T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT > Class Template Reference

#include <Potential_energy_parameters_libxml2.hpp>

Classes
class	Str_equal

Public Types
typedef T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >	Self
typedef SBL::IO::Loader_base	Base
typedef CovalentStructure	Covalent_structure
typedef UnitSystemTraits	Unit_system_traits
typedef CovalentStructure::Particle_rep	Particle_rep
typedef std::map< unsigned, std::string >	Index_to_type_map
typedef std::map< std::string, unsigned >	Name_to_index_map
typedef std::map< std::string, typename UnitSystemTraits::Length_quantity >	Unary_length_map
typedef std::map< std::string, Unary_length_map >	Binary_length_map
typedef std::map< std::string, Binary_length_map >	Ternary_length_map
typedef std::map< unsigned, typename UnitSystemTraits::Length_quantity >	Unary_length_nonbonded_map
typedef std::map< std::string, typename UnitSystemTraits::LJ_6_quantity >	Unary_attractive_map
typedef std::map< std::string, Unary_attractive_map >	Binary_attractive_map
typedef std::map< std::string, typename UnitSystemTraits::LJ_12_quantity >	Unary_repulsive_map
typedef std::map< std::string, Unary_repulsive_map >	Binary_repulsive_map
typedef std::map< std::string, typename UnitSystemTraits::Bond_force_constant_quantity >	Unary_length_energy_constant_map
typedef std::map< std::string, Unary_length_energy_constant_map >	Binary_length_energy_constant_map
typedef std::map< std::string, Binary_length_energy_constant_map >	Ternary_length_energy_constant_map
typedef std::map< std::string, typename UnitSystemTraits::Angle_quantity >	Unary_angle_map
typedef std::map< std::string, Unary_angle_map >	Binary_angle_map
typedef std::map< std::string, Binary_angle_map >	Ternary_angle_map
typedef std::map< unsigned, typename UnitSystemTraits::Angle_quantity >	Unary_torsion_angle_map
typedef std::map< std::string, Unary_torsion_angle_map >	Binary_torsion_angle_map
typedef std::map< std::string, Binary_torsion_angle_map >	Ternary_torsion_angle_map
typedef std::map< std::string, Ternary_torsion_angle_map >	Quaternary_torsion_angle_map
typedef std::map< std::string, Quaternary_torsion_angle_map >	Quinternary_torsion_angle_map
typedef std::map< std::string, typename UnitSystemTraits::Angle_force_constant_quantity >	Unary_angle_energy_map
typedef std::map< std::string, Unary_angle_energy_map >	Binary_angle_energy_map
typedef std::map< std::string, Binary_angle_energy_map >	Ternary_angle_energy_map
typedef std::map< unsigned, typename UnitSystemTraits::Angle_force_constant_quantity >	Unary_torsion_angle_energy_map
typedef std::map< std::string, Unary_torsion_angle_energy_map >	Binary_torsion_angle_energy_map
typedef std::map< std::string, Binary_torsion_angle_energy_map >	Ternary_torsion_angle_energy_map
typedef std::map< std::string, Ternary_torsion_angle_energy_map >	Quaternary_torsion_angle_energy_map
typedef std::map< std::string, Quaternary_torsion_angle_energy_map >	Quinternary_torsion_angle_energy_map
typedef std::map< unsigned, typename UnitSystemTraits::Charge_quantity >	Unary_charge_map
typedef std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity >	Unary_energy_nonbonded_map
typedef std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity >	Unary_torsion_energy_map
typedef std::map< std::string, Unary_torsion_energy_map >	Binary_torsion_energy_map
typedef std::map< std::string, Binary_torsion_energy_map >	Ternary_torsion_energy_map
typedef std::map< std::string, Ternary_torsion_energy_map >	Quaternary_torsion_energy_map
typedef std::map< std::string, Quaternary_torsion_energy_map >	Quinternary_torsion_energy_map
typedef std::vector< typename UnitSystemTraits::Molar_energy_quantity >	Unary_coefficients_parameters_map
typedef std::vector< Unary_coefficients_parameters_map >	Binary_coefficients_parameters_map
typedef std::map< FT, std::map< FT, FT > >	CMap_coefficients_map
typedef std::map< std::string, CMap_coefficients_map >	CMap_coefficients_map_1
typedef std::map< std::string, CMap_coefficients_map_1 >	CMap_coefficients_map_2
typedef std::map< std::string, CMap_coefficients_map_2 >	CMap_coefficients_map_3
typedef std::map< std::string, CMap_coefficients_map_3 >	CMap_coefficients_map_4
typedef std::map< std::string, CMap_coefficients_map_4 >	CMap_coefficients_map_5
typedef std::map< std::string, CMap_coefficients_map_5 >	CMap_coefficients_map_6
typedef std::map< std::string, CMap_coefficients_map_6 >	CMap_coefficients_map_7
typedef std::map< std::string, CMap_coefficients_map_7 >	CMap_coefficients_map_8
typedef std::map< std::string, unsigned >	CMap_resolution_map_1
typedef std::map< std::string, CMap_resolution_map_1 >	CMap_resolution_map_2
typedef std::map< std::string, CMap_resolution_map_2 >	CMap_resolution_map_3
typedef std::map< std::string, CMap_resolution_map_3 >	CMap_resolution_map_4
typedef std::map< std::string, CMap_resolution_map_4 >	CMap_resolution_map_5
typedef std::map< std::string, CMap_resolution_map_5 >	CMap_resolution_map_6
typedef std::map< std::string, CMap_resolution_map_6 >	CMap_resolution_map_7
typedef std::map< std::string, CMap_resolution_map_7 >	CMap_resolution_map_8
typedef SBL::CADS::T_Directed_acyclic_graph_with_layers< std::string >	Wildcards_DAG
typedef T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >	Self
typedef SBL::IO::Loader_base	Base
typedef CovalentStructure	Covalent_structure
typedef UnitSystemTraits	Unit_system_traits
typedef CovalentStructure::Particle_rep	Particle_rep
typedef std::map< unsigned, std::string >	Index_to_type_map
typedef std::map< std::string, unsigned >	Name_to_index_map
typedef std::map< std::string, typename UnitSystemTraits::Length_quantity >	Unary_length_map
typedef std::map< std::string, Unary_length_map >	Binary_length_map
typedef std::map< std::string, Binary_length_map >	Ternary_length_map
typedef std::map< unsigned, typename UnitSystemTraits::Length_quantity >	Unary_length_nonbonded_map
typedef std::map< std::string, typename UnitSystemTraits::LJ_6_quantity >	Unary_attractive_map
typedef std::map< std::string, Unary_attractive_map >	Binary_attractive_map
typedef std::map< std::string, typename UnitSystemTraits::LJ_12_quantity >	Unary_repulsive_map
typedef std::map< std::string, Unary_repulsive_map >	Binary_repulsive_map
typedef std::map< std::string, typename UnitSystemTraits::Bond_force_constant_quantity >	Unary_length_energy_constant_map
typedef std::map< std::string, Unary_length_energy_constant_map >	Binary_length_energy_constant_map
typedef std::map< std::string, Binary_length_energy_constant_map >	Ternary_length_energy_constant_map
typedef std::map< std::string, typename UnitSystemTraits::Angle_quantity >	Unary_angle_map
typedef std::map< std::string, Unary_angle_map >	Binary_angle_map
typedef std::map< std::string, Binary_angle_map >	Ternary_angle_map
typedef std::map< unsigned, typename UnitSystemTraits::Angle_quantity >	Unary_torsion_angle_map
typedef std::map< std::string, Unary_torsion_angle_map >	Binary_torsion_angle_map
typedef std::map< std::string, Binary_torsion_angle_map >	Ternary_torsion_angle_map
typedef std::map< std::string, Ternary_torsion_angle_map >	Quaternary_torsion_angle_map
typedef std::map< std::string, Quaternary_torsion_angle_map >	Quinternary_torsion_angle_map
typedef std::map< std::string, typename UnitSystemTraits::Angle_force_constant_quantity >	Unary_angle_energy_map
typedef std::map< std::string, Unary_angle_energy_map >	Binary_angle_energy_map
typedef std::map< std::string, Binary_angle_energy_map >	Ternary_angle_energy_map
typedef std::map< unsigned, typename UnitSystemTraits::Angle_force_constant_quantity >	Unary_torsion_angle_energy_map
typedef std::map< std::string, Unary_torsion_angle_energy_map >	Binary_torsion_angle_energy_map
typedef std::map< std::string, Binary_torsion_angle_energy_map >	Ternary_torsion_angle_energy_map
typedef std::map< std::string, Ternary_torsion_angle_energy_map >	Quaternary_torsion_angle_energy_map
typedef std::map< std::string, Quaternary_torsion_angle_energy_map >	Quinternary_torsion_angle_energy_map
typedef std::map< unsigned, typename UnitSystemTraits::Charge_quantity >	Unary_charge_map
typedef std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity >	Unary_energy_nonbonded_map
typedef std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity >	Unary_torsion_energy_map
typedef std::map< std::string, Unary_torsion_energy_map >	Binary_torsion_energy_map
typedef std::map< std::string, Binary_torsion_energy_map >	Ternary_torsion_energy_map
typedef std::map< std::string, Ternary_torsion_energy_map >	Quaternary_torsion_energy_map
typedef std::map< std::string, Quaternary_torsion_energy_map >	Quinternary_torsion_energy_map
typedef std::vector< typename UnitSystemTraits::Molar_energy_quantity >	Unary_coefficients_parameters_map
typedef std::vector< Unary_coefficients_parameters_map >	Binary_coefficients_parameters_map
typedef std::map< FT, std::map< FT, FT > >	CMap_coefficients_map
typedef std::map< std::string, CMap_coefficients_map >	CMap_coefficients_map_1
typedef std::map< std::string, CMap_coefficients_map_1 >	CMap_coefficients_map_2
typedef std::map< std::string, CMap_coefficients_map_2 >	CMap_coefficients_map_3
typedef std::map< std::string, CMap_coefficients_map_3 >	CMap_coefficients_map_4
typedef std::map< std::string, CMap_coefficients_map_4 >	CMap_coefficients_map_5
typedef std::map< std::string, CMap_coefficients_map_5 >	CMap_coefficients_map_6
typedef std::map< std::string, CMap_coefficients_map_6 >	CMap_coefficients_map_7
typedef std::map< std::string, CMap_coefficients_map_7 >	CMap_coefficients_map_8
typedef std::map< std::string, unsigned >	CMap_resolution_map_1
typedef std::map< std::string, CMap_resolution_map_1 >	CMap_resolution_map_2
typedef std::map< std::string, CMap_resolution_map_2 >	CMap_resolution_map_3
typedef std::map< std::string, CMap_resolution_map_3 >	CMap_resolution_map_4
typedef std::map< std::string, CMap_resolution_map_4 >	CMap_resolution_map_5
typedef std::map< std::string, CMap_resolution_map_5 >	CMap_resolution_map_6
typedef std::map< std::string, CMap_resolution_map_6 >	CMap_resolution_map_7
typedef std::map< std::string, CMap_resolution_map_7 >	CMap_resolution_map_8
typedef SBL::CADS::T_Directed_acyclic_graph_with_layers< std::string >	Wildcards_DAG

