ProDistanceInMolecule computes atom-to-atom distance in each molecule (also computes square of the distance). More...

#include <pro_distance_in_molecule.h>

Inheritance diagram for ProDistanceInMolecule:

Collaboration diagram for ProDistanceInMolecule:

Public Member Functions
	ProDistanceInMolecule (const ElPtr &mols, const ElPtr &atoms)
	Constructor of ProDistanceInMolecule class for a snapshot of simulation. More...

	ProDistanceInMolecule (const Vec< std::pair< ElPtr, ElPtr >> &pairs)
	Constructor of ProDistanceInMolecule class for multiple snapshots of simulation. More...

virtual void	prepare () override
	Resize distance2_traj. More...

virtual void	finish () override
	Fill distance2_array with values of distance2_traj. More...

void	set_indices (int index1_in_mol_, int index2_in_mol_)
	Specify two atoms in a molecule by zero-based index. Distance between the two atoms is computed for each molecule. More...

void	set_moltype (int target_moltype_)
	Specify a molecular type. Only molecules whose `type` property is the specified type are analyzed. If molecules have no `type` property, you do not need to use this method. More...

ArrayXXd	get_distance_array ()
	Get computed distances between two atoms in each molecule as a two-dimensional array: each row corresponds to each snapshot of a simulation and each column corresponds to each molecule. More...

const ArrayXXd &	get_distance2_array ()
	Get computed squared distances between two atoms in each molecule as a two-dimensional array: each row corresponds to each snapshot of a simulation and each column corresponds to each molecule. More...

Public Member Functions inherited from Processor
	Processor ()=default
	Constructor of Processor class (default).

virtual bool	run ()
	Run analysis using i th Generator object in generators, where i = i_generator. More...

void	startup ()
	Startup this Processor object. More...

Protected Member Functions
virtual void	run_impl (const int index) override
	Implementation of analysis using an element of generators. More...

Protected Member Functions inherited from Processor
template<class GEN >
void	register_generator (const ShPtr< GEN > &gen)

template<class GEN >
void	register_generators (const Vec< ShPtr< GEN >> &gens)

virtual void	use_generator_at (const int i)
	Call Generator::generate_data of i th Generator object in generators. More...

virtual void	finish_using_generator_at (const int i)
	Call Generator::finish_using_generated_data of i* th Generator object in generators. More...

Private Attributes
int	index1_in_mol = 0

int	index2_in_mol = 0

int	target_moltype = 1

Vec< RowArrayXd >	distance2_traj

ArrayXXd	distance2_array

Additional Inherited Members
Protected Attributes inherited from Processor
int	n_generators

Vec< ShPtr< Generator > >	generators

Detailed Description

ProDistanceInMolecule computes atom-to-atom distance in each molecule (also computes square of the distance).

An object of this class makes a two-dimensional array of distances between two atoms belonging to the same molecule. Each row of the array corresponds to each snapshot of a simulation, and each column of the array corresponds to each molecule.

About usage in Python, please see pybind::py_pro_distance_in_molecule.

Definition at line 26 of file pro_distance_in_molecule.h.

Constructor & Destructor Documentation

◆ ProDistanceInMolecule() [1/2]

ProDistanceInMolecule::ProDistanceInMolecule	(	const ElPtr &	mols,
		const ElPtr &	atoms
	)

Constructor of ProDistanceInMolecule class for a snapshot of simulation.

Parameters

mols

An Element object for molecules.

Required property

id : integer
atom-ids : array of integers

atoms

An Element object for atoms.

Required property

id : integer
xu : float
yu : float
zu : float

A GenDict object is constructed taking the mols and atoms, and then put into generators by register_generator.

Definition at line 17 of file pro_distance_in_molecule.cpp.

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◆ ProDistanceInMolecule() [2/2]

ProDistanceInMolecule::ProDistanceInMolecule ( const Vec< std::pair< ElPtr, ElPtr >> & pairs )

Constructor of ProDistanceInMolecule class for multiple snapshots of simulation.

Parameters

pairs

List of pairs of two Element objects: the first object is for molecules and the second object is for atoms. If each Element object has an array data, all the array should have the same length.

Required property (first)

atom-ids : array of integers

Required property (second)

id : integer
xu : float
yu : float
zu : float

GenDict objects are constructed taking each element of the pairs, and then put into generators by register_generators.

Definition at line 27 of file pro_distance_in_molecule.cpp.

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Member Function Documentation

◆ finish()

void ProDistanceInMolecule::finish ( )

overridevirtual

Fill distance2_array with values of distance2_traj.

Returns: None.

Each row of distance2_array corresponds to each element of distance2_traj.

