nnp::Prediction Class Reference

#include <Prediction.h>

Inheritance diagram for nnp::Prediction:

Collaboration diagram for nnp::Prediction:

Public Member Functions
	Prediction ()
void	readStructureFromFile (std::string const &fileName="input.data")
void	setup ()
void	predict ()
Public Member Functions inherited from nnp::Mode
	Mode ()
void	initialize ()
	Write welcome message with version information. More...
void	loadSettingsFile (std::string const &fileName="input.nn")
	Open settings file and load all keywords into memory. More...
void	setupGeneric (bool skipNormalize=false)
	Combine multiple setup routines and provide a basic NNP setup. More...
void	setupNormalization (bool standalone=true)
	Set up normalization. More...
virtual void	setupElementMap ()
	Set up the element map. More...
virtual void	setupElements ()
	Set up all Element instances. More...
void	setupCutoff ()
	Set up cutoff function for all symmetry functions. More...
virtual void	setupSymmetryFunctions ()
	Set up all symmetry functions. More...
void	setupSymmetryFunctionScalingNone ()
	Set up "empy" symmetry function scaling. More...
virtual void	setupSymmetryFunctionScaling (std::string const &fileName="scaling.data")
	Set up symmetry function scaling from file. More...
virtual void	setupSymmetryFunctionGroups ()
	Set up symmetry function groups. More...
virtual void	setupSymmetryFunctionCache (bool verbose=false)
	Set up symmetry function cache. More...
void	setupSymmetryFunctionMemory (bool verbose=false)
	Extract required memory dimensions for symmetry function derivatives. More...
void	setupSymmetryFunctionStatistics (bool collectStatistics, bool collectExtrapolationWarnings, bool writeExtrapolationWarnings, bool stopOnExtrapolationWarnings)
	Set up symmetry function statistics collection. More...
virtual void	setupNeuralNetwork ()
	Set up neural networks for all elements. More...
virtual void	setupNeuralNetworkWeights (std::string const &fileNameFormatShort="weights.%03zu.data", std::string const &fileNameFormatCharge="weightse.%03zu.data")
	Set up neural network weights from files. More...
void	calculateSymmetryFunctions (Structure &structure, bool const derivatives)
	Calculate all symmetry functions for all atoms in given structure. More...
void	calculateSymmetryFunctionGroups (Structure &structure, bool const derivatives)
	Calculate all symmetry function groups for all atoms in given structure. More...
void	calculateAtomicNeuralNetworks (Structure &structure, bool const derivatives)
	Calculate a single atomic neural network for a given atom and nn type. More...
void	calculateEnergy (Structure &structure) const
	Calculate potential energy for a given structure. More...
void	calculateCharge (Structure &structure) const
	Calculate total charge for a given structure. More...
void	calculateForces (Structure &structure) const
	Calculate forces for all atoms in given structure. More...
void	addEnergyOffset (Structure &structure, bool ref=true)
	Add atomic energy offsets to reference energy. More...
void	removeEnergyOffset (Structure &structure, bool ref=true)
	Remove atomic energy offsets from reference energy. More...
double	getEnergyOffset (Structure const &structure) const
	Get atomic energy offset for given structure. More...
double	getEnergyWithOffset (Structure const &structure, bool ref=true) const
	Add atomic energy offsets and return energy. More...
double	normalized (std::string const &property, double value) const
	Apply normalization to given property. More...
double	normalizedEnergy (Structure const &structure, bool ref=true) const
	Apply normalization to given energy of structure. More...
double	physical (std::string const &property, double value) const
	Undo normalization for a given property. More...
double	physicalEnergy (Structure const &structure, bool ref=true) const
	Undo normalization for a given energy of structure. More...
void	convertToNormalizedUnits (Structure &structure) const
	Convert one structure to normalized units. More...
void	convertToPhysicalUnits (Structure &structure) const
	Convert one structure to physical units. More...
std::size_t	getNumExtrapolationWarnings () const
	Count total number of extrapolation warnings encountered for all elements and symmetry functions. More...
void	resetExtrapolationWarnings ()
	Erase all extrapolation warnings and reset counters. More...
NNPType	getNnpType () const
	Getter for Mode::nnpType. More...
double	getMeanEnergy () const
	Getter for Mode::meanEnergy. More...
double	getConvEnergy () const
	Getter for Mode::convEnergy. More...
double	getConvLength () const
	Getter for Mode::convLength. More...
double	getMaxCutoffRadius () const
	Getter for Mode::maxCutoffRadius. More...
std::size_t	getNumElements () const
	Getter for Mode::numElements. More...
std::vector< std::size_t >	getNumSymmetryFunctions () const
	Get number of symmetry functions per element. More...
bool	useNormalization () const
	Check if normalization is enabled. More...
bool	settingsKeywordExists (std::string const &keyword) const
	Check if keyword was found in settings file. More...
std::string	settingsGetValue (std::string const &keyword) const
	Get value for given keyword in Settings instance. More...
std::vector< std::size_t >	pruneSymmetryFunctionsRange (double threshold)
	Prune symmetry functions according to their range and write settings file. More...
std::vector< std::size_t >	pruneSymmetryFunctionsSensitivity (double threshold, std::vector< std::vector< double > > sensitivity)
	Prune symmetry functions with sensitivity analysis data. More...
void	writePrunedSettingsFile (std::vector< std::size_t > prune, std::string fileName="output.nn") const
	Copy settings file but comment out lines provided. More...
void	writeSettingsFile (std::ofstream *const &file) const
	Write complete settings file. More...

