- PairwisePotentialInterface (class in pele.potentials._pele)
- Parameters (class in pele.systems)
- params() (pele.transition_states.FindTransitionState class method)
- ParticleExchange (class in pele.takestep)
- pbinary_double (C function)
- pbinary_int64 (C function)
-
pele.accept_tests
-
pele.angleaxis
-
pele.concurrent
-
pele.gui
-
pele.landscape
-
pele.mindist
-
pele.optimize
-
pele.potentials
-
pele.rates
-
pele.storage
-
pele.systems
-
pele.takestep
-
pele.thermodynamics
-
pele.transition_states
-
pele.utils
-
pele.utils.amber
-
pele.utils.frozen_atoms
-
pele.utils.hessian
-
pele.utils.histogram
-
pele.utils.neighbor_list
-
pele.utils.pymolwrapper
-
pele.utils.rbtools
-
pele.utils.rotations
-
pele.utils.xyz
- pele::aa_to_quaternion (C++ function)
- pele::aa_to_rot_mat (C++ function)
- pele::AbstractStopCriterion (C++ class)
- pele::AbstractStopCriterion::stop_criterion_satisfied (C++ function)
- pele::AbstractStopCriterion::~AbstractStopCriterion (C++ function)
- pele::accumulate_energies_omp (C++ function)
- pele::accumulate_gradient (C++ function)
- pele::accumulate_hessian (C++ function)
- pele::add_symmetry_offset (C++ function)
- pele::add_translation_offset_2d (C++ function)
- pele::Array (C++ class)
- pele::Array::Array (C++ function), [1], [2], [3], [4], [5], [6]
- pele::Array::assign (C++ function), [1]
- pele::Array::begin (C++ function), [1]
- pele::Array::const_iterator (C++ type)
- pele::Array::copy (C++ function)
- pele::Array::data (C++ function), [1]
- pele::Array::empty (C++ function)
- pele::Array::end (C++ function), [1]
- pele::Array::free (C++ function)
- pele::Array::get_max (C++ function)
- pele::Array::get_min (C++ function)
- pele::Array::iterator (C++ type)
- pele::Array::operator!= (C++ function)
- pele::Array::operator* (C++ function)
- pele::Array::operator*= (C++ function), [1]
- pele::Array::operator+ (C++ function)
- pele::Array::operator+= (C++ function), [1]
- pele::Array::operator- (C++ function), [1]
- pele::Array::operator-= (C++ function), [1]
- pele::Array::operator/= (C++ function), [1]
- pele::Array::operator== (C++ function)
- pele::Array::operator[] (C++ function), [1]
- pele::Array::prod (C++ function)
- pele::Array::reference_count (C++ function)
- pele::Array::size (C++ function)
- pele::Array::sum (C++ function)
- pele::Array::to_std_vector_copy (C++ function)
- pele::Array::view (C++ function)
- pele::Array::wrap (C++ function)
- pele::ATLJ (C++ class)
- pele::ATLJ::ATLJ (C++ function)
- pele::ATLJ::get_energy (C++ function)
- pele::ATLJ::~ATLJ (C++ function)
- pele::AtomListPotential (C++ class)
- pele::AtomListPotential::add_energy_gradient (C++ function)
- pele::AtomListPotential::add_energy_gradient_hessian (C++ function)
- pele::AtomListPotential::AtomListPotential (C++ function), [1], [2]
- pele::AtomListPotential::get_energy (C++ function)
- pele::BacktrackingLineSearch (C++ class)
- pele::BacktrackingLineSearch::BacktrackingLineSearch (C++ function)
- pele::BacktrackingLineSearch::get_initial_stpsize (C++ function)
- pele::BacktrackingLineSearch::get_step_moving_away_from_min (C++ function)
- pele::BacktrackingLineSearch::line_search (C++ function)
- pele::BacktrackingLineSearch::set_g_f_ptr (C++ function)
- pele::BacktrackingLineSearch::set_xold_gold_ (C++ function)
- pele::BacktrackingLineSearch::~BacktrackingLineSearch (C++ function)
- pele::BaseAccumulator (C++ class)
- pele::BaseAccumulator::BaseAccumulator (C++ function)
- pele::BaseAccumulator::calculate_dist_data_in_thread (C++ function)
- pele::BaseAccumulator::calculate_distance_data (C++ function)
- pele::BaseAccumulator::m_coords (C++ member)
- pele::BaseAccumulator::m_cutoff (C++ member)
- pele::BaseAccumulator::m_dist (C++ member)
- pele::BaseAccumulator::m_distance_datas (C++ member)
- pele::BaseAccumulator::m_interaction (C++ member)
- pele::BaseAccumulator::m_ndim (C++ member)
- pele::BaseAccumulator::m_radii (C++ member)
- pele::BaseAccumulator::reset_data (C++ function)
- pele::BaseHarmonic (C++ class)
- pele::BaseHarmonic::BaseHarmonic (C++ function)
- pele::BaseHarmonic::get_energy (C++ function)
- pele::BaseHarmonic::get_energy_gradient (C++ function)
- pele::BaseHarmonic::get_k (C++ function)
- pele::BaseHarmonic::set_k (C++ function)
- pele::BaseHarmonic::~BaseHarmonic (C++ function)
- pele::BaseInteraction (C++ struct)
- pele::BaseInteraction::energy (C++ function)
- pele::BaseInteraction::energy_gradient (C++ function)
- pele::BaseInteraction::energy_gradient_hessian (C++ function)
- pele::BasePotential (C++ class)
- pele::BasePotential::add_energy_gradient (C++ function)
- pele::BasePotential::add_energy_gradient_hessian (C++ function)
- pele::BasePotential::add_hessian (C++ function)
- pele::BasePotential::compute_norm (C++ function)
- pele::BasePotential::find_rattlers (C++ function)
- pele::BasePotential::get_energy (C++ function)
- pele::BasePotential::get_energy_change (C++ function)
- pele::BasePotential::get_energy_gradient (C++ function), [1], [2]
- pele::BasePotential::get_energy_gradient_hessian (C++ function)
- pele::BasePotential::get_energy_gradient_hessian_rattlers (C++ function)
- pele::BasePotential::get_hessian (C++ function)
- pele::BasePotential::get_ndim (C++ function)
- pele::BasePotential::numerical_gradient (C++ function)
- pele::BasePotential::numerical_hessian (C++ function)
- pele::BasePotential::~BasePotential (C++ function)
- pele::BaseRadialGaussian (C++ class)
- pele::BaseRadialGaussian::BaseRadialGaussian (C++ function)
- pele::BaseRadialGaussian::get_energy (C++ function)
- pele::BaseRadialGaussian::get_energy_gradient (C++ function)
- pele::BaseRadialGaussian::get_k (C++ function)
- pele::BaseRadialGaussian::get_l0 (C++ function)
- pele::BaseRadialGaussian::get_log_prefactor (C++ function)
- pele::BaseRadialGaussian::get_r_cutoff (C++ function)
- pele::BaseRadialGaussian::set_k (C++ function)
- pele::BaseRadialGaussian::set_l0 (C++ function)
- pele::BaseRadialGaussian::set_log_prefactor (C++ function)
- pele::BaseRadialGaussian::set_r_cutoff (C++ function)
- pele::BaseRadialGaussian::~BaseRadialGaussian (C++ function)
- pele::BerthierDistribution3d (C++ class)
- pele::BerthierDistribution3d::BerthierDistribution3d (C++ function)
- pele::BerthierDistribution3d::pdf (C++ function)
- pele::BerthierDistribution3d::sample (C++ function)
- pele::BracketingLineSearch (C++ class)
- pele::BracketingLineSearch::BracketingLineSearch (C++ function)
- pele::BracketingLineSearch::line_search (C++ function)
- pele::BracketingLineSearch::set_g_f_ptr (C++ function)
- pele::BracketingLineSearch::set_xold_gold_ (C++ function)
- pele::BracketingLineSearch::~BracketingLineSearch (C++ function)
- pele::cartesian_distance (C++ struct)
- pele::cartesian_distance::get_rij (C++ function)
- pele::cartesian_distance::put_atom_in_box (C++ function), [1]
- pele::CartesianDistanceWrapper (C++ class)
- pele::CartesianDistanceWrapper::get_rij (C++ function)
- pele::cell_t (C++ type)
- pele::CellListPotential (C++ class)
- pele::CellListPotential::add_energy_gradient (C++ function)
- pele::CellListPotential::add_energy_gradient_hessian (C++ function)
- pele::CellListPotential::add_energy_hessian (C++ function)
- pele::CellListPotential::add_hessian (C++ function)
- pele::CellListPotential::CellListPotential (C++ function), [1], [2]
- pele::CellListPotential::compute_norm (C++ function)
- pele::CellListPotential::exact_gradient (C++ member)
- pele::CellListPotential::exact_gradient_initialized (C++ member)
- pele::CellListPotential::exact_sum (C++ member)
- pele::CellListPotential::get_atom_order (C++ function)
- pele::CellListPotential::get_energy (C++ function)
- pele::CellListPotential::get_energy_change (C++ function)
- pele::CellListPotential::get_energy_gradient (C++ function)
