ring Namespace Reference

Topological network criteria functions. More...

Enumerations

enum  strucType {
  unclassified , DDC , HCbasal , HCprismatic ,
  bothBasal , bothPrismatic , Prism , deformedPrism ,
  mixedPrismRing
}
 

Functions

std::vector< std::vector< int > > getSingleRingSize (std::vector< std::vector< int >> rings, int ringSize)
 Returns a vector of vectors of rings of a single size. More...
 
bool hasCommonElements (std::vector< int > ring1, std::vector< int > ring2)
 
bool compareRings (std::vector< int > ring1, std::vector< int > ring2)
 
bool findTripletInRing (std::vector< int > ring, std::vector< int > triplet)
 Searches a particular ring for a triplet. More...
 
bool commonElementsInThreeRings (std::vector< int > ring1, std::vector< int > ring2, std::vector< int > ring3)
 Common elements in 3 rings. More...
 
std::vector< int > findsCommonElements (std::vector< int > ring1, std::vector< int > ring2)
 Returns the common elements of two rings. More...
 
int clearRingList (std::vector< std::vector< int >> &rings)
 Erases memory for a vector of vectors for a list of rings. More...
 
int topoBulkAnalysis (std::string path, std::vector< std::vector< int >> rings, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int firstFrame, bool onlyTetrahedral=true)
 
std::vector< int > findDDC (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, std::vector< int > listHC, std::vector< cage::Cage > *cageList)
 
std::vector< int > findMixedRings (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, std::vector< int > *listDDC, std::vector< int > *listHC)
 
std::vector< int > findHC (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, std::vector< std::vector< int >> nList, std::vector< cage::Cage > *cageList)
 
bool conditionOneDDC (std::vector< std::vector< int >> rings, std::vector< int > *peripheralRings, int iring)
 
bool conditionTwoDDC (std::vector< std::vector< int >> rings, std::vector< int > *peripheralRings, int iring)
 
bool conditionThreeDDC (std::vector< std::vector< int >> rings, std::vector< int > *peripheralRings)
 
bool basalConditions (std::vector< std::vector< int >> nList, std::vector< int > *basal1, std::vector< int > *basal2)
 Tests whether two rings are basal rings (true) or not (false) More...
 
bool basalNeighbours (std::vector< std::vector< int >> nList, std::vector< int > *triplet, int atomOne, int atomTwo)
 
bool notNeighboursOfRing (std::vector< std::vector< int >> nList, std::vector< int > *triplet, std::vector< int > *ring)
 
int findPrismatic (std::vector< std::vector< int >> rings, std::vector< int > *listHC, std::vector< strucType > *ringType, int iring, int jring, std::vector< int > *prismaticRings)
 Finds the prismatic rings from basal rings iring and jring. More...
 
int getAtomTypesTopoBulk (std::vector< std::vector< int >> rings, std::vector< ring::strucType > ringType, std::vector< cage::iceType > *atomTypes)
 
int getStrucNumbers (std::vector< ring::strucType > ringType, std::vector< cage::Cage > cageList, int *numHC, int *numDDC, int *mixedRings, int *prismaticRings, int *basalRings)
 Determines the number of HCs, DDCs, Mixed rings, prismatic and basal rings. More...
 
std::vector< int > findPrisms (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, int *nPerfectPrisms, int *nImperfectPrisms, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< double > *rmsdPerAtom, bool doShapeMatching=false)
 
bool basalPrismConditions (std::vector< std::vector< int >> nList, std::vector< int > *basal1, std::vector< int > *basal2)
 
bool relaxedPrismConditions (std::vector< std::vector< int >> nList, std::vector< int > *basal1, std::vector< int > *basal2)
 
bool discardExtraTetragonBlocks (std::vector< int > *basal1, std::vector< int > *basal2, molSys::PointCloud< molSys::Point< double >, double > *yCloud)
 
std::vector< std::vector< int > > keepAxialRingsOnly (std::vector< std::vector< int >> rings, molSys::PointCloud< molSys::Point< double >, double > *yCloud)
 Saves only axial rings out of all possible rings. More...
 
int prismAnalysis (std::string path, std::vector< std::vector< int >> rings, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int maxDepth, int *atomID, int firstFrame, int currentFrame, bool doShapeMatching=false)
 
int assignPrismType (std::vector< std::vector< int >> rings, std::vector< int > listPrism, int ringSize, std::vector< ring::strucType > ringType, std::vector< int > *atomTypes, std::vector< ring::strucType > *atomState)
 
int deformedPrismTypes (std::vector< ring::strucType > atomState, std::vector< int > *atomTypes, int maxDepth)
 Get the atom type values for deformed prisms. More...
 
int rmAxialTranslations (molSys::PointCloud< molSys::Point< double >, double > *yCloud, int *atomID, int firstFrame, int currentFrame)
 Shift the entire ice nanotube and remove axial translations. More...
 
int polygonRingAnalysis (std::string path, std::vector< std::vector< int >> rings, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int maxDepth, double sheetArea, int firstFrame)
 
int assignPolygonType (std::vector< std::vector< int >> rings, std::vector< int > *atomTypes, std::vector< int > nRings)
 

Detailed Description

Topological network criteria functions.

This namespace contains functions for the topological network criteria for bulk and confined systems both.

Although the namespace is shared by bulk and confined topological network criteria, the functions are split into files specific to each set of criteria.

All the topological network criteria are based on the identification of primitive rings (using the Franzblau algorithm for primitive rings), following which specific rules for combinations of primitive rings are used to identify quasi-one-dimensional, quasi-two-dimensional and bulk ices.

Changelog