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

#include <SymGrpCompRad.h>

Inheritance diagram for nnp::SymGrpCompRad:

Collaboration diagram for nnp::SymGrpCompRad:

[legend]

Public Member Functions
	SymGrpCompRad (ElementMap const &elementMap)
	Constructor, sets type = 20. More...

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

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

virtual bool	addMember (SymFnc const *const symmetryFunction)
	Potentially add a member to group. More...

virtual void	sortMembers ()
	Sort member symmetry functions. More...

virtual void	setScalingFactors ()
	Fill scalingFactors with values from member symmetry functions. More...

virtual void	calculate (Atom &atom, bool const derivatives) const
	Calculate all symmetry functions of this group for one atom. More...

virtual std::vector< std::string >	parameterLines () const
	Give symmetry function group parameters on multiple lines. More...

Public Member Functions inherited from nnp::SymGrpBaseComp
double	getRmin () const
	Getter for rmin. More...

double	getRmax () const
	Getter for rmax. More...

Public Member Functions inherited from nnp::SymGrp
virtual	~SymGrp ()
	Virtual destructor. More...

virtual bool	operator== (SymGrp const &rhs) const =0
	Overload == operator. More...

virtual bool	operator< (SymGrp const &rhs) const =0
	Overload < operator. More...

bool	operator!= (SymGrp const &rhs) const
	Overload != operator. More...

bool	operator> (SymGrp const &rhs) const
	Overload > operator. More...

bool	operator<= (SymGrp const &rhs) const
	Overload <= operator. More...

bool	operator>= (SymGrp const &rhs) const
	Overload >= operator. More...

virtual bool	addMember (SymFnc const *const symmetryFunction)=0
	Potentially add a member to group. More...

virtual void	sortMembers ()=0
	Sort member symmetry functions. More...

virtual void	setScalingFactors ()=0
	Fill scalingFactors with values from member symmetry functions. More...

virtual void	calculate (Atom &atom, bool const derivatives) const =0
	Calculate all symmetry functions of this group for one atom. More...

virtual std::vector< std::string >	parameterLines () const =0
	Give symmetry function group parameters on multiple lines. More...

void	setIndex (std::size_t index)
	Set private index member variable. More...

std::size_t	getIndex () const
	Get private index member variable. More...

std::size_t	getType () const
	Get private type member variable. More...

std::size_t	getEc () const
	Get private ec member variable. More...

Private Attributes
std::size_t	e1
	Element index of neighbor atom (common feature). More...

std::vector< SymFncCompRad const * >	members
	Vector of all group member pointers. More...

std::vector< double >	mrl
	Member rl. More...

std::vector< double >	mrc
	Member rc. More...

std::vector< std::vector< std::size_t > >	mci
	Member cache indices for actual neighbor element. More...

Additional Inherited Members
Protected Types inherited from nnp::SymGrp
typedef std::map< std::string, std::pair< std::string, std::string > >	PrintFormat

typedef std::vector< std::string >	PrintOrder

Protected Member Functions inherited from nnp::SymGrpBaseComp
	SymGrpBaseComp (std::size_t type, ElementMap const &elementMap)
	Constructor, sets type. More...

Protected Member Functions inherited from nnp::SymGrp
	SymGrp (std::size_t type, ElementMap const &elementMap)
	Constructor, sets type. More...

std::string	getPrintFormatCommon () const
	Get common parameter line format string. More...

std::string	getPrintFormatMember () const
	Get member parameter line format string. More...

Static Protected Member Functions inherited from nnp::SymGrp
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::SymGrpBaseComp
double	rmin
	Minimum radius within group. More...

double	rmax
	Maximum radius within group. More...

Protected Attributes inherited from nnp::SymGrp
std::size_t	type
	Symmetry function type. More...