- pele::CellListPotential::get_energy_gradient_hessian (C++ function)
- pele::CellListPotential::get_energy_hessian (C++ function)
- pele::CellListPotential::get_interaction_energy_gradient (C++ function)
- pele::CellListPotential::get_interaction_energy_gradient_hessian (C++ function)
- pele::CellListPotential::get_ndim (C++ function), [1]
- pele::CellListPotential::get_neighbors (C++ function)
- pele::CellListPotential::get_neighbors_picky (C++ function)
- pele::CellListPotential::get_overlaps (C++ function)
- pele::CellListPotential::get_rij (C++ function)
- pele::CellListPotential::m_cell_lists (C++ member)
- pele::CellListPotential::m_dist (C++ member)
- pele::CellListPotential::m_eAcc (C++ member)
- pele::CellListPotential::m_eAccExact (C++ member)
- pele::CellListPotential::m_egAcc (C++ member)
- pele::CellListPotential::m_egAccExact (C++ member)
- pele::CellListPotential::m_eghAcc (C++ member)
- pele::CellListPotential::m_eghAccExact (C++ member)
- pele::CellListPotential::m_ehAcc (C++ member)
- pele::CellListPotential::m_interaction (C++ member)
- pele::CellListPotential::m_ndim (C++ member)
- pele::CellListPotential::m_radii_sca (C++ member)
- pele::CellListPotential::update_iterator (C++ function)
- pele::CellListPotential::~CellListPotential (C++ function)
- pele::CellLists (C++ class)
- pele::CellLists::add_atom_queue (C++ member)
- pele::CellLists::build_cell_neighbors_list (C++ function)
- pele::CellLists::CellLists (C++ function)
- pele::CellLists::get_atom_pair_looper (C++ function)
- pele::CellLists::get_nr_cells (C++ function)
- pele::CellLists::get_nr_cellsx (C++ function)
- pele::CellLists::get_order (C++ function)
- pele::CellLists::m_container (C++ member)
- pele::CellLists::m_initialized (C++ member)
- pele::CellLists::m_lattice_tool (C++ member)
- pele::CellLists::m_ndim (C++ member)
- pele::CellLists::print_warnings (C++ function)
- pele::CellLists::reset_container (C++ function)
- pele::CellLists::update (C++ function)
- pele::CellLists::update_container (C++ function)
- pele::CellLists::update_container_specific (C++ function)
- pele::CellLists::update_specific (C++ function)
- pele::CellLists::~CellLists (C++ function)
- pele::CellListsContainer (C++ class)
- pele::CellListsContainer::add_atom_to_cell (C++ function)
- pele::CellListsContainer::CellListsContainer (C++ function)
- pele::CellListsContainer::m_cell_atoms (C++ member)
- pele::CellListsContainer::m_cell_neighbor_pairs_boundary (C++ member)
- pele::CellListsContainer::m_cell_neighbor_pairs_inner (C++ member)
- pele::CellListsContainer::m_cell_neighbors (C++ member)
- pele::CellListsContainer::remove_atom_from_cell (C++ function)
- pele::CellListsContainer::remove_atom_from_cell_ind (C++ function)
- pele::CellListsContainer::reset (C++ function)
- pele::CellListsContainer::setup_cells (C++ function)
- pele::CellListsLoop (C++ class)
- pele::CellListsLoop::cell_vec_t (C++ type)
- pele::CellListsLoop::CellListsLoop (C++ function)
- pele::CellListsLoop::loop_cell_pairs (C++ function)
- pele::CellListsLoop::loop_cell_pairs_specific (C++ function)
- pele::CellListsLoop::loop_through_atom_pairs (C++ function)
- pele::CellListsLoop::loop_through_atom_pairs_specific (C++ function)
- pele::CellListsLoop::loop_through_cell_neighbors_for_unique_pairs (C++ function)
- pele::CellListsLoop::loop_through_unique_pairs_containing_iatoms (C++ function)
- pele::CellListsLoop::m_container (C++ member)
- pele::CellListsLoop::m_lattice_tool (C++ member)
- pele::CellListsLoop::m_ndim (C++ member)
- pele::CellListsLoop::m_visitor (C++ member)
- pele::check_sundials_retval (C++ function)
- pele::color_type (C++ type)
- pele::combination_generator (C++ class)
- pele::combination_generator::combination_generator (C++ function)
- pele::combination_generator::operator() (C++ function)
- pele::CombinedPotential (C++ class)
- pele::CombinedPotential::add_potential (C++ function)
- pele::CombinedPotential::CombinedPotential (C++ function)
- pele::CombinedPotential::get_energy (C++ function)
- pele::CombinedPotential::get_energy_gradient (C++ function)
- pele::CombinedPotential::get_energy_gradient_hessian (C++ function)
- pele::CombinedPotential::get_hessian (C++ function)
- pele::CombinedPotential::~CombinedPotential (C++ function)
- pele::compare_degree (C++ function)
- pele::CoordsAdaptor (C++ class)
- pele::CoordsAdaptor::CoordsAdaptor (C++ function)
- pele::CoordsAdaptor::get_atom_positions (C++ function)
- pele::CoordsAdaptor::get_coords (C++ function)
- pele::CoordsAdaptor::get_rb_position (C++ function)
- pele::CoordsAdaptor::get_rb_positions (C++ function)
- pele::CoordsAdaptor::get_rb_rotation (C++ function)
- pele::CoordsAdaptor::get_rb_rotations (C++ function)
- pele::CosineGradientDescent (C++ class)
- pele::CosineGradientDescent::CosineGradientDescent (C++ function)
- pele::CosineGradientDescent::one_iteration (C++ function)
- pele::CosineGradientDescent::reset (C++ function)
- pele::CosineGradientDescent::~CosineGradientDescent (C++ function)
- pele::cross_shifted (C++ function)
- pele::CVODEBDFOptimizer (C++ class)
- pele::CVODEBDFOptimizer::CVODEBDFOptimizer (C++ function), [1]
- pele::CVODEBDFOptimizer::get_nhev (C++ function)
- pele::CVODEBDFOptimizer::H02 (C++ member)
- pele::CVODEBDFOptimizer::one_iteration (C++ function)
- pele::CVODEBDFOptimizer::operator= (C++ function)
- pele::CVODEBDFOptimizer::reset (C++ function)
- pele::CVODEBDFOptimizer::stop_criterion_satisfied (C++ function)
- pele::CVODEBDFOptimizer::~CVODEBDFOptimizer (C++ function)
- pele::digits (C++ member)
- pele::DistanceData (C++ class)
- pele::DistanceData::dij (C++ member)
- pele::DistanceData::DistanceData (C++ function)
- pele::DistanceData::dr (C++ member)
- pele::DistanceData::r2 (C++ member)
- pele::DistanceData::reset (C++ function)
- pele::DistanceData::xi_off (C++ member)
- pele::DistanceData::xj_off (C++ member)
- pele::DistanceInterface (C++ class)
- pele::DistanceInterface::get_rij (C++ function)
- pele::DistanceInterface::~DistanceInterface (C++ function)
- pele::dot (C++ function), [1], [2], [3]
- pele::Edge (C++ class)
- pele::Edge::Edge (C++ function)
- pele::Edge::head (C++ function)
- pele::Edge::head_ (C++ member)
- pele::Edge::P (C++ member)
- pele::Edge::tail (C++ function)
- pele::Edge::tail_ (C++ member)
- pele::edge_ptr (C++ type)
- pele::eig_eq_pele (C++ function)
- pele::eig_eq_pele_data (C++ function)
- pele::eig_mat_eq_pele (C++ function)
- pele::EnergyAccumulator (C++ class)
- pele::EnergyAccumulator::EnergyAccumulator (C++ function)
- pele::EnergyAccumulator::get_energy (C++ function)
- pele::EnergyAccumulator::insert_atom_pair (C++ function)
- pele::EnergyAccumulator::reset_data (C++ function)
- pele::EnergyAccumulator::~EnergyAccumulator (C++ function)
- pele::EnergyAccumulatorExact (C++ class)
- pele::EnergyAccumulatorExact::EnergyAccumulatorExact (C++ function)
- pele::EnergyAccumulatorExact::get_energy (C++ function)
- pele::EnergyAccumulatorExact::insert_atom_pair (C++ function)
- pele::EnergyAccumulatorExact::reset_data (C++ function)
- pele::EnergyAccumulatorExact::~EnergyAccumulatorExact (C++ function)
- pele::EnergyGradientAccumulator (C++ class)
- pele::EnergyGradientAccumulator::EnergyGradientAccumulator (C++ function)
- pele::EnergyGradientAccumulator::get_energy (C++ function)
- pele::EnergyGradientAccumulator::insert_atom_pair (C++ function)
- pele::EnergyGradientAccumulator::m_gradient (C++ member)
- pele::EnergyGradientAccumulator::reset_data (C++ function)
- pele::EnergyGradientAccumulator::~EnergyGradientAccumulator (C++ function)
- pele::EnergyGradientAccumulatorExact (C++ class)
- pele::EnergyGradientAccumulatorExact::EnergyGradientAccumulatorExact (C++ function)