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module. More...
static bool	has_options (void)
static void	delete_options (void)
static void	initialize_options (const std::string &caption)

Attributes
static std::string	s_file_name = ""
	Input file name for this force field. More...
static bool	s_is_nanometer = false
	Multiplicative factor for distance terms. More...
static bool	s_is_kilojoule = false
static bool	s_is_degree = false
	Tag for the unit for angles. If degree, convert them in radian. More...
static bool	s_is_coulomb = false
	Tag for the unit for electric charge. If coulomb, convert them in q electron. More...
static bool	s_ignore_1_3_interactions = false
static unsigned	s_nb_sse_types = 0
	Number of secondary structure element types. More...
static Index_to_type_map	s_index_to_type
static Name_to_index_map	s_name_to_index
static std::vector< unsigned >	s_secondary_structure
static Binary_length_map	s_equilibrium_bond_length
	For bond length potential energy calculations. More...
static Binary_length_energy_constant_map	s_bond_length_force_constant
	name rk_r/2 in Wales code More...
static Ternary_angle_map	s_equilibrium_bond_angle
	For bond angle potential energy calculations. More...
static Ternary_angle_energy_map	s_bond_angle_force_constant
	name rk_theta/2 in Wales code More...
static Ternary_length_map	s_equilibrium_Urey_Bradley
	For Urey Bradley potential energy calculations. More...
static Ternary_length_energy_constant_map	s_Urey_Bradley_force_constant
	For Urey Bradley potential energy calculations. More...
static Quinternary_torsion_angle_map	s_equilibrium_torsion_angle
	For torsion angle potential energy calculations. More...
static Quinternary_torsion_energy_map	s_torsion_angle_force_constant
	For torsion angle potential energy calculations. More...
static Quinternary_torsion_angle_map	s_equilibrium_improper_angle
	For torsion angle potential energy calculations. More...
static CMap_coefficients_map_8	s_cmap_coefficients
	For cmap correction calculations. More...
static CMap_resolution_map_8	s_cmap_resolutions
	For cmap correction calculations. More...
static Quinternary_torsion_angle_energy_map	s_improper_angle_force_constant
	For torsion angle potential energy calculations. More...
static Binary_coefficients_parameters_map	s_dihedral_coefficients
	Defines the four coefficients for each secondary structure element. More...
static Binary_attractive_map	s_Lennard_Jones_attractive_constants
	For attractive vdW potential energy calculations. More...
static Binary_repulsive_map	s_Lennard_Jones_repulsive_constants
	For repulsive vdW potential energy calculations. More...
static Unary_energy_nonbonded_map	s_Lennard_Jones_epsilon_constants
	For epsilon vdW potential energy calculations. More...
static Unary_length_nonbonded_map	s_Lennard_Jones_sigma_constants
	For sigma vdW potential energy calculations. More...
static FT	s_fudge_LJ_constant = 1
	fudge Lennard Jones constant More...
static FT	s_fudge_LJ14_constant = 1
static Unary_charge_map	s_electrostatic_charges
	electrostatic charges (default is 0 for all) More...
static FT	s_fudge_QQ_constant = 1
	fudge screening factor constant More...
static FT	s_fudge_QQ14_constant = 1
static Wildcards_DAG	s_dag
static UnitSystemTraits::Length_quantity	get_input_length_unit (void)
static UnitSystemTraits::Molar_energy_quantity	get_input_molar_energy_unit (void)
static UnitSystemTraits::Angle_quantity	get_input_angle_unit (void)
static UnitSystemTraits::Charge_quantity	get_input_charge_unit (void)
static void	set_equilibrium_bond_length (const std::string &p1, const std::string &p2, const FT &v)
static void	set_bond_length_force_constant (const std::string &p1, const std::string &p2, const FT &v)
static void	set_equilibrium_bond_angle (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_bond_angle_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_equilibrium_Urey_Bradley (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_Urey_Bradley_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_equilibrium_torsion_angle (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_torsion_angle_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_equilibrium_improper_angle (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_improper_angle_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_cmap_resolution (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, const std::string &p5, const std::string &p6, const std::string &p7, const std::string &p8, unsigned resolution)
static void	set_cmap_coefficients (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, const std::string &p5, const std::string &p6, const std::string &p7, const std::string &p8, const std::map< FT, std::map< FT, FT > > &coefficients)
static void	set_dihedral_coefficient (unsigned ss_rep, unsigned num_coeff, const FT &v)
static void	set_Lennard_Jones_attractive_constant (const std::string &p1, const std::string &p2, const FT &v)
static void	set_Lennard_Jones_repulsive_constant (const std::string &p1, const std::string &p2, const FT &v)
static void	set_Lennard_Jones_epsilon_constant (unsigned index, const FT &v)
static void	set_Lennard_Jones_sigma_constant (unsigned index, const FT &v)
static void	set_fudge_LJ_constant (const FT &v)
static void	set_fudge_LJ14_constant (const FT &v)
static void	set_electrostatic_charge (unsigned index, const FT &v)
static void	set_fudge_QQ_constant (const FT &v)
static void	set_fudge_QQ14_constant (const FT &v)
static UnitSystemTraits::Length_quantity	get_input_length_unit (void)
static UnitSystemTraits::Molar_energy_quantity	get_input_molar_energy_unit (void)
static UnitSystemTraits::Angle_quantity	get_input_angle_unit (void)
static UnitSystemTraits::Charge_quantity	get_input_charge_unit (void)
static void	set_equilibrium_bond_length (const std::string &p1, const std::string &p2, const FT &v)
static void	set_bond_length_force_constant (const std::string &p1, const std::string &p2, const FT &v)
static void	set_equilibrium_bond_angle (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_bond_angle_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_equilibrium_Urey_Bradley (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_Urey_Bradley_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const FT &v)
static void	set_equilibrium_torsion_angle (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_torsion_angle_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_equilibrium_improper_angle (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_improper_angle_force_constant (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, unsigned n, const FT &v)
static void	set_cmap_resolution (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, const std::string &p5, const std::string &p6, const std::string &p7, const std::string &p8, unsigned resolution)
static void	set_cmap_coefficients (const std::string &p1, const std::string &p2, const std::string &p3, const std::string &p4, const std::string &p5, const std::string &p6, const std::string &p7, const std::string &p8, const std::map< FT, std::map< FT, FT > > &coefficients)
static void	set_dihedral_coefficient (unsigned ss_rep, unsigned num_coeff, const FT &v)
static void	set_Lennard_Jones_attractive_constant (const std::string &p1, const std::string &p2, const FT &v)
static void	set_Lennard_Jones_repulsive_constant (const std::string &p1, const std::string &p2, const FT &v)
static void	set_Lennard_Jones_epsilon_constant (unsigned index, const FT &v)
static void	set_Lennard_Jones_sigma_constant (unsigned index, const FT &v)
static void	set_fudge_LJ_constant (const FT &v)
static void	set_fudge_LJ14_constant (const FT &v)
static void	set_electrostatic_charge (unsigned index, const FT &v)
static void	set_fudge_QQ_constant (const FT &v)
static void	set_fudge_QQ14_constant (const FT &v)

