Index

_

__init__() (AmberFD.AmberFD method) (AmberFD.AmberFD.AmberFDSimulation method) (AmberFD.AmberFD.MoleculeImporter method) (AmberFD.DispersionPauli method) (AmberFD.Energies method) (AmberFD.FlucDens method) (AmberFD.ParticleInfo method)

A

A_mat_save (AmberFD.FlucDens property) add() (AmberFD.Energies method) add_del_frz_exclusion() (AmberFD.FlucDens method) add_exclusion() (AmberFD.DispersionPauli method) add_fragment() (AmberFD.AmberFD method) (AmberFD.FlucDens method) add_frz_frz_exclusion() (AmberFD.FlucDens method) add_particle() (AmberFD.AmberFD method) All (AmberFD.FlucDens attribute) AmberFD (C++ class) (class in AmberFD) AmberFD.PDBReporter module AmberFD::add_fragment (C++ function) AmberFD::add_particle (C++ function) AmberFD::AmberFD (C++ function), [1] AmberFD::calc_energy_forces (C++ function) AmberFD::calc_one_pair (C++ function) AmberFD::create_disp_pauli_force (C++ function)

AmberFD::create_fluc_dens_force (C++ function) AmberFD::dump_to_file (C++ function) AmberFD::get_disp_pauli_force (C++ function) AmberFD::get_fluc_dens_force (C++ function) AmberFD::get_forces (C++ function) AmberFD::get_index_mapping (C++ function) AmberFD::get_num_particles (C++ function) AmberFD::get_parallel_time (C++ function) AmberFD::get_use_PBC (C++ function) AmberFD::getDeltaR (C++ function) AmberFD::load_from_file (C++ function) AmberFD::set_threads (C++ function) AmberFD::set_use_PBC (C++ function), [1] AmberFD::~AmberFD (C++ function) AMBERFD_H (C macro) AmberFDSimulation (class in AmberFD.AmberFD) ANG2BOHR (C macro) apply_field_to_system() (AmberFD.FlucDens method) AU_2_KJ_PER_MOL (C macro)

B

B_vec_save (AmberFD.FlucDens property)

C

calc_density() (AmberFD.FlucDens method) calc_energy() (AmberFD.DispersionPauli method) (AmberFD.FlucDens method) calc_energy_forces() (AmberFD.AmberFD method) calc_frz_ext_field_energy() (AmberFD.FlucDens method) calc_one_electro() (AmberFD.FlucDens method) calc_one_frozen() (AmberFD.FlucDens method) calc_one_pair() (AmberFD.AmberFD method) (AmberFD.DispersionPauli method)

calc_overlap() (AmberFD.FlucDens method) create_disp_pauli_force() (AmberFD.AmberFD method) create_exclusions_from_bonds() (AmberFD.DispersionPauli method) create_exclusions_from_fragment() (AmberFD.DispersionPauli method) create_fluc_dens_force() (AmberFD.AmberFD method) create_frz_exclusions_from_bonds() (AmberFD.FlucDens method) create_repulsion_sites() (AmberFD.DispersionPauli method)

D

Delta (AmberFD.FlucDens attribute) DeltaR (C++ class) DeltaR::DeltaR (C++ function), [1], [2], [3] DeltaR::dR (C++ member) DeltaR::get_pointer (C++ function) DeltaR::getDeltaR (C++ function), [1], [2], [3] DeltaR::r (C++ member) DeltaR::r2 (C++ member) DeltaR::r_inv (C++ member) describeNextReport() (AmberFD.PDBReporter.PDBReporterExtra method) disp (AmberFD.Energies property) DispersionPauli (C++ class) (class in AmberFD) DispersionPauli::add_exclusion (C++ function) DispersionPauli::calc_energy (C++ function) DispersionPauli::calc_one_pair (C++ function), [1] DispersionPauli::create_exclusions_from_bonds (C++ function) DispersionPauli::create_exclusions_from_fragment (C++ function) DispersionPauli::create_repulsion_sites (C++ function) DispersionPauli::DispersionPauli (C++ function) DispersionPauli::get_C6_coeff (C++ function) DispersionPauli::get_C6_map (C++ function) DispersionPauli::get_disp_energy (C++ function)