- pele::EnergyGradientAccumulatorExact::get_energy (C++ function)
- pele::EnergyGradientAccumulatorExact::insert_atom_pair (C++ function)
- pele::EnergyGradientAccumulatorExact::m_gradient (C++ member)
- pele::EnergyGradientAccumulatorExact::reset_data (C++ function)
- pele::EnergyGradientAccumulatorExact::~EnergyGradientAccumulatorExact (C++ function)
- pele::EnergyGradientHessianAccumulator (C++ class)
- pele::EnergyGradientHessianAccumulator::EnergyGradientHessianAccumulator (C++ function)
- pele::EnergyGradientHessianAccumulator::get_energy (C++ function)
- pele::EnergyGradientHessianAccumulator::insert_atom_pair (C++ function)
- pele::EnergyGradientHessianAccumulator::m_gradient (C++ member)
- pele::EnergyGradientHessianAccumulator::m_hessian (C++ member)
- pele::EnergyGradientHessianAccumulator::reset_data (C++ function)
- pele::EnergyGradientHessianAccumulator::~EnergyGradientHessianAccumulator (C++ function)
- pele::EnergyGradientHessianAccumulatorExact (C++ class)
- pele::EnergyGradientHessianAccumulatorExact::EnergyGradientHessianAccumulatorExact (C++ function)
- pele::EnergyGradientHessianAccumulatorExact::get_energy (C++ function)
- pele::EnergyGradientHessianAccumulatorExact::insert_atom_pair (C++ function)
- pele::EnergyGradientHessianAccumulatorExact::m_gradient (C++ member)
- pele::EnergyGradientHessianAccumulatorExact::m_hessian (C++ member)
- pele::EnergyGradientHessianAccumulatorExact::reset_data (C++ function)
- pele::EnergyGradientHessianAccumulatorExact::~EnergyGradientHessianAccumulatorExact (C++ function)
- pele::EnergyHessianAccumulator (C++ class)
- pele::EnergyHessianAccumulator::EnergyHessianAccumulator (C++ function)
- pele::EnergyHessianAccumulator::get_energy (C++ function)
- pele::EnergyHessianAccumulator::insert_atom_pair (C++ function)
- pele::EnergyHessianAccumulator::reset_data (C++ function)
- pele::EnergyHessianAccumulator::~EnergyHessianAccumulator (C++ function)
- pele::ExtendedMixedOptimizer (C++ class)
- pele::ExtendedMixedOptimizer::ExtendedMixedOptimizer (C++ function)
- pele::ExtendedMixedOptimizer::free_cvode_objects (C++ function)
- pele::ExtendedMixedOptimizer::get_n_failed_phase_2_steps (C++ function)
- pele::ExtendedMixedOptimizer::get_n_phase_1_steps (C++ function)
- pele::ExtendedMixedOptimizer::get_n_phase_2_steps (C++ function)
- pele::ExtendedMixedOptimizer::get_nhev (C++ function)
- pele::ExtendedMixedOptimizer::get_nhev_extended (C++ function)
- pele::ExtendedMixedOptimizer::one_iteration (C++ function)
- pele::ExtendedMixedOptimizer::reset (C++ function)
- pele::ExtendedMixedOptimizer::reset_cvode (C++ function)
- pele::ExtendedMixedOptimizer::reset_newton (C++ function)
- pele::ExtendedMixedOptimizer::~ExtendedMixedOptimizer (C++ function)
- pele::ExtendedPotential (C++ class)
- pele::ExtendedPotential::ExtendedPotential (C++ function)
- pele::ExtendedPotential::get_energy (C++ function)
- pele::ExtendedPotential::get_energy_gradient (C++ function)
- pele::ExtendedPotential::get_energy_gradient_hessian (C++ function)
- pele::ExtendedPotential::get_hessian (C++ function)
- pele::ExtendedPotential::get_hessian_extended (C++ function)
- pele::ExtendedPotential::get_neev_extension (C++ function)
- pele::ExtendedPotential::get_nfev_extension (C++ function)
- pele::ExtendedPotential::get_nhev_extension (C++ function)
- pele::ExtendedPotential::get_use_extended_potential (C++ function)
- pele::ExtendedPotential::switch_off_extended_potential (C++ function)
- pele::ExtendedPotential::switch_on_extended_potential (C++ function)
- pele::f (C++ function), [1]
- pele::Factorial (C++ struct)
- pele::Factorial::[anonymous] (C++ enum)
- pele::Factorial::[anonymous]::value (C++ enumerator)
- pele::Factorial<0> (C++ struct)
- pele::Factorial<0>::[anonymous] (C++ enum)
- pele::Factorial<0>::[anonymous]::value (C++ enumerator)
- pele::FlatHarmonic (C++ class)
- pele::FlatHarmonic::FlatHarmonic (C++ function)
- pele::FlatHarmonic::get_energy (C++ function)
- pele::FlatHarmonic::get_energy_gradient (C++ function)
- pele::FlatHarmonic::get_energy_gradient_hessian (C++ function)
- pele::FlatHarmonic::~FlatHarmonic (C++ function)
- pele::Frenkel (C++ class)
- pele::Frenkel::Frenkel (C++ function)
- pele::frenkel_interaction (C++ struct)
- pele::frenkel_interaction::energy (C++ function)
- pele::frenkel_interaction::energy_gradient (C++ function)
- pele::frenkel_interaction::energy_gradient_hessian (C++ function)
- pele::frenkel_interaction::frenkel_interaction (C++ function)
- pele::FrenkelPeriodic (C++ class)
- pele::FrenkelPeriodic::FrenkelPeriodic (C++ function)
- pele::FrenkelPeriodicCellLists (C++ class)
- pele::FrenkelPeriodicCellLists::FrenkelPeriodicCellLists (C++ function)
- pele::FrozenCoordsConverter (C++ class)
- pele::FrozenCoordsConverter::FrozenCoordsConverter (C++ function)
- pele::FrozenCoordsConverter::get_frozen_dof (C++ function)
- pele::FrozenCoordsConverter::get_full_coords (C++ function)
- pele::FrozenCoordsConverter::get_full_grad (C++ function)
- pele::FrozenCoordsConverter::get_mobile_dof (C++ function)
- pele::FrozenCoordsConverter::get_reduced_coords (C++ function)
- pele::FrozenCoordsConverter::get_reduced_hessian (C++ function)
- pele::FrozenCoordsConverter::ndof (C++ function)
- pele::FrozenCoordsConverter::ndof_frozen (C++ function)
- pele::FrozenCoordsConverter::ndof_mobile (C++ function)
- pele::FrozenPotentialWrapper (C++ class)
- pele::FrozenPotentialWrapper::coords_converter (C++ member)
- pele::FrozenPotentialWrapper::FrozenPotentialWrapper (C++ function)
- pele::FrozenPotentialWrapper::get_energy (C++ function)
- pele::FrozenPotentialWrapper::get_energy_gradient (C++ function)
- pele::FrozenPotentialWrapper::get_energy_gradient_hessian (C++ function)
- pele::FrozenPotentialWrapper::get_frozen_dof (C++ function)
- pele::FrozenPotentialWrapper::get_full_coords (C++ function)
- pele::FrozenPotentialWrapper::get_mobile_dof (C++ function)
- pele::FrozenPotentialWrapper::get_reduced_coords (C++ function)
- pele::FrozenPotentialWrapper::~FrozenPotentialWrapper (C++ function)
- pele::GaussianPot (C++ class)
- pele::GaussianPot::add_energy_gradient (C++ function)
- pele::GaussianPot::add_energy_gradient_hessian (C++ function)
- pele::GaussianPot::GaussianPot (C++ function)
- pele::GaussianPot::get_energy (C++ function)
- pele::GaussianPot::get_energy_gradient (C++ function)
- pele::GaussianPot::get_energy_gradient_hessian (C++ function)
- pele::generate_2d_symmetries (C++ function)
- pele::generate_3d_symmetries (C++ function)
- pele::generate_bidisperse_radii (C++ function)
- pele::generate_random_coordinates (C++ function)
- pele::GenericMixedDescent (C++ class)
- pele::GenericMixedDescent::GenericMixedDescent (C++ function)
- pele::GenericMixedDescent::get_n_phase_1_steps (C++ function)
- pele::GenericMixedDescent::get_n_phase_2_steps (C++ function)
- pele::GenericMixedDescent::get_x (C++ function)
- pele::GenericMixedDescent::one_iteration (C++ function)
- pele::GenericMixedDescent::stop_criterion_satisfied (C++ function)
- pele::get_box_length (C++ function)
- pele::get_ncellx_scale (C++ function)
- pele::get_symmetries (C++ function)
- pele::GradientDescent (C++ class)
- pele::GradientDescent::GradientDescent (C++ function)
- pele::GradientDescent::one_iteration (C++ function)
- pele::GradientDescent::reset (C++ function)
- pele::GradientDescent::~GradientDescent (C++ function)
- pele::GradientOptimizer (C++ class)
- pele::GradientOptimizer::compute_func_gradient (C++ function), [1]
- pele::GradientOptimizer::compute_pot_norm (C++ function)
- pele::GradientOptimizer::f_ (C++ member)
- pele::GradientOptimizer::func_initialized_ (C++ member)
- pele::GradientOptimizer::g_ (C++ member)
- pele::GradientOptimizer::get_f (C++ function)
