Derived Cabana class for element-specific data. More...

#include <ElementCabana.h>

Inheritance diagram for nnp::ElementCabana:

Collaboration diagram for nnp::ElementCabana:

Public Member Functions
	ElementCabana (std::size_t const index)
	Constructor using index.

	~ElementCabana ()
	Destructor.

template<class t_SF, class h_t_int>
void	addSymmetryFunction (std::string const &parameters, std::vector< std::string > elementStrings, int attype, t_SF SF, double convLength, h_t_int h_numSFperElem)
	Add one symmetry function.

void	changeLengthUnitSymmetryFunctions (double convLength)
	Change length unit for all symmetry functions.

template<class t_SF, class h_t_int>
void	sortSymmetryFunctions (t_SF SF, h_t_int h_numSFperElem, int attype)
	Sort all symmetry function.

template<class t_SF>
bool	compareSF (t_SF SF, int attype, int index1, int index2)
	Print symmetry function parameter value information.

template<class t_SF, class h_t_int>
std::vector< std::string >	infoSymmetryFunctionParameters (t_SF SF, int attype, h_t_int h_numSFperElem) const
	Print symmetry function parameter value information.

template<class t_SF, class t_SFscaling, class h_t_int>
std::vector< std::string >	infoSymmetryFunctionScaling (ScalingType scalingType, t_SF SF, t_SFscaling SFscaling, int attype, h_t_int h_numSFperElem) const
	Print symmetry function scaling information.

template<class t_SF, class t_SFGmemberlist, class h_t_int>
void	setupSymmetryFunctionGroups (t_SF SF, t_SFGmemberlist SFGmemberlist, int attype, h_t_int h_numSFperElem, h_t_int h_numSFGperElem, int maxSFperElem)
	Set up symmetry function groups.

template<class t_SF, class t_SFGmemberlist, class h_t_int>
std::vector< std::string >	infoSymmetryFunctionGroups (t_SF SF, t_SFGmemberlist SFGmemberlist, int attype, h_t_int h_numSFGperElem) const
	Print symmetry function group info.

template<class t_SF, class h_t_int>
void	setCutoffFunction (CutoffFunction::CutoffType const cutoffType, double const cutoffAlpha, t_SF SF, int attype, h_t_int h_numSFperElem)
	Set cutoff function for all symmetry functions.

template<class t_SF, class t_SFscaling, class h_t_int>
void	setScaling (ScalingType scalingType, std::vector< std::string > const &statisticsLine, double minS, double maxS, t_SF SF, t_SFscaling SFscaling, int attype, h_t_int h_numSFperElem) const
	Set scaling of all symmetry functions.

template<class h_t_int>
std::size_t	numSymmetryFunctions (int attype, h_t_int h_numSFperElem) const
	Get number of symmetry functions.

template<class t_SF>
std::size_t	getMinNeighbors (int attype, t_SF SF, int nSF) const
	Get maximum of required minimum number of neighbors for all symmetry functions for this element.

template<class t_SF, class h_t_int>
double	getMinCutoffRadius (t_SF SF, int attype, h_t_int h_numSFperElem) const
	Get minimum cutoff radius of all symmetry functions.

template<class t_SF, class h_t_int>
double	getMaxCutoffRadius (t_SF SF, int attype, h_t_int h_numSFperElem) const
	Get maximum cutoff radius of all symmetry functions.

template<class t_SFscaling>
void	setScalingType (ScalingType scalingType, std::string statisticsLine, double Smin, double Smax, t_SFscaling SFscaling, int attype, int k) const
	Symmetry function statistics.

template<class t_SFscaling>
std::string	scalingLine (ScalingType scalingType, t_SFscaling SFscaling, int attype, int k) const
	Print scaling for one symmetry function.

template<class t_SFscaling>
double	unscale (int attype, double value, int k, t_SFscaling SFscaling)
	Unscale one symmetry function.

template<class t_SF, class h_t_int>
vector< string >	infoSymmetryFunctionParameters (t_SF SF, int attype, h_t_int h_numSFperElem) const

template<class t_SF, class t_SFscaling, class h_t_int>
vector< string >	infoSymmetryFunctionScaling (ScalingType scalingType, t_SF SF, t_SFscaling SFscaling, int attype, h_t_int h_numSFperElem) const

template<class t_SF, class t_SFGmemberlist, class h_t_int>
vector< string >	infoSymmetryFunctionGroups (t_SF SF, t_SFGmemberlist SFGmemberlist, int attype, h_t_int h_numSFGperElem) const

template<class t_SF>
size_t	getMinNeighbors (int attype, t_SF SF, int nSF) const

Public Member Functions inherited from nnp::Element
	Element ()
	Default constructor.

