Functions | |
bool | isDirExist (const std::string &path) |
int | makePath (const std::string &path) |
int | 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 | writePrismNum (std::string path, std::vector< int > nPrisms, std::vector< int > nDefPrisms, std::vector< double > heightPercent, int maxDepth, int currentFrame, int firstFrame) |
int | 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 | printRDF (std::string fileName, std::vector< double > *rdfValues, double binwidth, int nbin) |
Function for printing out the RDF, given the filename. More... | |
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, molSys::PointCloud< molSys::Point< double >, double > *yCloud) |
Function for writing out each prism. More... | |
int | writeClusterStats (std::string path, int currentFrame, int largestCluster, int numOfClusters, int smallestCluster, double avgClusterSize, int firstFrame) |
Function for writing out cluster statistics. More... | |
int | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | writeHisto (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::vector< double > avgQ6) |
int | 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 | 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... | |
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inline |
Inline function for checking if the directory exists or not
[in] | path | The path of the directory |
Definition at line 40 of file seams_output.hpp.
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inline |
Inline function for creating the desried directory.
[in] | path | The path of the directory |
Definition at line 60 of file seams_output.hpp.
int sout::printRDF | ( | std::string | fileName, |
std::vector< double > * | rdfValues, | ||
double | binwidth, | ||
int | nbin | ||
) |
Function for printing out the RDF, given the filename.
Function for printing out the RDF to a file, given that the file already exists and given the filename.
Definition at line 1024 of file seams_output.cpp.
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 | ||
) |
Write out all cages of all types into a folder called cages inside the output directory
Function for writing out all the cages of all types to a folder in the output
Definition at line 283 of file seams_output.cpp.
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.
Function for printing out the basal rings only of the hexagonal cage described by the number cageNum Uses Boost!
Definition at line 437 of file seams_output.cpp.
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.
Function for printing out the basal rings of the prism blocks described by the number prismNum. Uses Boost!
Definition at line 646 of file seams_output.cpp.
int sout::writeCluster | ( | molSys::PointCloud< molSys::Point< double >, double > * | yCloud, |
std::string | fileName = "cluster.txt" , |
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bool | isSlice = false , |
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int | largestIceCluster = 0 |
||
) |
Function for printing the largest ice cluster.
Function to print out the largest ice cluster
Definition at line 2094 of file seams_output.cpp.
int sout::writeClusterStats | ( | std::string | path, |
int | currentFrame, | ||
int | largestCluster, | ||
int | numOfClusters, | ||
int | smallestCluster, | ||
double | avgClusterSize, | ||
int | firstFrame | ||
) |
Function for writing out cluster statistics.
Function for printing out cluster statistics
Definition at line 836 of file seams_output.cpp.
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.
Function for printing out info in PairCorrel struct
Definition at line 1949 of file seams_output.cpp.
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.
Function for printing out each cage's coordinates, when there is no volume slice Uses Boost!
Definition at line 344 of file seams_output.cpp.
int sout::writeHisto | ( | molSys::PointCloud< molSys::Point< double >, double > * | yCloud, |
std::vector< std::vector< int >> | nList, | ||
std::vector< double > | avgQ6 | ||
) |
Function for printing out Q6, Cij and averaged Q3 values as single columns to text files The file names are cij, q6, q3
Function for printing out values of averaged Q6, averaged Q3 and Cij values
Definition at line 2053 of file seams_output.cpp.
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.
Prints out a LAMMPS data file, with some default options. Only Oxygen atoms are printed out
Definition at line 18 of file seams_output.cpp.
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.
Prints out a LAMMPS data file for all the prisms for a single frame, with some default options. Only Oxygen atoms are printed out. Bonds are inferred from the rings vector of vectors
Definition at line 1251 of file seams_output.cpp.
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.
Prints out a LAMMPS data file for all the rings for a single frame, with some default options. Only Oxygen atoms are printed out. Bonds are inferred from the rings vector of vectors
Definition at line 1385 of file seams_output.cpp.
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" |
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) |
Write out a lammps data file for DDCs or HCs, assuming that there is no slice
Prints out a LAMMPS data file for the either the DDCs or HCs, with some default options. Only Oxygen atoms are printed out
Definition at line 1737 of file seams_output.cpp.
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" |
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) |
Write a data file for prisms of a single type.
Prints out a LAMMPS data file for the prisms, with some default options. Only Oxygen atoms are printed out
Definition at line 1507 of file seams_output.cpp.
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 |
||
) |
Write a data file for a particular frame, writing out topological bulk ice structures (DDCs/HCs)
Prints out a LAMMPS data file for all the topological bulk ice for a single frame, with some default options. Only Oxygen atoms are printed out. Bonds are inferred from the neighbour list
Definition at line 2111 of file seams_output.cpp.
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.
Prints out a LAMMPS dump file for all the cages in bulk ice, for every frame, printing the RMSD per atom as well
Definition at line 1086 of file seams_output.cpp.
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.
Prints out a LAMMPS dump file for all the prisms, for every frame, printing the RMSD per atom as well
Definition at line 1176 of file seams_output.cpp.
int sout::writePrismNum | ( | std::string | path, |
std::vector< int > | nPrisms, | ||
std::vector< int > | nDefPrisms, | ||
std::vector< double > | heightPercent, | ||
int | maxDepth, | ||
int | currentFrame, | ||
int | firstFrame | ||
) |
Function for printing out the number of prism blocks, with or without slices. Be careful when using slices!
Function for printing out prism info, when there is no volume slice
Definition at line 872 of file seams_output.cpp.
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.
Function for printing out each info, when there is no volume slice Uses Boost!
Definition at line 212 of file seams_output.cpp.
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 | ||
) |
Function for printing out the coverage area and the number of rings of each type
Function for printing out ring info, for a monolayer
Definition at line 918 of file seams_output.cpp.
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.
Function for printing out ring info, when there is no volume slice Uses Boost!
Definition at line 178 of file seams_output.cpp.
int sout::writeTopoBulkData | ( | std::string | path, |
int | currentFrame, | ||
int | numHC, | ||
int | numDDC, | ||
int | mixedRings, | ||
int | basalRings, | ||
int | prismaticRings, | ||
int | firstFrame | ||
) |
Function for printing out the number of DDCs, HCs, mixed rings, basal and prismatic rings
Function for out the number of DDCs, HCs, mixed rings, basal and prismatic rings.
Definition at line 1049 of file seams_output.cpp.
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.
Function for writing out the XYZ file of a particular cluster. The vector atoms contains the atom indices of the atoms to be written out
Definition at line 2264 of file seams_output.cpp.