ElementMap	elementMap
	Copy of element map. More...

std::size_t	index
	Symmetry function group index. More...

std::size_t	ec
	Element index of center atom (common feature). More...

double	convLength
	Data set normalization length conversion factor. More...

std::vector< size_t >	memberIndex
	Vector containing indices of all member symmetry functions. More...

std::vector< double >	scalingFactors
	Scaling factors of all member symmetry functions. More...

std::set< std::string >	parametersCommon
	Set of common parameters IDs. More...

std::set< std::string >	parametersMember
	Set of common parameters IDs. More...

std::vector< std::vector< std::size_t > >	memberIndexPerElement
	Vector containing per-element indices of all member symmetry functions. More...

Static Protected Attributes inherited from nnp::SymGrp
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

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 \(\left[x_\text{low}, x_\text{high}\right]\).

Common features:

element of central atom
element of neighbor atom

Definition at line 47 of file SymGrpCompRad.h.

Constructor & Destructor Documentation

◆ SymGrpCompRad()

SymGrpCompRad::SymGrpCompRad ( ElementMap const & elementMap )

Constructor, sets type = 20.

Definition at line 31 of file SymGrpCompRad.cpp.

                                            :
    SymGrpBaseComp(20, elementMap),
    e1(0)
{
    parametersCommon.insert("e1");
}

References nnp::SymGrp::parametersCommon.

Member Function Documentation

◆ operator==()

bool SymGrpCompRad::operator== ( SymGrp const & rhs ) const

virtual

Overload == operator.

Implements nnp::SymGrp.

Definition at line 39 of file SymGrpCompRad.cpp.

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

References e1, nnp::SymGrp::ec, nnp::SymGrp::getEc(), nnp::SymGrp::getType(), and nnp::SymGrp::type.

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◆ operator<()

bool SymGrpCompRad::operator< ( SymGrp const & rhs ) const

virtual

Overload < operator.

Implements nnp::SymGrp.

Definition at line 48 of file SymGrpCompRad.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;
    SymGrpCompRad const& c = dynamic_cast<SymGrpCompRad const&>(rhs);
    if      (e1 < c.e1) return true;
    else if (e1 > c.e1) return false;
    return false;
}

References e1, nnp::SymGrp::ec, nnp::SymGrp::getEc(), nnp::SymGrp::getType(), and nnp::SymGrp::type.

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◆ addMember()

bool SymGrpCompRad::addMember ( SymFnc const *const symmetryFunction )

virtual

Potentially add a member to group.

Parameters

[in] symmetryFunction Candidate symmetry function.

Returns: If addition was successful.

If symmetry function is compatible with common feature list its pointer will be added to members.

Implements nnp::SymGrp.

Definition at line 60 of file SymGrpCompRad.cpp.

{
    if (symmetryFunction->getType() != type) return false;
 
    SymFncCompRad const* sf =
        dynamic_cast<SymFncCompRad const*>(symmetryFunction);
 
    if (members.empty())
    {
        ec          = sf->getEc();
        e1          = sf->getE1();
        convLength  = sf->getConvLength();
    }
 
    if (sf->getEc()          != ec         ) return false;
    if (sf->getE1()          != e1         ) return false;
    if (sf->getConvLength()  != convLength )
    {
        throw runtime_error("ERROR: Unable to add symmetry function members "
                            "with different conversion factors.\n");
    }
 
    if (sf->getRl() <= 0.0) rmin = 0.0;
    else rmin = min( rmin, sf->getRl() );
    rmax = max( rmax, sf->getRc() );
 
    members.push_back(sf);
 
    return true;
}

References nnp::SymGrp::convLength, e1, nnp::SymGrp::ec, nnp::SymFnc::getConvLength(), nnp::SymFncCompRad::getE1(), nnp::SymFnc::getEc(), nnp::SymFnc::getRc(), nnp::SymFncBaseComp::getRl(), nnp::SymFnc::getType(), members, nnp::SymGrpBaseComp::rmax, nnp::SymGrpBaseComp::rmin, and nnp::SymGrp::type.

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◆ sortMembers()

void SymGrpCompRad::sortMembers ( )

virtual

Sort member symmetry functions.

Also allocate and precalculate additional stuff.

Implements nnp::SymGrp.

Definition at line 91 of file SymGrpCompRad.cpp.