Mandatory Requirements
static void	set_file_name (const std::string &file_name)
static void	set_is_nanometer (bool is_nanometer)
	Set a multiplicative factor for changing the metric unit of the force field. More...
static void	set_is_kilojoule (bool is_kilojoule)
	Set a multiplicative factor for changing the force constant unit of the force field. More...
static void	set_is_degree (bool is_degree)
	If true, angles are assumed to be expressed in degree rather than radian. More...
static void	set_is_coulomb (bool is_coulomb)
	If true, electric charge are assumed to be expressed in coulombs rather than q-electron. More...
static void	set_ignore_1_3_interactions (bool ignore_angles)
	When using a non-bonded visitor with a threshold, one can ignore 1_3 interactions here. More...
static bool	ignore_1_3_interactions (void)
static void	set_file_name (const std::string &file_name)
static void	set_is_nanometer (bool is_nanometer)
	Set a multiplicative factor for changing the metric unit of the force field. More...
static void	set_is_kilojoule (bool is_kilojoule)
	Set a multiplicative factor for changing the force constant unit of the force field. More...
static void	set_is_degree (bool is_degree)
	If true, angles are assumed to be expressed in degree rather than radian. More...
static void	set_is_coulomb (bool is_coulomb)
	If true, electric charge are assumed to be expressed in coulombs rather than q-electron. More...
static void	set_ignore_1_3_interactions (bool ignore_angles)
	When using a non-bonded visitor with a threshold, one can ignore 1_3 interactions here. More...
static bool	ignore_1_3_interactions (void)
boost::program_options::options_description	add_options (void) const
	Virtual method for adding options to the module. More...
bool	load (unsigned verbose=0, std::ostream &out=std::cout)
	Loads the data. More...
bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. More...
std::string	get_output_prefix (void) const
	Returns a prefix that concatains the input line options used when running the module. More...
std::string	get_name (void) const
	Return the name of the class itself. More...
boost::program_options::options_description	add_options (void) const
	Virtual method for adding options to the module. More...
bool	load (unsigned verbose=0, std::ostream &out=std::cout)
	Loads the data. More...
bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. More...
std::string	get_output_prefix (void) const
	Returns a prefix that concatains the input line options used when running the module. More...
std::string	get_name (void) const
	Return the name of the class itself. More...

Accessors
static UnitSystemTraits::Length_quantity	get_equilibrium_bond_length (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Length_quantity	get_equilibrium_bond_length (const Covalent_structure &C, const typename Covalent_structure::Bond_rep &b)
static UnitSystemTraits::Bond_force_constant_quantity	get_bond_length_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Bond_force_constant_quantity	get_bond_length_force_constant (const Covalent_structure &C, const typename Covalent_structure::Bond_rep &b)
static UnitSystemTraits::Angle_quantity	get_equilibrium_bond_angle (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Angle_quantity	get_equilibrium_bond_angle (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static UnitSystemTraits::Angle_force_constant_quantity	get_bond_angle_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Angle_force_constant_quantity	get_bond_angle_force_constant (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static UnitSystemTraits::Length_quantity	get_equilibrium_Urey_Bradley (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Length_quantity	get_equilibrium_Urey_Bradley (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static UnitSystemTraits::Bond_force_constant_quantity	get_Urey_Bradley_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Bond_force_constant_quantity	get_Urey_Bradley_force_constant (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static const std::map< unsigned, typename UnitSystemTraits::Angle_quantity > *	get_equilibrium_torsion_angles (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static const std::map< unsigned, typename UnitSystemTraits::Angle_quantity > *	get_equilibrium_torsion_angles (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static const std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity > *	get_torsion_angle_force_constants (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static const std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity > *	get_torsion_angle_force_constants (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static unsigned	get_torsion_angle_number_of_periods (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Molar_energy_quantity >	get_torsion_angle_parameters (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b, unsigned i)
static std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Angle_force_constant_quantity >	get_improper_angle_parameters (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static UnitSystemTraits::Angle_quantity	get_equilibrium_improper_angle (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static UnitSystemTraits::Angle_quantity	get_equilibrium_improper_angle (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static UnitSystemTraits::Angle_force_constant_quantity	get_improper_angle_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static UnitSystemTraits::Angle_force_constant_quantity	get_improper_angle_force_constant (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static unsigned	get_cmap_resolution (const Covalent_structure &C, const Particle_rep &p1, const Particle_rep &p2, const Particle_rep &p3, const Particle_rep &p4, const Particle_rep &q1, const Particle_rep &q2, const Particle_rep &q3, const Particle_rep &q4)
static const CMap_coefficients_map *	get_cmap_coefficients (const Covalent_structure &C, const Particle_rep &p1, const Particle_rep &p2, const Particle_rep &p3, const Particle_rep &p4, const Particle_rep &q1, const Particle_rep &q2, const Particle_rep &q3, const Particle_rep &q4)
static UnitSystemTraits::Molar_energy_quantity	get_dihedral_coefficient (const Covalent_structure &C, const Particle_rep &p, unsigned i)
static UnitSystemTraits::LJ_6_quantity	get_Lennard_Jones_attractive_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::LJ_12_quantity	get_Lennard_Jones_repulsive_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Molar_energy_quantity	get_Lennard_Jones_epsilon_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Charge_quantity	get_electrostatic_charge (const Covalent_structure &C, const Particle_rep &p)
static UnitSystemTraits::Dielectric_constant_quantity	get_dielectric_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Length_quantity	get_equilibrium_bond_length (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Length_quantity	get_equilibrium_bond_length (const Covalent_structure &C, const typename Covalent_structure::Bond_rep &b)
static UnitSystemTraits::Bond_force_constant_quantity	get_bond_length_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Bond_force_constant_quantity	get_bond_length_force_constant (const Covalent_structure &C, const typename Covalent_structure::Bond_rep &b)
static UnitSystemTraits::Angle_quantity	get_equilibrium_bond_angle (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Angle_quantity	get_equilibrium_bond_angle (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static UnitSystemTraits::Angle_force_constant_quantity	get_bond_angle_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Angle_force_constant_quantity	get_bond_angle_force_constant (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static UnitSystemTraits::Length_quantity	get_equilibrium_Urey_Bradley (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Length_quantity	get_equilibrium_Urey_Bradley (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static UnitSystemTraits::Bond_force_constant_quantity	get_Urey_Bradley_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r)
static UnitSystemTraits::Bond_force_constant_quantity	get_Urey_Bradley_force_constant (const Covalent_structure &C, const typename Covalent_structure::Bond_angle_rep &b)
static const std::map< unsigned, typename UnitSystemTraits::Angle_quantity > *	get_equilibrium_torsion_angles (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static const std::map< unsigned, typename UnitSystemTraits::Angle_quantity > *	get_equilibrium_torsion_angles (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static const std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity > *	get_torsion_angle_force_constants (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static const std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity > *	get_torsion_angle_force_constants (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static unsigned	get_torsion_angle_number_of_periods (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Molar_energy_quantity >	get_torsion_angle_parameters (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b, unsigned i)
static std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Angle_force_constant_quantity >	get_improper_angle_parameters (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static UnitSystemTraits::Angle_quantity	get_equilibrium_improper_angle (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static UnitSystemTraits::Angle_quantity	get_equilibrium_improper_angle (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static UnitSystemTraits::Angle_force_constant_quantity	get_improper_angle_force_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q, const Particle_rep &r, const Particle_rep &t)
static UnitSystemTraits::Angle_force_constant_quantity	get_improper_angle_force_constant (const Covalent_structure &C, const typename Covalent_structure::Torsion_angle_rep &b)
static unsigned	get_cmap_resolution (const Covalent_structure &C, const Particle_rep &p1, const Particle_rep &p2, const Particle_rep &p3, const Particle_rep &p4, const Particle_rep &q1, const Particle_rep &q2, const Particle_rep &q3, const Particle_rep &q4)
static const CMap_coefficients_map *	get_cmap_coefficients (const Covalent_structure &C, const Particle_rep &p1, const Particle_rep &p2, const Particle_rep &p3, const Particle_rep &p4, const Particle_rep &q1, const Particle_rep &q2, const Particle_rep &q3, const Particle_rep &q4)
static UnitSystemTraits::Molar_energy_quantity	get_dihedral_coefficient (const Covalent_structure &C, const Particle_rep &p, unsigned i)
static UnitSystemTraits::LJ_6_quantity	get_Lennard_Jones_attractive_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::LJ_12_quantity	get_Lennard_Jones_repulsive_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Molar_energy_quantity	get_Lennard_Jones_epsilon_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)
static UnitSystemTraits::Charge_quantity	get_electrostatic_charge (const Covalent_structure &C, const Particle_rep &p)
static UnitSystemTraits::Dielectric_constant_quantity	get_dielectric_constant (const Covalent_structure &C, const Particle_rep &p, const Particle_rep &q)

