Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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, FTSelf
 
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_mapBinary_length_map
 
typedef std::map< std::string, Binary_length_mapTernary_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_mapBinary_attractive_map
 
typedef std::map< std::string, typename UnitSystemTraits::LJ_12_quantity > Unary_repulsive_map
 
typedef std::map< std::string, Unary_repulsive_mapBinary_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_mapBinary_length_energy_constant_map
 
typedef std::map< std::string, Binary_length_energy_constant_mapTernary_length_energy_constant_map
 
typedef std::map< std::string, typename UnitSystemTraits::Angle_quantity > Unary_angle_map
 
typedef std::map< std::string, Unary_angle_mapBinary_angle_map
 
typedef std::map< std::string, Binary_angle_mapTernary_angle_map
 
typedef std::map< unsigned, typename UnitSystemTraits::Angle_quantity > Unary_torsion_angle_map
 
typedef std::map< std::string, Unary_torsion_angle_mapBinary_torsion_angle_map
 
typedef std::map< std::string, Binary_torsion_angle_mapTernary_torsion_angle_map
 
typedef std::map< std::string, Ternary_torsion_angle_mapQuaternary_torsion_angle_map
 
typedef std::map< std::string, Quaternary_torsion_angle_mapQuinternary_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_mapBinary_angle_energy_map
 
typedef std::map< std::string, Binary_angle_energy_mapTernary_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_mapBinary_torsion_angle_energy_map
 
typedef std::map< std::string, Binary_torsion_angle_energy_mapTernary_torsion_angle_energy_map
 
typedef std::map< std::string, Ternary_torsion_angle_energy_mapQuaternary_torsion_angle_energy_map
 
typedef std::map< std::string, Quaternary_torsion_angle_energy_mapQuinternary_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_mapBinary_torsion_energy_map
 
typedef std::map< std::string, Binary_torsion_energy_mapTernary_torsion_energy_map
 
typedef std::map< std::string, Ternary_torsion_energy_mapQuaternary_torsion_energy_map
 
typedef std::map< std::string, Quaternary_torsion_energy_mapQuinternary_torsion_energy_map
 
typedef std::vector< typename UnitSystemTraits::Molar_energy_quantity > Unary_coefficients_parameters_map
 
typedef std::vector< Unary_coefficients_parameters_mapBinary_coefficients_parameters_map
 
typedef std::map< FT, std::map< FT, FT > > CMap_coefficients_map
 
typedef std::map< std::string, CMap_coefficients_mapCMap_coefficients_map_1
 
typedef std::map< std::string, CMap_coefficients_map_1CMap_coefficients_map_2
 
typedef std::map< std::string, CMap_coefficients_map_2CMap_coefficients_map_3
 
typedef std::map< std::string, CMap_coefficients_map_3CMap_coefficients_map_4
 
typedef std::map< std::string, CMap_coefficients_map_4CMap_coefficients_map_5
 
typedef std::map< std::string, CMap_coefficients_map_5CMap_coefficients_map_6
 
typedef std::map< std::string, CMap_coefficients_map_6CMap_coefficients_map_7
 
typedef std::map< std::string, CMap_coefficients_map_7CMap_coefficients_map_8
 
typedef std::map< std::string, unsigned > CMap_resolution_map_1
 
typedef std::map< std::string, CMap_resolution_map_1CMap_resolution_map_2
 
typedef std::map< std::string, CMap_resolution_map_2CMap_resolution_map_3
 
typedef std::map< std::string, CMap_resolution_map_3CMap_resolution_map_4
 
typedef std::map< std::string, CMap_resolution_map_4CMap_resolution_map_5
 
typedef std::map< std::string, CMap_resolution_map_5CMap_resolution_map_6
 
typedef std::map< std::string, CMap_resolution_map_6CMap_resolution_map_7
 
typedef std::map< std::string, CMap_resolution_map_7CMap_resolution_map_8
 
typedef SBL::CADS::T_Directed_acyclic_graph_with_layers< std::string > Wildcards_DAG
 
typedef T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FTSelf
 
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_mapBinary_length_map
 
typedef std::map< std::string, Binary_length_mapTernary_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_mapBinary_attractive_map
 
typedef std::map< std::string, typename UnitSystemTraits::LJ_12_quantity > Unary_repulsive_map
 
typedef std::map< std::string, Unary_repulsive_mapBinary_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_mapBinary_length_energy_constant_map
 
typedef std::map< std::string, Binary_length_energy_constant_mapTernary_length_energy_constant_map
 
typedef std::map< std::string, typename UnitSystemTraits::Angle_quantity > Unary_angle_map
 
typedef std::map< std::string, Unary_angle_mapBinary_angle_map
 
typedef std::map< std::string, Binary_angle_mapTernary_angle_map
 
typedef std::map< unsigned, typename UnitSystemTraits::Angle_quantity > Unary_torsion_angle_map
 
typedef std::map< std::string, Unary_torsion_angle_mapBinary_torsion_angle_map
 
typedef std::map< std::string, Binary_torsion_angle_mapTernary_torsion_angle_map
 
typedef std::map< std::string, Ternary_torsion_angle_mapQuaternary_torsion_angle_map
 
