pele Namespace Reference

Classes
class	CoordsAdaptor
class	TransformPolicy
class	TransformAACluster
class	MeasureAngleAxisCluster
class	RigidFragment
class	RBTopology
class	RBPotentialWrapper
class	_ArrayMemory
class	Array
class	AtomListPotential
class	BasePotential
class	EnergyAccumulator
class	EnergyGradientAccumulator
class	EnergyGradientHessianAccumulator
class	CellListPotential
class	CellListsLoop
class	CellLists
class	stupid_counter
class	CombinedPotential
struct	meta_dist
struct	meta_dist< 1 >
struct	cartesian_distance
struct	meta_periodic_distance
struct	meta_periodic_distance< 1 >
struct	meta_image
struct	meta_image< 1 >
class	periodic_distance
class	DistanceInterface
class	CartesianDistanceWrapper
class	PeriodicDistanceWrapper
class	FrozenCoordsConverter
class	FrozenPotentialWrapper
class	Edge
class	Node
class	Graph
class	BaseHarmonic
class	Harmonic
class	HarmonicCOM
struct	harmonic_interaction
class	HarmonicAtomList
class	HarmonicNeighborList
struct	sf_HS_WCA_interaction
struct	HS_WCA_interaction
class	HS_WCA
class	HS_WCAPeriodic
class	HS_WCACellLists
class	HS_WCAPeriodicCellLists
class	HS_WCAFrozen
class	HS_WCAPeriodicFrozen
class	HS_WCACellListsFrozen
class	HS_WCAPeriodicCellListsFrozen
class	HS_WCANeighborList
struct	InversePower_interaction
struct	InverseIntPower_interaction
struct	InverseHalfIntPower_interaction
class	InversePower
class	InversePowerPeriodic
class	InverseIntPower
class	InverseIntPowerPeriodic
class	InverseHalfIntPower
class	InverseHalfIntPowerPeriodic
class	InversePowerCellLists
class	InversePowerPeriodicCellLists
class	LBFGS
struct	lj_interaction
class	LJ
class	LJPeriodic
class	LJFrozen
class	LJNeighborList
struct	lj_interaction_cut_smooth
class	LJCut
class	LJCutPeriodic
class	LJCutAtomList
class	LJCutPeriodicAtomList
class	LJCutPeriodicCellLists
class	Orthogonalize
class	OrthogonalizeTranslational
class	LowestEigPotential
class	MatrixAdapter
struct	meta_pow
struct	meta_pow< T, 0 >
class	MODIFIED_FIRE
struct	morse_interaction
class	Morse
class	NGT
class	Optimizer
class	GradientOptimizer
class	PythonPotential
class	SimplePairwiseNeighborList
class	SimplePairwisePotential
class	VecN
class	MatrixNM
struct	WCA_interaction
class	WCA
class	WCA2D
class	WCAPeriodic
class	WCAPeriodic2D
class	WCANeighborList
class	WCAAtomList
Typedefs
typedef size_t	node_id
typedef Node *	node_ptr
typedef Edge *	edge_ptr
typedef int	color_type
Functions
MatrixNM< 3, 3 >	aa_to_rot_mat (pele::VecN< 3 > const &p)
pele::VecN< 4 >	rot_mat_to_quaternion (pele::MatrixNM< 3, 3 > const &mx)
pele::VecN< 3 >	quaternion_to_aa (pele::VecN< 4 > const &qin)
pele::VecN< 4 >	aa_to_quaternion (pele::VecN< 3 > const &aa)
pele::VecN< 4 >	quaternion_multiply (pele::VecN< 4 > const &q0, pele::VecN< 4 > const &q1)
void	rot_mat_derivatives_small_theta (pele::VecN< 3 > const &p, MatrixNM< 3, 3 > &rmat, MatrixNM< 3, 3 > &drm1, MatrixNM< 3, 3 > &drm2, MatrixNM< 3, 3 > &drm3, bool with_grad)
void	rot_mat_derivatives (pele::VecN< 3 > const &p, MatrixNM< 3, 3 > &rmat, MatrixNM< 3, 3 > &drm1, MatrixNM< 3, 3 > &drm2, MatrixNM< 3, 3 > &drm3)
template<class dtype >
std::ostream &	operator<< (std::ostream &out, const Array< dtype > &a)
double	dot (Array< double > const &v1, Array< double > const &v2)
double	norm (Array< double > const &v)
template<class T , class U >
Array< T >	operator* (const U rhs, const Array< T > &lhs)
std::ostream &	operator<< (std::ostream &out, std::shared_ptr< Graph > g)
void	zero_modes_translational (std::vector< pele::Array< double > > &zev, size_t natoms, size_t bdim)
template<class dtype >
MatrixAdapter< dtype >	hacky_mat_mul (MatrixAdapter< dtype > const &A, MatrixAdapter< dtype > const &B)
template<class dtype >
std::ostream &	operator<< (std::ostream &out, const pele::MatrixAdapter< dtype > &a)
template<int N, class T >
T	pos_int_pow (const T x)
template<int N, class T >
T	neg_int_pow (const T x)
template<int N, class T >
T	pos_half_int_pow (const T x)
template<int N, class T >
T	neg_half_int_pow (const T x)
bool	compare_degree (node_ptr u, node_ptr v)
pele::VecN< 3 >	rot_mat_to_aa (pele::MatrixNM< 3, 3 > const &mx)
pele::VecN< 3 >	rotate_aa (pele::VecN< 3 > const &p1, pele::VecN< 3 > const &p2)
template<size_t N>
double	dot (VecN< N > const &v1, VecN< N > const &v2)
template<size_t N>
double	norm (VecN< N > const &v)
template<size_t N, size_t L, size_t M>
MatrixNM< N, M >	dot (MatrixNM< N, L > const &A, MatrixNM< L, M > const &B)
template<size_t N, size_t M>
pele::VecN< N >	dot (MatrixNM< N, M > const &A, pele::VecN< M > const &v)
template<size_t N, size_t M>
pele::MatrixNM< M, N >	transpose (MatrixNM< N, M > const &A)
template<size_t N>
pele::MatrixNM< N, N >	identity ()
template<size_t N, size_t M>
std::ostream &	operator<< (std::ostream &out, const MatrixNM< N, M > &a)
template<size_t N>
std::ostream &	operator<< (std::ostream &out, const VecN< N > &a)
Variables
color_type	color_white = 0
color_type	color_grey = 1
color_type	color_black = 4