Management
void	set_loader_instance_name (const std::string &loader_instance_name)
const std::string &	get_loader_instance_name (void) const

Member Typedef Documentation

Base [1/2]

typedef SBL::IO::Loader_base Base

Base [2/2]

typedef SBL::IO::Loader_base Base

Binary_angle_energy_map [1/2]

typedef std::map<std::string, Unary_angle_energy_map> Binary_angle_energy_map

Binary_angle_energy_map [2/2]

typedef std::map<std::string, Unary_angle_energy_map> Binary_angle_energy_map

Binary_angle_map [1/2]

typedef std::map<std::string, Unary_angle_map> Binary_angle_map

Binary_angle_map [2/2]

typedef std::map<std::string, Unary_angle_map> Binary_angle_map

Binary_attractive_map [1/2]

typedef std::map<std::string, Unary_attractive_map> Binary_attractive_map

Binary_attractive_map [2/2]

typedef std::map<std::string, Unary_attractive_map> Binary_attractive_map

Binary_coefficients_parameters_map [1/2]

typedef std::vector<Unary_coefficients_parameters_map> Binary_coefficients_parameters_map

Binary_coefficients_parameters_map [2/2]

typedef std::vector<Unary_coefficients_parameters_map> Binary_coefficients_parameters_map

Binary_length_energy_constant_map [1/2]

typedef std::map<std::string, Unary_length_energy_constant_map> Binary_length_energy_constant_map

Binary_length_energy_constant_map [2/2]

typedef std::map<std::string, Unary_length_energy_constant_map> Binary_length_energy_constant_map

Binary_length_map [1/2]

typedef std::map<std::string, Unary_length_map> Binary_length_map

Binary_length_map [2/2]

typedef std::map<std::string, Unary_length_map> Binary_length_map

Binary_repulsive_map [1/2]

typedef std::map<std::string, Unary_repulsive_map> Binary_repulsive_map

Binary_repulsive_map [2/2]

typedef std::map<std::string, Unary_repulsive_map> Binary_repulsive_map

Binary_torsion_angle_energy_map [1/2]

typedef std::map<std::string, Unary_torsion_angle_energy_map> Binary_torsion_angle_energy_map

Binary_torsion_angle_energy_map [2/2]

typedef std::map<std::string, Unary_torsion_angle_energy_map> Binary_torsion_angle_energy_map

Binary_torsion_angle_map [1/2]

typedef std::map<std::string, Unary_torsion_angle_map> Binary_torsion_angle_map

Binary_torsion_angle_map [2/2]

typedef std::map<std::string, Unary_torsion_angle_map> Binary_torsion_angle_map

Binary_torsion_energy_map [1/2]

typedef std::map<std::string, Unary_torsion_energy_map> Binary_torsion_energy_map

Binary_torsion_energy_map [2/2]

typedef std::map<std::string, Unary_torsion_energy_map> Binary_torsion_energy_map

CMap_coefficients_map [1/2]

typedef std::map<FT, std::map<FT, FT> > CMap_coefficients_map

CMap_coefficients_map [2/2]

typedef std::map<FT, std::map<FT, FT> > CMap_coefficients_map

CMap_coefficients_map_1 [1/2]

typedef std::map<std::string, CMap_coefficients_map> CMap_coefficients_map_1

CMap_coefficients_map_1 [2/2]

typedef std::map<std::string, CMap_coefficients_map> CMap_coefficients_map_1

CMap_coefficients_map_2 [1/2]

typedef std::map<std::string, CMap_coefficients_map_1> CMap_coefficients_map_2

CMap_coefficients_map_2 [2/2]

typedef std::map<std::string, CMap_coefficients_map_1> CMap_coefficients_map_2

CMap_coefficients_map_3 [1/2]

typedef std::map<std::string, CMap_coefficients_map_2> CMap_coefficients_map_3

CMap_coefficients_map_3 [2/2]

typedef std::map<std::string, CMap_coefficients_map_2> CMap_coefficients_map_3

CMap_coefficients_map_4 [1/2]

typedef std::map<std::string, CMap_coefficients_map_3> CMap_coefficients_map_4

CMap_coefficients_map_4 [2/2]

typedef std::map<std::string, CMap_coefficients_map_3> CMap_coefficients_map_4

CMap_coefficients_map_5 [1/2]

typedef std::map<std::string, CMap_coefficients_map_4> CMap_coefficients_map_5

CMap_coefficients_map_5 [2/2]

typedef std::map<std::string, CMap_coefficients_map_4> CMap_coefficients_map_5

CMap_coefficients_map_6 [1/2]

typedef std::map<std::string, CMap_coefficients_map_5> CMap_coefficients_map_6

CMap_coefficients_map_6 [2/2]

typedef std::map<std::string, CMap_coefficients_map_5> CMap_coefficients_map_6

CMap_coefficients_map_7 [1/2]

typedef std::map<std::string, CMap_coefficients_map_6> CMap_coefficients_map_7

CMap_coefficients_map_7 [2/2]

typedef std::map<std::string, CMap_coefficients_map_6> CMap_coefficients_map_7

CMap_coefficients_map_8 [1/2]

typedef std::map<std::string, CMap_coefficients_map_7> CMap_coefficients_map_8

CMap_coefficients_map_8 [2/2]

typedef std::map<std::string, CMap_coefficients_map_7> CMap_coefficients_map_8

CMap_resolution_map_1 [1/2]

typedef std::map<std::string, unsigned> CMap_resolution_map_1

CMap_resolution_map_1 [2/2]

typedef std::map<std::string, unsigned> CMap_resolution_map_1

CMap_resolution_map_2 [1/2]

typedef std::map<std::string, CMap_resolution_map_1> CMap_resolution_map_2

CMap_resolution_map_2 [2/2]

typedef std::map<std::string, CMap_resolution_map_1> CMap_resolution_map_2

CMap_resolution_map_3 [1/2]

typedef std::map<std::string, CMap_resolution_map_2> CMap_resolution_map_3

CMap_resolution_map_3 [2/2]

typedef std::map<std::string, CMap_resolution_map_2> CMap_resolution_map_3

CMap_resolution_map_4 [1/2]

typedef std::map<std::string, CMap_resolution_map_3> CMap_resolution_map_4

CMap_resolution_map_4 [2/2]

typedef std::map<std::string, CMap_resolution_map_3> CMap_resolution_map_4

CMap_resolution_map_5 [1/2]

typedef std::map<std::string, CMap_resolution_map_4> CMap_resolution_map_5

CMap_resolution_map_5 [2/2]

typedef std::map<std::string, CMap_resolution_map_4> CMap_resolution_map_5

CMap_resolution_map_6 [1/2]

typedef std::map<std::string, CMap_resolution_map_5> CMap_resolution_map_6

CMap_resolution_map_6 [2/2]

typedef std::map<std::string, CMap_resolution_map_5> CMap_resolution_map_6

CMap_resolution_map_7 [1/2]

typedef std::map<std::string, CMap_resolution_map_6> CMap_resolution_map_7

CMap_resolution_map_7 [2/2]

typedef std::map<std::string, CMap_resolution_map_6> CMap_resolution_map_7

CMap_resolution_map_8 [1/2]

typedef std::map<std::string, CMap_resolution_map_7> CMap_resolution_map_8

CMap_resolution_map_8 [2/2]

typedef std::map<std::string, CMap_resolution_map_7> CMap_resolution_map_8

Covalent_structure [1/2]

typedef CovalentStructure Covalent_structure

Covalent_structure [2/2]

typedef CovalentStructure Covalent_structure

Index_to_type_map [1/2]

typedef std::map<unsigned, std::string> Index_to_type_map

Index_to_type_map [2/2]

typedef std::map<unsigned, std::string> Index_to_type_map

Name_to_index_map [1/2]

typedef std::map<std::string, unsigned> Name_to_index_map

Name_to_index_map [2/2]

typedef std::map<std::string, unsigned> Name_to_index_map

Particle_rep [1/2]

typedef CovalentStructure::Particle_rep Particle_rep

Particle_rep [2/2]

typedef CovalentStructure::Particle_rep Particle_rep

Quaternary_torsion_angle_energy_map [1/2]

typedef std::map<std::string, Ternary_torsion_angle_energy_map> Quaternary_torsion_angle_energy_map

