#include <aatopology.h>

Public Member Functions
	RigidFragment (pele::Array< double > atom_positions, Array< double > cog, double M, double W, Array< double > S, Array< double > inversion, bool can_invert, std::shared_ptr< DistanceInterface > distance_function)
size_t	natoms () const
void	add_symmetry_rotation (pele::Array< double > R)
std::vector< pele::MatrixNM < 3, 3 > > const &	get_symmetry_rotations () const
pele::Array< double >	to_atomistic (pele::Array< double > const com, pele::VecN< 3 > const &p)
void	transform_grad (pele::VecN< 3 > const &p, pele::Array< double > const g, pele::VecN< 3 > &g_com, pele::VecN< 3 > &g_rot)
void	transform_grad (pele::Array< double > const p, pele::Array< double > const g, pele::Array< double > g_com, pele::Array< double > g_rot)
pele::VecN< 3 >	get_smallest_rij (pele::VecN< 3 > const &com1, pele::VecN< 3 > const &com2) const
double	distance_squared (pele::VecN< 3 > const &com1, pele::VecN< 3 > const &p1, pele::VecN< 3 > const &com2, pele::VecN< 3 > const &p2) const
void	distance_squared_grad (pele::VecN< 3 > const &com1, pele::VecN< 3 > const &p1, pele::VecN< 3 > const &com2, pele::VecN< 3 > const &p2, VecN< 3 > &g_M, VecN< 3 > &g_P) const

Detailed Description

represent a single rigid body

Definition at line 199 of file aatopology.h.

Constructor & Destructor Documentation

pele::RigidFragment::RigidFragment	(	pele::Array< double >	atom_positions,
		Array< double >	cog,
		double	M,
		double	W,
		Array< double >	S,
		Array< double >	inversion,
		bool	can_invert,
		std::shared_ptr< DistanceInterface >	distance_function
	)		`[inline]`

Definition at line 219 of file aatopology.h.

void pele::RigidFragment::add_symmetry_rotation ( pele::Array< double > R ) [inline]

add a symmetry rotation

Definition at line 254 of file aatopology.h.

double pele::RigidFragment::distance_squared	(	pele::VecN< 3 > const &	com1,
		pele::VecN< 3 > const &	p1,
		pele::VecN< 3 > const &	com2,
		pele::VecN< 3 > const &	p2
	)		const

compute the squared distance between two configurations of the rigid fragment

Definition at line 79 of file aatopology.cpp.

void pele::RigidFragment::distance_squared_grad	(	pele::VecN< 3 > const &	com1,
		pele::VecN< 3 > const &	p1,
		pele::VecN< 3 > const &	com2,
		pele::VecN< 3 > const &	p2,
		VecN< 3 > &	g_M,
		VecN< 3 > &	g_P
	)		const

Definition at line 98 of file aatopology.cpp.

pele::VecN<3> pele::RigidFragment::get_smallest_rij	(	pele::VecN< 3 > const &	com1,
		pele::VecN< 3 > const &	com2
	)		const `[inline]`

return the shortest vector from com1 to com2

this could be replaced by periodic distances for instance

Definition at line 317 of file aatopology.h.

std::vector<pele::MatrixNM<3,3> > const& pele::RigidFragment::get_symmetry_rotations ( ) const [inline]

access the vector of symmetry rotations

Definition at line 262 of file aatopology.h.

size_t pele::RigidFragment::natoms ( ) const [inline]

return the number of atoms in the rigid body

Definition at line 249 of file aatopology.h.

pele::Array< double > pele::RigidFragment::to_atomistic	(	pele::Array< double > const	com,
		pele::VecN< 3 > const &	p
	)

convert a center of mass and a angle axis rotation to a set of atomistic coordinates

Definition at line 8 of file aatopology.cpp.

void pele::RigidFragment::transform_grad	(	pele::VecN< 3 > const &	p,
		pele::Array< double > const	g,
		pele::VecN< 3 > &	g_com,
		pele::VecN< 3 > &	g_rot
	)

transform an atomistic gradient into a gradient in the rigid body coordinates

Definition at line 32 of file aatopology.cpp.

void pele::RigidFragment::transform_grad	(	pele::Array< double > const	p,
		pele::Array< double > const	g,
		pele::Array< double >	g_com,
		pele::Array< double >	g_rot
	)		`[inline]`

transform an atomistic gradient into a gradient in the rigid body coordinates

This is simply a wrapper. This copies the data into VecN objects, calls transform_grad and copies it back.

copy the data back into the arrays

Definition at line 291 of file aatopology.h.

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