typedef std::map< std::string, Quaternary_torsion_angle_mapQuinternary_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_mapBinary_angle_energy_map
 
typedef std::map< std::string, Binary_angle_energy_mapTernary_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_mapBinary_torsion_angle_energy_map
 
typedef std::map< std::string, Binary_torsion_angle_energy_mapTernary_torsion_angle_energy_map
 
typedef std::map< std::string, Ternary_torsion_angle_energy_mapQuaternary_torsion_angle_energy_map
 
typedef std::map< std::string, Quaternary_torsion_angle_energy_mapQuinternary_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_mapBinary_torsion_energy_map
 
typedef std::map< std::string, Binary_torsion_energy_mapTernary_torsion_energy_map
 
typedef std::map< std::string, Ternary_torsion_energy_mapQuaternary_torsion_energy_map
 
typedef std::map< std::string, Quaternary_torsion_energy_mapQuinternary_torsion_energy_map
 
typedef std::vector< typename UnitSystemTraits::Molar_energy_quantity > Unary_coefficients_parameters_map
 
typedef std::vector< Unary_coefficients_parameters_mapBinary_coefficients_parameters_map
 
typedef std::map< FT, std::map< FT, FT > > CMap_coefficients_map
 
typedef std::map< std::string, CMap_coefficients_mapCMap_coefficients_map_1
 
typedef std::map< std::string, CMap_coefficients_map_1CMap_coefficients_map_2
 
typedef std::map< std::string, CMap_coefficients_map_2CMap_coefficients_map_3
 
typedef std::map< std::string, CMap_coefficients_map_3CMap_coefficients_map_4
 
typedef std::map< std::string, CMap_coefficients_map_4CMap_coefficients_map_5
 
typedef std::map< std::string, CMap_coefficients_map_5CMap_coefficients_map_6
 
typedef std::map< std::string, CMap_coefficients_map_6CMap_coefficients_map_7
 
typedef std::map< std::string, CMap_coefficients_map_7CMap_coefficients_map_8
 
typedef std::map< std::string, unsigned > CMap_resolution_map_1
 
typedef std::map< std::string, CMap_resolution_map_1CMap_resolution_map_2
 
typedef std::map< std::string, CMap_resolution_map_2CMap_resolution_map_3
 
typedef std::map< std::string, CMap_resolution_map_3CMap_resolution_map_4
 
typedef std::map< std::string, CMap_resolution_map_4CMap_resolution_map_5
 
typedef std::map< std::string, CMap_resolution_map_5CMap_resolution_map_6
 
typedef std::map< std::string, CMap_resolution_map_6CMap_resolution_map_7
 
typedef std::map< std::string, CMap_resolution_map_7CMap_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)
 

Management

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

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_mapget_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_mapget_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)
 

Member Typedef Documentation

◆ Base [1/2]

◆ Base [2/2]

◆ 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]

◆ Binary_coefficients_parameters_map [2/2]

◆ Binary_length_energy_constant_map [1/2]

◆ Binary_length_energy_constant_map [2/2]

◆ 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]

◆ Binary_torsion_angle_energy_map [2/2]

◆ 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]

◆ Quaternary_torsion_angle_energy_map [2/2]

◆ Quaternary_torsion_angle_map [1/2]

◆ Quaternary_torsion_angle_map [2/2]

◆ Quaternary_torsion_energy_map [1/2]

◆ Quaternary_torsion_energy_map [2/2]

◆ Quinternary_torsion_angle_energy_map [1/2]

◆ Quinternary_torsion_angle_energy_map [2/2]

◆ Quinternary_torsion_angle_map [1/2]

◆ Quinternary_torsion_angle_map [2/2]

◆ Quinternary_torsion_energy_map [1/2]

◆ Quinternary_torsion_energy_map [2/2]

◆ 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]

◆ Ternary_length_energy_constant_map [2/2]

◆ 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]

◆ Ternary_torsion_angle_energy_map [2/2]

◆ 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]

◆ Wildcards_DAG [2/2]

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<>.

◆ 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<>.

◆ 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<>.

◆ 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<>.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_bond_angle_force_constant() [1/4]

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() [2/4]

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() [3/4]

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() [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]

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() [2/4]

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() [3/4]

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() [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]

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_coefficients() [2/2]

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_resolution() [1/2]

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_cmap_resolution() [2/2]

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_dielectric_constant() [1/2]

static 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]

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]

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

◆ get_dihedral_coefficient() [2/2]

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

◆ get_electrostatic_charge() [1/2]

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

◆ get_electrostatic_charge() [2/2]

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

◆ get_equilibrium_bond_angle() [1/4]

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() [2/4]

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() [3/4]

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() [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]

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() [2/4]

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

◆ get_equilibrium_bond_length() [3/4]

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

◆ get_equilibrium_bond_length() [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]

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() [2/4]

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() [3/4]

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() [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]

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() [2/4]

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() [3/4]

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() [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]

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() [2/4]

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() [3/4]