---

Detailed Description

This is a partial c++ implementation of the tools needed to interact with systems of rigid bodies. This is not a complete reimplementation, only the parts that were too slow in python were implemented here.

References on round etc: http://www.cplusplus.com/reference/cmath/floor/ http://www.cplusplus.com/reference/cmath/ceil/ http://www.cplusplus.com/reference/cmath/round/ These classes and structs are used by the potentials to compute distances. They must have a member function get_rij() with signature

void get_rij(double * r_ij, double const * const r1, double const * const r2)

Where r1 and r2 are the position of the two atoms and r_ij is an array of size 3 which will be used to return the distance vector from r1 to r2.

References: Used here: general reference on template meta-programming and recursive template functions: http://www.itp.phys.ethz.ch/education/hs12/programming_techniques

---

Typedef Documentation

typedef int pele::color_type

Definition at line 39 of file graph.hpp.

typedef Edge* pele::edge_ptr

Definition at line 38 of file graph.hpp.

typedef size_t pele::node_id

Definition at line 35 of file graph.hpp.

typedef Node* pele::node_ptr

Definition at line 37 of file graph.hpp.

---

Function Documentation

pele::VecN< 4 > pele::aa_to_quaternion

(

pele::VecN< 3 > const &

aa

)

Definition at line 119 of file rotations.cpp.

pele::MatrixNM< 3, 3 > pele::aa_to_rot_mat

(

pele::VecN< 3 > const &

p

)

make a rotation matrix from an angle axis

Definition at line 10 of file rotations.cpp.

bool pele::compare_degree	(	node_ptr	u,
		node_ptr	v
	)

Definition at line 29 of file ngt.hpp.

template<size_t N>

double pele::dot	(	VecN< N > const &	v1,
		VecN< N > const &	v2
	)		[inline]

compute the dot product of two Arrays

Definition at line 296 of file vecn.h.

template<size_t N, size_t L, size_t M>

MatrixNM<N,M> pele::dot	(	MatrixNM< N, L > const &	A,
		MatrixNM< L, M > const &	B
	)

matrix_multiplication

This is a really simple implementation of matrix multiplication. It is order N*M*L but can be done with much better scaling

Definition at line 322 of file vecn.h.

template<size_t N, size_t M>

pele::VecN<N> pele::dot	(	MatrixNM< N, M > const &	A,
		pele::VecN< M > const &	v
	)

multiply a matrix times an vector

Definition at line 341 of file vecn.h.

double pele::dot	(	Array< double > const &	v1,
		Array< double > const &	v2
	)		[inline]

compute the dot product of two Arrays

Definition at line 438 of file array.h.

template<class dtype >

MatrixAdapter<dtype> pele::hacky_mat_mul	(	MatrixAdapter< dtype > const &	A,
		MatrixAdapter< dtype > const &	B
	)

multiply two matrices. Note, this is a very inefficient way of doing matrix multiplication. If you have large matrices or care about speed you should use something else.