Public Attributes
std::string	fileNameSettings
std::string	fileNameScaling
std::string	formatWeightsFilesShort
std::string	formatWeightsFilesCharge
Structure	structure
Public Attributes inherited from nnp::Mode
ElementMap	elementMap
	Global element map, populated by setupElementMap(). More...
Log	log
	Global log file. More...

Additional Inherited Members
Public Types inherited from nnp::Mode
enum class	NNPType { SHORT_ONLY , SHORT_CHARGE_NN }
Protected Member Functions inherited from nnp::Mode
void	readNeuralNetworkWeights (std::string const &type, std::string const &fileName)
	Read in weights for a specific type of neural network. More...
Protected Attributes inherited from nnp::Mode
NNPType	nnpType
bool	normalize
bool	checkExtrapolationWarnings
bool	useChargeNN
std::size_t	numElements
std::vector< std::size_t >	minNeighbors
std::vector< double >	minCutoffRadius
double	maxCutoffRadius
double	cutoffAlpha
double	meanEnergy
double	convEnergy
double	convLength
Settings	settings
SymFnc::ScalingType	scalingType
CutoffFunction::CutoffType	cutoffType
std::vector< Element >	elements

Detailed Description

Definition at line 27 of file Prediction.h.

Constructor & Destructor Documentation

Prediction()

Prediction::Prediction

(

)

Definition at line 25 of file Prediction.cpp.

                       : Mode(),
                           fileNameSettings        ("input.nn"          ),
                           fileNameScaling         ("scaling.data"      ),
                           formatWeightsFilesShort ("weights.%03zu.data" ),
                           formatWeightsFilesCharge("weightse.%03zu.data")
{
}

Member Function Documentation

readStructureFromFile()

void Prediction::readStructureFromFile

(

std::string const &

fileName = "input.data"

)

Definition at line 44 of file Prediction.cpp.

{
    ifstream file;
    file.open(fileName.c_str());
    structure.reset();
    structure.setElementMap(elementMap);
    structure.readFromFile(fileName);
    removeEnergyOffset(structure);
    if (normalize)
    {
        structure.toNormalizedUnits(meanEnergy, convEnergy, convLength);
    }
    file.close();
 
    return;
}

References nnp::Mode::convEnergy, nnp::Mode::convLength, nnp::Mode::elementMap, nnp::Mode::meanEnergy, nnp::Mode::normalize, nnp::Structure::readFromFile(), nnp::Mode::removeEnergyOffset(), nnp::Structure::reset(), nnp::Structure::setElementMap(), structure, and nnp::Structure::toNormalizedUnits().

Referenced by main().

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setup()

void Prediction::setup

(

)

Definition at line 33 of file Prediction.cpp.

{
    initialize();
    loadSettingsFile(fileNameSettings);
    setupGeneric();
    setupSymmetryFunctionScaling(fileNameScaling);
    setupNeuralNetworkWeights(formatWeightsFilesShort,
                              formatWeightsFilesCharge);
    setupSymmetryFunctionStatistics(false, false, true, false);
}

References fileNameScaling, fileNameSettings, formatWeightsFilesCharge, formatWeightsFilesShort, nnp::Mode::initialize(), nnp::Mode::loadSettingsFile(), nnp::Mode::setupGeneric(), nnp::Mode::setupNeuralNetworkWeights(), nnp::Mode::setupSymmetryFunctionScaling(), and nnp::Mode::setupSymmetryFunctionStatistics().

Referenced by main().

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predict()

void Prediction::predict

(

)

Definition at line 61 of file Prediction.cpp.

{
    structure.calculateNeighborList(maxCutoffRadius);
#ifdef N2P2_NO_SF_GROUPS
    calculateSymmetryFunctions(structure, true);
#else
    calculateSymmetryFunctionGroups(structure, true);
#endif
    calculateAtomicNeuralNetworks(structure, true);
    calculateEnergy(structure);
    if (nnpType == NNPType::SHORT_CHARGE_NN) calculateCharge(structure);
    calculateForces(structure);
    if (normalize)
    {
        structure.toPhysicalUnits(meanEnergy, convEnergy, convLength);
    }
    addEnergyOffset(structure, false);
    addEnergyOffset(structure, true);
 
    return;
}

References nnp::Mode::addEnergyOffset(), nnp::Mode::calculateAtomicNeuralNetworks(), nnp::Mode::calculateCharge(), nnp::Mode::calculateEnergy(), nnp::Mode::calculateForces(), nnp::Structure::calculateNeighborList(), nnp::Mode::calculateSymmetryFunctionGroups(), nnp::Mode::calculateSymmetryFunctions(), nnp::Mode::convEnergy, nnp::Mode::convLength, nnp::Mode::maxCutoffRadius, nnp::Mode::meanEnergy, nnp::Mode::nnpType, nnp::Mode::normalize, nnp::Mode::SHORT_CHARGE_NN, structure, and nnp::Structure::toPhysicalUnits().

Referenced by main().

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Member Data Documentation

fileNameSettings

std::string nnp::Prediction::fileNameSettings

Definition at line 35 of file Prediction.h.

Referenced by setup().

fileNameScaling

std::string nnp::Prediction::fileNameScaling

Definition at line 36 of file Prediction.h.

Referenced by setup().

formatWeightsFilesShort

std::string nnp::Prediction::formatWeightsFilesShort

Definition at line 37 of file Prediction.h.

Referenced by setup().

formatWeightsFilesCharge

std::string nnp::Prediction::formatWeightsFilesCharge

Definition at line 38 of file Prediction.h.

Referenced by setup().

structure

Structure nnp::Prediction::structure

Definition at line 39 of file Prediction.h.

Referenced by main(), predict(), and readStructureFromFile().

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

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