	Element (std::size_t const index, ElementMap const &elementMap)
	Constructor using index.

virtual	~Element ()
	Destructor.

void	clearSymmetryFunctions ()
	Clear all symmetry functions and groups.

void	setAtomicEnergyOffset (double atomicEnergyOffset)
	Set atomicEnergyOffset.

void	setHardness (double hardness)
	Set hardness.

void	setQsigma (double qsigma)
	Set qsigma.

std::size_t	getIndex () const
	Get index.

std::size_t	getAtomicNumber () const
	Get atomicNumber.

double	getAtomicEnergyOffset () const
	Get atomicEnergyOffset.

double	getHardness () const
	Get hardness.

double	getQsigma () const
	Get qsigma.

std::string	getSymbol () const
	Get symbol.

void	addSymmetryFunction (std::string const &parameters, std::size_t const &lineNumber)
	Add one symmetry function.

void	changeLengthUnitSymmetryFunctions (double convLength)
	Change length unit for all symmetry functions.

void	sortSymmetryFunctions ()
	Sort all symmetry function.

std::vector< std::string >	infoSymmetryFunctionParameters () const
	Print symmetry function parameter value information.

std::vector< std::string >	infoSymmetryFunction (std::size_t index) const
	Print symmetry function parameter names and values.

std::vector< std::string >	infoSymmetryFunctionScaling () const
	Print symmetry function scaling information.

void	setupSymmetryFunctionGroups ()
	Set up symmetry function groups.

void	setupSymmetryFunctionMemory ()
	Extract relevant symmetry function combinations for derivative memory.

std::vector< std::string >	infoSymmetryFunctionGroups () const
	Print symmetry function group info.

void	setCutoffFunction (CutoffFunction::CutoffType const cutoffType, double const cutoffAlpha)
	Set cutoff function for all symmetry functions.

void	setScalingNone () const
	Set no scaling of symmetry function.

void	setScaling (SymFnc::ScalingType scalingType, std::vector< std::string > const &statisticsLine, double minS, double maxS) const
	Set scaling of all symmetry functions.

std::size_t	numSymmetryFunctions () const
	Get number of symmetry functions.

std::size_t	getMinNeighbors () const
	Get maximum of required minimum number of neighbors for all symmetry functions for this element.

double	getMinCutoffRadius () const
	Get minimum cutoff radius of all symmetry functions.

double	getMaxCutoffRadius () const
	Get maximum cutoff radius of all symmetry functions.

void	getCutoffRadii (std::vector< double > &cutoffs) const
	Get all different cutoff radii belonging to this element.

std::vector< std::size_t > const &	getSymmetryFunctionNumTable () const
	Get number of relevant symmetry functions per element.

std::vector< std::vector< std::size_t > > const &	getSymmetryFunctionTable () const
	Get symmetry function element relevance table.

void	calculateSymmetryFunctions (Atom &atom, bool const derivatives) const
	Calculate symmetry functions.

void	calculateSymmetryFunctionGroups (Atom &atom, bool const derivatives) const
	Calculate symmetry functions via groups.

std::size_t	updateSymmetryFunctionStatistics (Atom const &atom)
	Update symmetry function statistics.

SymFnc const &	getSymmetryFunction (std::size_t index) const
	Get symmetry function instance.

void	setCacheIndices (std::vector< std::vector< SFCacheList > > cacheLists)
	Set cache indices for all symmetry functions of this element.

std::vector< std::size_t >	getCacheSizes () const
	Get cache sizes for each neighbor atom element.

Private Attributes
std::size_t	index
	Global index of this element.

std::size_t	atomicNumber
	Atomic number of this element.

double	atomicEnergyOffset
	Offset energy for every atom of this element.

std::string	symbol
	Element symbol.

Additional Inherited Members
Public Attributes inherited from nnp::Element
std::map< std::string, NeuralNetwork >	neuralNetworks
	Neural networks for this element.

SymFncStatistics	statistics
	Symmetry function statistics.

Protected Attributes inherited from nnp::Element
ElementMap	elementMap
	Copy of element map.

std::size_t	index
	Global index of this element.

std::size_t	atomicNumber
	Atomic number of this element.

double	atomicEnergyOffset
	Offset energy for every atom of this element.

double	hardness
	Atomic hardness for global charge equilibration.

double	qsigma
	Gaussian width of charge distribution.

std::string	symbol
	Element symbol.

std::vector< std::size_t >	symmetryFunctionNumTable
	Number of relevant symmetry functions for each neighbor element.

std::vector< std::vector< std::size_t > >	symmetryFunctionTable
	List of symmetry function indices relevant for each neighbor element.

std::vector< std::vector< SFCacheList > >	cacheLists
	Symmetry function cache lists.

std::vector< SymFnc * >	symmetryFunctions
	Vector of pointers to symmetry functions.

std::vector< SymGrp * >	symmetryFunctionGroups
	Vector of pointers to symmetry function groups.

Detailed Description

Derived Cabana class for element-specific data.

Definition at line 35 of file ElementCabana.h.

Constructor & Destructor Documentation

◆ ElementCabana()

nnp::ElementCabana::ElementCabana ( std::size_t const index )

Constructor using index.

Definition at line 31 of file ElementCabana_impl.h.

    : Element()
{
    index = _index;
    atomicEnergyOffset = 0.0;
    neuralNetwork = NULL;
}

References atomicEnergyOffset, nnp::Element::Element(), and index.

