topo_bulk.hpp File Reference

File containing functions used specific to bulk topological network critera. More...

#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <math.h>
#include <memory>
#include <sstream>
#include <string>
#include <sys/stat.h>
#include <vector>
#include <cage.hpp>
#include <mol_sys.hpp>
#include <order_parameter.hpp>
#include <ring.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>
#include <shapeMatch.hpp>
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Namespaces

 ring
 Topological network criteria functions.
 
 prism3
 

Functions

int ring::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 > ring::findDDC (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, std::vector< int > listHC, std::vector< cage::Cage > *cageList)
 
std::vector< int > ring::findMixedRings (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, std::vector< int > *listDDC, std::vector< int > *listHC)
 
std::vector< int > ring::findHC (std::vector< std::vector< int >> rings, std::vector< strucType > *ringType, std::vector< std::vector< int >> nList, std::vector< cage::Cage > *cageList)
 
bool ring::conditionOneDDC (std::vector< std::vector< int >> rings, std::vector< int > *peripheralRings, int iring)
 
bool ring::conditionTwoDDC (std::vector< std::vector< int >> rings, std::vector< int > *peripheralRings, int iring)
 
bool ring::conditionThreeDDC (std::vector< std::vector< int >> rings, std::vector< int > *peripheralRings)
 
bool ring::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 ring::basalNeighbours (std::vector< std::vector< int >> nList, std::vector< int > *triplet, int atomOne, int atomTwo)
 
bool ring::notNeighboursOfRing (std::vector< std::vector< int >> nList, std::vector< int > *triplet, std::vector< int > *ring)
 
int ring::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 ring::getAtomTypesTopoBulk (std::vector< std::vector< int >> rings, std::vector< ring::strucType > ringType, std::vector< cage::iceType > *atomTypes)
 
int ring::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...
 
int prism3::findBulkPrisms (std::vector< std::vector< int >> rings, std::vector< ring::strucType > *ringType, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< double > *rmsdPerAtom, double heightCutoff=8)
 Find out which rings are prisms. More...
 
bool prism3::basalPrismConditions (std::vector< std::vector< int >> nList, std::vector< int > *basal1, std::vector< int > *basal2)
 
bool prism3::relaxedPrismConditions (std::vector< std::vector< int >> nList, std::vector< int > *basal1, std::vector< int > *basal2)
 
bool prism3::basalRingsSeparation (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< int > basal1, std::vector< int > basal2, double heightCutoff=8)
 Check to see that candidate basal prisms are not really far from each other. More...
 

Detailed Description

File containing functions used specific to bulk topological network critera.

Definition in file topo_bulk.hpp.