncCompRad.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)];
    rl      = atof(splitLine.at(3).c_str());
    rc      = atof(splitLine.at(4).c_str());
    subtype = splitLine.at(5);
 
    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);
 
    return;
}

References nnp::SymFncBaseComp::cr, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, nnp::SymFnc::rc, nnp::reduce(), nnp::SymFncBaseComp::rl, nnp::SymFncBaseComp::setCompactFunction(), nnp::split(), nnp::SymFncBaseComp::subtype, and nnp::SymFnc::type.

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changeLengthUnit()

void SymFncCompRad::changeLengthUnit ( double convLength )

virtual

Change length unit.

Parameters

[in]

convLength

Multiplicative length unit conversion factor.

Implements nnp::SymFnc.

Definition at line 101 of file SymFncCompRad.cpp.

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

References nnp::SymFnc::convLength, nnp::SymFncBaseComp::cr, nnp::SymFnc::rc, and nnp::SymFncBaseComp::rl.

getSettingsLine()

string SymFncCompRad::getSettingsLine ( ) const

virtual

Get settings file line from currently set parameters.

Returns

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

Implements nnp::SymFnc.

Definition at line 112 of file SymFncCompRad.cpp.

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

References nnp::SymFnc::convLength, e1, 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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calculate()

void SymFncCompRad::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 125 of file SymFncCompRad.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.numNeighbors; ++j)
    {
        Atom::Neighbor& n = atom.neighbors[j];
        if (e1 == n.element && n.d > rl && n.d < rc)
        {
            // Energy calculation.
            double const rij = n.d;
 
            double rad;
            double drad;
            double r = rij;
#ifndef N2P2_NO_SF_CACHE
            if (unique) cr.fdf(r, rad, drad);
            else
            {
                double& crad = n.cache[c0];
                double& cdrad = n.cache[c1];
                if (crad < 0) cr.fdf(r, crad, cdrad);
                rad = crad;
                drad = cdrad;
            }
#else
            cr.fdf(r, rad, drad);
#endif
            result += rad;
 
            // Force calculation.
            if (!derivatives) continue;
            double const p1 = scalingFactor * drad / 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::SymFncBaseComp::cr, nnp::Atom::Neighbor::d, nnp::Atom::dGdr, nnp::Atom::Neighbor::dGdr, nnp::Atom::Neighbor::dr, e1, nnp::Atom::Neighbor::element, nnp::Atom::G, nnp::SymFnc::index, nnp::SymFnc::indexPerElement, nnp::Atom::neighbors, nnp::Atom::numNeighbors, nnp::SymFnc::rc, nnp::SymFncBaseComp::rl, nnp::SymFnc::scale(), and nnp::SymFnc::scalingFactor.

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getCompactOnly()

void nnp::SymFncCompRad::getCompactOnly ( double const x, double & fx, double & dfx ) const

inline

Definition at line 148 of file SymFncCompRad.h.

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

References nnp::SymFncBaseComp::cr.

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

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parameterLine()

string SymFncCompRad::parameterLine ( ) const

virtual

Give symmetry function parameters in one line.

Returns

String containing symmetry function parameter values.

Implements nnp::SymFnc.

Definition at line 185 of file SymFncCompRad.cpp.

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

References nnp::SymFnc::convLength, e1, 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 > SymFncCompRad::parameterInfo ( ) const

virtual

Get description with parameter names and values.

Returns

Vector of parameter description strings.

Reimplemented from nnp::SymFncBaseComp.

Definition at line 198 of file SymFncCompRad.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()));
 
    return v;
}

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

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getE1()

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

inline

Get private e1 member variable.

Definition at line 146 of file SymFncCompRad.h.

{ return e1; }

References e1.

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

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calculateRadialPart()

double SymFncCompRad::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 210 of file SymFncCompRad.cpp.

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

References nnp::SymFnc::convLength, and nnp::SymFncBaseComp::cr.

calculateAngularPart()

double SymFncCompRad::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 217 of file SymFncCompRad.cpp.

{
    return 1.0;
}

checkRelevantElement()

bool SymFncCompRad::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 222 of file SymFncCompRad.cpp.

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

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

getCacheIdentifiers()

vector< string > SymFncCompRad::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 229 of file SymFncCompRad.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);
 
    return v;
}

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

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Member Data Documentation

e1

std::size_t nnp::SymFncCompRad::e1

private

Element index of neighbor atom.

Definition at line 139 of file SymFncCompRad.h.

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

---

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

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