seams_output.hpp File Reference

#include <bond.hpp>
#include <cage.hpp>
#include <generic.hpp>
#include <iostream>
#include <memory>
#include <mol_sys.hpp>
#include <filesystem>

Go to the source code of this file.

Namespaces
namespace	sout

Functions
int	sout::makePath (const std::string &path)
	Inline function for creating the desired directory (and parents).
int	sout::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	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)
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)
int	sout::writeRingNumBulk (std::string path, int currentFrame, const std::vector< int > &nRings, int maxDepth, int firstFrame)
int	sout::printRDF (std::string fileName, std::vector< double > &rdfValues, double binwidth, int nbin)
	Function for printing out the RDF, given the filename.
int	sout::writeTopoBulkData (std::string path, int currentFrame, int numHC, int numDDC, int mixedRings, int basalRings, int prismaticRings, int firstFrame)
int	sout::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	sout::writeClusterStats (std::string path, int currentFrame, int largestCluster, int numOfClusters, int smallestCluster, double avgClusterSize, int firstFrame)
	Function for writing out cluster statistics.
int	sout::writeMoleculeIDsInSlice (std::string path, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
int	sout::writeMoleculeIDsExpressionSelectOVITO (std::string path, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
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")
	Write a data file for rings.
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)
	Write out a LAMMPS dump file containing the RMSD per atom.
int	sout::writeLAMMPSdumpSlice (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, std::string path)
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)
	Write out a LAMMPS dump file containing the RMSD per atom for bulk ice.
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)
	Write a data file for prisms of every type.
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)
	Write a data file for rings of every type for a monolayer.
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)
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")
	Write a data file for prisms of a single type.
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")
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)
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)
	Write out a particular cage to a file.
int	sout::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	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)
	Write out the basal rings for a particular prism.
int	sout::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	sout::writeHisto (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, const std::vector< double > &avgQ6)
int	sout::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	sout::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.