seams_output.hpp File Reference
#include <bond.hpp>
#include <cage.hpp>
#include <errno.h>
#include <generic.hpp>
#include <iostream>
#include <memory>
#include <mol_sys.hpp>
#include <sys/stat.h>
#include "boost/filesystem/operations.hpp"
#include "boost/filesystem/path.hpp"
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Namespaces

 sout
 

Functions

bool sout::isDirExist (const std::string &path)
 
int sout::makePath (const std::string &path)
 
int sout::writeRings (std::vector< std::vector< int >> rings, std::string filename="rings.dat")
 Function for printing out ring info, when there is no volume slice. More...
 
int sout::writePrismNum (std::string path, std::vector< int > nPrisms, std::vector< int > nDefPrisms, std::vector< double > heightPercent, int maxDepth, int currentFrame, int firstFrame)
 
int sout::writeRingNum (std::string path, int currentFrame, std::vector< int > nRings, std::vector< double > coverageAreaXY, std::vector< double > coverageAreaXZ, std::vector< double > coverageAreaYZ, 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. More...
 
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, molSys::PointCloud< molSys::Point< double >, double > *yCloud)
 Function for writing out each prism. More...
 
int sout::writeClusterStats (std::string path, int currentFrame, int largestCluster, int numOfClusters, int smallestCluster, double avgClusterSize, int firstFrame)
 Function for writing out cluster statistics. More...
 
int sout::writeLAMMPSdata (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. More...
 
int sout::writeLAMMPSdumpINT (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< double > rmsdPerAtom, std::vector< int > atomTypes, int maxDepth, std::string path)
 Write out a LAMMPS dump file containing the RMSD per atom. More...
 
int sout::writeLAMMPSdumpCages (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< double > rmsdPerAtom, std::vector< int > atomTypes, std::string path, int firstFrame)
 Write out a LAMMPS dump file containing the RMSD per atom for bulk ice. More...
 
int sout::writeLAMMPSdataAllPrisms (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::vector< int > atomTypes, int maxDepth, std::string path, bool doShapeMatching=false)
 Write a data file for prisms of every type. More...
 
int sout::writeLAMMPSdataAllRings (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::vector< int > atomTypes, int maxDepth, std::string path)
 Write a data file for rings of every type for a monolayer. More...
 
int sout::writeLAMMPSdataTopoBulk (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::vector< cage::iceType > atomTypes, std::string path, bool bondsBetweenDummy=false)
 
int sout::writeLAMMPSdataPrisms (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> rings, bool useBondFile, std::string bondFile, std::vector< int > listPrism, std::vector< std::vector< int >> nList, std::string filename="system-prisms.data")
 Write a data file for prisms of a single type. More...
 
int sout::writeLAMMPSdataCages (molSys::PointCloud< molSys::Point< double >, double > *yCloud, 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, std::vector< std::vector< int >> rings, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int currentFrame)
 
int sout::writeEachCage (std::vector< int > currentCage, int cageNum, cage::cageType type, std::vector< std::vector< int >> rings, molSys::PointCloud< molSys::Point< double >, double > *yCloud)
 Write out a particular cage to a file. More...
 
int sout::writeBasalRingsHex (std::vector< int > currentCage, int cageNum, std::vector< std::vector< int >> nList, std::vector< std::vector< int >> rings)
 Write out the basal rings of a particular Hexagonal cage. More...
 
int sout::writeBasalRingsPrism (std::vector< int > *basal1, std::vector< int > *basal2, int prismNum, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, bool isDeformed)
 Write out the basal rings for a particular prism. More...
 
int sout::writeDump (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::string path, std::string outFile)
 Generic function for writing out to a dump file. More...
 
int sout::writeHisto (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::vector< double > avgQ6)
 
int sout::writeCluster (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. More...
 
int sout::writeXYZcluster (std::string path, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< int > atoms, int clusterID, cage::cageType type)
 Function for writing out the XYZ files for each cluster. More...