- pele::GradientOptimizer::get_g (C++ function)
- pele::GradientOptimizer::get_gradient_norm_ (C++ function)
- pele::GradientOptimizer::get_last_step_failed (C++ function)
- pele::GradientOptimizer::get_maxiter (C++ function)
- pele::GradientOptimizer::get_maxstep (C++ function)
- pele::GradientOptimizer::get_nfev (C++ function)
- pele::GradientOptimizer::get_nhev (C++ function)
- pele::GradientOptimizer::get_niter (C++ function)
- pele::GradientOptimizer::get_potential (C++ function)
- pele::GradientOptimizer::get_rms (C++ function)
- pele::GradientOptimizer::get_step_norm_ (C++ function)
- pele::GradientOptimizer::get_tol (C++ function)
- pele::GradientOptimizer::get_verbosity_ (C++ function)
- pele::GradientOptimizer::get_x (C++ function)
- pele::GradientOptimizer::gradient_norm_ (C++ member)
- pele::GradientOptimizer::GradientOptimizer (C++ function), [1], [2]
- pele::GradientOptimizer::initialize_func_gradient (C++ function)
- pele::GradientOptimizer::iprint_ (C++ member)
- pele::GradientOptimizer::iter_number_ (C++ member)
- pele::GradientOptimizer::iterations_before_save_ (C++ member)
- pele::GradientOptimizer::last_step_failed_ (C++ member)
- pele::GradientOptimizer::maxiter_ (C++ member)
- pele::GradientOptimizer::maxstep_ (C++ member)
- pele::GradientOptimizer::nfev_ (C++ member)
- pele::GradientOptimizer::nhev_ (C++ member)
- pele::GradientOptimizer::one_iteration (C++ function)
- pele::GradientOptimizer::potential_ (C++ member)
- pele::GradientOptimizer::print_stats (C++ function)
- pele::GradientOptimizer::reset (C++ function)
- pele::GradientOptimizer::run (C++ function), [1]
- pele::GradientOptimizer::save_trajectory_ (C++ member)
- pele::GradientOptimizer::set_f (C++ function)
- pele::GradientOptimizer::set_func_gradient (C++ function)
- pele::GradientOptimizer::set_iprint (C++ function)
- pele::GradientOptimizer::set_max_iter (C++ function)
- pele::GradientOptimizer::set_maxstep (C++ function)
- pele::GradientOptimizer::set_potential (C++ function)
- pele::GradientOptimizer::set_rms (C++ function)
- pele::GradientOptimizer::set_tol (C++ function)
- pele::GradientOptimizer::set_tolerance (C++ function)
- pele::GradientOptimizer::set_verbosity (C++ function)
- pele::GradientOptimizer::set_x (C++ function)
- pele::GradientOptimizer::step_norm_ (C++ member)
- pele::GradientOptimizer::stop_criterion (C++ member)
- pele::GradientOptimizer::stop_criterion_satisfied (C++ function)
- pele::GradientOptimizer::succeeded_ (C++ member)
- pele::GradientOptimizer::success (C++ function)
- pele::GradientOptimizer::tol_ (C++ member)
- pele::GradientOptimizer::update_cheap_trajectory_info (C++ function)
- pele::GradientOptimizer::update_costly_trajectory_info (C++ function)
- pele::GradientOptimizer::verbosity_ (C++ member)
- pele::GradientOptimizer::x_ (C++ member)
- pele::GradientOptimizer::~GradientOptimizer (C++ function)
- pele::GradientStopCriterion (C++ class)
- pele::GradientStopCriterion::GradientStopCriterion (C++ function)
- pele::GradientStopCriterion::stop_criterion_satisfied (C++ function)
- pele::Graph (C++ class)
- pele::Graph::add_edge (C++ function)
- pele::Graph::add_node (C++ function), [1]
- pele::Graph::add_nodes (C++ function)
- pele::Graph::edge_list_ (C++ member)
- pele::Graph::edge_list_t (C++ type)
- pele::Graph::get_node (C++ function)
- pele::Graph::Graph (C++ function), [1]
- pele::Graph::next_node_id_ (C++ member)
- pele::Graph::node_map_ (C++ member)
- pele::Graph::node_map_t (C++ type)
- pele::Graph::number_of_edges (C++ function)
- pele::Graph::number_of_nodes (C++ function)
- pele::Graph::remove_node (C++ function)
- pele::Graph::~Graph (C++ function)
- pele::hacky_mat_mul (C++ function)
- pele::Harmonic (C++ class)
- pele::Harmonic::Harmonic (C++ function)
- pele::harmonic_interaction (C++ struct)
- pele::harmonic_interaction::energy (C++ function)
- pele::harmonic_interaction::energy_gradient (C++ function)
- pele::harmonic_interaction::energy_gradient_hessian (C++ function)
- pele::harmonic_interaction::harmonic_interaction (C++ function)
- pele::harmonic_interaction::m_k (C++ member)
- pele::HarmonicAtomList (C++ class)
- pele::HarmonicAtomList::HarmonicAtomList (C++ function), [1]
- pele::HarmonicCOM (C++ class)
- pele::HarmonicCOM::HarmonicCOM (C++ function)
- pele::HarmonicNeighborList (C++ class)
- pele::HarmonicNeighborList::HarmonicNeighborList (C++ function)
- pele::HessianType (C++ enum)
- pele::HessianType::DENSE (C++ enumerator)
- pele::HessianType::ITERATIVE (C++ enumerator)
- pele::HS_halfint_pairwise_power_interaction (C++ struct)
- pele::HS_halfint_pairwise_power_interaction::energy (C++ function)
- pele::HS_halfint_pairwise_power_interaction::energy_gradient (C++ function)
- pele::HS_halfint_pairwise_power_interaction::energy_gradient_hessian (C++ function)
- pele::HS_halfint_pairwise_power_interaction::HS_halfint_pairwise_power_interaction (C++ function)
- pele::HS_WCA (C++ class)
- pele::HS_WCA::HS_WCA (C++ function)
- pele::HS_WCA_interaction (C++ struct)
- pele::HS_WCA_interaction::compute_energy (C++ function)
- pele::HS_WCA_interaction::energy (C++ function)
- pele::HS_WCA_interaction::energy_gradient (C++ function)
- pele::HS_WCA_interaction::energy_gradient_hessian (C++ function)
- pele::HS_WCA_interaction::evaluate_pair_potential (C++ function)
- pele::HS_WCA_interaction::HS_WCA_interaction (C++ function)
- pele::HS_WCACellLists (C++ class)
- pele::HS_WCACellLists::get_nr_unique_pairs (C++ function)
- pele::HS_WCACellLists::HS_WCACellLists (C++ function)
- pele::HS_WCALeesEdwards (C++ class)
- pele::HS_WCALeesEdwards::HS_WCALeesEdwards (C++ function)
- pele::HS_WCALeesEdwardsCellLists (C++ class)
- pele::HS_WCALeesEdwardsCellLists::get_nr_unique_pairs (C++ function)
- pele::HS_WCALeesEdwardsCellLists::HS_WCALeesEdwardsCellLists (C++ function)
- pele::HS_WCANeighborList (C++ class)
- pele::HS_WCANeighborList::HS_WCANeighborList (C++ function)
- pele::HS_WCAPeriodic (C++ class)
- pele::HS_WCAPeriodic::HS_WCAPeriodic (C++ function)
- pele::HS_WCAPeriodicCellLists (C++ class)
- pele::HS_WCAPeriodicCellLists::get_nr_unique_pairs (C++ function)
- pele::HS_WCAPeriodicCellLists::HS_WCAPeriodicCellLists (C++ function)
- pele::HSHalfIntPairwisePower (C++ class)
- pele::HSHalfIntPairwisePower::HSHalfIntPairwisePower (C++ function)
- pele::HSHalfIntPairwisePowerPeriodic (C++ class)
- pele::HSHalfIntPairwisePowerPeriodic::HSHalfIntPairwisePowerPeriodic (C++ function)
- pele::HSHalfIntPairwisePowerPeriodicCellLists (C++ class)
- pele::HSHalfIntPairwisePowerPeriodicCellLists::HSHalfIntPairwisePowerPeriodicCellLists (C++ function)
- pele::identity (C++ function)
- pele::init_distance_datas (C++ function)
- pele::init_energies (C++ function)
- pele::InverseHalfIntPower (C++ class)
- pele::InverseHalfIntPower::InverseHalfIntPower (C++ function)
- pele::InverseHalfIntPower_interaction (C++ struct)
- pele::InverseHalfIntPower_interaction::energy (C++ function)
- pele::InverseHalfIntPower_interaction::energy_gradient (C++ function)
- pele::InverseHalfIntPower_interaction::energy_gradient_hessian (C++ function)
- pele::InverseHalfIntPower_interaction::InverseHalfIntPower_interaction (C++ function)
- pele::InverseHalfIntPowerHS (C++ class)
- pele::InverseHalfIntPowerHS::InverseHalfIntPowerHS (C++ function)
- pele::InverseHalfIntPowerHS_interaction (C++ struct)
- pele::InverseHalfIntPowerHS_interaction::energy (C++ function)
- pele::InverseHalfIntPowerHS_interaction::energy_gradient (C++ function)
- pele::InverseHalfIntPowerHS_interaction::energy_gradient_hessian (C++ function)
- pele::InverseHalfIntPowerHS_interaction::InverseHalfIntPowerHS_interaction (C++ function)
- pele::InverseHalfIntPowerHSPeriodic (C++ class)
