#include <SetupAnalysis.h>

Inheritance diagram for nnp::SetupAnalysis:

Collaboration diagram for nnp::SetupAnalysis:

Public Member Functions
void	writeSymmetryFunctionShape (std::size_t numPoints, std::string const fileNameFormat="sf.%03zu.%04zu.out")
	Write radial and angular part of symmetry functions to file. More...

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 (std::string const &nnpDir="", bool skipNormalize=false, bool initialHardness=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...

void	setupCutoffMatrix ()
	Setup matrix storing all symmetry function cut-offs for each element. More...

virtual void	setupNeuralNetwork ()
	Set up neural networks for all elements. More...

virtual void	setupNeuralNetworkWeights (std::map< std::string, std::string > fileNameFormats=std::map< std::string, std::string >())
	Set up neural network weights from files with given name format. More...

virtual void	setupNeuralNetworkWeights (std::string directoryPrefix, std::map< std::string, std::string > fileNameFormats=std::map< std::string, std::string >())
	Set up neural network weights from files with given name format. More...

virtual void	setupElectrostatics (bool initialHardness=false, std::string directoryPrefix="", std::string fileNameFormat="hardness.%03zu.data")
	Set up electrostatics related stuff (hardness, screening, ...). 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, std::string id="")
	Calculate atomic neural networks for all atoms in given structure. More...

void	chargeEquilibration (Structure &structure, bool const derivativesElec)
	Perform global charge equilibration method. 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	evaluateNNP (Structure &structure, bool useForces=true, bool useDEdG=true)
	Evaluate neural network potential (includes total energy, optionally forces and in some cases charges. 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...

void	logEwaldCutoffs ()
	Logs Ewald params whenever they change. 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	getConvCharge () const
	Getter for Mode::convCharge. 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...

Additional Inherited Members
Public Types inherited from nnp::Mode
enum class	NNPType { HDNNP_2G = 2 , HDNNP_4G = 4 , HDNNP_Q = 10 }

Public Attributes inherited from nnp::Mode
ElementMap	elementMap
	Global element map, populated by setupElementMap(). More...

Log	log
	Global log file. More...

Protected Member Functions inherited from nnp::Mode
void	readNeuralNetworkWeights (std::string const &id, 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

std::size_t	numElements

std::vector< std::size_t >	minNeighbors

std::vector< double >	minCutoffRadius

double	maxCutoffRadius

double	cutoffAlpha

double	meanEnergy

double	convEnergy

double	convLength

double	convCharge

double	fourPiEps

EwaldSetup	ewaldSetup

settings::Settings	settings

SymFnc::ScalingType	scalingType

CutoffFunction::CutoffType	cutoffType

ScreeningFunction	screeningFunction

std::vector< Element >	elements

std::vector< std::string >	nnk

std::map< std::string, NNSetup >	nns

std::vector< std::vector< double > >	cutoffs
	Matrix storing all symmetry function cut-offs for all elements. More...

ErfcBuf	erfcBuf

Detailed Description

Definition at line 26 of file SetupAnalysis.h.

Member Function Documentation

◆ writeSymmetryFunctionShape()

void SetupAnalysis::writeSymmetryFunctionShape	(	std::size_t	numPoints,
		std::string const	fileNameFormat = `"sf.%03zu.%04zu.out"`
	)

Write radial and angular part of symmetry functions to file.

Parameters

[in]	numPoints	Number of symmetry function points to plot.
[in]	fileNameFormat	File name with place holder for element and symmetry function number.

Definition at line 24 of file SetupAnalysis.cpp.

{
    log << "\n";
    log << "*** ANALYSIS: SYMMETRY FUNCTION SHAPE ***"
           "**************************************\n";
    log << "\n";
 
    log << strpr("Symmetry function file name format: %s\n",
                 fileNameFormat.c_str());
    log << strpr("Number of points                  : %zu\n", numPoints);
    double dr = getMaxCutoffRadius() / numPoints;
    log << strpr("Distance step                     : %f\n", dr);
    double da = M_PI / numPoints;
    log << strpr("Angle step (radians)              : %f\n", da);
 
    for (size_t i = 0; i < numElements; ++i)
    {
        Element const& e = elements.at(i);
        for (size_t j = 0; j < e.numSymmetryFunctions(); ++j)
        {
            SymFnc const& s = e.getSymmetryFunction(j);
            ofstream file;
            file.open(strpr(fileNameFormat.c_str(),
                            e.getAtomicNumber(),
                            j + 1).c_str());
            vector<string> info = e.infoSymmetryFunction(s.getIndex());
            for (vector<string>::const_iterator it = info.begin();
                 it != info.end(); ++it)
            {
                file << strpr("#SFINFO %s\n", it->c_str());
            }
 
            // File header.
            vector<string> title;
            vector<string> colName;
            vector<string> colInfo;
            vector<size_t> colSize;
            title.push_back("Symmetry function shape.");
            colSize.push_back(16);
            colName.push_back("distance");
            colInfo.push_back("Distance from center.");
            colSize.push_back(16);
            colName.push_back("sf_radial");
            colInfo.push_back("Radial part of symmetry function at given "
                              "distance.");
            colSize.push_back(16);
            colName.push_back("angle");
            colInfo.push_back("Angle in degrees.");
            colSize.push_back(16);
            colName.push_back("sf_angular");
            colInfo.push_back("Angular part of symmetry function at given "
                              "angle.");
            appendLinesToFile(file,
                              createFileHeader(title,
                                               colSize,
                                               colName,
                                               colInfo));
 
            for (size_t k = 0; k < numPoints + 1; ++k)
            {
                file << strpr("%16.8E %16.8E %16.8E %16.8E\n",
                              k * dr,
                              s.calculateRadialPart(k * dr),
                              k * da,
                              s.calculateAngularPart(k * da));
            }
            file.close();
        }
    }
 
    log << "*****************************************"
           "**************************************\n";
 
    return;
}

References nnp::appendLinesToFile(), nnp::SymFnc::calculateAngularPart(), nnp::SymFnc::calculateRadialPart(), nnp::createFileHeader(), nnp::Mode::elements, nnp::Element::getAtomicNumber(), nnp::SymFnc::getIndex(), nnp::Mode::getMaxCutoffRadius(), nnp::Element::getSymmetryFunction(), nnp::Element::infoSymmetryFunction(), nnp::Mode::log, nnp::Mode::numElements, nnp::Element::numSymmetryFunctions(), and nnp::strpr().

Referenced by main().

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ writeSymmetryFunctionShape()