{
    sort(members.begin(),
         members.end(),
         comparePointerTargets<SymFncCompRad const>);
 
    for (size_t i = 0; i < members.size(); i++)
    {
        memberIndex.push_back(members[i]->getIndex());
        memberIndexPerElement.push_back(members[i]->getIndexPerElement());
    }
 
    mrl.resize(members.size(), 0.0);
    mrc.resize(members.size(), 0.0);
    for (size_t i = 0; i < members.size(); i++)
    {
        mrl.at(i) = members[i]->getRl();
        mrc.at(i) = members[i]->getRc();
    }
 
#ifndef N2P2_NO_SF_CACHE
    mci.resize(members.size());
    for (size_t k = 0; k < members.size(); ++k)
    {
        mci.at(k) = members.at(k)->getCacheIndices()[e1];
    }
#endif
 
    return;
}

References e1, nnp::SymGrp::getIndex(), mci, nnp::SymGrp::memberIndex, nnp::SymGrp::memberIndexPerElement, members, mrc, and mrl.

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◆ setScalingFactors()

void SymGrpCompRad::setScalingFactors ( )

virtual

Fill scalingFactors with values from member symmetry functions.

Implements nnp::SymGrp.

Definition at line 122 of file SymGrpCompRad.cpp.

{
    scalingFactors.resize(members.size(), 0.0);
    for (size_t i = 0; i < members.size(); i++)
    {
        scalingFactors.at(i) = members[i]->getScalingFactor();
    }
 
    return;
}

References members, and nnp::SymGrp::scalingFactors.

◆ calculate()

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

virtual

Calculate all symmetry functions of this group for one atom.

Parameters

[in,out]	atom	Atom for which symmetry functions are caluclated.
[in]	derivatives	If also symmetry function derivatives will be calculated and saved.

Implements nnp::SymGrp.

Definition at line 139 of file SymGrpCompRad.cpp.

{
    double* result = new double[members.size()];
    for (size_t k = 0; k < members.size(); ++k)
    {
        result[k] = 0.0;
    }
 
    for (size_t j = 0; j < atom.numNeighbors; ++j)
    {
        Atom::Neighbor& n = atom.neighbors[j];
        double const rij = n.d;
        if (e1 == n.element && rij < rmax && rij > rmin)
        {
            // Energy calculation.
            double const* const d1 = n.dr.r;
            for (size_t k = 0; k < members.size(); ++k)
            {
                SymFncCompRad const& sf = *(members[k]);
                if (rij <= mrl[k] || rij >= mrc[k]) continue;
                double rad;
                double drad;
#ifndef N2P2_NO_SF_CACHE
                if (mci[k].size() == 0) sf.getCompactOnly(rij, rad, drad);
                else
                {
                    double& crad = n.cache[mci[k][0]];
                    double& cdrad = n.cache[mci[k][1]];
                    if (crad < 0) sf.getCompactOnly(rij, crad, cdrad);
                    rad = crad;
                    drad = cdrad;
                }
#else
                sf.getCompactOnly(rij, rad, drad);
#endif
                result[k] += rad;
 
                // Force calculation.
                if (!derivatives || drad == 0.0) continue;
                drad *= scalingFactors[k] / rij;
                // SIMPLE EXPRESSIONS:
                //Vec3D const dij = p1 * atom.neighbors[j].dr;
                double const p1drijx = drad * d1[0];
                double const p1drijy = drad * d1[1];
                double const p1drijz = drad * d1[2];
 
                // Save force contributions in Atom storage.
#ifndef N2P2_FULL_SFD_MEMORY
                size_t ki = memberIndex[k];
#else
                size_t const ki = memberIndex[k];
#endif
                // SIMPLE EXPRESSIONS:
                //atom.dGdr[ki]              += dij;
                //atom.neighbors[j].dGdr[ki] -= dij;
 
                double* dGdr = atom.dGdr[ki].r;
                dGdr[0] += p1drijx;
                dGdr[1] += p1drijy;
                dGdr[2] += p1drijz;
 