- pele::InverseHalfIntPowerHSPeriodic::InverseHalfIntPowerHSPeriodic (C++ function)
- pele::InverseHalfIntPowerHSPeriodicCellLists (C++ class)
- pele::InverseHalfIntPowerHSPeriodicCellLists::InverseHalfIntPowerHSPeriodicCellLists (C++ function)
- pele::InverseHalfIntPowerPeriodic (C++ class)
- pele::InverseHalfIntPowerPeriodic::InverseHalfIntPowerPeriodic (C++ function)
- pele::InverseHalfIntPowerPeriodicCellLists (C++ class)
- pele::InverseHalfIntPowerPeriodicCellLists::InverseHalfIntPowerPeriodicCellLists (C++ function)
- pele::InverseIntPower (C++ class)
- pele::InverseIntPower::InverseIntPower (C++ function)
- pele::InverseIntPower_interaction (C++ struct)
- pele::InverseIntPower_interaction::energy (C++ function)
- pele::InverseIntPower_interaction::energy_gradient (C++ function)
- pele::InverseIntPower_interaction::energy_gradient_hessian (C++ function)
- pele::InverseIntPower_interaction::InverseIntPower_interaction (C++ function)
- pele::InverseIntPowerHS (C++ class)
- pele::InverseIntPowerHS::InverseIntPowerHS (C++ function)
- pele::InverseIntPowerHS_interaction (C++ struct)
- pele::InverseIntPowerHS_interaction::energy (C++ function)
- pele::InverseIntPowerHS_interaction::energy_gradient (C++ function)
- pele::InverseIntPowerHS_interaction::energy_gradient_hessian (C++ function)
- pele::InverseIntPowerHS_interaction::InverseIntPowerHS_interaction (C++ function)
- pele::InverseIntPowerHSPeriodic (C++ class)
- pele::InverseIntPowerHSPeriodic::InverseIntPowerHSPeriodic (C++ function)
- pele::InverseIntPowerHSPeriodicCellLists (C++ class)
- pele::InverseIntPowerHSPeriodicCellLists::InverseIntPowerHSPeriodicCellLists (C++ function)
- pele::InverseIntPowerPeriodic (C++ class)
- pele::InverseIntPowerPeriodic::InverseIntPowerPeriodic (C++ function)
- pele::InverseIntPowerPeriodicCellLists (C++ class)
- pele::InverseIntPowerPeriodicCellLists::InverseIntPowerPeriodicCellLists (C++ function)
- pele::InversePower (C++ class)
- pele::InversePower::InversePower (C++ function)
- pele::InversePower_interaction (C++ struct)
- pele::InversePower_interaction::energy (C++ function)
- pele::InversePower_interaction::energy_gradient (C++ function)
- pele::InversePower_interaction::energy_gradient_hessian (C++ function)
- pele::InversePower_interaction::InversePower_interaction (C++ function)
- pele::InversePowerHS (C++ class)
- pele::InversePowerHS::InversePowerHS (C++ function)
- pele::InversePowerHS_interaction (C++ struct)
- pele::InversePowerHS_interaction::energy (C++ function)
- pele::InversePowerHS_interaction::energy_gradient (C++ function)
- pele::InversePowerHS_interaction::energy_gradient_hessian (C++ function)
- pele::InversePowerHS_interaction::InversePowerHS_interaction (C++ function)
- pele::InversePowerHSPeriodic (C++ class)
- pele::InversePowerHSPeriodic::InversePowerHSPeriodic (C++ function)
- pele::InversePowerHSPeriodicCellLists (C++ class)
- pele::InversePowerHSPeriodicCellLists::InversePowerHSPeriodicCellLists (C++ function)
- pele::InversePowerPeriodic (C++ class)
- pele::InversePowerPeriodic::InversePowerPeriodic (C++ function)
- pele::InversePowerPeriodicCellLists (C++ class)
- pele::InversePowerPeriodicCellLists::InversePowerPeriodicCellLists (C++ function)
- pele::InversePowerStillinger (C++ class)
- pele::InversePowerStillinger::InversePowerStillinger (C++ function)
- pele::InversePowerStillinger_cut_interaction (C++ struct)
- pele::InversePowerStillinger_cut_interaction::energy (C++ function)
- pele::InversePowerStillinger_cut_interaction::energy_gradient (C++ function)
- pele::InversePowerStillinger_cut_interaction::energy_gradient_hessian (C++ function)
- pele::InversePowerStillinger_cut_interaction::InversePowerStillinger_cut_interaction (C++ function)
- pele::InversePowerStillinger_cut_interaction::m_pow (C++ member)
- pele::InversePowerStillinger_cut_interaction::m_q0 (C++ member)
- pele::InversePowerStillinger_cut_interaction::m_q1 (C++ member)
- pele::InversePowerStillinger_cut_interaction::m_q2 (C++ member)
- pele::InversePowerStillinger_cut_interaction::m_rcut (C++ member)
- pele::InversePowerStillinger_cut_interaction::m_rcut2 (C++ member)
- pele::InversePowerStillinger_cut_interaction::power (C++ function)
- pele::InversePowerStillinger_cut_interaction::power_inp2 (C++ function)
- pele::InversePowerStillinger_interaction (C++ struct)
- pele::InversePowerStillinger_interaction::energy (C++ function)
- pele::InversePowerStillinger_interaction::energy_gradient (C++ function)
- pele::InversePowerStillinger_interaction::energy_gradient_hessian (C++ function)
- pele::InversePowerStillinger_interaction::InversePowerStillinger_interaction (C++ function)
- pele::InversePowerStillinger_interaction::m_pow (C++ member)
- pele::InversePowerStillinger_interaction::power (C++ function)
- pele::InversePowerStillinger_interaction::power_inp2 (C++ function)
- pele::InversePowerStillingerCut (C++ class)
- pele::InversePowerStillingerCut::InversePowerStillingerCut (C++ function)
- pele::InversePowerStillingerCutPeriodic (C++ class)
- pele::InversePowerStillingerCutPeriodic::InversePowerStillingerCutPeriodic (C++ function)
- pele::InversePowerStillingerCutPeriodicCellLists (C++ class)
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- pele::InversePowerStillingerCutPeriodicCellLists::InversePowerStillingerCutPeriodicCellLists (C++ function)
- pele::InversePowerStillingerCutQuad (C++ class)
- pele::InversePowerStillingerCutQuad::InversePowerStillingerCutQuad (C++ function)
- pele::InversePowerStillingerCutQuadInt (C++ class)
- pele::InversePowerStillingerCutQuadInt::InversePowerStillingerCutQuadInt (C++ function)
- pele::InversePowerStillingerCutQuadIntPeriodic (C++ class)
- pele::InversePowerStillingerCutQuadIntPeriodic::InversePowerStillingerCutQuadIntPeriodic (C++ function)
- pele::InversePowerStillingerCutQuadIntPeriodicCellLists (C++ class)
- pele::InversePowerStillingerCutQuadIntPeriodicCellLists::InversePowerStillingerCutQuadIntPeriodicCellLists (C++ function)
- pele::InversePowerStillingerCutQuadPeriodic (C++ class)
- pele::InversePowerStillingerCutQuadPeriodic::InversePowerStillingerCutQuadPeriodic (C++ function)
- pele::InversePowerStillingerCutQuadPeriodicCellLists (C++ class)
- pele::InversePowerStillingerCutQuadPeriodicCellLists::InversePowerStillingerCutQuadPeriodicCellLists (C++ function)
- pele::InversePowerStillingerPeriodic (C++ class)
- pele::InversePowerStillingerPeriodic::InversePowerStillingerPeriodic (C++ function)
- pele::InversePowerStillingerQuadCutInteraction (C++ struct)
- pele::InversePowerStillingerQuadCutInteraction::c0 (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::c2 (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::c4 (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::energy (C++ function)
- pele::InversePowerStillingerQuadCutInteraction::energy_gradient (C++ function)
- pele::InversePowerStillingerQuadCutInteraction::energy_gradient_hessian (C++ function)
- pele::InversePowerStillingerQuadCutInteraction::InversePowerStillingerQuadCutInteraction (C++ function)
- pele::InversePowerStillingerQuadCutInteraction::m_cutoff_factor (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::m_cutoff_factor2 (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::m_pow (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::m_pow_by_2 (C++ member)
- pele::InversePowerStillingerQuadCutInteraction::m_v0 (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt (C++ struct)
- pele::InversePowerStillingerQuadCutInteractionInt::c0 (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::c2 (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::c4 (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::energy (C++ function)
- pele::InversePowerStillingerQuadCutInteractionInt::energy_gradient (C++ function)