Quaternary_torsion_angle_energy_map [2/2]

typedef std::map<std::string, Ternary_torsion_angle_energy_map> Quaternary_torsion_angle_energy_map

Quaternary_torsion_angle_map [1/2]

typedef std::map<std::string, Ternary_torsion_angle_map> Quaternary_torsion_angle_map

Quaternary_torsion_angle_map [2/2]

typedef std::map<std::string, Ternary_torsion_angle_map> Quaternary_torsion_angle_map

Quaternary_torsion_energy_map [1/2]

typedef std::map<std::string, Ternary_torsion_energy_map> Quaternary_torsion_energy_map

Quaternary_torsion_energy_map [2/2]

typedef std::map<std::string, Ternary_torsion_energy_map> Quaternary_torsion_energy_map

Quinternary_torsion_angle_energy_map [1/2]

typedef std::map<std::string, Quaternary_torsion_angle_energy_map> Quinternary_torsion_angle_energy_map

Quinternary_torsion_angle_energy_map [2/2]

typedef std::map<std::string, Quaternary_torsion_angle_energy_map> Quinternary_torsion_angle_energy_map

Quinternary_torsion_angle_map [1/2]

typedef std::map<std::string, Quaternary_torsion_angle_map> Quinternary_torsion_angle_map

Quinternary_torsion_angle_map [2/2]

typedef std::map<std::string, Quaternary_torsion_angle_map> Quinternary_torsion_angle_map

Quinternary_torsion_energy_map [1/2]

typedef std::map<std::string, Quaternary_torsion_energy_map> Quinternary_torsion_energy_map

Quinternary_torsion_energy_map [2/2]

typedef std::map<std::string, Quaternary_torsion_energy_map> Quinternary_torsion_energy_map

Self [1/2]

typedef T_Potential_energy_parameters<CovalentStructure, UnitSystemTraits, FT> Self

Self [2/2]

typedef T_Potential_energy_parameters<CovalentStructure, UnitSystemTraits, FT> Self

Ternary_angle_energy_map [1/2]

typedef std::map<std::string, Binary_angle_energy_map> Ternary_angle_energy_map

Ternary_angle_energy_map [2/2]

typedef std::map<std::string, Binary_angle_energy_map> Ternary_angle_energy_map

Ternary_angle_map [1/2]

typedef std::map<std::string, Binary_angle_map> Ternary_angle_map

Ternary_angle_map [2/2]

typedef std::map<std::string, Binary_angle_map> Ternary_angle_map

Ternary_length_energy_constant_map [1/2]

typedef std::map<std::string, Binary_length_energy_constant_map> Ternary_length_energy_constant_map

Ternary_length_energy_constant_map [2/2]

typedef std::map<std::string, Binary_length_energy_constant_map> Ternary_length_energy_constant_map

Ternary_length_map [1/2]

typedef std::map<std::string, Binary_length_map> Ternary_length_map

Ternary_length_map [2/2]

typedef std::map<std::string, Binary_length_map> Ternary_length_map

Ternary_torsion_angle_energy_map [1/2]

typedef std::map<std::string, Binary_torsion_angle_energy_map> Ternary_torsion_angle_energy_map

Ternary_torsion_angle_energy_map [2/2]

typedef std::map<std::string, Binary_torsion_angle_energy_map> Ternary_torsion_angle_energy_map

Ternary_torsion_angle_map [1/2]

typedef std::map<std::string, Binary_torsion_angle_map> Ternary_torsion_angle_map

Ternary_torsion_angle_map [2/2]

typedef std::map<std::string, Binary_torsion_angle_map> Ternary_torsion_angle_map

Ternary_torsion_energy_map [1/2]

typedef std::map<std::string, Binary_torsion_energy_map> Ternary_torsion_energy_map

Ternary_torsion_energy_map [2/2]

typedef std::map<std::string, Binary_torsion_energy_map> Ternary_torsion_energy_map

Unary_angle_energy_map [1/2]

typedef std::map<std::string, typename UnitSystemTraits::Angle_force_constant_quantity> Unary_angle_energy_map

Unary_angle_energy_map [2/2]

typedef std::map<std::string, typename UnitSystemTraits::Angle_force_constant_quantity> Unary_angle_energy_map

Unary_angle_map [1/2]

typedef std::map<std::string, typename UnitSystemTraits::Angle_quantity> Unary_angle_map

Unary_angle_map [2/2]

typedef std::map<std::string, typename UnitSystemTraits::Angle_quantity> Unary_angle_map

Unary_attractive_map [1/2]

typedef std::map<std::string, typename UnitSystemTraits::LJ_6_quantity> Unary_attractive_map

Unary_attractive_map [2/2]

typedef std::map<std::string, typename UnitSystemTraits::LJ_6_quantity> Unary_attractive_map

Unary_charge_map [1/2]

typedef std::map<unsigned, typename UnitSystemTraits::Charge_quantity> Unary_charge_map

Unary_charge_map [2/2]

typedef std::map<unsigned, typename UnitSystemTraits::Charge_quantity> Unary_charge_map

Unary_coefficients_parameters_map [1/2]

typedef std::vector<typename UnitSystemTraits::Molar_energy_quantity> Unary_coefficients_parameters_map

Unary_coefficients_parameters_map [2/2]

typedef std::vector<typename UnitSystemTraits::Molar_energy_quantity> Unary_coefficients_parameters_map

Unary_energy_nonbonded_map [1/2]

typedef std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity> Unary_energy_nonbonded_map

Unary_energy_nonbonded_map [2/2]

typedef std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity> Unary_energy_nonbonded_map

Unary_length_energy_constant_map [1/2]

typedef std::map<std::string, typename UnitSystemTraits::Bond_force_constant_quantity> Unary_length_energy_constant_map

Unary_length_energy_constant_map [2/2]

typedef std::map<std::string, typename UnitSystemTraits::Bond_force_constant_quantity> Unary_length_energy_constant_map

Unary_length_map [1/2]

typedef std::map<std::string, typename UnitSystemTraits::Length_quantity> Unary_length_map

Unary_length_map [2/2]

typedef std::map<std::string, typename UnitSystemTraits::Length_quantity> Unary_length_map

Unary_length_nonbonded_map [1/2]

typedef std::map<unsigned, typename UnitSystemTraits::Length_quantity> Unary_length_nonbonded_map

Unary_length_nonbonded_map [2/2]

typedef std::map<unsigned, typename UnitSystemTraits::Length_quantity> Unary_length_nonbonded_map

Unary_repulsive_map [1/2]

typedef std::map<std::string, typename UnitSystemTraits::LJ_12_quantity> Unary_repulsive_map

Unary_repulsive_map [2/2]

typedef std::map<std::string, typename UnitSystemTraits::LJ_12_quantity> Unary_repulsive_map

Unary_torsion_angle_energy_map [1/2]

typedef std::map<unsigned, typename UnitSystemTraits::Angle_force_constant_quantity> Unary_torsion_angle_energy_map

Unary_torsion_angle_energy_map [2/2]

typedef std::map<unsigned, typename UnitSystemTraits::Angle_force_constant_quantity> Unary_torsion_angle_energy_map

Unary_torsion_angle_map [1/2]

typedef std::map<unsigned, typename UnitSystemTraits::Angle_quantity> Unary_torsion_angle_map

Unary_torsion_angle_map [2/2]

typedef std::map<unsigned, typename UnitSystemTraits::Angle_quantity> Unary_torsion_angle_map

Unary_torsion_energy_map [1/2]

typedef std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity> Unary_torsion_energy_map

Unary_torsion_energy_map [2/2]

typedef std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity> Unary_torsion_energy_map