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◆ ~ElementCabana()

nnp::ElementCabana::~ElementCabana ( )

Destructor.

Definition at line 39 of file ElementCabana_impl.h.

39{}

Member Function Documentation

◆ addSymmetryFunction()

template<class t_SF, class h_t_int>

void nnp::ElementCabana::addSymmetryFunction	(	std::string const &	parameters,
		std::vector< std::string >	elementStrings,
		int	attype,
		t_SF	SF,
		double	convLength,
		h_t_int	h_numSFperElem )

Add one symmetry function.

Parameters

[in]	parameters	String containing settings for symmetry function.
[in]	lineNumber	Line number of symmetry function in settings file.
[in]	attype	Atom type.
[in]	SF	Kokkos host View of symmetry functions.
[in]	convLength	Length unit conversion factor.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

Definition at line 42 of file ElementCabana_impl.h.

{
    vector<string> args = split( reduce( parameters ) );
    size_t type = (size_t)atoi( args.at( 1 ).c_str() );
    const char *estring;
    int el = 0;
 
    vector<string> splitLine = split( reduce( parameters ) );
    if ( type == 2 )
    {
        estring = splitLine.at( 0 ).c_str();
        for ( size_t i = 0; i < elementStrings.size(); ++i )
        {
            if ( strcmp( elementStrings[i].c_str(), estring ) == 0 )
                el = i;
        }
        SF( attype, h_numSFperElem( attype ), 0 ) = el;   // ec
        SF( attype, h_numSFperElem( attype ), 1 ) = type; // type
 
        estring = splitLine.at( 2 ).c_str();
        for ( size_t i = 0; i < elementStrings.size(); ++i )
        {
            if ( strcmp( elementStrings[i].c_str(), estring ) == 0 )
                el = i;
        }
        SF( attype, h_numSFperElem( attype ), 2 ) = el; // e1
        // set e2 to arbit high number for ease in creating groups
        SF( attype, h_numSFperElem( attype ), 3 ) = 100000; // e2
 
        SF( attype, h_numSFperElem( attype ), 4 ) =
            atof( splitLine.at( 3 ).c_str() ) /
            ( convLength * convLength ); // eta
        SF( attype, h_numSFperElem( attype ), 8 ) =
            atof( splitLine.at( 4 ).c_str() ) * convLength; // rs
        SF( attype, h_numSFperElem( attype ), 7 ) =
            atof( splitLine.at( 5 ).c_str() ) * convLength; // rc
 
        SF( attype, h_numSFperElem( attype ), 13 ) = h_numSFperElem( attype );
        h_numSFperElem( attype )++;
    }
 
    else if ( type == 3 )
    {
        if ( type != (size_t)atoi( splitLine.at( 1 ).c_str() ) )
            throw runtime_error( "ERROR: Incorrect symmetry function type.\n" );
        estring = splitLine.at( 0 ).c_str();
        for ( size_t i = 0; i < elementStrings.size(); ++i )
        {
            if ( strcmp( elementStrings[i].c_str(), estring ) == 0 )
                el = i;
        }
        SF( attype, h_numSFperElem( attype ), 0 ) = el;   // ec
        SF( attype, h_numSFperElem( attype ), 1 ) = type; // type
 
        estring = splitLine.at( 2 ).c_str();
        for ( size_t i = 0; i < elementStrings.size(); ++i )
        {
            if ( strcmp( elementStrings[i].c_str(), estring ) == 0 )
                el = i;
        }
        SF( attype, h_numSFperElem( attype ), 2 ) = el; // e1
 
        estring = splitLine.at( 3 ).c_str();
        for ( size_t i = 0; i < elementStrings.size(); ++i )
        {
            if ( strcmp( elementStrings[i].c_str(), estring ) == 0 )
                el = i;
        }
 
        SF( attype, h_numSFperElem( attype ), 3 ) = el; // e2
        SF( attype, h_numSFperElem( attype ), 4 ) =
            atof( splitLine.at( 4 ).c_str() ) /
            ( convLength * convLength ); // eta
        SF( attype, h_numSFperElem( attype ), 5 ) =
            atof( splitLine.at( 5 ).c_str() ); // lambda
        SF( attype, h_numSFperElem( attype ), 6 ) =
            atof( splitLine.at( 6 ).c_str() ); // zeta
        SF( attype, h_numSFperElem( attype ), 7 ) =
            atof( splitLine.at( 7 ).c_str() ) * convLength; // rc
        // Shift parameter is optional.
        if ( splitLine.size() > 8 )
            SF( attype, h_numSFperElem( attype ), 8 ) =
                atof( splitLine.at( 8 ).c_str() ) * convLength; // rs
 
        T_INT e1 = SF( attype, h_numSFperElem( attype ), 2 );
        T_INT e2 = SF( attype, h_numSFperElem( attype ), 3 );
        if ( e1 > e2 )
        {
            size_t tmp = e1;
            e1 = e2;
            e2 = tmp;
        }
        SF( attype, h_numSFperElem( attype ), 2 ) = e1;
        SF( attype, h_numSFperElem( attype ), 3 ) = e2;
 