DispersionPauli::get_dispersion_params (C++ function) DispersionPauli::get_exclusions (C++ function) DispersionPauli::get_forces (C++ function) DispersionPauli::get_num_sites (C++ function) DispersionPauli::get_pauli_energy (C++ function) DispersionPauli::get_pauli_exp (C++ function) DispersionPauli::get_pauli_radii (C++ function) DispersionPauli::get_use_PBC (C++ function) DispersionPauli::get_vdw_radii (C++ function) DispersionPauli::get_vdw_radii_map (C++ function) DispersionPauli::initialize (C++ function) DispersionPauli::set_C6_map (C++ function) DispersionPauli::set_dispersion_params (C++ function) DispersionPauli::set_pauli_exp (C++ function), [1] DispersionPauli::set_pauli_radii (C++ function), [1] DispersionPauli::set_two_site_distance (C++ function) DispersionPauli::set_use_PBC (C++ function), [1] DispersionPauli::set_use_secondary_radii (C++ function) DispersionPauli::set_use_two_site_repulsion (C++ function) DispersionPauli::set_vdw_radii (C++ function) DispersionPauli::~DispersionPauli (C++ function) dot3Vec() (AmberFD.FlucDens static method) dump_to_file() (AmberFD.AmberFD method) dyn_exp (AmberFD.ParticleInfo property)

E

elec_elec (AmberFD.Energies property) elec_elec_energy() (AmberFD.FlucDens method) elec_nuc (AmberFD.Energies property) elec_nuclei_energy() (AmberFD.FlucDens method) Energies (C++ class) (class in AmberFD) Energies::add (C++ function) Energies::disp (C++ member) Energies::elec_elec (C++ member) Energies::elec_nuc (C++ member)

Energies::Energies (C++ function), [1] Energies::frz (C++ member) Energies::frz_ext (C++ member) Energies::nuc_nuc (C++ member) Energies::operator+= (C++ function) Energies::pauli (C++ member) Energies::pauli_wall (C++ member) Energies::pol (C++ member) Energies::total (C++ function) Energies::vct (C++ member) Energies::zero (C++ function)

F

fileReader (C++ class) fileReader::flines (C++ type) fileReader::flines_p (C++ type) fileReader::readFile (C++ function) fileReader::readFile_unparsed (C++ function) fileReader::readXYZ (C++ function) FlucDens (C++ class) (class in AmberFD) FlucDens::A_mat_save (C++ member) FlucDens::add_del_frz_exclusion (C++ function) FlucDens::add_fragment (C++ function) FlucDens::add_frz_frz_exclusion (C++ function) FlucDens::apply_field_to_system (C++ function) FlucDens::B_vec_save (C++ member) FlucDens::calc_density (C++ function) FlucDens::calc_energy (C++ function) FlucDens::calc_frz_ext_field_energy (C++ function) FlucDens::calc_one_electro (C++ function) FlucDens::calc_one_frozen (C++ function) FlucDens::calc_overlap (C++ function) FlucDens::create_frz_exclusions_from_bonds (C++ function) FlucDens::DampType (C++ enum) FlucDens::DampType::Linear (C++ enumerator) FlucDens::DampType::Quadratic (C++ enumerator) FlucDens::DensityType (C++ enum) FlucDens::DensityType::All (C++ enumerator) FlucDens::DensityType::Delta (C++ enumerator) FlucDens::DensityType::Frozen (C++ enumerator) FlucDens::DensityType::Nuclei (C++ enumerator) FlucDens::dot3Vec (C++ function) FlucDens::elec_elec_energy (C++ function) FlucDens::elec_nuclei_energy (C++ function) FlucDens::FlucDens (C++ function) FlucDens::frz_frz_overlap (C++ function) FlucDens::get_constraints (C++ function) FlucDens::get_ct_coeff (C++ function) FlucDens::get_ct_energy (C++ function) FlucDens::get_cutoff_distance (C++ function) FlucDens::get_dampening (C++ function) FlucDens::get_del_frz_exclusions (C++ function) FlucDens::get_delta_rho (C++ function) FlucDens::get_dipole (C++ function) FlucDens::get_dipoles (C++ function) FlucDens::get_energies (C++ function) FlucDens::get_forces (C++ function) FlucDens::get_fragments (C++ function) FlucDens::get_frozen_energy (C++ function)