- pele::InversePowerStillingerQuadCutInteractionInt::energy_gradient_hessian (C++ function)
- pele::InversePowerStillingerQuadCutInteractionInt::InversePowerStillingerQuadCutInteractionInt (C++ function)
- pele::InversePowerStillingerQuadCutInteractionInt::m_cutoff_factor (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::m_cutoff_factor2 (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::m_pow (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::m_pow_by_2 (C++ member)
- pele::InversePowerStillingerQuadCutInteractionInt::m_v0 (C++ member)
- pele::Jac (C++ function)
- pele::LAMMPSPotential (C++ class)
- pele::LAMMPSPotential::get_energy (C++ function)
- pele::LAMMPSPotential::get_energy_gradient (C++ function), [1], [2]
- pele::LAMMPSPotential::handle (C++ member)
- pele::LAMMPSPotential::LAMMPSPotential (C++ function)
- pele::LatticeNeighbors (C++ class)
- pele::LatticeNeighbors::calc_subdom_stats (C++ function)
- pele::LatticeNeighbors::cell_vec_t (C++ type)
- pele::LatticeNeighbors::cell_vec_to_global_ind (C++ function)
- pele::LatticeNeighbors::cell_vec_to_local_ind (C++ function)
- pele::LatticeNeighbors::cell_vec_to_position (C++ function)
- pele::LatticeNeighbors::find_all_global_neighbor_inds (C++ function)
- pele::LatticeNeighbors::find_global_neighbor_inds (C++ function)
- pele::LatticeNeighbors::find_global_neighbor_inds_nearest (C++ function)
- pele::LatticeNeighbors::find_neighbor_pairs (C++ function)
- pele::LatticeNeighbors::find_neighbor_pairs_subdom (C++ function)
- pele::LatticeNeighbors::get_subdomain (C++ function), [1]
- pele::LatticeNeighbors::global_ind_to_cell_vec (C++ function)
- pele::LatticeNeighbors::global_ind_to_local_ind (C++ function)
- pele::LatticeNeighbors::LatticeNeighbors (C++ function)
- pele::LatticeNeighbors::local_ind_to_cell_vec (C++ function)
- pele::LatticeNeighbors::local_ind_to_global_ind (C++ function)
- pele::LatticeNeighbors::m_boxvec (C++ member)
- pele::LatticeNeighbors::m_dist (C++ member)
- pele::LatticeNeighbors::m_inv_boxvec (C++ member)
- pele::LatticeNeighbors::m_ncells (C++ member)
- pele::LatticeNeighbors::m_ncells_vec (C++ member)
- pele::LatticeNeighbors::m_nsubdoms (C++ member)
- pele::LatticeNeighbors::m_rcell_vec (C++ member)
- pele::LatticeNeighbors::m_rcut (C++ member)
- pele::LatticeNeighbors::m_subdom_avg_len (C++ member)
- pele::LatticeNeighbors::m_subdom_limits (C++ member)
- pele::LatticeNeighbors::m_subdom_ncells (C++ member)
- pele::LatticeNeighbors::m_subdoms_balanced (C++ member)
- pele::LatticeNeighbors::minimum_distance (C++ function)
- pele::LatticeNeighbors::ndim (C++ member)
- pele::LatticeNeighbors::pos_direction_y (C++ function)
- pele::LatticeNeighbors::position_to_cell_vec (C++ function)
- pele::LatticeNeighbors::position_to_global_ind (C++ function)
- pele::LatticeNeighbors::position_to_local_ind (C++ function)
- pele::LBFGS (C++ class)
- pele::LBFGS::get_H0 (C++ function)
- pele::LBFGS::get_k (C++ function)
- pele::LBFGS::get_rho (C++ function)
- pele::LBFGS::get_s (C++ function)
- pele::LBFGS::get_y (C++ function)
- pele::LBFGS::LBFGS (C++ function)
- pele::LBFGS::one_iteration (C++ function)
- pele::LBFGS::reset (C++ function)
- pele::LBFGS::set_H0 (C++ function)
- pele::LBFGS::set_max_f_rise (C++ function)
- pele::LBFGS::set_state (C++ function)
- pele::LBFGS::set_use_relative_f (C++ function)
- pele::LBFGS::~LBFGS (C++ function)
- pele::LBFGSParam (C++ class)
- pele::LBFGSParam::check_param (C++ function)
- pele::LBFGSParam::delta (C++ member)
- pele::LBFGSParam::epsilon (C++ member)
- pele::LBFGSParam::epsilon_rel (C++ member)
- pele::LBFGSParam::ftol (C++ member)
- pele::LBFGSParam::LBFGSParam (C++ function)
- pele::LBFGSParam::linesearch (C++ member)
- pele::LBFGSParam::m (C++ member)
- pele::LBFGSParam::max_iterations (C++ member)
- pele::LBFGSParam::max_linesearch (C++ member)
- pele::LBFGSParam::max_step (C++ member)
- pele::LBFGSParam::min_step (C++ member)
- pele::LBFGSParam::past (C++ member)
- pele::LBFGSParam::wolfe (C++ member)
- pele::leesedwards_distance (C++ class)
- pele::leesedwards_distance::get_rij (C++ function)
- pele::leesedwards_distance::leesedwards_distance (C++ function), [1]
- pele::leesedwards_distance::put_atom_in_box (C++ function), [1]
- pele::leesedwards_distance::put_in_box (C++ function)
- pele::LeesEdwardsDistanceWrapper (C++ class)
- pele::LeesEdwardsDistanceWrapper::get_rij (C++ function)
- pele::LeesEdwardsDistanceWrapper::LeesEdwardsDistanceWrapper (C++ function)
- pele::LINE_SEARCH_TERMINATION_CONDITION (C++ enum)
- pele::LINE_SEARCH_TERMINATION_CONDITION::LINESEARCH_BACKTRACKING (C++ enumerator)
- pele::LINE_SEARCH_TERMINATION_CONDITION::LINESEARCH_BACKTRACKING_ARMIJO (C++ enumerator)
- pele::LINE_SEARCH_TERMINATION_CONDITION::LINESEARCH_BACKTRACKING_STRONG_WOLFE (C++ enumerator)
- pele::LINE_SEARCH_TERMINATION_CONDITION::LINESEARCH_BACKTRACKING_WOLFE (C++ enumerator)
- pele::LineSearch (C++ class)
- pele::LineSearch::end_energy (C++ member)
- pele::LineSearch::end_gradient (C++ member)
- pele::LineSearch::line_search (C++ function)
- pele::LineSearch::LineSearch (C++ function)
- pele::LineSearch::max_stepnorm_ (C++ member)
- pele::LineSearch::opt_ (C++ member)
- pele::LineSearch::set_max_stepnorm_ (C++ function)
- pele::LineSearch::stepnorm (C++ member)
- pele::LineSearch::~LineSearch (C++ function)
- pele::LJ (C++ class)
- pele::LJ::LJ (C++ function)
- pele::lj_interaction (C++ struct)
- pele::lj_interaction::energy (C++ function)
- pele::lj_interaction::energy_gradient (C++ function)
- pele::lj_interaction::energy_gradient_hessian (C++ function)
- pele::lj_interaction::lj_interaction (C++ function)
- pele::lj_interaction_cut_smooth (C++ struct)
- pele::lj_interaction_cut_smooth::energy (C++ function)
- pele::lj_interaction_cut_smooth::energy_gradient (C++ function)
- pele::lj_interaction_cut_smooth::energy_gradient_hessian (C++ function)
- pele::lj_interaction_cut_smooth::lj_interaction_cut_smooth (C++ function)
- pele::LJCut (C++ class)
- pele::LJCut::LJCut (C++ function)
- pele::LJCutAtomList (C++ class)
- pele::LJCutAtomList::LJCutAtomList (C++ function), [1]
- pele::LJCutPeriodic (C++ class)
- pele::LJCutPeriodic::LJCutPeriodic (C++ function)
- pele::LJCutPeriodicAtomList (C++ class)
- pele::LJCutPeriodicAtomList::LJCutPeriodicAtomList (C++ function), [1]
- pele::LJCutPeriodicCellLists (C++ class)
- pele::LJCutPeriodicCellLists::LJCutPeriodicCellLists (C++ function)
- pele::LJNeighborList (C++ class)
- pele::LJNeighborList::LJNeighborList (C++ function)
- pele::LJPeriodic (C++ class)
- pele::LJPeriodic::LJPeriodic (C++ function)
- pele::LowestEigPotential (C++ class)
- pele::LowestEigPotential::get_energy (C++ function)
- pele::LowestEigPotential::get_energy_gradient (C++ function)
- pele::LowestEigPotential::LowestEigPotential (C++ function)
- pele::LowestEigPotential::reset_coords (C++ function)
- pele::LowestEigPotential::set_x_opt (C++ function)
- pele::LowestEigPotential::x_opt (C++ member)
- pele::LowestEigPotential::~LowestEigPotential (C++ function)
- pele::make_combination_generator (C++ function)
- pele::MatrixAdapter (C++ class)
- pele::MatrixAdapter::MatrixAdapter (C++ function), [1], [2]
- pele::MatrixAdapter::operator() (C++ function), [1]
- pele::MatrixAdapter::shape (C++ function)
- pele::MatrixNM (C++ class)
- pele::MatrixNM::assign (C++ function)
- pele::MatrixNM::begin (C++ function), [1]
- pele::MatrixNM::const_iterator (C++ type)
- pele::MatrixNM::data (C++ function), [1]
- pele::MatrixNM::end (C++ function), [1]
- pele::MatrixNM::iterator (C++ type)
- pele::MatrixNM::MatrixNM (C++ function), [1], [2]
- pele::MatrixNM::operator() (C++ function), [1]
- pele::MatrixNM::operator*= (C++ function)