        T_FLOAT zeta = SF( attype, h_numSFperElem( attype ), 6 );
        T_INT zetaInt = round( zeta );
        if ( fabs( zeta - zetaInt ) <= numeric_limits<double>::min() )
            SF( attype, h_numSFperElem( attype ), 9 ) = 1;
        else
            SF( attype, h_numSFperElem( attype ), 9 ) = 0;
 
        SF( attype, h_numSFperElem( attype ), 13 ) = h_numSFperElem( attype );
        h_numSFperElem( attype )++;
    }
    // TODO: Add this later
    else if ( type == 9 )
    {
    }
    else if ( type == 12 )
    {
    }
    else if ( type == 13 )
    {
    }
    else
    {
        throw runtime_error( "ERROR: Unknown symmetry function type.\n" );
    }
 
    return;
}

References nnp::reduce(), and nnp::split().

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◆ changeLengthUnitSymmetryFunctions()

void nnp::ElementCabana::changeLengthUnitSymmetryFunctions ( double convLength )

Change length unit for all symmetry functions.

Parameters

[in] convLength Length unit conversion factor.

◆ sortSymmetryFunctions()

template<class t_SF, class h_t_int>

void nnp::ElementCabana::sortSymmetryFunctions	(	t_SF	SF,
		h_t_int	h_numSFperElem,
		int	attype )

Sort all symmetry function.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.
[in]	attype	Atom type.

Definition at line 169 of file ElementCabana_impl.h.

{
    int size = h_numSFperElem( attype );
    h_t_int h_SFsort( "SortSort", size );
    for ( int i = 0; i < size; ++i )
        h_SFsort( i ) = i;
 
    // naive insertion sort
    int i, j, tmp;
    for ( i = 1; i < size; ++i )
    {
        j = i;
        // explicit condition for sort
        while ( j > 0 &&
                compareSF( SF, attype, h_SFsort( j - 1 ), h_SFsort( j ) ) )
        {
            tmp = h_SFsort( j );
            h_SFsort( j ) = h_SFsort( j - 1 );
            h_SFsort( j - 1 ) = tmp;
            --j;
        }
    }
 
    int tmpindex;
    for ( int i = 0; i < size; ++i )
    {
        SF( attype, i, 13 ) = h_SFsort( i );
        tmpindex = SF( attype, i, 13 );
        SF( attype, tmpindex, 14 ) = i;
    }
 
    return;
}

References compareSF().

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◆ compareSF()

template<class t_SF>

bool nnp::ElementCabana::compareSF	(	t_SF	SF,
		int	attype,
		int	index1,
		int	index2 )

Print symmetry function parameter value information.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	attype	Atom type.
[in]	index1	First symmetry function index.
[in]	index2	Second symmetry function index.

Definition at line 205 of file ElementCabana_impl.h.

{
    if ( SF( attype, index2, 0 ) < SF( attype, index1, 0 ) )
        return true; // ec
    else if ( SF( attype, index2, 0 ) > SF( attype, index1, 0 ) )
        return false;
 
    if ( SF( attype, index2, 1 ) < SF( attype, index1, 1 ) )
        return true; // type
    else if ( SF( attype, index2, 1 ) > SF( attype, index1, 1 ) )
        return false;
 
    if ( SF( attype, index2, 11 ) < SF( attype, index1, 11 ) )
        return true; // cutofftype
    else if ( SF( attype, index2, 11 ) > SF( attype, index1, 11 ) )
        return false;
 
    if ( SF( attype, index2, 12 ) < SF( attype, index1, 12 ) )
        return true; // cutoffalpha
    else if ( SF( attype, index2, 12 ) > SF( attype, index1, 12 ) )
        return false;
 
    if ( SF( attype, index2, 7 ) < SF( attype, index1, 7 ) )
        return true; // rc
    else if ( SF( attype, index2, 7 ) > SF( attype, index1, 7 ) )
        return false;
 
    if ( SF( attype, index2, 4 ) < SF( attype, index1, 4 ) )
        return true; // eta
    else if ( SF( attype, index2, 4 ) > SF( attype, index1, 4 ) )
        return false;
 
    if ( SF( attype, index2, 8 ) < SF( attype, index1, 8 ) )
        return true; // rs
    else if ( SF( attype, index2, 8 ) > SF( attype, index1, 8 ) )
        return false;
 
    if ( SF( attype, index2, 6 ) < SF( attype, index1, 6 ) )
        return true; // zeta
    else if ( SF( attype, index2, 6 ) > SF( attype, index1, 6 ) )
        return false;
 
    if ( SF( attype, index2, 5 ) < SF( attype, index1, 5 ) )
        return true; // lambda
    else if ( SF( attype, index2, 5 ) > SF( attype, index1, 5 ) )
        return false;
 
    if ( SF( attype, index2, 2 ) < SF( attype, index1, 2 ) )
        return true; // e1
    else if ( SF( attype, index2, 2 ) > SF( attype, index1, 2 ) )
        return false;
 
    if ( SF( attype, index2, 3 ) < SF( attype, index1, 3 ) )
        return true; // e2
    else if ( SF( attype, index2, 3 ) > SF( attype, index1, 3 ) )
        return false;
 
    else
        return false;
}

Referenced by sortSymmetryFunctions().

