nnp::SymGrpExpRad Class Reference

Radial symmetry function group (type 2) More...

#include <SymGrpExpRad.h>

Inheritance diagram for nnp::SymGrpExpRad:

Collaboration diagram for nnp::SymGrpExpRad:

Public Member Functions
	SymGrpExpRad (ElementMap const &elementMap)
	Constructor, sets type = 2. 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::SymGrpBaseCutoff
double	getRc () const
	Get private rc member variable. 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< SymFncExpRad const * >	members
	Vector of all group member pointers. More...
std::vector< double >	eta
	Vector containing values of all member symmetry functions. More...
std::vector< double >	rs
	Vector containing values of all member symmetry functions. 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::SymGrpBaseCutoff
	SymGrpBaseCutoff (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::SymGrpBaseCutoff
double	rc
	Cutoff radius \(r_c\) (common feature). More...
double	cutoffAlpha
	Cutoff function parameter \(\alpha\) (common feature). More...
std::string	subtype
	Subtype string (specifies cutoff type) (common feature). More...
CutoffFunction	fc
	Cutoff function used by this symmetry function group. More...
CutoffFunction::CutoffType	cutoffType
	Cutoff type used by this symmetry function group (common feature). 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 group (type 2)

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

Common features:

• element of central atom
• element of neighbor atom
• cutoff type
• \(r_c\)
• \(\alpha\)

Definition at line 46 of file SymGrpExpRad.h.

Constructor & Destructor Documentation

SymGrpExpRad()

SymGrpExpRad::SymGrpExpRad

(

ElementMap const &

elementMap

)

Constructor, sets type = 2.

Definition at line 30 of file SymGrpExpRad.cpp.

                                                       :
    SymGrpBaseCutoff(2, elementMap),
    e1(0)
{
    parametersCommon.insert("e1");
 
    parametersMember.insert("eta");
    parametersMember.insert("rs/rl");
    parametersMember.insert("mindex");
    parametersMember.insert("sfindex");
}

References nnp::SymGrp::parametersCommon, and nnp::SymGrp::parametersMember.

Member Function Documentation

operator==()

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

virtual

Overload == operator.

Implements nnp::SymGrp.

Definition at line 42 of file SymGrpExpRad.cpp.

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

References nnp::SymGrpBaseCutoff::cutoffAlpha, nnp::SymGrpBaseCutoff::cutoffType, e1, nnp::SymGrp::ec, nnp::SymGrp::getEc(), nnp::SymGrp::getType(), nnp::SymGrpBaseCutoff::rc, and nnp::SymGrp::type.

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operator<()

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

virtual

Overload < operator.

Implements nnp::SymGrp.

Definition at line 54 of file SymGrpExpRad.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;
    SymGrpExpRad const& c = dynamic_cast<SymGrpExpRad 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      (e1          < c.e1         ) return true;
    else if (e1          > c.e1         ) return false;
    return false;
}

References nnp::SymGrpBaseCutoff::cutoffAlpha, nnp::SymGrpBaseCutoff::cutoffType, e1, nnp::SymGrp::ec, nnp::SymGrp::getEc(), nnp::SymGrp::getType(), nnp::SymGrpBaseCutoff::rc, and nnp::SymGrp::type.

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addMember()

bool SymGrpExpRad::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 72 of file SymGrpExpRad.cpp.

{
    if (symmetryFunction->getType() != type) return false;
 
    SymFncExpRad const* sf =
        dynamic_cast<SymFncExpRad const*>(symmetryFunction);
 
    if (members.empty())
    {
        cutoffType  = sf->getCutoffType();
        subtype     = sf->getSubtype();
        cutoffAlpha = sf->getCutoffAlpha();
        ec          = sf->getEc();
        rc          = sf->getRc();
        e1          = sf->getE1();
        convLength  = sf->getConvLength();
 
        fc.setCutoffType(cutoffType);
        fc.setCutoffRadius(rc);
        fc.setCutoffParameter(cutoffAlpha);
    }
 
    if (sf->getCutoffType()  != cutoffType ) return false;
    if (sf->getCutoffAlpha() != cutoffAlpha) return false;
    if (sf->getEc()          != ec         ) return false;
    if (sf->getRc()          != rc         ) 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");
    }
 
    members.push_back(sf);
 
    return true;
}

References nnp::SymGrp::convLength, nnp::SymGrpBaseCutoff::cutoffAlpha, nnp::SymGrpBaseCutoff::cutoffType, e1, nnp::SymGrp::ec, nnp::SymGrpBaseCutoff::fc, nnp::SymFnc::getConvLength(), nnp::SymFncBaseCutoff::getCutoffAlpha(), nnp::SymFncBaseCutoff::getCutoffType(), nnp::SymFncExpRad::getE1(), nnp::SymFnc::getEc(), nnp::SymFnc::getRc(), nnp::SymFncBaseCutoff::getSubtype(), nnp::SymFnc::getType(), members, nnp::SymGrpBaseCutoff::rc, nnp::CutoffFunction::setCutoffParameter(), nnp::CutoffFunction::setCutoffRadius(), nnp::CutoffFunction::setCutoffType(), nnp::SymGrpBaseCutoff::subtype, and nnp::SymGrp::type.