- pele::MatrixNM::operator- (C++ function)
- pele::MatrixNM::shape (C++ function)
- pele::MatrixNM::size (C++ function)
- pele::MatrixNM::trace (C++ function)
- pele::MeanFieldPSpinSpherical (C++ class)
- pele::MeanFieldPSpinSpherical::add_energy (C++ function)
- pele::MeanFieldPSpinSpherical::add_energy_gradient (C++ function)
- pele::MeanFieldPSpinSpherical::add_energy_gradient_hessian (C++ function)
- pele::MeanFieldPSpinSpherical::get_energy (C++ function)
- pele::MeanFieldPSpinSpherical::get_energy_gradient (C++ function)
- pele::MeanFieldPSpinSpherical::m_combination_generator (C++ member)
- pele::MeanFieldPSpinSpherical::m_combination_generator_grad (C++ member)
- pele::MeanFieldPSpinSpherical::m_combination_generator_hess (C++ member)
- pele::MeanFieldPSpinSpherical::m_get_index (C++ function)
- pele::MeanFieldPSpinSpherical::m_indexes (C++ member)
- pele::MeanFieldPSpinSpherical::m_interactions (C++ member)
- pele::MeanFieldPSpinSpherical::m_N (C++ member)
- pele::MeanFieldPSpinSpherical::m_N_prf (C++ member)
- pele::MeanFieldPSpinSpherical::m_normalize_spins (C++ function)
- pele::MeanFieldPSpinSpherical::m_orthogonalize (C++ function)
- pele::MeanFieldPSpinSpherical::m_p (C++ member)
- pele::MeanFieldPSpinSpherical::m_pf (C++ member)
- pele::MeanFieldPSpinSpherical::m_spins (C++ member)
- pele::MeanFieldPSpinSpherical::m_sqrt_N (C++ member)
- pele::MeanFieldPSpinSpherical::m_tol (C++ member)
- pele::MeanFieldPSpinSpherical::MeanFieldPSpinSpherical (C++ function)
- pele::MeanFieldPSpinSpherical::numerical_gradient (C++ function)
- pele::MeanFieldPSpinSpherical::numerical_hessian (C++ function)
- pele::MeanFieldPSpinSpherical::~MeanFieldPSpinSpherical (C++ function)
- pele::MeasureAngleAxisCluster (C++ class)
- pele::MeasureAngleAxisCluster::align (C++ function)
- pele::MeasureAngleAxisCluster::m_topology (C++ member)
- pele::MeasureAngleAxisCluster::MeasureAngleAxisCluster (C++ function)
- pele::meta_dist (C++ struct)
- pele::meta_dist::f (C++ function)
- pele::meta_dist<1> (C++ struct)
- pele::meta_dist<1>::f (C++ function)
- pele::meta_image (C++ struct)
- pele::meta_image::f (C++ function), [1]
- pele::meta_image<1> (C++ struct)
- pele::meta_image<1>::f (C++ function), [1]
- pele::meta_leesedwards_distance (C++ struct)
- pele::meta_leesedwards_distance::f (C++ function)
- pele::meta_leesedwards_distance<2> (C++ struct)
- pele::meta_leesedwards_distance<2>::f (C++ function)
- pele::meta_leesedwards_image (C++ struct)
- pele::meta_leesedwards_image::f (C++ function), [1]
- pele::meta_leesedwards_image<2> (C++ struct)
- pele::meta_leesedwards_image<2>::f (C++ function), [1]
- pele::meta_periodic_distance (C++ struct)
- pele::meta_periodic_distance::f (C++ function)
- pele::meta_periodic_distance<1> (C++ struct)
- pele::meta_periodic_distance<1>::f (C++ function)
- pele::meta_pow (C++ struct)
- pele::meta_pow::f (C++ function)
- pele::meta_pow<T, 0> (C++ struct)
- pele::meta_pow<T, 0>::f (C++ function)
- pele::meta_pow<T, 10> (C++ struct)
- pele::meta_pow<T, 10>::f (C++ function)
- pele::meta_pow<T, 12> (C++ struct)
- pele::meta_pow<T, 12>::f (C++ function)
- pele::meta_pow<T, 4> (C++ struct)
- pele::meta_pow<T, 4>::f (C++ function)
- pele::meta_pow<T, 6> (C++ struct)
- pele::meta_pow<T, 6>::f (C++ function)
- pele::meta_pow<T, 8> (C++ struct)
- pele::meta_pow<T, 8>::f (C++ function)
- pele::meta_pow<T, 9> (C++ struct)
- pele::meta_pow<T, 9>::f (C++ function)
- pele::MixedDescentEndOnly (C++ class)
- pele::MixedDescentEndOnly::get_nfev (C++ function)
- pele::MixedDescentEndOnly::get_nhev (C++ function)
- pele::MixedDescentEndOnly::get_niter (C++ function)
- pele::MixedDescentEndOnly::get_step_vec (C++ function)
- pele::MixedDescentEndOnly::MixedDescentEndOnly (C++ function)
- pele::MixedDescentEndOnly::one_iteration (C++ function)
- pele::MixedDescentEndOnly::stop_criterion_satisfied (C++ function)
- pele::MixedDescentEndOnly::~MixedDescentEndOnly (C++ function)
- pele::MODIFIED_FIRE (C++ class)
- pele::MODIFIED_FIRE::initialize_func_gradient (C++ function)
- pele::MODIFIED_FIRE::MODIFIED_FIRE (C++ function)
- pele::MODIFIED_FIRE::one_iteration (C++ function)
- pele::MODIFIED_FIRE::reset (C++ function)
- pele::MODIFIED_FIRE::set_func_gradient (C++ function)
- pele::MODIFIED_FIRE::~MODIFIED_FIRE (C++ function)
- pele::MoreThuente (C++ class)
- pele::MoreThuente::cstep (C++ function)
- pele::MoreThuente::cvsrch (C++ function)
- pele::MoreThuente::line_search (C++ function)
- pele::MoreThuente::MoreThuente (C++ function)
- pele::MoreThuente::search (C++ function)
- pele::MoreThuente::set_g_f_ptr (C++ function)
- pele::MoreThuente::set_xold_gold_ (C++ function)
- pele::MoreThuente::~MoreThuente (C++ function)
- pele::Morse (C++ class)
- pele::Morse::Morse (C++ function)
- pele::morse_interaction (C++ struct)
- pele::morse_interaction::energy (C++ function)
- pele::morse_interaction::energy_gradient (C++ function)
- pele::morse_interaction::energy_gradient_hessian (C++ function)
- pele::morse_interaction::morse_interaction (C++ function)
- pele::N_Vector_eq_pele (C++ function)
- pele::neg_half_int_pow (C++ function)
- pele::neg_int_pow (C++ function)
- pele::NeighborAccumulator (C++ class)
- pele::NeighborAccumulator::insert_atom_pair (C++ function)
- pele::NeighborAccumulator::m_neighbor_displacements (C++ member)
- pele::NeighborAccumulator::m_neighbor_indexes (C++ member)
- pele::NeighborAccumulator::NeighborAccumulator (C++ function)
- pele::Newton (C++ class)
- pele::Newton::compute_func_gradient (C++ function)
- pele::Newton::compute_step (C++ function)
- pele::Newton::compute_trust_region_step (C++ function)
- pele::Newton::delta_k (C++ member)
- pele::Newton::delta_max (C++ member)
- pele::Newton::eta (C++ member)
- pele::Newton::ev (C++ function)
- pele::Newton::get_nhev (C++ function)
- pele::Newton::get_rattler_details (C++ function)
- pele::Newton::get_rho_k (C++ function)
- pele::Newton::get_step (C++ function)
- pele::Newton::is_jammed (C++ function)
- pele::Newton::Newton (C++ function)
- pele::Newton::one_iteration (C++ function)
- pele::Newton::p_k (C++ member)
- pele::Newton::prev_e (C++ member)
- pele::Newton::reset (C++ function)
- pele::Newton::solve_subproblem (C++ function)
- pele::Newton::x_k (C++ member)
- pele::Newton::~Newton (C++ function)
- pele::NewtonStopCriterion (C++ class)
- pele::NewtonStopCriterion::NewtonStopCriterion (C++ function)
- pele::NewtonStopCriterion::stop_criterion_satisfied (C++ function)
- pele::NewtonWithExtendedPotential (C++ class)
- pele::NewtonWithExtendedPotential::get_nhev (C++ function)
- pele::NewtonWithExtendedPotential::get_step (C++ function)
- pele::NewtonWithExtendedPotential::NewtonWithExtendedPotential (C++ function)
- pele::NewtonWithExtendedPotential::one_iteration (C++ function)
- pele::NewtonWithExtendedPotential::reset (C++ function)
- pele::NewtonWithExtendedPotential::set_hessian (C++ function)
- pele::NewtonWithExtendedPotential::~NewtonWithExtendedPotential (C++ function)
- pele::NGT (C++ class)
- pele::NGT::add_edge (C++ function)
- pele::NGT::compute_rates (C++ function)
- pele::NGT::compute_rates_and_committors (C++ function)
- pele::NGT::debug (C++ member)
- pele::NGT::final_committors (C++ member)
- pele::NGT::final_omPxx (C++ member)
- pele::NGT::final_tau (C++ member)
- pele::NGT::get_committors (C++ function)
- pele::NGT::get_node_one_minus_P (C++ function)
- pele::NGT::get_node_P (C++ function)
- pele::NGT::get_P (C++ function)
- pele::NGT::get_PxB (C++ function)
- pele::NGT::get_rate_AB (C++ function)
- pele::NGT::get_rate_AB_SS (C++ function)
- pele::NGT::get_rate_BA (C++ function)
- pele::NGT::get_rate_BA_SS (C++ function)
- pele::NGT::get_tau (C++ function)
- pele::NGT::initial_tau (C++ member)