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() [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]

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() [2/4]

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() [3/4]

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() [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]

static UnitSystemTraits::Angle_quantity get_input_angle_unit ( void  )
inlinestatic

◆ get_input_angle_unit() [2/2]

UnitSystemTraits::Angle_quantity get_input_angle_unit ( void  )
inlinestatic

◆ get_input_charge_unit() [1/2]

static UnitSystemTraits::Charge_quantity get_input_charge_unit ( void  )
inlinestatic

◆ get_input_charge_unit() [2/2]

UnitSystemTraits::Charge_quantity get_input_charge_unit ( void  )
inlinestatic

◆ get_input_length_unit() [1/2]

static UnitSystemTraits::Length_quantity get_input_length_unit ( void  )
inlinestatic

◆ get_input_length_unit() [2/2]

UnitSystemTraits::Length_quantity get_input_length_unit ( void  )
inlinestatic

◆ get_input_molar_energy_unit() [1/2]

static UnitSystemTraits::Molar_energy_quantity get_input_molar_energy_unit ( void  )
inlinestatic

◆ get_input_molar_energy_unit() [2/2]

UnitSystemTraits::Molar_energy_quantity get_input_molar_energy_unit ( void  )
inlinestatic

◆ get_Lennard_Jones_attractive_constant() [1/2]

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_attractive_constant() [2/2]

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_epsilon_constant() [1/2]

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_epsilon_constant() [2/2]

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_repulsive_constant() [1/2]

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

◆ get_Lennard_Jones_repulsive_constant() [2/2]

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<>.

◆ 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<>.

◆ get_torsion_angle_force_constants() [1/4]

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() [2/4]

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() [3/4]

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() [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]

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() [2/4]

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() [3/4]

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() [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]

static bool ignore_1_3_interactions ( void  )
inlinestatic

◆ ignore_1_3_interactions() [2/2]

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]

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_angle_force_constant() [2/2]

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

◆ set_bond_length_force_constant() [1/2]

static 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]

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

◆ set_cmap_coefficients() [1/2]

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_coefficients() [2/2]

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_resolution() [1/2]

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_cmap_resolution() [2/2]

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_dihedral_coefficient() [1/2]

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

◆ set_dihedral_coefficient() [2/2]

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

◆ set_electrostatic_charge() [1/2]

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

◆ set_electrostatic_charge() [2/2]

void set_electrostatic_charge ( unsigned  index,
const FT v 
)
inlinestatic

◆ set_equilibrium_bond_angle() [1/2]

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_angle() [2/2]

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

◆ set_equilibrium_bond_length() [1/2]

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

◆ set_equilibrium_bond_length() [2/2]

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

◆ set_equilibrium_improper_angle() [1/2]

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_improper_angle() [2/2]

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_torsion_angle() [1/2]

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_torsion_angle() [2/2]

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_Urey_Bradley() [1/2]

static 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]

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]

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

◆ set_file_name() [2/2]

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

◆ set_fudge_LJ14_constant() [1/2]

static void set_fudge_LJ14_constant ( const FT v)
inlinestatic

◆ set_fudge_LJ14_constant() [2/2]

void set_fudge_LJ14_constant ( const FT v)
inlinestatic

◆ set_fudge_LJ_constant() [1/2]

static void set_fudge_LJ_constant ( const FT v)
inlinestatic

◆ set_fudge_LJ_constant() [2/2]

void set_fudge_LJ_constant ( const FT v)
inlinestatic

◆ set_fudge_QQ14_constant() [1/2]

static void set_fudge_QQ14_constant ( const FT v)
inlinestatic

◆ set_fudge_QQ14_constant() [2/2]

void set_fudge_QQ14_constant ( const FT v)
inlinestatic

◆ set_fudge_QQ_constant() [1/2]

static void set_fudge_QQ_constant ( const FT v)
inlinestatic

◆ set_fudge_QQ_constant() [2/2]

void set_fudge_QQ_constant ( const FT v)
inlinestatic

◆ set_ignore_1_3_interactions() [1/2]

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_ignore_1_3_interactions() [2/2]

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_improper_angle_force_constant() [1/2]

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_improper_angle_force_constant() [2/2]

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_is_coulomb() [1/2]

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_coulomb() [2/2]

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_degree() [1/2]

static void set_is_degree ( bool  is_degree)
inlinestatic

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

◆ set_is_degree() [2/2]

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]

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_kilojoule() [2/2]

void set_is_kilojoule ( bool  is_kilojoule)
inlinestatic

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

◆ set_is_nanometer() [1/2]

static 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]

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]

static 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]

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]

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

◆ set_Lennard_Jones_epsilon_constant() [2/2]

void set_Lennard_Jones_epsilon_constant ( unsigned  index,
const FT v 
)
inlinestatic

◆ set_Lennard_Jones_repulsive_constant() [1/2]

static 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]

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]

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

◆ set_Lennard_Jones_sigma_constant() [2/2]

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]

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_torsion_angle_force_constant() [2/2]

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_Urey_Bradley_force_constant() [1/2]

static 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]

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.