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sortMembers()

void SymGrpExpRad::sortMembers ( )

virtual

Sort member symmetry functions.

Also allocate and precalculate additional stuff.

Implements nnp::SymGrp.

Definition at line 110 of file SymGrpExpRad.cpp.

{
    sort(members.begin(),
         members.end(),
         comparePointerTargets<SymFncExpRad const>);
 
    for (size_t i = 0; i < members.size(); i++)
    {
        memberIndex.push_back(members[i]->getIndex());
        eta.push_back(members[i]->getEta());
        rs.push_back(members[i]->getRs());
        memberIndexPerElement.push_back(members[i]->getIndexPerElement());
    }
 
    return;
}

References eta, nnp::SymGrp::getIndex(), nnp::SymGrp::memberIndex, nnp::SymGrp::memberIndexPerElement, members, and rs.

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setScalingFactors()

void SymGrpExpRad::setScalingFactors ( )

virtual

Fill scalingFactors with values from member symmetry functions.

Implements nnp::SymGrp.

Definition at line 127 of file SymGrpExpRad.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 SymGrpExpRad::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 144 of file SymGrpExpRad.cpp.

{
#ifndef N2P2_NO_SF_CACHE
    // Can use cache indices of any member because this group is defined via
    // identical symmetry function type, neighbors and cutoff functions.
    auto cacheIndices = members.at(0)->getCacheIndices();
    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
    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.getStoredMinNumNeighbors(rc); ++j)
    {
        Atom::Neighbor& n = atom.neighbors[j];
        if (e1 == n.element && n.d < rc)
        {
            // Energy calculation.
            double const rij = n.d;
 
            // 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
            double const* const d1 = n.dr.r;
            for (size_t k = 0; k < members.size(); ++k)
            {
                double pexp = exp(-eta[k] * (rij - rs[k]) * (rij - rs[k]));
                result[k] += pexp * pfc;
                // Force calculation.
                if (!derivatives) continue;
                double const p1 = scalingFactors[k] * (pdfc - 2.0 * eta[k]
                                * (rij - rs[k]) * pfc) * pexp / rij;
                // SIMPLE EXPRESSIONS:
                //Vec3D const dij = p1 * atom.neighbors[j].dr;
                double const p1drijx = p1 * d1[0];
                double const p1drijy = p1 * d1[1];
                double const p1drijz = p1 * 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, eta, nnp::SymGrpBaseCutoff::fc, nnp::CutoffFunction::fdf(), nnp::Atom::G, nnp::Atom::getStoredMinNumNeighbors(), nnp::SymGrp::memberIndex, nnp::SymGrp::memberIndexPerElement, members, nnp::Atom::neighbors, nnp::Vec3D::r, nnp::SymGrpBaseCutoff::rc, rs, and nnp::SymGrp::scalingFactors.

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parameterLines()

vector< string > SymGrpExpRad::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 241 of file SymGrpExpRad.cpp.

{
    vector<string> v;
 
    v.push_back(strpr(getPrintFormatCommon().c_str(),
                      index + 1,
                      elementMap[ec].c_str(),
                      type,
                      subtype.c_str(),
                      elementMap[e1].c_str(),
                      rc / convLength,
                      cutoffAlpha));
 
    for (size_t i = 0; i < members.size(); ++i)
    {
        v.push_back(strpr(getPrintFormatMember().c_str(),
                          members[i]->getEta() * convLength * convLength,
                          members[i]->getRs() / convLength,
                          members[i]->getLineNumber() + 1,
                          i + 1,
                          members[i]->getIndex() + 1));
    }
 
    return v;
}

References nnp::SymGrp::convLength, nnp::SymGrpBaseCutoff::cutoffAlpha, e1, nnp::SymGrp::ec, nnp::SymGrp::elementMap, nnp::SymGrp::getIndex(), nnp::SymGrp::getPrintFormatCommon(), nnp::SymGrp::getPrintFormatMember(), nnp::SymGrp::index, members, nnp::SymGrpBaseCutoff::rc, nnp::strpr(), nnp::SymGrpBaseCutoff::subtype, and nnp::SymGrp::type.

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Member Data Documentation

e1

std::size_t nnp::SymGrpExpRad::e1

private

Element index of neighbor atom (common feature).

Definition at line 91 of file SymGrpExpRad.h.

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

members

std::vector<SymFncExpRad const*> nnp::SymGrpExpRad::members

private

Vector of all group member pointers.

Definition at line 93 of file SymGrpExpRad.h.

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

eta

std::vector<double> nnp::SymGrpExpRad::eta

private

Vector containing values of all member symmetry functions.

Definition at line 95 of file SymGrpExpRad.h.

Referenced by calculate(), and sortMembers().

rs

std::vector<double> nnp::SymGrpExpRad::rs

private

Vector containing values of all member symmetry functions.

Definition at line 97 of file SymGrpExpRad.h.

Referenced by calculate(), and sortMembers().

---

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

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