MolSys

Data Structures
struct	molSys::Result
	This contains the bond classifier of enum class 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 class	molSys::bond_type { molSys::staggered , molSys::eclipsed , molSys::out_of_range }
enum class	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::unordered_multimap< int, int >	molSys::createMolIDAtomIDMultiMap (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...

Variables
bond_type	molSys::Result::classifier
double	molSys::Result::c_value
	Classifier according to CHILL, CHILL+ etc. More...
int	molSys::Point< T >::type
int	molSys::Point< T >::molID
int	molSys::Point< T >::atomID
T	molSys::Point< T >::x
	type ID, molID, atomID More...
T	molSys::Point< T >::y
T	molSys::Point< T >::z
std::vector< Result >	molSys::Point< T >::c_ij
	coordinates More...
atom_state_type	molSys::Point< T >::iceType
	Results (contains bond correlation type) More...
bool	molSys::Point< T >::inSlice = true
	Type of ice/water etc based on cij. More...
std::vector< S >	molSys::PointCloud< S, T >::pts
int	molSys::PointCloud< S, T >::currentFrame
	Collection of points. More...
int	molSys::PointCloud< S, T >::nop
	Current frame number. More...
std::vector< T >	molSys::PointCloud< S, T >::box
	Number of atoms. More...
std::vector< T >	molSys::PointCloud< S, T >::boxLow
	Periodic box lengths. More...
std::unordered_map< int, int >	molSys::PointCloud< S, T >::idIndexMap
	xlo, ylo, zlo More...

Detailed Description

Enumeration Type Documentation

atom_state_type

enum molSys::atom_state_type

strong

Enumerator
cubic	Ic, or particle type signifying Cubic Ice.
hexagonal	Ih, or particle type signifying Hexagonal Ice.
water	Liquid/amorphous phase.
interfacial	Interfacial ice: ice-like molecules which do not fulfill the strict criteria of the Ic or Ih phases.
clathrate	Clathrate ice phase.
interClathrate	Interfacial clathrate ice phase.
unclassified	Not classified into any other category.
reCubic	Reclassified as cubic ice, according to the \(q_6\) order parameter.
reHex	Reclassified as hexagonal ice, according to the \(q_6\) order parameter.

Definition at line 113 of file mol_sys.hpp.

                           {
  cubic,
  hexagonal,
  water,
  interfacial,
  clathrate,
  interClathrate,
  unclassified,
  reCubic,
  reHex
};

bond_type

enum molSys::bond_type

strong

Enumerator
staggered	The bond is a staggered bond, according to the \(a(i,j)\) or \(c(i,j)\) value.
eclipsed	The bond is an eclipsed bond.
out_of_range	The bond cannot be classified as either staggered or eclipsed.

Definition at line 75 of file mol_sys.hpp.

{ staggered, eclipsed, out_of_range };

Function Documentation

clearPointCloud()

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.

Parameters

[out]

yCloud

The cleared PointCloud

Definition at line 24 of file mol_sys.cpp.

                                                           {
  //
  std::vector<molSys::Point<double>> tempPts;
  std::vector<double> tempBox;
  //
  std::vector<double> tempBox1;
 
  tempPts.swap(yCloud->pts);
  tempBox.swap(yCloud->box);
  tempBox1.swap(yCloud->boxLow);
  yCloud->idIndexMap.clear();
 
  return *yCloud;
}

createIDMolIDmap()

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 44 of file mol_sys.cpp.

                                                           {
  std::unordered_map<int, int>
      idMolIDmap; // atom IDs as keys and mol IDs as values
  int iatomMolID; // molID of the current iatom
  int iatomID;    // atom ID of the current iatom
 
  // Loop through the atoms in yCloud
  for (int iatom = 0; iatom < yCloud->nop; iatom++) {
    iatomID = yCloud->pts[iatom].atomID;   // atom ID
    iatomMolID = yCloud->pts[iatom].molID; // molecular ID
    // Update the unordered map
    idMolIDmap[iatomID] = iatomMolID;
  } // end of loop through every iatom in pointCloud
 
  return idMolIDmap;
}

createMolIDAtomIDMultiMap()

std::unordered_multimap< int, int > molSys::createMolIDAtomIDMultiMap

(

molSys::PointCloud< molSys::Point< double >, double > *

yCloud

)

Creates an multimap with molecule IDs of the atoms as the keys and the atom IDs as the values. More than one atom can have the same molecule ID

Function for creating an unordered map with the atomIDs in the pointCloud as the keys and the molecular IDs as the values. More than one atom can have the same molecule ID.

Definition at line 67 of file mol_sys.cpp.