Unit_system_traits [1/2]

typedef UnitSystemTraits Unit_system_traits

Unit_system_traits [2/2]

typedef UnitSystemTraits Unit_system_traits

Wildcards_DAG [1/2]

typedef SBL::CADS::T_Directed_acyclic_graph_with_layers<std::string> Wildcards_DAG

Wildcards_DAG [2/2]

typedef SBL::CADS::T_Directed_acyclic_graph_with_layers<std::string> Wildcards_DAG

Member Function Documentation

add_options() [1/2]

boost::program_options::options_description add_options ( void  ) const

inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

add_options() [2/2]

boost::program_options::options_description add_options ( void  ) const

inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

check_options() [1/2]

bool check_options ( std::string &  message ) const

inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

check_options() [2/2]

bool check_options ( std::string &  message ) const

inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

delete_options()

static void delete_options ( void  )

inlinestaticinherited

get_bond_angle_force_constant() [1/4]

UnitSystemTraits::Angle_force_constant_quantity get_bond_angle_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_bond_angle_force_constant() [2/4]

static UnitSystemTraits::Angle_force_constant_quantity get_bond_angle_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_bond_angle_force_constant() [3/4]

static UnitSystemTraits::Angle_force_constant_quantity get_bond_angle_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_bond_angle_force_constant() [4/4]

static UnitSystemTraits::Angle_force_constant_quantity get_bond_angle_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_bond_length_force_constant() [1/4]

UnitSystemTraits::Bond_force_constant_quantity get_bond_length_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_bond_length_force_constant() [2/4]

static UnitSystemTraits::Bond_force_constant_quantity get_bond_length_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_bond_length_force_constant() [3/4]

static UnitSystemTraits::Bond_force_constant_quantity get_bond_length_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Bond_rep &  b  )

inlinestatic

get_bond_length_force_constant() [4/4]

static UnitSystemTraits::Bond_force_constant_quantity get_bond_length_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Bond_rep &  b  )

inlinestatic

get_cmap_coefficients() [1/2]

const T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::CMap_coefficients_map * get_cmap_coefficients ( const Covalent_structure &  C, const Particle_rep &  p1, const Particle_rep &  p2, const Particle_rep &  p3, const Particle_rep &  p4, const Particle_rep &  q1, const Particle_rep &  q2, const Particle_rep &  q3, const Particle_rep &  q4  )

inlinestatic

get_cmap_coefficients() [2/2]

static const CMap_coefficients_map* get_cmap_coefficients ( const Covalent_structure &  C, const Particle_rep &  p1, const Particle_rep &  p2, const Particle_rep &  p3, const Particle_rep &  p4, const Particle_rep &  q1, const Particle_rep &  q2, const Particle_rep &  q3, const Particle_rep &  q4  )

inlinestatic

get_cmap_resolution() [1/2]

unsigned get_cmap_resolution ( const Covalent_structure &  C, const Particle_rep &  p1, const Particle_rep &  p2, const Particle_rep &  p3, const Particle_rep &  p4, const Particle_rep &  q1, const Particle_rep &  q2, const Particle_rep &  q3, const Particle_rep &  q4  )

inlinestatic

get_cmap_resolution() [2/2]

static unsigned get_cmap_resolution ( const Covalent_structure &  C, const Particle_rep &  p1, const Particle_rep &  p2, const Particle_rep &  p3, const Particle_rep &  p4, const Particle_rep &  q1, const Particle_rep &  q2, const Particle_rep &  q3, const Particle_rep &  q4  )

inlinestatic

get_dielectric_constant() [1/2]

UnitSystemTraits::Dielectric_constant_quantity get_dielectric_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_dielectric_constant() [2/2]

static UnitSystemTraits::Dielectric_constant_quantity get_dielectric_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_dihedral_coefficient() [1/2]

UnitSystemTraits::Molar_energy_quantity get_dihedral_coefficient ( const Covalent_structure &  C, const Particle_rep &  p, unsigned  i  )

inlinestatic

get_dihedral_coefficient() [2/2]

static UnitSystemTraits::Molar_energy_quantity get_dihedral_coefficient ( const Covalent_structure &  C, const Particle_rep &  p, unsigned  i  )

inlinestatic

get_electrostatic_charge() [1/2]

UnitSystemTraits::Charge_quantity get_electrostatic_charge ( const Covalent_structure &  C, const Particle_rep &  p  )

inlinestatic

get_electrostatic_charge() [2/2]

static UnitSystemTraits::Charge_quantity get_electrostatic_charge ( const Covalent_structure &  C, const Particle_rep &  p  )

inlinestatic

get_equilibrium_bond_angle() [1/4]

UnitSystemTraits::Angle_quantity get_equilibrium_bond_angle ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_equilibrium_bond_angle() [2/4]

static UnitSystemTraits::Angle_quantity get_equilibrium_bond_angle ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_equilibrium_bond_angle() [3/4]

static UnitSystemTraits::Angle_quantity get_equilibrium_bond_angle ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_equilibrium_bond_angle() [4/4]

static UnitSystemTraits::Angle_quantity get_equilibrium_bond_angle ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_equilibrium_bond_length() [1/4]

UnitSystemTraits::Length_quantity get_equilibrium_bond_length ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_equilibrium_bond_length() [2/4]

static UnitSystemTraits::Length_quantity get_equilibrium_bond_length ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_equilibrium_bond_length() [3/4]

static UnitSystemTraits::Length_quantity get_equilibrium_bond_length ( const Covalent_structure &  C, const typename Covalent_structure::Bond_rep &  b  )

inlinestatic

get_equilibrium_bond_length() [4/4]

static UnitSystemTraits::Length_quantity get_equilibrium_bond_length ( const Covalent_structure &  C, const typename Covalent_structure::Bond_rep &  b  )

inlinestatic

get_equilibrium_improper_angle() [1/4]

UnitSystemTraits::Angle_quantity get_equilibrium_improper_angle ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_equilibrium_improper_angle() [2/4]

static UnitSystemTraits::Angle_quantity get_equilibrium_improper_angle ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_equilibrium_improper_angle() [3/4]

static UnitSystemTraits::Angle_quantity get_equilibrium_improper_angle ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_equilibrium_improper_angle() [4/4]

static UnitSystemTraits::Angle_quantity get_equilibrium_improper_angle ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_equilibrium_torsion_angles() [1/4]

const std::map< unsigned, typename UnitSystemTraits::Angle_quantity > * get_equilibrium_torsion_angles ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_equilibrium_torsion_angles() [2/4]

static const std::map<unsigned, typename UnitSystemTraits::Angle_quantity>* get_equilibrium_torsion_angles ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_equilibrium_torsion_angles() [3/4]

static const std::map<unsigned, typename UnitSystemTraits::Angle_quantity>* get_equilibrium_torsion_angles ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_equilibrium_torsion_angles() [4/4]

static const std::map<unsigned, typename UnitSystemTraits::Angle_quantity>* get_equilibrium_torsion_angles ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_equilibrium_Urey_Bradley() [1/4]

UnitSystemTraits::Length_quantity get_equilibrium_Urey_Bradley ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_equilibrium_Urey_Bradley() [2/4]

static UnitSystemTraits::Length_quantity get_equilibrium_Urey_Bradley ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_equilibrium_Urey_Bradley() [3/4]

static UnitSystemTraits::Length_quantity get_equilibrium_Urey_Bradley ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_equilibrium_Urey_Bradley() [4/4]

static UnitSystemTraits::Length_quantity get_equilibrium_Urey_Bradley ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_improper_angle_force_constant() [1/4]

UnitSystemTraits::Angle_force_constant_quantity get_improper_angle_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_improper_angle_force_constant() [2/4]

static UnitSystemTraits::Angle_force_constant_quantity get_improper_angle_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_improper_angle_force_constant() [3/4]

static UnitSystemTraits::Angle_force_constant_quantity get_improper_angle_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_improper_angle_force_constant() [4/4]

static UnitSystemTraits::Angle_force_constant_quantity get_improper_angle_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_improper_angle_parameters() [1/2]

static std::tuple<unsigned,typename UnitSystemTraits::Angle_quantity,typename UnitSystemTraits::Angle_force_constant_quantity> get_improper_angle_parameters ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_improper_angle_parameters() [2/2]

static std::tuple<unsigned,typename UnitSystemTraits::Angle_quantity,typename UnitSystemTraits::Angle_force_constant_quantity> get_improper_angle_parameters ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_input_angle_unit() [1/2]

UnitSystemTraits::Angle_quantity get_input_angle_unit ( void  )

inlinestatic

get_input_angle_unit() [2/2]

static UnitSystemTraits::Angle_quantity get_input_angle_unit ( void  )

inlinestatic

get_input_charge_unit() [1/2]