#ifndef N2P2_FULL_SFD_MEMORY
                ki = memberIndexPerElement[k][e1];
#endif
                dGdr = n.dGdr[ki].r;
                dGdr[0] -= p1drijx;
                dGdr[1] -= p1drijy;
                dGdr[2] -= p1drijz;
            }
        }
    }
 
    for (size_t k = 0; k < members.size(); ++k)
    {
        atom.G[memberIndex[k]] = members[k]->scale(result[k]);
    }
 
    delete[] result;
 
    return;
}

References nnp::Atom::Neighbor::cache, nnp::Atom::Neighbor::d, nnp::Atom::Neighbor::dGdr, nnp::Atom::dGdr, nnp::Atom::Neighbor::dr, e1, nnp::Atom::Neighbor::element, nnp::Atom::G, nnp::SymFncCompRad::getCompactOnly(), mci, nnp::SymGrp::memberIndex, nnp::SymGrp::memberIndexPerElement, members, mrc, mrl, nnp::Atom::neighbors, nnp::Atom::numNeighbors, nnp::Vec3D::r, nnp::SymGrpBaseComp::rmin, and nnp::SymGrp::scalingFactors.

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◆ parameterLines()

vector< string > SymGrpCompRad::parameterLines ( ) const

virtual

Give symmetry function group parameters on multiple lines.

Returns: Vector of string containing symmetry function parameters lines.

Implements nnp::SymGrp.

Definition at line 221 of file SymGrpCompRad.cpp.

{
    vector<string> v;
 
    v.push_back(strpr(getPrintFormatCommon().c_str(),
                      index + 1,
                      elementMap[ec].c_str(),
                      type,
                      elementMap[e1].c_str(),
                      rmin / convLength,
                      rmax / convLength));
 
    for (size_t i = 0; i < members.size(); ++i)
    {
        v.push_back(strpr(getPrintFormatMember().c_str(),
                          members[i]->getSubtype().c_str(),
                          members[i]->getRl() / convLength,
                          members[i]->getRc() / convLength,
                          members[i]->getLineNumber() + 1,
                          i + 1,
                          members[i]->getIndex() + 1));
    }
 
    return v;
}

References nnp::SymGrp::convLength, e1, nnp::SymGrp::ec, nnp::SymGrp::elementMap, nnp::SymGrp::getIndex(), nnp::SymGrp::getPrintFormatCommon(), nnp::SymGrp::getPrintFormatMember(), nnp::SymGrp::index, members, nnp::SymGrpBaseComp::rmax, nnp::SymGrpBaseComp::rmin, nnp::strpr(), and nnp::SymGrp::type.

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Member Data Documentation

◆ e1

std::size_t nnp::SymGrpCompRad::e1

private

Element index of neighbor atom (common feature).

Definition at line 92 of file SymGrpCompRad.h.

Referenced by addMember(), calculate(), operator<(), operator==(), parameterLines(), and sortMembers().

◆ members

std::vector<SymFncCompRad const*> nnp::SymGrpCompRad::members

private

Vector of all group member pointers.

Definition at line 94 of file SymGrpCompRad.h.

Referenced by addMember(), calculate(), parameterLines(), setScalingFactors(), and sortMembers().

◆ mrl

std::vector<double> nnp::SymGrpCompRad::mrl

private

Member rl.

Definition at line 96 of file SymGrpCompRad.h.

Referenced by calculate(), and sortMembers().

◆ mrc

std::vector<double> nnp::SymGrpCompRad::mrc

private

Member rc.

Definition at line 98 of file SymGrpCompRad.h.

Referenced by calculate(), and sortMembers().

◆ mci

std::vector<std::vector<std::size_t> > nnp::SymGrpCompRad::mci

private

Member cache indices for actual neighbor element.

Definition at line 101 of file SymGrpCompRad.h.

Referenced by calculate(), and sortMembers().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SymGrpCompRad()

Member Function Documentation

◆ operator==()

◆ operator<()

◆ addMember()

◆ sortMembers()

◆ setScalingFactors()

◆ calculate()

◆ parameterLines()

Member Data Documentation

◆ e1

◆ members

◆ mrl

◆ mrc

◆ mci