                                                           {
  std::unordered_multimap<int, int>
      molIDAtomIDmap; // atom IDs as keys and mol IDs as values
  int iatomMolID; // molID of the current iatom
  int iatomID;    // atom ID of the current iatom
 
  // Loop through the atoms in yCloud
  for (int iatom = 0; iatom < yCloud->nop; iatom++) {
    iatomID = yCloud->pts[iatom].atomID;   // atom ID
    iatomMolID = yCloud->pts[iatom].molID; // molecular ID
    // Update the unordered multimap
    molIDAtomIDmap.emplace(iatomMolID,iatomID);
  } // end of loop through every iatom in pointCloud
 
  return molIDAtomIDmap;
}

hAtomMolList()

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 89 of file mol_sys.cpp.

                                                           {
  std::vector<std::vector<int>>
      hMolList; // the first column contains the molecular IDs, and the next
                // two elements in the row are the hydrogen bond atoms in the
                // molecule
  int iMolID;   // Current molecular ID
  int nHatoms;  // No. of h atoms found for a particular molID.
 
  for (int iatom = 0; iatom < oCloud->nop; iatom++) {
    // Get the molID
    iMolID = oCloud->pts[iatom].molID;
 
    hMolList.push_back(std::vector<int>()); // Empty vector for the index iatom
    // Fill the first element with the molecular ID
    hMolList[iatom].push_back(iMolID);
 
    nHatoms = 0; // init (no. of h atoms for the particular molID)
 
    // Now search through the hydrogen atom pointCloud for this particular molID
    for (int jatom = 0; jatom < hCloud->nop; jatom++) {
      if (hCloud->pts[jatom].molID == iMolID) {
        hMolList[iatom].push_back(jatom); // fill the hatom index
        nHatoms++;
        // If the two hydrogens have been found, break out of the loop
        if (nHatoms == 2) {
          break;
        } // end of break
      }   // end of check to see if jatom is part of iMolID
    }     // end of loop through the hydrogen atom pointCloud
  }       // end of looping through every oxygen atom
 
  return hMolList;
} // end of function

searchMolList()

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

Returns

the index found in molList

-1 if not found

Definition at line 131 of file mol_sys.cpp.

                                           {
  int index = -1; // init invalid index
 
  for (int iatom = 0; iatom < molList.size(); iatom++) {
    // If the molecular ID is equal, return the index in the array
    if (molList[iatom][0] == molIDtoFind) {
      index = iatom;
      return index;
    } // end of check
  }   // end of looping through iatom
 
  return index;
}

Variable Documentation

atomID

template<typename T >

int molSys::Point< T >::atomID

Definition at line 150 of file mol_sys.hpp.

box

template<typename S , typename T >

std::vector<T> molSys::PointCloud< S, T >::box

Number of atoms.

Definition at line 174 of file mol_sys.hpp.

boxLow

template<typename S , typename T >

std::vector<T> molSys::PointCloud< S, T >::boxLow

Periodic box lengths.

Definition at line 175 of file mol_sys.hpp.

c_ij

template<typename T >

std::vector<Result> molSys::Point< T >::c_ij

coordinates

Definition at line 152 of file mol_sys.hpp.

c_value

double molSys::Result::c_value

Classifier according to CHILL, CHILL+ etc.

Definition at line 134 of file mol_sys.hpp.

classifier

bond_type molSys::Result::classifier

Definition at line 133 of file mol_sys.hpp.

currentFrame

template<typename S , typename T >

int molSys::PointCloud< S, T >::currentFrame

Collection of points.

Definition at line 172 of file mol_sys.hpp.

iceType

template<typename T >

atom_state_type molSys::Point< T >::iceType

Initial value:

=
      molSys::atom_state_type::unclassified

Results (contains bond correlation type)

Definition at line 153 of file mol_sys.hpp.

idIndexMap

template<typename S , typename T >

std::unordered_map<int, int> molSys::PointCloud< S, T >::idIndexMap

xlo, ylo, zlo

Definition at line 176 of file mol_sys.hpp.

inSlice

template<typename T >

bool molSys::Point< T >::inSlice = true

Type of ice/water etc based on cij.

Definition at line 155 of file mol_sys.hpp.

molID

template<typename T >

int molSys::Point< T >::molID

Definition at line 150 of file mol_sys.hpp.

nop

template<typename S , typename T >

int molSys::PointCloud< S, T >::nop

Current frame number.

Definition at line 173 of file mol_sys.hpp.

pts

template<typename S , typename T >

std::vector<S> molSys::PointCloud< S, T >::pts

Definition at line 171 of file mol_sys.hpp.

type

template<typename T >

int molSys::Point< T >::type

Definition at line 150 of file mol_sys.hpp.

x

template<typename T >

T molSys::Point< T >::x

type ID, molID, atomID

Definition at line 151 of file mol_sys.hpp.

y

template<typename T >

T molSys::Point< T >::y

Definition at line 151 of file mol_sys.hpp.

z

template<typename T >

T molSys::Point< T >::z

Definition at line 151 of file mol_sys.hpp.