Data Structures | |
struct | molSys::Result |
This contains the bond classifier of enum type bond_type, and the bond correlation factor. More... | |
struct | molSys::Point< T > |
This contains per-particle information. More... | |
struct | molSys::PointCloud< S, T > |
This contains a collection of points; contains information for a particular frame. More... | |
Enumerations | |
enum | molSys::bond_type { molSys::staggered , molSys::eclipsed , molSys::out_of_range } |
enum | molSys::atom_state_type { molSys::cubic , molSys::hexagonal , molSys::water , molSys::interfacial , molSys::clathrate , molSys::interClathrate , molSys::unclassified , molSys::reCubic , molSys::reHex } |
Functions | |
std::unordered_map< int, int > | molSys::createIDMolIDmap (molSys::PointCloud< molSys::Point< double >, double > *yCloud) |
std::vector< std::vector< int > > | molSys::hAtomMolList (molSys::PointCloud< molSys::Point< double >, double > *hCloud, molSys::PointCloud< molSys::Point< double >, double > *oCloud) |
int | molSys::searchMolList (std::vector< std::vector< int >> molList, int molIDtoFind) |
molSys::PointCloud< molSys::Point< double >, double > | molSys::clearPointCloud (molSys::PointCloud< molSys::Point< double >, double > *yCloud) |
//! Function for clearing vectors in PointCloud after multiple usage More... | |
Definition at line 109 of file mol_sys.hpp.
enum molSys::bond_type |
Definition at line 71 of file mol_sys.hpp.
molSys::PointCloud< molSys::Point< double >, double > molSys::clearPointCloud | ( | molSys::PointCloud< molSys::Point< double >, double > * | yCloud | ) |
//! Function for clearing vectors in PointCloud after multiple usage
Function for clearing PointCloud if it is already filled. This should be called before every frame is read in.
[out] | yCloud | The cleared PointCloud |
Definition at line 20 of file mol_sys.cpp.
std::unordered_map< int, int > molSys::createIDMolIDmap | ( | molSys::PointCloud< molSys::Point< double >, double > * | yCloud | ) |
Creates an unordered map, with the atomIDs as keys and molecular IDs as the values
Function for creating an unordered map with the atomIDs in the pointCloud as the keys and the molecular IDs as the values
Definition at line 40 of file mol_sys.cpp.
std::vector< std::vector< int > > molSys::hAtomMolList | ( | molSys::PointCloud< molSys::Point< double >, double > * | hCloud, |
molSys::PointCloud< molSys::Point< double >, double > * | oCloud | ||
) |
Returns a vector of vectors, which contains the molIDs in the first column, and the hydrogen atom indices (not atom IDs) in the row
Function that returns a vector of vectors, which contains the hydrogen atoms for each molID in the oxygen atom pointCloud
Definition at line 62 of file mol_sys.cpp.
int molSys::searchMolList | ( | std::vector< std::vector< int >> | molList, |
int | molIDtoFind | ||
) |
This function searches a vector of vectors molList, for a particular molecular ID, and returns the index in molList
Function for searching a vector of vectors for a particular molecular ID, and
Definition at line 104 of file mol_sys.cpp.
int molSys::Point< T >::atomID |
Definition at line 146 of file mol_sys.hpp.
std::vector<T> molSys::PointCloud< S, T >::box |
Number of atoms.
Definition at line 170 of file mol_sys.hpp.
std::vector<T> molSys::PointCloud< S, T >::boxLow |
Periodic box lengths.
Definition at line 171 of file mol_sys.hpp.
std::vector<Result> molSys::Point< T >::c_ij |
coordinates
Definition at line 148 of file mol_sys.hpp.
double molSys::Result::c_value |
Classifier according to CHILL, CHILL+ etc.
Definition at line 130 of file mol_sys.hpp.
bond_type molSys::Result::classifier |
Definition at line 129 of file mol_sys.hpp.
int molSys::PointCloud< S, T >::currentFrame |
Collection of points.
Definition at line 168 of file mol_sys.hpp.
atom_state_type molSys::Point< T >::iceType |
Results (contains bond correlation type)
Definition at line 149 of file mol_sys.hpp.
std::unordered_map<int, int> molSys::PointCloud< S, T >::idIndexMap |
xlo, ylo, zlo
Definition at line 172 of file mol_sys.hpp.
bool molSys::Point< T >::inSlice = true |
Type of ice/water etc based on cij.
Definition at line 151 of file mol_sys.hpp.
int molSys::Point< T >::molID |
Definition at line 146 of file mol_sys.hpp.
int molSys::PointCloud< S, T >::nop |
Current frame number.
Definition at line 169 of file mol_sys.hpp.
std::vector<S> molSys::PointCloud< S, T >::pts |
Definition at line 167 of file mol_sys.hpp.
int molSys::Point< T >::type |
Definition at line 146 of file mol_sys.hpp.
T molSys::Point< T >::x |
type ID, molID, atomID
Definition at line 147 of file mol_sys.hpp.
T molSys::Point< T >::y |
Definition at line 147 of file mol_sys.hpp.
T molSys::Point< T >::z |
Definition at line 147 of file mol_sys.hpp.