UnitSystemTraits::Charge_quantity get_input_charge_unit ( void  )

inlinestatic

get_input_charge_unit() [2/2]

static UnitSystemTraits::Charge_quantity get_input_charge_unit ( void  )

inlinestatic

get_input_length_unit() [1/2]

UnitSystemTraits::Length_quantity get_input_length_unit ( void  )

inlinestatic

get_input_length_unit() [2/2]

static UnitSystemTraits::Length_quantity get_input_length_unit ( void  )

inlinestatic

get_input_molar_energy_unit() [1/2]

UnitSystemTraits::Molar_energy_quantity get_input_molar_energy_unit ( void  )

inlinestatic

get_input_molar_energy_unit() [2/2]

static UnitSystemTraits::Molar_energy_quantity get_input_molar_energy_unit ( void  )

inlinestatic

get_Lennard_Jones_attractive_constant() [1/2]

UnitSystemTraits::LJ_6_quantity get_Lennard_Jones_attractive_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_Lennard_Jones_attractive_constant() [2/2]

static UnitSystemTraits::LJ_6_quantity get_Lennard_Jones_attractive_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_Lennard_Jones_epsilon_constant() [1/2]

UnitSystemTraits::Molar_energy_quantity get_Lennard_Jones_epsilon_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_Lennard_Jones_epsilon_constant() [2/2]

static UnitSystemTraits::Molar_energy_quantity get_Lennard_Jones_epsilon_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_Lennard_Jones_repulsive_constant() [1/2]

UnitSystemTraits::LJ_12_quantity get_Lennard_Jones_repulsive_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_Lennard_Jones_repulsive_constant() [2/2]

static UnitSystemTraits::LJ_12_quantity get_Lennard_Jones_repulsive_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q  )

inlinestatic

get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const

inlineinherited

get_name() [1/2]

std::string get_name ( void  ) const

inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

get_name() [2/2]

std::string get_name ( void  ) const

inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

get_options()

static boost::program_options::options_description*& get_options ( void  )

inlinestaticinherited

Access to the options' description of the module.

get_output_prefix() [1/2]

std::string get_output_prefix ( void  ) const

inlinevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

get_output_prefix() [2/2]

std::string get_output_prefix ( void  ) const

inlinevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

get_torsion_angle_force_constants() [1/4]

const std::map< unsigned, typename UnitSystemTraits::Molar_energy_quantity > * get_torsion_angle_force_constants ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_torsion_angle_force_constants() [2/4]

static const std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity>* get_torsion_angle_force_constants ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r, const Particle_rep &  t  )

inlinestatic

get_torsion_angle_force_constants() [3/4]

static const std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity>* get_torsion_angle_force_constants ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_torsion_angle_force_constants() [4/4]

static const std::map<unsigned, typename UnitSystemTraits::Molar_energy_quantity>* get_torsion_angle_force_constants ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_torsion_angle_number_of_periods() [1/2]

static unsigned get_torsion_angle_number_of_periods ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_torsion_angle_number_of_periods() [2/2]

static unsigned get_torsion_angle_number_of_periods ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b  )

inlinestatic

get_torsion_angle_parameters() [1/2]

static std::tuple<unsigned,typename UnitSystemTraits::Angle_quantity,typename UnitSystemTraits::Molar_energy_quantity> get_torsion_angle_parameters ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b, unsigned  i  )

inlinestatic

get_torsion_angle_parameters() [2/2]

static std::tuple<unsigned,typename UnitSystemTraits::Angle_quantity,typename UnitSystemTraits::Molar_energy_quantity> get_torsion_angle_parameters ( const Covalent_structure &  C, const typename Covalent_structure::Torsion_angle_rep &  b, unsigned  i  )

inlinestatic

get_Urey_Bradley_force_constant() [1/4]

UnitSystemTraits::Bond_force_constant_quantity get_Urey_Bradley_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_Urey_Bradley_force_constant() [2/4]

static UnitSystemTraits::Bond_force_constant_quantity get_Urey_Bradley_force_constant ( const Covalent_structure &  C, const Particle_rep &  p, const Particle_rep &  q, const Particle_rep &  r  )

inlinestatic

get_Urey_Bradley_force_constant() [3/4]

static UnitSystemTraits::Bond_force_constant_quantity get_Urey_Bradley_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

get_Urey_Bradley_force_constant() [4/4]

static UnitSystemTraits::Bond_force_constant_quantity get_Urey_Bradley_force_constant ( const Covalent_structure &  C, const typename Covalent_structure::Bond_angle_rep &  b  )

inlinestatic

has_options()

static bool has_options ( void  )

inlinestaticinherited

ignore_1_3_interactions() [1/2]

bool ignore_1_3_interactions ( void  )

inlinestatic

ignore_1_3_interactions() [2/2]

static bool ignore_1_3_interactions ( void  )

inlinestatic

initialize_options()

static void initialize_options ( const std::string &  caption )

inlinestaticinherited

load() [1/2]

bool load ( unsigned  verbose = 0, std::ostream &  out = std::cout  )

inlinevirtual

Loads the data.

Reimplemented from Loader_base.

load() [2/2]

bool load ( unsigned  verbose = 0, std::ostream &  out = std::cout  )

inlinevirtual

Loads the data.

Reimplemented from Loader_base.

set_bond_angle_force_constant() [1/2]

void set_bond_angle_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_bond_angle_force_constant() [2/2]

static void set_bond_angle_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_bond_length_force_constant() [1/2]

void set_bond_length_force_constant ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_bond_length_force_constant() [2/2]

static void set_bond_length_force_constant ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_cmap_coefficients() [1/2]

void set_cmap_coefficients ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, const std::string &  p5, const std::string &  p6, const std::string &  p7, const std::string &  p8, const std::map< FT, std::map< FT, FT > > &  coefficients  )

inlinestatic

set_cmap_coefficients() [2/2]

static void set_cmap_coefficients ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, const std::string &  p5, const std::string &  p6, const std::string &  p7, const std::string &  p8, const std::map< FT, std::map< FT, FT > > &  coefficients  )

inlinestatic

set_cmap_resolution() [1/2]

void set_cmap_resolution ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, const std::string &  p5, const std::string &  p6, const std::string &  p7, const std::string &  p8, unsigned  resolution  )

inlinestatic

set_cmap_resolution() [2/2]

static void set_cmap_resolution ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, const std::string &  p5, const std::string &  p6, const std::string &  p7, const std::string &  p8, unsigned  resolution  )

inlinestatic

set_dihedral_coefficient() [1/2]

void set_dihedral_coefficient ( unsigned  ss_rep, unsigned  num_coeff, const FT &  v  )

inlinestatic

set_dihedral_coefficient() [2/2]

static void set_dihedral_coefficient ( unsigned  ss_rep, unsigned  num_coeff, const FT &  v  )

inlinestatic

set_electrostatic_charge() [1/2]

void set_electrostatic_charge ( unsigned  index, const FT &  v  )

inlinestatic

set_electrostatic_charge() [2/2]

static void set_electrostatic_charge ( unsigned  index, const FT &  v  )

inlinestatic

set_equilibrium_bond_angle() [1/2]

void set_equilibrium_bond_angle ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_equilibrium_bond_angle() [2/2]

static void set_equilibrium_bond_angle ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_equilibrium_bond_length() [1/2]

void set_equilibrium_bond_length ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_equilibrium_bond_length() [2/2]

static void set_equilibrium_bond_length ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_equilibrium_improper_angle() [1/2]

void set_equilibrium_improper_angle ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_equilibrium_improper_angle() [2/2]

static void set_equilibrium_improper_angle ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_equilibrium_torsion_angle() [1/2]

void set_equilibrium_torsion_angle ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_equilibrium_torsion_angle() [2/2]

static void set_equilibrium_torsion_angle ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_equilibrium_Urey_Bradley() [1/2]

void set_equilibrium_Urey_Bradley ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_equilibrium_Urey_Bradley() [2/2]

static void set_equilibrium_Urey_Bradley ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_file_name() [1/2]

void set_file_name ( const std::string &  file_name )

inlinestatic

set_file_name() [2/2]

static void set_file_name ( const std::string &  file_name )

inlinestatic

set_fudge_LJ14_constant() [1/2]

void set_fudge_LJ14_constant ( const FT &  v )

inlinestatic

set_fudge_LJ14_constant() [2/2]

static void set_fudge_LJ14_constant ( const FT &  v )

inlinestatic

set_fudge_LJ_constant() [1/2]

void set_fudge_LJ_constant ( const FT &  v )

inlinestatic

set_fudge_LJ_constant() [2/2]

static void set_fudge_LJ_constant ( const FT &  v )

inlinestatic

set_fudge_QQ14_constant() [1/2]

void set_fudge_QQ14_constant ( const FT &  v )

inlinestatic

set_fudge_QQ14_constant() [2/2]

static void set_fudge_QQ14_constant ( const FT &  v )

inlinestatic

set_fudge_QQ_constant() [1/2]

void set_fudge_QQ_constant ( const FT &  v )

inlinestatic

set_fudge_QQ_constant() [2/2]

static void set_fudge_QQ_constant ( const FT &  v )

inlinestatic

set_ignore_1_3_interactions() [1/2]

void set_ignore_1_3_interactions ( bool  ignore_angles )

inlinestatic

When using a non-bonded visitor with a threshold, one can ignore 1_3 interactions here.