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◆ infoSymmetryFunctionParameters() [1/2]

template<class t_SF, class h_t_int>

std::vector< std::string > nnp::ElementCabana::infoSymmetryFunctionParameters	(	t_SF	SF,
		int	attype,
		h_t_int	h_numSFperElem ) const

Print symmetry function parameter value information.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

◆ infoSymmetryFunctionScaling() [1/2]

template<class t_SF, class t_SFscaling, class h_t_int>

std::vector< std::string > nnp::ElementCabana::infoSymmetryFunctionScaling	(	ScalingType	scalingType,
		t_SF	SF,
		t_SFscaling	SFscaling,
		int	attype,
		h_t_int	h_numSFperElem ) const

Print symmetry function scaling information.

Parameters

[in]	scalingType	Type of scaling see SymmetryFunction::ScalingType.
[in]	SF	Kokkos host View of symmetry functions.
[in]	SFscaling	Kokkos host View of symmetry function scaling.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

◆ setupSymmetryFunctionGroups()

template<class t_SF, class t_SFGmemberlist, class h_t_int>

void nnp::ElementCabana::setupSymmetryFunctionGroups	(	t_SF	SF,
		t_SFGmemberlist	SFGmemberlist,
		int	attype,
		h_t_int	h_numSFperElem,
		h_t_int	h_numSFGperElem,
		int	maxSFperElem )

Set up symmetry function groups.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	SFGmemberlist	Kokkos host View of symmetry function groups.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.
[in]	h_numSFGperElem	Kokkos host View of number of symmetry function groups per element.
[in]	maxSFperElem	Maximum number of symmetry functions per element.

Definition at line 308 of file ElementCabana_impl.h.

{
    int num_group = h_numSFperElem.extent( 0 );
    h_t_int h_numGR( "RadialCounter", num_group );
    h_t_int h_numGA( "AngularCounter", num_group );
    int SFindex;
    for ( int k = 0; k < h_numSFperElem( attype ); ++k )
    {
        bool createNewGroup = true;
        SFindex = SF( attype, k, 13 );
        for ( int l = 0; l < h_numSFGperElem( attype ); ++l )
        {
            if ( ( SF( attype, SFindex, 0 ) ==
                   SF( attype, SFGmemberlist( attype, l, 0 ),
                       0 ) ) && // same ec
                 ( SF( attype, SFindex, 2 ) ==
                   SF( attype, SFGmemberlist( attype, l, 0 ),
                       2 ) ) && // same e1
                 ( SF( attype, SFindex, 3 ) ==
                   SF( attype, SFGmemberlist( attype, l, 0 ),
                       3 ) ) && // same e2
                 ( SF( attype, SFindex, 7 ) ==
                   SF( attype, SFGmemberlist( attype, l, 0 ),
                       7 ) ) && // same rc
                 ( SF( attype, SFindex, 11 ) ==
                   SF( attype, SFGmemberlist( attype, l, 0 ),
                       11 ) ) && // same cutoffType
                 ( SF( attype, SFindex, 12 ) ==
                   SF( attype, SFGmemberlist( attype, l, 0 ),
                       12 ) ) ) // same cutoffAlpha
            {
                createNewGroup = false;
                if ( SF( attype, SFindex, 1 ) == 2 )
                {
                    SFGmemberlist( attype, l, h_numGR( l ) ) = SFindex;
                    h_numGR( l )++;
                    SFGmemberlist( attype, l, maxSFperElem )++;
                    break;
                }
 
                else if ( SF( attype, SFindex, 1 ) == 3 )
                {
                    SFGmemberlist( attype, l, h_numGA( l ) ) = SFindex;
                    h_numGA( l )++;
                    SFGmemberlist( attype, l, maxSFperElem )++;
                    break;
                }
            }
        }
 
        if ( createNewGroup )
        {
            int l = h_numSFGperElem( attype );
            h_numSFGperElem( attype )++;
            if ( SF( attype, SFindex, 1 ) == 2 )
            {
                SFGmemberlist( attype, l, 0 ) = SFindex;
                if ( l >= (int)h_numGR.extent( 0 ) )
                    Kokkos::resize( h_numGR, l+1 );
                h_numGR( l ) = 1;
                SFGmemberlist( attype, l, maxSFperElem )++;
            }
            else if ( SF( attype, SFindex, 1 ) == 3 )
            {
                SFGmemberlist( attype, l, 0 ) = SFindex;
                if ( l >= (int)h_numGA.extent( 0 ) )
                    Kokkos::resize( h_numGA, l+1 );
                h_numGA( l ) = 1;
                SFGmemberlist( attype, l, maxSFperElem )++;
            }
        }
    }
 
    return;
}

◆ infoSymmetryFunctionGroups() [1/2]

template<class t_SF, class t_SFGmemberlist, class h_t_int>

std::vector< std::string > nnp::ElementCabana::infoSymmetryFunctionGroups	(	t_SF	SF,
		t_SFGmemberlist	SFGmemberlist,
		int	attype,
		h_t_int	h_numSFGperElem ) const

Print symmetry function group info.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	SFGmemberlist	Kokkos host View of symmetry function groups.
[in]	attype	Atom type.
[in]	h_numSFGperElem	Kokkos host View of number of symmetry function groups per element.

