pteros::ForceField Class Reference

Force field parameters of the system. More...

#include <force_field.h>

Public Member Functions
	ForceField ()
	Constructor.
	ForceField (const ForceField &other)
	Copy constructor.
ForceField &	operator= (ForceField other)
	Assignment operator.
void	clear ()
void	setup_kernels ()
Eigen::Vector2f	pair_energy (int at1, int at2, float r, float q1, float q2, int type1, int type2)
float	get_cutoff ()
	Returns "natural" cutoff (currenly min of rcoulomb and rvdw)

Public Attributes
int	natoms
std::vector< std::unordered_set< int > >	exclusions
	Exclusions. More...
Eigen::MatrixXf	LJ_C6
	Matrices of normal (not excluded, not 1-4) LJ interactions. More...
Eigen::MatrixXf	LJ_C12
std::vector< Eigen::Vector2f >	LJ14_interactions
	The list of distinct types of LJ14 interactions in the format [C6,C12].
std::unordered_map< int, int >	LJ14_pairs
	The list of LJ14 pairs. More...
float	fudgeQQ
	Scaling factor of 1-4 Coulomb interactions.
float	rcoulomb
float	epsilon_r
float	epsilon_rf
float	rcoulomb_switch
float	rvdw_switch
float	rvdw
std::string	coulomb_type
std::string	coulomb_modifier
std::string	vdw_type
std::string	vdw_modifier
std::vector< Eigen::Vector2i >	bonds
	Bonds.
std::vector< Eigen::Vector2i >	molecules
bool	ready
	Is the force field properly set up?
float(*	coulomb_kernel_ptr )(float, float, float, const ForceField &)
	Pointer to chosen coulomb kernel.
float(*	LJ_kernel_ptr )(float, float, float, const ForceField &)
	Pointer to chosen VDW kernel.
float	coulomb_prefactor
float	k_rf
float	c_rf
Eigen::Vector3f	shift_1
Eigen::Vector3f	shift_6
Eigen::Vector3f	shift_12

Detailed Description

Force field parameters of the system.

MD packages usually separate topology and force filed i.e. interaction parameters and chemical identity and connectivity (bonds, angles, atom types, etc). This doesn't make much sense since atom types are part of particular force field and at the same time part of chemical identity, etc. In Pteros the force field is all information, which is needed to compute interactomic energies and forces in addition to what is stored already in Atom.

Atom already contains the following information: mass, charge, type and type_name. All the rest is stored in this class.

Member Data Documentation

exclusions

std::vector<std::unordered_set<int> > pteros::ForceField::exclusions

Exclusions.

The storage order is: (atom)-->[i1,i2,i3...in] which means that all interactions (atom:i1), (atom:i2) ... (atom:in) are excluded If atom has no exclusions the set is empty

LJ_C6

Eigen::MatrixXf pteros::ForceField::LJ_C6

Matrices of normal (not excluded, not 1-4) LJ interactions.

The size of the matrix == the number of distinct LJ types. The types themselves are integers and are stored in Atom.type Matrices are symmetric.

LJ14_pairs

std::unordered_map<int,int> pteros::ForceField::LJ14_pairs

The list of LJ14 pairs.

The mapping is (a*Natoms+b)->index in LJ14_interactions a<=b! This is important

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

• include/pteros/core/force_field.h
• src/core/force_field.cpp