set_ignore_1_3_interactions() [2/2]

static void set_ignore_1_3_interactions ( bool  ignore_angles )

inlinestatic

When using a non-bonded visitor with a threshold, one can ignore 1_3 interactions here.

set_improper_angle_force_constant() [1/2]

void set_improper_angle_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_improper_angle_force_constant() [2/2]

static void set_improper_angle_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_is_coulomb() [1/2]

void set_is_coulomb ( bool  is_coulomb )

inlinestatic

If true, electric charge are assumed to be expressed in coulombs rather than q-electron.

set_is_coulomb() [2/2]

static void set_is_coulomb ( bool  is_coulomb )

inlinestatic

If true, electric charge are assumed to be expressed in coulombs rather than q-electron.

set_is_degree() [1/2]

void set_is_degree ( bool  is_degree )

inlinestatic

If true, angles are assumed to be expressed in degree rather than radian.

set_is_degree() [2/2]

static void set_is_degree ( bool  is_degree )

inlinestatic

If true, angles are assumed to be expressed in degree rather than radian.

set_is_kilojoule() [1/2]

void set_is_kilojoule ( bool  is_kilojoule )

inlinestatic

Set a multiplicative factor for changing the force constant unit of the force field.

set_is_kilojoule() [2/2]

static void set_is_kilojoule ( bool  is_kilojoule )

inlinestatic

Set a multiplicative factor for changing the force constant unit of the force field.

set_is_nanometer() [1/2]

void set_is_nanometer ( bool  is_nanometer )

inlinestatic

Set a multiplicative factor for changing the metric unit of the force field.

set_is_nanometer() [2/2]

static void set_is_nanometer ( bool  is_nanometer )

inlinestatic

Set a multiplicative factor for changing the metric unit of the force field.

set_Lennard_Jones_attractive_constant() [1/2]

void set_Lennard_Jones_attractive_constant ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_Lennard_Jones_attractive_constant() [2/2]

static void set_Lennard_Jones_attractive_constant ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_Lennard_Jones_epsilon_constant() [1/2]

void set_Lennard_Jones_epsilon_constant ( unsigned  index, const FT &  v  )

inlinestatic

set_Lennard_Jones_epsilon_constant() [2/2]

static void set_Lennard_Jones_epsilon_constant ( unsigned  index, const FT &  v  )

inlinestatic

set_Lennard_Jones_repulsive_constant() [1/2]

void set_Lennard_Jones_repulsive_constant ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_Lennard_Jones_repulsive_constant() [2/2]

static void set_Lennard_Jones_repulsive_constant ( const std::string &  p1, const std::string &  p2, const FT &  v  )

inlinestatic

set_Lennard_Jones_sigma_constant() [1/2]

void set_Lennard_Jones_sigma_constant ( unsigned  index, const FT &  v  )

inlinestatic

set_Lennard_Jones_sigma_constant() [2/2]

static void set_Lennard_Jones_sigma_constant ( unsigned  index, const FT &  v  )

inlinestatic

set_loader_instance_name()

void set_loader_instance_name ( const std::string &  loader_instance_name )

inlineinherited

set_torsion_angle_force_constant() [1/2]

void set_torsion_angle_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_torsion_angle_force_constant() [2/2]

static void set_torsion_angle_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const std::string &  p4, unsigned  n, const FT &  v  )

inlinestatic

set_Urey_Bradley_force_constant() [1/2]

void set_Urey_Bradley_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

set_Urey_Bradley_force_constant() [2/2]

static void set_Urey_Bradley_force_constant ( const std::string &  p1, const std::string &  p2, const std::string &  p3, const FT &  v  )

inlinestatic

Member Data Documentation

s_bond_angle_force_constant

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Ternary_angle_energy_map s_bond_angle_force_constant

static

name rk_theta/2 in Wales code

s_bond_length_force_constant

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Binary_length_energy_constant_map s_bond_length_force_constant

static

name rk_r/2 in Wales code

s_cmap_coefficients

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::CMap_coefficients_map_8 s_cmap_coefficients

static

For cmap correction calculations.

s_cmap_resolutions

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::CMap_resolution_map_8 s_cmap_resolutions

static

For cmap correction calculations.

s_dag

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Wildcards_DAG s_dag

static

s_dihedral_coefficients

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Binary_coefficients_parameters_map s_dihedral_coefficients

static

Defines the four coefficients for each secondary structure element.

s_electrostatic_charges

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Unary_charge_map s_electrostatic_charges

static

electrostatic charges (default is 0 for all)

s_equilibrium_bond_angle

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Ternary_angle_map s_equilibrium_bond_angle

static

For bond angle potential energy calculations.

s_equilibrium_bond_length

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Binary_length_map s_equilibrium_bond_length

static

For bond length potential energy calculations.

s_equilibrium_improper_angle

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Quinternary_torsion_angle_map s_equilibrium_improper_angle

static

For torsion angle potential energy calculations.

s_equilibrium_torsion_angle

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Quinternary_torsion_angle_map s_equilibrium_torsion_angle

static

For torsion angle potential energy calculations.

s_equilibrium_Urey_Bradley

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Ternary_length_map s_equilibrium_Urey_Bradley

static

For Urey Bradley potential energy calculations.

s_file_name

std::string s_file_name = ""

static

Input file name for this force field.

s_fudge_LJ14_constant

FT s_fudge_LJ14_constant = 1

static

s_fudge_LJ_constant

FT s_fudge_LJ_constant = 1

static

fudge Lennard Jones constant

s_fudge_QQ14_constant

FT s_fudge_QQ14_constant = 1

static

s_fudge_QQ_constant

FT s_fudge_QQ_constant = 1

static

fudge screening factor constant

s_ignore_1_3_interactions

bool s_ignore_1_3_interactions = false

static

s_improper_angle_force_constant

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Quinternary_torsion_angle_energy_map s_improper_angle_force_constant

static

For torsion angle potential energy calculations.

s_index_to_type

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Index_to_type_map s_index_to_type

static

Molecule types : mapping between their name and their representation here for accessing the parameters.

s_is_coulomb

bool s_is_coulomb = false

static

Tag for the unit for electric charge. If coulomb, convert them in q electron.

s_is_degree

bool s_is_degree = false

static

Tag for the unit for angles. If degree, convert them in radian.

s_is_kilojoule

bool s_is_kilojoule = false

static

s_is_nanometer

bool s_is_nanometer = false

static

Multiplicative factor for distance terms.

s_Lennard_Jones_attractive_constants

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Binary_attractive_map s_Lennard_Jones_attractive_constants

static

For attractive vdW potential energy calculations.

s_Lennard_Jones_epsilon_constants

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Unary_energy_nonbonded_map s_Lennard_Jones_epsilon_constants

static

For epsilon vdW potential energy calculations.

s_Lennard_Jones_repulsive_constants

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Binary_repulsive_map s_Lennard_Jones_repulsive_constants

static

For repulsive vdW potential energy calculations.

s_Lennard_Jones_sigma_constants

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Unary_length_nonbonded_map s_Lennard_Jones_sigma_constants

static

For sigma vdW potential energy calculations.

s_name_to_index

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Name_to_index_map s_name_to_index

static

s_nb_sse_types

unsigned s_nb_sse_types = 0

static

Number of secondary structure element types.

s_secondary_structure

std::vector< unsigned > s_secondary_structure

static

Secondary structure associated to the input molecule, if any : the integer corresponds to the secondary structure type index in corresponding arrays

s_torsion_angle_force_constant

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Quinternary_torsion_energy_map s_torsion_angle_force_constant

static

For torsion angle potential energy calculations.

s_Urey_Bradley_force_constant

T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >::Ternary_length_energy_constant_map s_Urey_Bradley_force_constant

static

For Urey Bradley potential energy calculations.