◆ setCutoffFunction()

template<class t_SF, class h_t_int>

void nnp::ElementCabana::setCutoffFunction	(	CutoffFunction::CutoffType const	cutoffType,
		double const	cutoffAlpha,
		t_SF	SF,
		int	attype,
		h_t_int	h_numSFperElem )

Set cutoff function for all symmetry functions.

Parameters

[in]	cutoffType	Type of cutoff function.
[in]	cutoffAlpha	Cutoff parameter for all functions.
[in]	SF	Kokkos host View of symmetry functions.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

Definition at line 412 of file ElementCabana_impl.h.

{
    for ( int k = 0; k < h_numSFperElem( attype ); ++k )
    {
        SF( attype, k, 10 ) = cutoffType;
        SF( attype, k, 11 ) = cutoffAlpha;
    }
    return;
}

◆ setScaling()

template<class t_SF, class t_SFscaling, class h_t_int>

void nnp::ElementCabana::setScaling	(	ScalingType	scalingType,
		std::vector< std::string > const &	statisticsLine,
		double	minS,
		double	maxS,
		t_SF	SF,
		t_SFscaling	SFscaling,
		int	attype,
		h_t_int	h_numSFperElem ) const

Set scaling of all symmetry functions.

Parameters

[in]	scalingType	Type of scaling, see SymmetryFunction::ScalingType.
[in]	statisticsLine	Vector of strings containing statistics for all symmetry functions.
[in]	minS	Minimum for scaling range.
[in]	maxS	Maximum for scaling range.
[in]	SF	Kokkos host View of symmetry functions.
[in]	SFscaling	Kokkos host View of symmetry function scaling.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

Definition at line 425 of file ElementCabana_impl.h.

{
    int index;
    for ( int k = 0; k < h_numSFperElem( attype ); ++k )
    {
        index = SF( attype, k, 13 );
        setScalingType( scalingType, statisticsLine.at( k ), Smin, Smax,
                        SFscaling, attype, index );
    }
    // TODO: groups
    // for (int k = 0; k < h_numSFperElem(attype); ++k)
    //    setScalingFactors(SF,attype,k);
 
    return;
}

References index, and setScalingType().

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◆ numSymmetryFunctions()

template<class h_t_int>

std::size_t nnp::ElementCabana::numSymmetryFunctions	(	int	attype,
		h_t_int	h_numSFperElem ) const

inline

Get number of symmetry functions.

Parameters

[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

Returns: Number of symmetry functions.

Definition at line 278 of file ElementCabana.h.

{
    return h_numSFperElem( attype );
}

◆ getMinNeighbors() [1/2]

template<class t_SF>

std::size_t nnp::ElementCabana::getMinNeighbors	(	int	attype,
		t_SF	SF,
		int	nSF ) const

Get maximum of required minimum number of neighbors for all symmetry functions for this element.

Parameters

[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.
[in]	nSF	Number of symmetry function for this type.

Returns: Minimum number of neighbors required.

References nnp::Element::atomicEnergyOffset, nnp::Element::atomicNumber, nnp::Element::index, and nnp::Element::symbol.

◆ getMinCutoffRadius()

template<class t_SF, class h_t_int>

double nnp::ElementCabana::getMinCutoffRadius	(	t_SF	SF,
		int	attype,
		h_t_int	h_numSFperElem ) const

Get minimum cutoff radius of all symmetry functions.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

Returns: Minimum cutoff radius.

Definition at line 465 of file ElementCabana_impl.h.

{
    double minCutoffRadius = numeric_limits<double>::max();
 
    for ( int k = 0; k < h_numSFperElem( attype ); ++k )
        minCutoffRadius = min( SF( attype, k, 7 ), minCutoffRadius );
 
    return minCutoffRadius;
}

◆ getMaxCutoffRadius()

template<class t_SF, class h_t_int>

double nnp::ElementCabana::getMaxCutoffRadius	(	t_SF	SF,
		int	attype,
		h_t_int	h_numSFperElem ) const

Get maximum cutoff radius of all symmetry functions.

Parameters

[in]	SF	Kokkos host View of symmetry functions.
[in]	attype	Atom type.
[in]	h_numSFperElem	Kokkos host View of number of symmetry functions per element.

Returns: Maximum cutoff radius.

Definition at line 477 of file ElementCabana_impl.h.

{
    double maxCutoffRadius = 0.0;
 
    for ( int k = 0; k < h_numSFperElem( attype ); ++k )
        maxCutoffRadius = max( SF( attype, k, 7 ), maxCutoffRadius );
 
    return maxCutoffRadius;
}

◆ setScalingType()

template<class t_SFscaling>

void nnp::ElementCabana::setScalingType	(	ScalingType	scalingType,
		std::string	statisticsLine,
		double	Smin,
		double	Smax,
		t_SFscaling	SFscaling,
		int	attype,
		int	k ) const

inline

Symmetry function statistics.