Definition at line 80 of file matrix.h.

template<size_t N>

pele::MatrixNM<N,N> pele::identity

(

)

Definition at line 367 of file vecn.h.

template<int N, class T >

T pele::neg_half_int_pow

(

const T

x

)

[inline]

pow(x, - N / 2) where N >= 0, integer usage: neg_half_int_pow<-N>(x)

Definition at line 74 of file meta_pow.h.

template<int N, class T >

T pele::neg_int_pow

(

const T

x

)

[inline]

pow(x, - N) where N >= 0, integer usage: neg_int_pow<-N>(x)

Definition at line 52 of file meta_pow.h.

template<size_t N>

double pele::norm

(

VecN< N > const &

v

)

[inline]

compute the L2 norm of an Array

Definition at line 309 of file vecn.h.

double pele::norm

(

Array< double > const &

v

)

[inline]

compute the L2 norm of an Array

Definition at line 447 of file array.h.

template<class T , class U >

Array<T> pele::operator*	(	const U	rhs,
		const Array< T > &	lhs
	)

Definition at line 453 of file array.h.

template<class dtype >

std::ostream& pele::operator<<	(	std::ostream &	out,
		const pele::MatrixAdapter< dtype > &	a
	)

multiply a matrix times an vector

Definition at line 123 of file matrix.h.

std::ostream& pele::operator<<	(	std::ostream &	out,
		std::shared_ptr< Graph >	g
	)		[inline]

Definition at line 303 of file graph.hpp.

template<size_t N, size_t M>

std::ostream& pele::operator<<	(	std::ostream &	out,
		const MatrixNM< N, M > &	a
	)		[inline]

Definition at line 378 of file vecn.h.

template<size_t N>

std::ostream& pele::operator<<	(	std::ostream &	out,
		const VecN< N > &	a
	)		[inline]

Definition at line 393 of file vecn.h.

template<class dtype >

std::ostream& pele::operator<<	(	std::ostream &	out,
		const Array< dtype > &	a
	)		[inline]

Definition at line 424 of file array.h.

template<int N, class T >

T pele::pos_half_int_pow

(

const T

x

)

[inline]

pow(x, N / 2) where N >= 0, integer usage: pos_half_int_pow<N>(x)

Definition at line 63 of file meta_pow.h.

template<int N, class T >

T pele::pos_int_pow

(

const T

x

)

[inline]

pow(x, N) where N >= 0, integer usage: pos_int_pow<N>(x)

Definition at line 41 of file meta_pow.h.

pele::VecN< 4 > pele::quaternion_multiply	(	pele::VecN< 4 > const &	q0,
		pele::VecN< 4 > const &	q1
	)

Definition at line 145 of file rotations.cpp.

pele::VecN< 3 > pele::quaternion_to_aa

(

pele::VecN< 4 > const &

qin

)

Definition at line 94 of file rotations.cpp.

void pele::rot_mat_derivatives	(	pele::VecN< 3 > const &	p,
		MatrixNM< 3, 3 > &	rmat,
		MatrixNM< 3, 3 > &	drm1,
		MatrixNM< 3, 3 > &	drm2,
		MatrixNM< 3, 3 > &	drm3
	)

make a rotation matrix and it's derivatives from an angle axis

Definition at line 232 of file rotations.cpp.

void pele::rot_mat_derivatives_small_theta	(	pele::VecN< 3 > const &	p,
		MatrixNM< 3, 3 > &	rmat,
		MatrixNM< 3, 3 > &	drm1,
		MatrixNM< 3, 3 > &	drm2,
		MatrixNM< 3, 3 > &	drm3,
		bool	with_grad
	)

compute the rotation matrix and it's derivatives from an angle axis vector if the rotation angle is very small

Definition at line 159 of file rotations.cpp.

pele::VecN<3> pele::rot_mat_to_aa

(

pele::MatrixNM< 3, 3 > const &

mx

)

[inline]

Definition at line 18 of file rotations.h.

pele::VecN< 4 > pele::rot_mat_to_quaternion

(

pele::MatrixNM< 3, 3 > const &

mx

)

Definition at line 55 of file rotations.cpp.

pele::VecN<3> pele::rotate_aa	(	pele::VecN< 3 > const &	p1,
		pele::VecN< 3 > const &	p2
	)		[inline]

change angle axis rotation p1 by the rotation p2

Definition at line 26 of file rotations.h.

template<size_t N, size_t M>

pele::MatrixNM<M,N> pele::transpose

(

MatrixNM< N, M > const &

A

)

Definition at line 355 of file vecn.h.

void pele::zero_modes_translational	(	std::vector< pele::Array< double > > &	zev,
		size_t	natoms,
		size_t	bdim
	)		[inline]

Definition at line 13 of file lowest_eig_potential.h.

---

Variable Documentation

color_type pele::color_black = 4

Definition at line 42 of file graph.hpp.

color_type pele::color_grey = 1

Definition at line 41 of file graph.hpp.

color_type pele::color_white = 0

Definition at line 40 of file graph.hpp.