MolSys

Namespaces
namespace	molSys
	Bare-bones structs used throughout the architecture.

Concepts
concept	molSys::CoordinateScalar
concept	molSys::molSys::CoordinateScalar
	The arithmetic type a coordinate may take.

Classes
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::bond_type::staggered , molSys::bond_type::eclipsed , molSys::bond_type::out_of_range }
enum class	molSys::atom_state_type {   molSys::atom_state_type::cubic , molSys::atom_state_type::hexagonal , molSys::atom_state_type::water , molSys::atom_state_type::interfacial ,   molSys::atom_state_type::clathrate , molSys::atom_state_type::interClathrate , molSys::atom_state_type::unclassified , molSys::atom_state_type::reCubic ,   molSys::atom_state_type::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 (const 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

Variables
bond_type	molSys::Result::classifier
double	molSys::Result::c_value
	Classifier according to CHILL, CHILL+ etc.
int	molSys::Point< T >::type = 0
int	molSys::Point< T >::molID = 0
int	molSys::Point< T >::atomID = 0
T	molSys::Point< T >::x = 0
	type ID, molID, atomID
T	molSys::Point< T >::y = 0
T	molSys::Point< T >::z = 0
std::vector< Result >	molSys::Point< T >::c_ij
	coordinates
atom_state_type	molSys::Point< T >::iceType
	Results (contains bond correlation type).
bool	molSys::Point< T >::inSlice = true
	Type of ice/water etc based on cij.
std::vector< S >	molSys::PointCloud< S, T >::pts
int	molSys::PointCloud< S, T >::currentFrame = 0
	Collection of points.
int	molSys::PointCloud< S, T >::nop = 0
	Current frame number.
std::vector< T >	molSys::PointCloud< S, T >::box
	Number of atoms.
std::vector< T >	molSys::PointCloud< S, T >::boxLow
	Periodic box lengths.
std::unordered_map< int, int >	molSys::PointCloud< S, T >::idIndexMap
	xlo, ylo, zlo

Detailed Description

Enumeration Type Documentation

atom_state_type

enum class 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 107 of file mol_sys.hpp.

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

bond_type

enum class 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 69 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

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

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

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

searchMolList()

int molSys::searchMolList ( const std::vector< std::vector< int > > & molList, int molIDtoFind )

nodiscard

This function searches a vector of vectors molList, for a particular molecular ID, and returns the index in molList

Variable Documentation

atomID

template<CoordinateScalar T>

int molSys::Point< T >::atomID = 0

Definition at line 153 of file mol_sys.hpp.

box

template<typename S, CoordinateScalar T>

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

Number of atoms.

Definition at line 177 of file mol_sys.hpp.

boxLow

template<typename S, CoordinateScalar T>

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

Periodic box lengths.

Definition at line 178 of file mol_sys.hpp.

c_ij

template<CoordinateScalar T>

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

coordinates

Definition at line 155 of file mol_sys.hpp.

c_value

double molSys::Result::c_value

Classifier according to CHILL, CHILL+ etc.

Definition at line 128 of file mol_sys.hpp.

classifier

bond_type molSys::Result::classifier

Definition at line 127 of file mol_sys.hpp.

currentFrame

template<typename S, CoordinateScalar T>

int molSys::PointCloud< S, T >::currentFrame = 0

Collection of points.

Definition at line 175 of file mol_sys.hpp.

iceType

template<CoordinateScalar T>

atom_state_type molSys::Point< T >::iceType

Initial value:

                    =
atom_state_type::unclassified

Results (contains bond correlation type).

Definition at line 156 of file mol_sys.hpp.

idIndexMap

template<typename S, CoordinateScalar T>

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

xlo, ylo, zlo

Definition at line 179 of file mol_sys.hpp.

inSlice

template<CoordinateScalar T>

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

Type of ice/water etc based on cij.

Definition at line 158 of file mol_sys.hpp.

molID

template<CoordinateScalar T>

int molSys::Point< T >::molID = 0

Definition at line 153 of file mol_sys.hpp.

nop

template<typename S, CoordinateScalar T>

int molSys::PointCloud< S, T >::nop = 0

Current frame number.

Definition at line 176 of file mol_sys.hpp.

pts

template<typename S, CoordinateScalar T>

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

Definition at line 174 of file mol_sys.hpp.

type

template<CoordinateScalar T>

int molSys::Point< T >::type = 0

Definition at line 153 of file mol_sys.hpp.

x

template<CoordinateScalar T>

T molSys::Point< T >::x = 0

type ID, molID, atomID

Definition at line 154 of file mol_sys.hpp.

y

template<CoordinateScalar T>

T molSys::Point< T >::y = 0

Definition at line 154 of file mol_sys.hpp.

z

template<CoordinateScalar T>

T molSys::Point< T >::z = 0

Definition at line 154 of file mol_sys.hpp.