Set scaling type of one symmetry function

Parameters

[in]	scalingType	Type of scaling, see SymmetryFunction::ScalingType.
[in]	statisticsLine	Output string for this symmetry function.
[in]	Smin	Minimum for scaling range.
[in]	Smax	Maximum for scaling range.
[in]	SFscaling	Kokkos host View of symmetry function scaling.
[in]	attype	Atom type.
[in]	k	Symmetry function index.

Definition at line 286 of file ElementCabana.h.

{
    double Gmin, Gmax, Gmean, Gsigma = 0, scalingFactor = 0;
    std::vector<std::string> s = split( reduce( statisticsLine ) );
 
    Gmin = atof( s.at( 2 ).c_str() );
    Gmax = atof( s.at( 3 ).c_str() );
    Gmean = atof( s.at( 4 ).c_str() );
    SFscaling( attype, k, 0 ) = Gmin;
    SFscaling( attype, k, 1 ) = Gmax;
    SFscaling( attype, k, 2 ) = Gmean;
 
    // Older versions may not supply sigma.
    if ( s.size() > 5 )
        Gsigma = atof( s.at( 5 ).c_str() );
    SFscaling( attype, k, 3 ) = Gsigma;
 
    SFscaling( attype, k, 4 ) = Smin;
    SFscaling( attype, k, 5 ) = Smax;
    SFscaling( attype, k, 7 ) = scalingType;
 
    if ( scalingType == ST_NONE )
        scalingFactor = 1.0;
    else if ( scalingType == ST_SCALE )
        scalingFactor = ( Smax - Smin ) / ( Gmax - Gmin );
    else if ( scalingType == ST_CENTER )
        scalingFactor = 1.0;
    else if ( scalingType == ST_SCALECENTER )
        scalingFactor = ( Smax - Smin ) / ( Gmax - Gmin );
    else if ( scalingType == ST_SCALESIGMA )
        scalingFactor = ( Smax - Smin ) / Gsigma;
    SFscaling( attype, k, 6 ) = scalingFactor;
 
    return;
}

References nnp::reduce(), nnp::split(), ST_CENTER, ST_NONE, ST_SCALE, ST_SCALECENTER, and ST_SCALESIGMA.

Referenced by setScaling().

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◆ scalingLine()

template<class t_SFscaling>

std::string nnp::ElementCabana::scalingLine	(	ScalingType	scalingType,
		t_SFscaling	SFscaling,
		int	attype,
		int	k ) const

inline

Print scaling for one symmetry function.

Parameters

[in]	scalingType	Type of scaling, see SymmetryFunction::ScalingType.
[in]	SFscaling	Kokkos host View of symmetry function scaling.
[in]	attype	Atom type.
[in]	k	Symmetry function index.

Definition at line 327 of file ElementCabana.h.

{
    return strpr( "%4zu %9.2E %9.2E %9.2E %9.2E %9.2E %5.2f %5.2f %d\n",
                  k + 1, SFscaling( attype, k, 0 ),
                  SFscaling( attype, k, 1 ), SFscaling( attype, k, 2 ),
                  SFscaling( attype, k, 3 ), SFscaling( attype, k, 6 ),
                  SFscaling( attype, k, 4 ), SFscaling( attype, k, 5 ),
                  scalingType );
}

References nnp::strpr().

Referenced by infoSymmetryFunctionScaling().

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◆ unscale()

template<class t_SFscaling>

double nnp::ElementCabana::unscale	(	int	attype,
		double	value,
		int	k,
		t_SFscaling	SFscaling )

inline

Unscale one symmetry function.

Parameters

[in]	attype	Atom type.
[in]	value	Unscaled symmetry function value.
[in]	k	Symmetry function index.
[in]	SFscaling	Kokkos host View of symmetry function scaling.

Definition at line 340 of file ElementCabana.h.

{
    double scalingType = SFscaling( attype, k, 7 );
    double scalingFactor = SFscaling( attype, k, 6 );
    double Gmin = SFscaling( attype, k, 0 );
    // double Gmax = SFscaling(attype,k,1);
    double Gmean = SFscaling( attype, k, 2 );
    // double Gsigma = SFscaling(attype,k,3);
    double Smin = SFscaling( attype, k, 4 );
    // double Smax = SFscaling(attype,k,5);
 
    if ( scalingType == 0.0 )
    {
        return value;
    }
    else if ( scalingType == 1.0 )
    {
        return ( value - Smin ) / scalingFactor + Gmin;
    }
    else if ( scalingType == 2.0 )
    {
        return value + Gmean;
    }
    else if ( scalingType == 3.0 )
    {
        return ( value - Smin ) / scalingFactor + Gmean;
    }
    else if ( scalingType == 4.0 )
    {
        return ( value - Smin ) / scalingFactor + Gmean;
    }
    else
    {
        return 0.0;
    }
}

◆ infoSymmetryFunctionParameters() [2/2]

template<class t_SF, class h_t_int>

vector< string > nnp::ElementCabana::infoSymmetryFunctionParameters	(	t_SF	SF,
		int	attype,
		h_t_int	h_numSFperElem ) const

Definition at line 268 of file ElementCabana_impl.h.