FlucDens::get_frz_frz_exclusions (C++ function) FlucDens::get_num_constraints (C++ function) FlucDens::get_num_fragments (C++ function) FlucDens::get_num_frz_frz_exclusions (C++ function) FlucDens::get_param_names (C++ function) FlucDens::get_params_by_name (C++ function) FlucDens::get_polarization_energy (C++ function) FlucDens::get_rho_coulomb_mat (C++ function) FlucDens::get_rho_pot_vec (C++ function) FlucDens::get_site_params (C++ function) FlucDens::get_total_time (C++ function) FlucDens::get_use_cutoff (C++ function) FlucDens::get_use_PBC (C++ function) FlucDens::get_use_SR_cutoff (C++ function) FlucDens::initialize_calculation (C++ function) FlucDens::print_params (C++ function) FlucDens::set_additional_hardness (C++ function), [1] FlucDens::set_calc_forces (C++ function) FlucDens::set_ct_coeff (C++ function) FlucDens::set_cutoff_distance (C++ function) FlucDens::set_dampening (C++ function) FlucDens::set_dyn_exp (C++ function), [1] FlucDens::set_external_field (C++ function) FlucDens::set_frag_constraints (C++ function) FlucDens::set_frz_exp (C++ function) FlucDens::set_site_params (C++ function) FlucDens::set_use_cutoff (C++ function) FlucDens::set_use_PBC (C++ function), [1] FlucDens::set_use_SR_cutoff (C++ function) FlucDens::solve_minimization (C++ function) FlucDens::~FlucDens (C++ function) FlucDensEnergies (C++ class) FlucDensEnergies::elec_elec (C++ member) FlucDensEnergies::elec_nuc (C++ member) FlucDensEnergies::FlucDensEnergies (C++ function) FlucDensEnergies::frz (C++ member) FlucDensEnergies::nuc_nuc (C++ member) FlucDensEnergies::pol (C++ member) FlucDensEnergies::reset (C++ function) FlucDensEnergies::total (C++ function) FlucDensEnergies::vct (C++ member) Frozen (AmberFD.FlucDens attribute) frz (AmberFD.Energies property) frz_chg (AmberFD.ParticleInfo property) frz_exp (AmberFD.ParticleInfo property) frz_ext (AmberFD.Energies property) frz_frz_overlap() (AmberFD.FlucDens method)

G

get_C6_coeff() (AmberFD.DispersionPauli method) get_C6_map() (AmberFD.DispersionPauli method) get_constraints() (AmberFD.FlucDens method) get_ct_coeff() (AmberFD.FlucDens method) get_ct_energy() (AmberFD.FlucDens method) get_cutoff_distance() (AmberFD.FlucDens method) get_dampening() (AmberFD.FlucDens method) get_del_frz_exclusions() (AmberFD.FlucDens method) get_delta_rho() (AmberFD.FlucDens method) get_dipole() (AmberFD.FlucDens method) get_dipoles() (AmberFD.FlucDens method) get_disp_energy() (AmberFD.DispersionPauli method) get_disp_pauli_force() (AmberFD.AmberFD method) get_dispersion_params() (AmberFD.DispersionPauli method) get_energies() (AmberFD.FlucDens method) get_exclusions() (AmberFD.DispersionPauli method) get_fluc_dens_force() (AmberFD.AmberFD method) get_forces() (AmberFD.AmberFD method) (AmberFD.DispersionPauli method) (AmberFD.FlucDens method) get_fragments() (AmberFD.FlucDens method) get_frozen_energy() (AmberFD.FlucDens method) get_frz_frz_exclusions() (AmberFD.FlucDens method) get_index_mapping() (AmberFD.AmberFD method)

get_num_constraints() (AmberFD.FlucDens method) get_num_fragments() (AmberFD.FlucDens method) get_num_frz_frz_exclusions() (AmberFD.FlucDens method) get_num_particles() (AmberFD.AmberFD method) get_num_sites() (AmberFD.DispersionPauli method) get_parallel_time() (AmberFD.AmberFD method) get_param_names() (AmberFD.FlucDens method) get_params_by_name() (AmberFD.FlucDens method) get_pauli_energy() (AmberFD.DispersionPauli method) get_pauli_exp() (AmberFD.DispersionPauli method) get_pauli_radii() (AmberFD.DispersionPauli method) get_polarization_energy() (AmberFD.FlucDens method) get_rho_coulomb_mat() (AmberFD.FlucDens method) get_rho_pot_vec() (AmberFD.FlucDens method) get_site_params() (AmberFD.FlucDens method) get_total_time() (AmberFD.FlucDens method) get_use_cutoff() (AmberFD.FlucDens method) get_use_PBC() (AmberFD.AmberFD method) (AmberFD.DispersionPauli method) (AmberFD.FlucDens method) get_use_SR_cutoff() (AmberFD.FlucDens method) get_vdw_radii() (AmberFD.DispersionPauli method) get_vdw_radii_map() (AmberFD.DispersionPauli method) getDeltaR() (AmberFD.AmberFD method)

I

Info (C++ class) Info::Info (C++ function) Info::one (C++ member)

Info::three (C++ member) Info::two (C++ member) initialize() (AmberFD.DispersionPauli method) initialize_calculation() (AmberFD.FlucDens method)

L

Linear (AmberFD.FlucDens attribute) load_from_file() (AmberFD.AmberFD method)

loadCheckpoint() (AmberFD.AmberFD.AmberFDSimulation method) loadState() (AmberFD.AmberFD.AmberFDSimulation method)

M

map_id (C++ type) minimizeEnergy() (AmberFD.AmberFD.AmberFDSimulation method)

module AmberFD.PDBReporter MoleculeImporter (class in AmberFD.AmberFD)

