Functions
int	makePath (const std::string &path)
	Inline function for creating the desired directory (and parents).
int	writeRings (const std::vector< std::vector< int > > &rings, std::string filename="rings.dat")
	Function for printing out ring info, when there is no volume slice.
int	writePrismNum (std::string path, const std::vector< int > &nPrisms, const std::vector< int > &nDefPrisms, const std::vector< double > &heightPercent, int maxDepth, int currentFrame, int firstFrame)
int	writeRingNum (std::string path, int currentFrame, const std::vector< int > &nRings, const std::vector< double > &coverageAreaXY, const std::vector< double > &coverageAreaXZ, const std::vector< double > &coverageAreaYZ, int maxDepth, int firstFrame)
int	writeRingNumBulk (std::string path, int currentFrame, const std::vector< int > &nRings, int maxDepth, int firstFrame)
int	printRDF (std::string fileName, std::vector< double > &rdfValues, double binwidth, int nbin)
	Function for printing out the RDF, given the filename.
int	writeTopoBulkData (std::string path, int currentFrame, int numHC, int numDDC, int mixedRings, int basalRings, int prismaticRings, int firstFrame)
int	writePrisms (std::vector< int > &basal1, std::vector< int > &basal2, int prismNum, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
	Function for writing out each prism.
int	writeClusterStats (std::string path, int currentFrame, int largestCluster, int numOfClusters, int smallestCluster, double avgClusterSize, int firstFrame)
	Function for writing out cluster statistics.
int	writeMoleculeIDsInSlice (std::string path, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
int	writeMoleculeIDsExpressionSelectOVITO (std::string path, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
int	writeLAMMPSdata (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, std::vector< std::vector< int > > rings, std::vector< std::vector< int > > bonds, std::string filename="system-rings.data")
	Write a data file for rings.
int	writeLAMMPSdumpINT (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< double > &rmsdPerAtom, const std::vector< int > &atomTypes, int maxDepth, std::string path)
	Write out a LAMMPS dump file containing the RMSD per atom.
int	writeLAMMPSdumpSlice (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, std::string path)
int	writeLAMMPSdumpCages (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< double > &rmsdPerAtom, const std::vector< int > &atomTypes, std::string path, int firstFrame)
	Write out a LAMMPS dump file containing the RMSD per atom for bulk ice.
int	writeLAMMPSdataAllPrisms (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, const std::vector< int > &atomTypes, int maxDepth, std::string path, bool doShapeMatching=false)
	Write a data file for prisms of every type.
int	writeLAMMPSdataAllRings (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, const std::vector< int > &atomTypes, int maxDepth, std::string path, bool isMonolayer=true)
	Write a data file for rings of every type for a monolayer.
int	writeLAMMPSdataTopoBulk (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, const std::vector< cage::iceType > &atomTypes, std::string path, bool bondsBetweenDummy=false)
int	writeLAMMPSdataPrisms (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &rings, bool useBondFile, std::string bondFile, const std::vector< int > &listPrism, const std::vector< std::vector< int > > &nList, std::string filename="system-prisms.data")
	Write a data file for prisms of a single type.
int	writeLAMMPSdataCages (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &rings, std::vector< cage::Cage > &cageList, cage::cageType type, int numCages, std::string filename="system-cages.data")
int	writeAllCages (std::string path, std::vector< cage::Cage > &cageList, const std::vector< std::vector< int > > &rings, const std::vector< std::vector< int > > &nList, const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int currentFrame)
int	writeEachCage (const std::vector< int > &currentCage, int cageNum, cage::cageType type, const std::vector< std::vector< int > > &rings, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
	Write out a particular cage to a file.
int	writeBasalRingsHex (const std::vector< int > &currentCage, int cageNum, const std::vector< std::vector< int > > &nList, const std::vector< std::vector< int > > &rings)
	Write out the basal rings of a particular Hexagonal cage.
int	writeBasalRingsPrism (std::vector< int > &basal1, std::vector< int > &basal2, int prismNum, const std::vector< std::vector< int > > &nList, const molSys::PointCloud< molSys::Point< double >, double > &yCloud, bool isDeformed)
	Write out the basal rings for a particular prism.
int	writeDump (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, std::string path, std::string outFile)
	Generic function for writing out to a dump file.
int	writeHisto (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, const std::vector< double > &avgQ6)
int	writeCluster (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, std::string fileName="cluster.txt", bool isSlice=false, int largestIceCluster=0)
	Function for printing the largest ice cluster.
int	writeXYZcluster (std::string path, const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< int > &atoms, int clusterID, cage::cageType type)
	Function for writing out the XYZ files for each cluster.