{
    vector<string> v;
    string pushstring = "";
    int index;
    float writestring;
    for ( int i = 0; i < h_numSFperElem( attype ); ++i )
    {
        index = SF( attype, i, 13 );
        // TODO: improve function
        for ( int j = 1; j < 12; ++j )
        {
            writestring = SF( attype, index, j );
            pushstring += to_string( writestring ) + " ";
        }
        pushstring += "\n";
    }
    v.push_back( pushstring );
 
    return v;
}

References index.

◆ infoSymmetryFunctionScaling() [2/2]

template<class t_SF, class t_SFscaling, class h_t_int>

vector< string > nnp::ElementCabana::infoSymmetryFunctionScaling	(	ScalingType	scalingType,
		t_SF	SF,
		t_SFscaling	SFscaling,
		int	attype,
		h_t_int	h_numSFperElem ) const

Definition at line 293 of file ElementCabana_impl.h.

{
    vector<string> v;
    int index;
    for ( int k = 0; k < h_numSFperElem( attype ); ++k )
    {
        index = SF( attype, k, 13 );
        v.push_back( scalingLine( scalingType, SFscaling, attype, index ) );
    }
    return v;
}

References index, and scalingLine().

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◆ infoSymmetryFunctionGroups() [2/2]

template<class t_SF, class t_SFGmemberlist, class h_t_int>

vector< string > nnp::ElementCabana::infoSymmetryFunctionGroups	(	t_SF	SF,
		t_SFGmemberlist	SFGmemberlist,
		int	attype,
		h_t_int	h_numSFGperElem ) const

Definition at line 390 of file ElementCabana_impl.h.

{
    vector<string> v;
    string pushstring = "";
    for ( int groupIndex = 0; groupIndex < h_numSFGperElem( attype );
          ++groupIndex )
    {
        // TODO: improve function
        for ( int j = 0; j < 8; ++j )
            pushstring +=
                to_string(
                    SF( attype, SFGmemberlist( attype, groupIndex, 0 ), j ) ) +
                " ";
        pushstring += "\n";
    }
    v.push_back( pushstring );
 
    return v;
}

◆ getMinNeighbors() [2/2]

template<class t_SF>

size_t nnp::ElementCabana::getMinNeighbors	(	int	attype,
		t_SF	SF,
		int	nSF ) const

Definition at line 445 of file ElementCabana_impl.h.

{
    // get max number of minNeighbors
    size_t global_minNeighbors = 0;
    size_t minNeighbors = 0;
    int SFtype;
    for ( int k = 0; k < nSF; ++k )
    {
        SFtype = SF( attype, k, 1 );
        if ( SFtype == 2 )
            minNeighbors = 1;
        else if ( SFtype == 3 )
            minNeighbors = 2;
        global_minNeighbors = max( minNeighbors, global_minNeighbors );
    }
 
    return global_minNeighbors;
}

Member Data Documentation

◆ index

std::size_t nnp::Element::index

private

Global index of this element.

Definition at line 255 of file Element.h.

Referenced by ElementCabana(), infoSymmetryFunctionParameters(), infoSymmetryFunctionScaling(), and setScaling().

◆ atomicNumber

std::size_t nnp::Element::atomicNumber

private

Atomic number of this element.

Definition at line 257 of file Element.h.

◆ atomicEnergyOffset

double nnp::Element::atomicEnergyOffset

private

Offset energy for every atom of this element.

Definition at line 259 of file Element.h.

Referenced by ElementCabana().

◆ symbol

std::string nnp::Element::symbol

private

Element symbol.

Definition at line 265 of file Element.h.

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

/home/runner/work/n2p2/n2p2/src/libnnpif/CabanaMD/ElementCabana.h
/home/runner/work/n2p2/n2p2/src/libnnpif/CabanaMD/ElementCabana_impl.h

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ElementCabana()

◆ ~ElementCabana()

Member Function Documentation

◆ addSymmetryFunction()

◆ changeLengthUnitSymmetryFunctions()

◆ sortSymmetryFunctions()

◆ compareSF()

◆ infoSymmetryFunctionParameters() [1/2]

◆ infoSymmetryFunctionScaling() [1/2]

◆ setupSymmetryFunctionGroups()

◆ infoSymmetryFunctionGroups() [1/2]

◆ setCutoffFunction()

◆ setScaling()

◆ numSymmetryFunctions()

◆ getMinNeighbors() [1/2]

◆ getMinCutoffRadius()

◆ getMaxCutoffRadius()

◆ setScalingType()

◆ scalingLine()

◆ unscale()

◆ infoSymmetryFunctionParameters() [2/2]

◆ infoSymmetryFunctionScaling() [2/2]

◆ infoSymmetryFunctionGroups() [2/2]

◆ getMinNeighbors() [2/2]

Member Data Documentation

◆ index

◆ atomicNumber

◆ atomicEnergyOffset

◆ symbol