Reimplemented from Processor.

Definition at line 92 of file pro_distance_in_molecule.cpp.

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◆ get_distance2_array()

const ArrayXXd & ProDistanceInMolecule::get_distance2_array ( )

Get computed squared distances between two atoms in each molecule as a two-dimensional array: each row corresponds to each snapshot of a simulation and each column corresponds to each molecule.

Returns: distance2_array.

Definition at line 142 of file pro_distance_in_molecule.cpp.

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◆ get_distance_array()

ArrayXXd ProDistanceInMolecule::get_distance_array ( )

Get computed distances between two atoms in each molecule as a two-dimensional array: each row corresponds to each snapshot of a simulation and each column corresponds to each molecule.

Returns: Square rooted distance2_array.

Definition at line 135 of file pro_distance_in_molecule.cpp.

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◆ prepare()

void ProDistanceInMolecule::prepare ( )

overridevirtual

Resize distance2_traj.

Returns: None.

Reimplemented from Processor.

Definition at line 85 of file pro_distance_in_molecule.cpp.

◆ run_impl()

void ProDistanceInMolecule::run_impl ( const int index )

overrideprotectedvirtual

Implementation of analysis using an element of generators.

Parameters

index An index in generators for a Generator object to be analyzed.

Returns: None.

To be compatible with multithreading computation, class members should not be modified in this method. If modification of some members is necessary, please consider defining them as Vec, and modifying only their i th element, where i = index.

I am sorry to say that the best documentation for this method is its source code...

Implements Processor.

Definition at line 43 of file pro_distance_in_molecule.cpp.

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◆ set_indices()

void ProDistanceInMolecule::set_indices	(	int	index1_in_mol_,
		int	index2_in_mol_
	)

Specify two atoms in a molecule by zero-based index. Distance between the two atoms is computed for each molecule.

Parameters

index1_in_mol_	A zero-based index in a molecule specifying a target atom. This parameter is assigned to index1_in_mol.
index2_in_mol_	A zero-based index in a molecule specifying the other target atom. This parameter is assigned to index2_in_mol.

Returns: None.

Definition at line 117 of file pro_distance_in_molecule.cpp.

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◆ set_moltype()

void ProDistanceInMolecule::set_moltype ( int target_moltype_ )

Specify a molecular type. Only molecules whose type property is the specified type are analyzed. If molecules have no type property, you do not need to use this method.

Parameters

target_moltype_ An integer for molecular type. This parameter is assigned to target_moltype.

Returns: None.

Definition at line 127 of file pro_distance_in_molecule.cpp.

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Member Data Documentation

◆ distance2_array

ArrayXXd ProDistanceInMolecule::distance2_array

private

A two-dimensional array of computed distances. Each column corresponds to a sequence of the distance for each molecule, and each row corresponds to each element of generators.

Definition at line 57 of file pro_distance_in_molecule.h.

◆ distance2_traj

Vec<RowArrayXd> ProDistanceInMolecule::distance2_traj

private

List in which RowArrayXd objects of computed distances of each molecule are stored. Indices in this list corresponds those in generators.

Definition at line 51 of file pro_distance_in_molecule.h.

◆ index1_in_mol

int ProDistanceInMolecule::index1_in_mol = 0

private

Zero-based index for an atom in a molecule. Distance between two atoms specified by index1_in_mol and index2_in_mol is calculated for each molecule.

Definition at line 32 of file pro_distance_in_molecule.h.

◆ index2_in_mol

int ProDistanceInMolecule::index2_in_mol = 0

private

Zero-based index for an atom in a molecule. Distance between two atoms specified by index1_in_mol and index2_in_mol is calculated for each molecule.

Definition at line 38 of file pro_distance_in_molecule.h.

◆ target_moltype

int ProDistanceInMolecule::target_moltype = 1

private

Specify a type of molecules to be analyzed (default is 1). Only molecules whose type is target_moltype are analyzed. Note that if molecules do not have type property, 1 is used as their types.

Definition at line 45 of file pro_distance_in_molecule.h.

The documentation for this class was generated from the following files:

src/processors/pro_distance_in_molecule.h
src/processors/pro_distance_in_molecule.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProDistanceInMolecule() [1/2]

◆ ProDistanceInMolecule() [2/2]

Member Function Documentation

◆ finish()

◆ get_distance2_array()

◆ get_distance_array()

◆ prepare()

◆ run_impl()

◆ set_indices()

◆ set_moltype()

Member Data Documentation

◆ distance2_array

◆ distance2_traj

◆ index1_in_mol

◆ index2_in_mol

◆ target_moltype