nnp::SymFncBaseComp Class Reference

Symmetry function base class for SFs with compact support. More...

#include <SymFncBaseComp.h>

Inheritance diagram for nnp::SymFncBaseComp:

Collaboration diagram for nnp::SymFncBaseComp:

Public Member Functions
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
	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
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

Symmetry function base class for SFs with compact support.

Definition at line 31 of file SymFncBaseComp.h.

Constructor & Destructor Documentation

SymFncBaseComp()

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

protected

Constructor, initializes type.

Definition at line 94 of file SymFncBaseComp.cpp.

                                                             :
    SymFnc(type, elementMap),
    asymmetric(false),
    rl        (0.0  ),
    subtype   (""   )
{
    // Add compact-related parameter IDs to set.
    parameters.insert("rs/rl");
    parameters.insert("subtype");
}

References nnp::SymFnc::parameters.

Member Function Documentation

parameterInfo()

vector< string > SymFncBaseComp::parameterInfo ( ) const

virtual

Get description with parameter names and values.

Returns

Vector of parameter description strings.

Reimplemented from nnp::SymFnc.

Reimplemented in nnp::SymFncBaseCompAng, nnp::SymFncBaseCompAngWeighted, nnp::SymFncCompRad, and nnp::SymFncCompRadWeighted.

Definition at line 25 of file SymFncBaseComp.cpp.

{
    vector<string> v = SymFnc::parameterInfo();
    string s;
    size_t w = sfinfoWidth;
 
    s = "subtype";
    v.push_back(strpr((pad(s, w) + "%s"    ).c_str(), subtype.c_str()));
    s = "rl";
    v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), rl / convLength));
 
    return v;
}

References nnp::SymFnc::convLength, nnp::pad(), nnp::SymFnc::parameterInfo(), rl, nnp::SymFnc::sfinfoWidth, nnp::strpr(), and subtype.

Referenced by nnp::SymFncBaseCompAng::parameterInfo(), nnp::SymFncBaseCompAngWeighted::parameterInfo(), nnp::SymFncCompRad::parameterInfo(), and nnp::SymFncCompRadWeighted::parameterInfo().

Here is the call graph for this function:

Here is the caller graph for this function:

setCompactFunction()

void SymFncBaseComp::setCompactFunction

(

std::string

subtype

)

Set radial compact function.

Parameters

[in]

subtype

Core function specification.

The subtype argument determines which CoreFunction::Type is used to generate the CompactFunction used by symmetry functions. The following strings are accepted (without the apostrophes):

• "e": CoreFunction::Type::EXP
• "pN", where "N" is one of "1,2,3,4", corresponding to the polynomial CoreFunction::Type POLYN, respectively. "pN" can be followed by the letter "a", which will enable the asymmetric version of the compact function, i.e. \(2x - x^2\) is used as argument. Examples: "p2", "p3a", "p4".

Definition at line 39 of file SymFncBaseComp.cpp.

{
    if (subtype.size() < 1 || subtype.size() > 3)
    {
        throw runtime_error(strpr("ERROR: Invalid compact function type "
                                  "specification: \"%s\".\n",
                                  subtype.c_str()));
    }
 
    using CFT = CoreFunction::Type;
    // Check for polynomials.
    if (subtype.front() == 'p')
    {
        if      (subtype.at(1) == '1') cr.setCoreFunction(CFT::POLY1);
        else if (subtype.at(1) == '2') cr.setCoreFunction(CFT::POLY2);
        else if (subtype.at(1) == '3') cr.setCoreFunction(CFT::POLY3);
        else if (subtype.at(1) == '4') cr.setCoreFunction(CFT::POLY4);
        else
        {
            throw runtime_error(strpr("ERROR: Invalid polynom type: \"%s\".\n",
                                      subtype.c_str()));
        }
        if (subtype.size() == 3)
        {
            if (subtype.at(2) == 'a')
            {
#ifndef N2P2_NO_ASYM_POLY
                asymmetric = true;
                cr.setAsymmetric(true);
#else
                throw runtime_error("ERROR: Compiled without support for "
                                    "asymmetric polynomial symmetry functions "
                                    "(-DN2P2_NO_ASYM_POLY).\n");
#endif
            }
            else
            {
                throw runtime_error(strpr("ERROR: Invalid polynom specifier: "
                                          "\"%s\".\n", subtype.c_str()));
            }
        }
    }
    else if (subtype.front() == 'e')
    {
        cr.setCoreFunction(CFT::EXP);
    }
    else
    {
        throw runtime_error(strpr("ERROR: Unknown compact SF type: \"%s\".\n",
                                  subtype.c_str()));
    }
 