N

Nonbonded (C++ class) Nonbonded::add_Vec3_to_vector (C++ function) Nonbonded::calc_dR (C++ function) Nonbonded::calc_exclusions_from_bonds (C++ function) Nonbonded::dot3 (C++ function) Nonbonded::num_threads (C++ member) Nonbonded::R2Idx (C++ member) Nonbonded::RIdx (C++ member)

Nonbonded::RInvIdx (C++ member) Nonbonded::RMaxIdx (C++ member) Nonbonded::use_threads (C++ member) Nonbonded::XIdx (C++ member) Nonbonded::YIdx (C++ member) Nonbonded::ZIdx (C++ member) nuc_nuc (AmberFD.Energies property) Nuclei (AmberFD.FlucDens attribute) nuclei (AmberFD.ParticleInfo property)

O

operator* (C++ function)

operator<< (C++ function)

P

ParticleInfo (C++ class) (class in AmberFD) ParticleInfo::dyn_exp (C++ member) ParticleInfo::frz_chg (C++ member) ParticleInfo::frz_exp (C++ member) ParticleInfo::nuclei (C++ member) ParticleInfo::ParticleInfo (C++ function) ParticleInfo::pauli_exp (C++ member) ParticleInfo::pauli_radii (C++ member) pauli (AmberFD.Energies property) pauli_exp (AmberFD.ParticleInfo property)

pauli_radii (AmberFD.ParticleInfo property) pauli_wall (AmberFD.Energies property) PDBReporterExtra (class in AmberFD.PDBReporter) Periodicity (C++ class) Periodicity::box_size (C++ member) Periodicity::box_vectors (C++ member) Periodicity::inv_box_size (C++ member) Periodicity::is_periodic (C++ member) Periodicity::Periodicity (C++ function) Periodicity::set (C++ function) pol (AmberFD.Energies property) print_params() (AmberFD.FlucDens method)

Q

Quadratic (AmberFD.FlucDens attribute)

R

report() (AmberFD.PDBReporter.PDBReporterExtra method)

runForClockTime() (AmberFD.AmberFD.AmberFDSimulation method)

S

saveCheckpoint() (AmberFD.AmberFD.AmberFDSimulation method) saveState() (AmberFD.AmberFD.AmberFDSimulation method) set_additional_hardness() (AmberFD.FlucDens method) set_C6_map() (AmberFD.DispersionPauli method) set_calc_forces() (AmberFD.FlucDens method) set_ct_coeff() (AmberFD.FlucDens method) set_cutoff_distance() (AmberFD.FlucDens method) set_dampening() (AmberFD.FlucDens method) set_dispersion_params() (AmberFD.DispersionPauli method) set_dyn_exp() (AmberFD.FlucDens method) set_external_field() (AmberFD.FlucDens method) set_frag_constraints() (AmberFD.FlucDens method) set_frz_exp() (AmberFD.FlucDens method) set_pauli_exp() (AmberFD.DispersionPauli method)

set_pauli_radii() (AmberFD.DispersionPauli method) set_site_params() (AmberFD.FlucDens method) set_threads() (AmberFD.AmberFD method) set_two_site_distance() (AmberFD.DispersionPauli method) set_use_cutoff() (AmberFD.FlucDens method) set_use_PBC() (AmberFD.AmberFD method) (AmberFD.DispersionPauli method) (AmberFD.FlucDens method) set_use_secondary_radii() (AmberFD.DispersionPauli method) set_use_SR_cutoff() (AmberFD.FlucDens method) set_use_two_site_repulsion() (AmberFD.DispersionPauli method) set_vdw_radii() (AmberFD.DispersionPauli method) solve_minimization() (AmberFD.FlucDens method) step() (AmberFD.AmberFD.AmberFDSimulation method)

T

thisown (AmberFD.AmberFD property) (AmberFD.DispersionPauli property) (AmberFD.Energies property) (AmberFD.FlucDens property) (AmberFD.ParticleInfo property)

total() (AmberFD.Energies method)

V

vct (AmberFD.Energies property) Vec3 (C++ class) Vec3::cross (C++ function) Vec3::dot (C++ function) Vec3::operator!= (C++ function) Vec3::operator* (C++ function) Vec3::operator*= (C++ function) Vec3::operator+ (C++ function), [1] Vec3::operator+= (C++ function)

Vec3::operator- (C++ function), [1] Vec3::operator-= (C++ function) Vec3::operator/ (C++ function) Vec3::operator/= (C++ function) Vec3::operator== (C++ function) Vec3::operator[] (C++ function), [1] Vec3::Vec3 (C++ function), [1] vec_d (C++ type) vec_f (C++ type) vec_i (C++ type)

Z

zero() (AmberFD.Energies method)