Function Documentation

◆ makePath()

int sout::makePath ( const std::string & path )

inlinenodiscard

Inline function for creating the desired directory (and parents).

Uses std::filesystem for portability.

Parameters

[in] path The path of the directory

Returns: 0 on success, 1 on failure

Definition at line 36 of file seams_output.hpp.

                                                         {
  std::error_code ec;
  if (fs::is_directory(path)) {
    return 0;
  }
  if (fs::create_directories(path, ec)) {
    return 0;
  }
  return ec ? 1 : 0;
}

◆ printRDF()

int sout::printRDF	(	std::string	fileName,
		std::vector< double > &	rdfValues,
		double	binwidth,
		int	nbin )

nodiscard

Function for printing out the RDF, given the filename.

◆ writeAllCages()

int sout::writeAllCages	(	std::string	path,
		std::vector< cage::Cage > &	cageList,
		const std::vector< std::vector< int > > &	rings,
		const std::vector< std::vector< int > > &	nList,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		int	currentFrame )

nodiscard

Write out all cages of all types into a folder called cages inside the output directory

◆ writeBasalRingsHex()

int sout::writeBasalRingsHex	(	const std::vector< int > &	currentCage,
		int	cageNum,
		const std::vector< std::vector< int > > &	nList,
		const std::vector< std::vector< int > > &	rings )

nodiscard

Write out the basal rings of a particular Hexagonal cage.

◆ writeBasalRingsPrism()

int sout::writeBasalRingsPrism	(	std::vector< int > &	basal1,
		std::vector< int > &	basal2,
		int	prismNum,
		const std::vector< std::vector< int > > &	nList,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		bool	isDeformed )

nodiscard

Write out the basal rings for a particular prism.

◆ writeCluster()

int sout::writeCluster	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		std::string	fileName = "cluster.txt",
		bool	isSlice = false,
		int	largestIceCluster = 0 )

nodiscard

Function for printing the largest ice cluster.

◆ writeClusterStats()

int sout::writeClusterStats	(	std::string	path,
		int	currentFrame,
		int	largestCluster,
		int	numOfClusters,
		int	smallestCluster,
		double	avgClusterSize,
		int	firstFrame )

nodiscard

Function for writing out cluster statistics.

◆ writeDump()

int sout::writeDump	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		std::string	path,
		std::string	outFile )

nodiscard

Generic function for writing out to a dump file.

◆ writeEachCage()

int sout::writeEachCage	(	const std::vector< int > &	currentCage,
		int	cageNum,
		cage::cageType	type,
		const std::vector< std::vector< int > > &	rings,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud )

nodiscard

Write out a particular cage to a file.

◆ writeHisto()

int sout::writeHisto	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	nList,
		const std::vector< double > &	avgQ6 )

nodiscard

Function for printing out Q6, Cij and averaged Q3 values as single columns to text files The file names are cij, q6, q3

◆ writeLAMMPSdata()

int sout::writeLAMMPSdata	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		std::vector< std::vector< int > >	rings,
		std::vector< std::vector< int > >	bonds,
		std::string	filename = "system-rings.data" )

nodiscard

Write a data file for rings.

◆ writeLAMMPSdataAllPrisms()

int sout::writeLAMMPSdataAllPrisms	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	nList,
		const std::vector< int > &	atomTypes,
		int	maxDepth,
		std::string	path,
		bool	doShapeMatching = false )

nodiscard

Write a data file for prisms of every type.

◆ writeLAMMPSdataAllRings()

int sout::writeLAMMPSdataAllRings	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	nList,
		const std::vector< int > &	atomTypes,
		int	maxDepth,
		std::string	path,
		bool	isMonolayer = true )

nodiscard

Write a data file for rings of every type for a monolayer.

◆ writeLAMMPSdataCages()

int sout::writeLAMMPSdataCages	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	rings,
		std::vector< cage::Cage > &	cageList,
		cage::cageType	type,
		int	numCages,
		std::string	filename = "system-cages.data" )

nodiscard

Write out a lammps data file for DDCs or HCs, assuming that there is no slice

◆ writeLAMMPSdataPrisms()

int sout::writeLAMMPSdataPrisms	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	rings,
		bool	useBondFile,
		std::string	bondFile,
		const std::vector< int > &	listPrism,
		const std::vector< std::vector< int > > &	nList,
		std::string	filename = "system-prisms.data" )

nodiscard

Write a data file for prisms of a single type.