    return;
}

References asymmetric, cr, nnp::CompactFunction::setAsymmetric(), nnp::CompactFunction::setCoreFunction(), nnp::strpr(), and subtype.

Referenced by nnp::SymFncBaseCompAng::setParameters(), nnp::SymFncBaseCompAngWeighted::setParameters(), nnp::SymFncCompRad::setParameters(), and nnp::SymFncCompRadWeighted::setParameters().

Here is the call graph for this function:

Here is the caller graph for this function:

getSubtype()

std::string nnp::SymFncBaseComp::getSubtype ( ) const

inline

Get private subtype member variable.

Definition at line 81 of file SymFncBaseComp.h.

{ return subtype; }

References subtype.

Referenced by nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngnWeighted::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngwWeighted::operator<(), nnp::SymFncCompRad::operator<(), nnp::SymFncCompRadWeighted::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngnWeighted::operator==(), nnp::SymFncCompAngw::operator==(), nnp::SymFncCompAngwWeighted::operator==(), nnp::SymFncCompRad::operator==(), and nnp::SymFncCompRadWeighted::operator==().

Here is the caller graph for this function:

getRl()

double nnp::SymFncBaseComp::getRl ( ) const

inline

Get private rl member variable.

Definition at line 82 of file SymFncBaseComp.h.

{ return rl; }

References rl.

Referenced by nnp::SymGrpCompAngn::addMember(), nnp::SymGrpCompAngnWeighted::addMember(), nnp::SymGrpCompAngw::addMember(), nnp::SymGrpCompAngwWeighted::addMember(), nnp::SymGrpCompRad::addMember(), and nnp::SymGrpCompRadWeighted::addMember().

Here is the caller graph for this function:

Member Data Documentation

asymmetric

bool nnp::SymFncBaseComp::asymmetric

protected

If asymmetric version of polynomials should be used.

Definition at line 64 of file SymFncBaseComp.h.

Referenced by setCompactFunction().

rl

double nnp::SymFncBaseComp::rl

protected

Lower bound of compact function, \(r_{l}\).

Definition at line 66 of file SymFncBaseComp.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngw::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRad::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncBaseCompAng::changeLengthUnit(), nnp::SymFncBaseCompAngWeighted::changeLengthUnit(), nnp::SymFncCompRad::changeLengthUnit(), nnp::SymFncCompRadWeighted::changeLengthUnit(), nnp::SymFncBaseCompAng::getCacheIdentifiers(), nnp::SymFncBaseCompAngWeighted::getCacheIdentifiers(), nnp::SymFncCompRad::getCacheIdentifiers(), nnp::SymFncCompRadWeighted::getCacheIdentifiers(), getRl(), nnp::SymFncBaseCompAng::getSettingsLine(), nnp::SymFncBaseCompAngWeighted::getSettingsLine(), nnp::SymFncCompRad::getSettingsLine(), nnp::SymFncCompRadWeighted::getSettingsLine(), nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngnWeighted::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngwWeighted::operator<(), nnp::SymFncCompRad::operator<(), nnp::SymFncCompRadWeighted::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngnWeighted::operator==(), nnp::SymFncCompAngw::operator==(), nnp::SymFncCompAngwWeighted::operator==(), nnp::SymFncCompRad::operator==(), nnp::SymFncCompRadWeighted::operator==(), parameterInfo(), nnp::SymFncBaseCompAng::parameterLine(), nnp::SymFncBaseCompAngWeighted::parameterLine(), nnp::SymFncCompRad::parameterLine(), nnp::SymFncCompRadWeighted::parameterLine(), nnp::SymFncBaseCompAng::setParameters(), nnp::SymFncBaseCompAngWeighted::setParameters(), nnp::SymFncCompRad::setParameters(), and nnp::SymFncCompRadWeighted::setParameters().

subtype

std::string nnp::SymFncBaseComp::subtype

protected

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

Definition at line 68 of file SymFncBaseComp.h.

Referenced by nnp::SymFncBaseCompAng::getCacheIdentifiers(), nnp::SymFncBaseCompAngWeighted::getCacheIdentifiers(), nnp::SymFncCompRad::getCacheIdentifiers(), nnp::SymFncCompRadWeighted::getCacheIdentifiers(), nnp::SymFncBaseCompAng::getSettingsLine(), nnp::SymFncBaseCompAngWeighted::getSettingsLine(), nnp::SymFncCompRad::getSettingsLine(), nnp::SymFncCompRadWeighted::getSettingsLine(), getSubtype(), nnp::SymFncCompAngn::operator<(), nnp::SymFncCompAngnWeighted::operator<(), nnp::SymFncCompAngw::operator<(), nnp::SymFncCompAngwWeighted::operator<(), nnp::SymFncCompRad::operator<(), nnp::SymFncCompRadWeighted::operator<(), nnp::SymFncCompAngn::operator==(), nnp::SymFncCompAngnWeighted::operator==(), nnp::SymFncCompAngw::operator==(), nnp::SymFncCompAngwWeighted::operator==(), nnp::SymFncCompRad::operator==(), nnp::SymFncCompRadWeighted::operator==(), parameterInfo(), nnp::SymFncBaseCompAng::parameterLine(), nnp::SymFncBaseCompAngWeighted::parameterLine(), nnp::SymFncCompRad::parameterLine(), nnp::SymFncCompRadWeighted::parameterLine(), setCompactFunction(), nnp::SymFncBaseCompAng::setParameters(), nnp::SymFncBaseCompAngWeighted::setParameters(), nnp::SymFncCompRad::setParameters(), and nnp::SymFncCompRadWeighted::setParameters().

cr

CompactFunction nnp::SymFncBaseComp::cr

protected

Compact function for radial part.

Definition at line 70 of file SymFncBaseComp.h.

Referenced by nnp::SymFncCompAngn::calculate(), nnp::SymFncCompAngnWeighted::calculate(), nnp::SymFncCompAngw::calculate(), nnp::SymFncCompAngwWeighted::calculate(), nnp::SymFncCompRad::calculate(), nnp::SymFncCompRadWeighted::calculate(), nnp::SymFncBaseCompAng::calculateRadialPart(), nnp::SymFncBaseCompAngWeighted::calculateRadialPart(), nnp::SymFncCompRad::calculateRadialPart(), nnp::SymFncCompRadWeighted::calculateRadialPart(), nnp::SymFncBaseCompAng::changeLengthUnit(), nnp::SymFncBaseCompAngWeighted::changeLengthUnit(), nnp::SymFncCompRad::changeLengthUnit(), nnp::SymFncCompRadWeighted::changeLengthUnit(), nnp::SymFncCompRad::getCompactOnly(), nnp::SymFncCompRadWeighted::getCompactOnly(), nnp::SymFncBaseCompAng::getCompactRadial(), nnp::SymFncBaseCompAngWeighted::getCompactRadial(), setCompactFunction(), nnp::SymFncBaseCompAng::setParameters(), nnp::SymFncBaseCompAngWeighted::setParameters(), nnp::SymFncCompRad::setParameters(), and nnp::SymFncCompRadWeighted::setParameters().

---

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

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