◆ writeLAMMPSdataTopoBulk()

int sout::writeLAMMPSdataTopoBulk	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	nList,
		const std::vector< cage::iceType > &	atomTypes,
		std::string	path,
		bool	bondsBetweenDummy = false )

nodiscard

Write a data file for a particular frame, writing out topological bulk ice structures (DDCs/HCs)

◆ writeLAMMPSdumpCages()

int sout::writeLAMMPSdumpCages	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< double > &	rmsdPerAtom,
		const std::vector< int > &	atomTypes,
		std::string	path,
		int	firstFrame )

nodiscard

Write out a LAMMPS dump file containing the RMSD per atom for bulk ice.

◆ writeLAMMPSdumpINT()

int sout::writeLAMMPSdumpINT	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< double > &	rmsdPerAtom,
		const std::vector< int > &	atomTypes,
		int	maxDepth,
		std::string	path )

nodiscard

Write out a LAMMPS dump file containing the RMSD per atom.

◆ writeLAMMPSdumpSlice()

int sout::writeLAMMPSdumpSlice	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		std::string	path )

nodiscard

Write out a LAMMPS dump file containing the inSlice value for each atom for a user-defined slice

◆ writeMoleculeIDsExpressionSelectOVITO()

int sout::writeMoleculeIDsExpressionSelectOVITO	(	std::string	path,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud )

nodiscard

Function for printing out the molecule IDs present in the slice (compatible with the OVITO Expression Select command

◆ writeMoleculeIDsInSlice()

int sout::writeMoleculeIDsInSlice	(	std::string	path,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud )

nodiscard

Function for printing out the molecule IDs present in the slice (compatible with the LAMMPS group command

◆ writePrismNum()

int sout::writePrismNum	(	std::string	path,
		const std::vector< int > &	nPrisms,
		const std::vector< int > &	nDefPrisms,
		const std::vector< double > &	heightPercent,
		int	maxDepth,
		int	currentFrame,
		int	firstFrame )

nodiscard

Function for printing out the number of prism blocks, with or without slices. Be careful when using slices!

◆ writePrisms()

int sout::writePrisms	(	std::vector< int > &	basal1,
		std::vector< int > &	basal2,
		int	prismNum,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud )

nodiscard

Function for writing out each prism.

◆ writeRingNum()

int sout::writeRingNum	(	std::string	path,
		int	currentFrame,
		const std::vector< int > &	nRings,
		const std::vector< double > &	coverageAreaXY,
		const std::vector< double > &	coverageAreaXZ,
		const std::vector< double > &	coverageAreaYZ,
		int	maxDepth,
		int	firstFrame )

nodiscard

Function for printing out the coverage area and the number of rings of each type

◆ writeRingNumBulk()

int sout::writeRingNumBulk	(	std::string	path,
		int	currentFrame,
		const std::vector< int > &	nRings,
		int	maxDepth,
		int	firstFrame )

nodiscard

Function for printing out the number of rings of each type in a bulk system

◆ writeRings()

int sout::writeRings	(	const std::vector< std::vector< int > > &	rings,
		std::string	filename = "rings.dat" )

nodiscard

Function for printing out ring info, when there is no volume slice.

◆ writeTopoBulkData()

int sout::writeTopoBulkData	(	std::string	path,
		int	currentFrame,
		int	numHC,
		int	numDDC,
		int	mixedRings,
		int	basalRings,
		int	prismaticRings,
		int	firstFrame )

nodiscard

Function for printing out the number of DDCs, HCs, mixed rings, basal and prismatic rings

◆ writeXYZcluster()

int sout::writeXYZcluster	(	std::string	path,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< int > &	atoms,
		int	clusterID,
		cage::cageType	type )

nodiscard

Function for writing out the XYZ files for each cluster.

Functions

Function Documentation

◆ makePath()

◆ printRDF()

◆ writeAllCages()

◆ writeBasalRingsHex()

◆ writeBasalRingsPrism()

◆ writeCluster()

◆ writeClusterStats()

◆ writeDump()

◆ writeEachCage()

◆ writeHisto()

◆ writeLAMMPSdata()

◆ writeLAMMPSdataAllPrisms()

◆ writeLAMMPSdataAllRings()

◆ writeLAMMPSdataCages()

◆ writeLAMMPSdataPrisms()

◆ writeLAMMPSdataTopoBulk()

◆ writeLAMMPSdumpCages()

◆ writeLAMMPSdumpINT()

◆ writeLAMMPSdumpSlice()

◆ writeMoleculeIDsExpressionSelectOVITO()

◆ writeMoleculeIDsInSlice()

◆ writePrismNum()

◆ writePrisms()

◆ writeRingNum()

◆ writeRingNumBulk()

◆ writeRings()

◆ writeTopoBulkData()

◆ writeXYZcluster()