- pele::NGT::intermediates (C++ member)
- pele::NGT::NGT (C++ function), [1]
- pele::NGT::phase_one (C++ function)
- pele::NGT::phase_two (C++ function)
- pele::NGT::rate_map_t (C++ type)
- pele::NGT::reduce_all_in_group (C++ function)
- pele::NGT::remove_intermediates (C++ function)
- pele::NGT::remove_node (C++ function)
- pele::NGT::set_debug (C++ function)
- pele::NGT::set_node_occupation_probabilities (C++ function)
- pele::NGT::set_P (C++ function)
- pele::NGT::set_tau (C++ function)
- pele::NGT::sort_intermediates (C++ function)
- pele::NGT::update_edge (C++ function)
- pele::NGT::update_node (C++ function)
- pele::NGT::weights (C++ member)
- pele::NGT::~NGT (C++ function)
- pele::NocedalWrightLineSearch (C++ class)
- pele::NocedalWrightLineSearch::line_search (C++ function)
- pele::NocedalWrightLineSearch::NocedalWrightLineSearch (C++ function)
- pele::NocedalWrightLineSearch::set_g_f_ptr (C++ function)
- pele::NocedalWrightLineSearch::set_xold_gold_ (C++ function)
- pele::NocedalWrightLineSearch::~NocedalWrightLineSearch (C++ function)
- pele::Node (C++ class)
- pele::Node::add_in_edge (C++ function)
- pele::Node::add_out_edge (C++ function)
- pele::Node::edge_iterator (C++ type)
- pele::Node::edge_list (C++ type)
- pele::Node::get_in_edges (C++ function)
- pele::Node::get_out_edges (C++ function)
- pele::Node::get_successor_edge (C++ function)
- pele::Node::id (C++ function)
- pele::Node::in_degree (C++ function)
- pele::Node::in_edge_begin (C++ function)
- pele::Node::in_edge_end (C++ function)
- pele::Node::in_out_degree (C++ function)
- pele::Node::in_out_neighbors (C++ function)
- pele::Node::Node (C++ function)
- pele::Node::out_degree (C++ function)
- pele::Node::out_edge_begin (C++ function)
- pele::Node::out_edge_end (C++ function)
- pele::Node::remove_in_edge (C++ function)
- pele::Node::remove_out_edge (C++ function)
- pele::Node::successor_map_ (C++ member)
- pele::Node::successor_map_t (C++ type)
- pele::Node::tau (C++ member)
- pele::node_id (C++ type)
- pele::node_ptr (C++ type)
- pele::NonAdditiveCutoffCalculator (C++ class)
- pele::NonAdditiveCutoffCalculator::get_cutoff (C++ function)
- pele::NonAdditiveCutoffCalculator::get_max_cutoff_distance (C++ function)
- pele::NonAdditiveCutoffCalculator::NonAdditiveCutoffCalculator (C++ function), [1]
- pele::norm (C++ function), [1]
- pele::ODEBasedOptimizer (C++ class)
- pele::ODEBasedOptimizer::get_coordinate_trajectory (C++ function)
- pele::ODEBasedOptimizer::get_costly_time_trajectory (C++ function)
- pele::ODEBasedOptimizer::get_distance_trajectory (C++ function)
- pele::ODEBasedOptimizer::get_energy_trajectory (C++ function)
- pele::ODEBasedOptimizer::get_gradient_norm_trajectory (C++ function)
- pele::ODEBasedOptimizer::get_gradient_trajectory (C++ function)
- pele::ODEBasedOptimizer::get_time_trajectory (C++ function)
- pele::ODEBasedOptimizer::ODEBasedOptimizer (C++ function), [1], [2]
- pele::ODEBasedOptimizer::time_ (C++ member)
- pele::ODEBasedOptimizer::update_cheap_trajectory_info (C++ function)
- pele::ODEBasedOptimizer::update_costly_trajectory_info (C++ function)
- pele::ODEBasedOptimizer::~ODEBasedOptimizer (C++ function)
- pele::OldLineSearch (C++ class)
- pele::OldLineSearch::line_search (C++ function)
- pele::OldLineSearch::OldLineSearch (C++ function)
- pele::OldLineSearch::set_g_f_ptr (C++ function)
- pele::OldLineSearch::set_xold_gold_ (C++ function)
- pele::operator* (C++ function)
- pele::operator<< (C++ function), [1], [2], [3], [4]
- pele::Optimizer (C++ class)
- pele::Optimizer::get_f (C++ function)
- pele::Optimizer::get_g (C++ function)
- pele::Optimizer::get_nfev (C++ function)
- pele::Optimizer::get_nhev (C++ function)
- pele::Optimizer::get_niter (C++ function)
- pele::Optimizer::get_rms (C++ function)
- pele::Optimizer::get_x (C++ function)
- pele::Optimizer::one_iteration (C++ function)
- pele::Optimizer::run (C++ function), [1]
- pele::Optimizer::success (C++ function)
- pele::Optimizer::~Optimizer (C++ function)
- pele::origin_in_hull_2d (C++ function)
- pele::Orthogonalize (C++ class)
- pele::Orthogonalize::orthogonalize (C++ function)
- pele::Orthogonalize::~Orthogonalize (C++ function)
- pele::OrthogonalizeTranslational (C++ class)
- pele::OrthogonalizeTranslational::orthogonalize (C++ function)
- pele::OrthogonalizeTranslational::OrthogonalizeTranslational (C++ function)
- pele::OrthogonalizeTranslational::~OrthogonalizeTranslational (C++ function)
- pele::OverlapAccumulator (C++ class)
- pele::OverlapAccumulator::insert_atom_pair (C++ function)
- pele::OverlapAccumulator::m_overlap_inds (C++ member)
- pele::OverlapAccumulator::OverlapAccumulator (C++ function)
- pele::PairwisePotentialInterface (C++ class)
- pele::PairwisePotentialInterface::find_rattlers (C++ function)
- pele::PairwisePotentialInterface::get_atom_order (C++ function)
- pele::PairwisePotentialInterface::get_interaction_energy_gradient (C++ function)
- pele::PairwisePotentialInterface::get_interaction_energy_gradient_hessian (C++ function)
- pele::PairwisePotentialInterface::get_max_cutoff (C++ function)
- pele::PairwisePotentialInterface::get_ndim (C++ function)
- pele::PairwisePotentialInterface::get_neighbors (C++ function)
- pele::PairwisePotentialInterface::get_neighbors_picky (C++ function)
- pele::PairwisePotentialInterface::get_non_additive_cutoff (C++ function)
- pele::PairwisePotentialInterface::get_overlaps (C++ function)
- pele::PairwisePotentialInterface::get_radii (C++ function)
- pele::PairwisePotentialInterface::get_rij (C++ function)
- pele::PairwisePotentialInterface::initialize (C++ function)
- pele::PairwisePotentialInterface::m_cutoff_calculator (C++ member)
- pele::PairwisePotentialInterface::m_radii (C++ member)
- pele::PairwisePotentialInterface::PairwisePotentialInterface (C++ function), [1], [2]
- pele::PairwisePotentialInterface::print_neighbor_index_and_displacements (C++ function)
- pele::PairwisePotentialInterface::~PairwisePotentialInterface (C++ function)
- pele::pele_eq_eig (C++ function)
- pele::pele_eq_eig_data (C++ function)
- pele::pele_eq_N_Vector (C++ function)
- pele::periodic_distance (C++ class)
- pele::periodic_distance::get_box (C++ function)
- pele::periodic_distance::get_ndim (C++ function)
- pele::periodic_distance::get_rij (C++ function)
- pele::periodic_distance::m_box (C++ member)
- pele::periodic_distance::m_ibox (C++ member)
- pele::periodic_distance::periodic_distance (C++ function), [1]
- pele::periodic_distance::put_atom_in_box (C++ function), [1]
- pele::periodic_distance::put_in_box (C++ function)
- pele::PeriodicDistanceWrapper (C++ class)
- pele::PeriodicDistanceWrapper::get_rij (C++ function)
- pele::PeriodicDistanceWrapper::PeriodicDistanceWrapper (C++ function)
- pele::pos_half_int_pow (C++ function)
- pele::pos_int_pow (C++ function)
- pele::PoweredCosineSum (C++ class)
- pele::PoweredCosineSum::add_energy_gradient (C++ function)
- pele::PoweredCosineSum::add_energy_gradient_hessian (C++ function)
- pele::PoweredCosineSum::add_hessian (C++ function)
- pele::PoweredCosineSum::get_energy (C++ function)
- pele::PoweredCosineSum::get_energy_gradient (C++ function)
- pele::PoweredCosineSum::get_energy_gradient_hessian (C++ function)
- pele::PoweredCosineSum::PoweredCosineSum (C++ function)
- pele::PoweredCosineSum::~PoweredCosineSum (C++ function)
- pele::pressure_tensor (C++ function)
- pele::print_matrix (C++ function)
- pele::print_vector (C++ function)
- pele::PythonPotential (C++ class)
- pele::PythonPotential::get_energy (C++ function)
- pele::PythonPotential::get_energy_gradient (C++ function)
- pele::PythonPotential::PythonPotential (C++ function)
- pele::PythonPotential::~PythonPotential (C++ function)
- pele::quaternion_multiply (C++ function)
- pele::quaternion_to_aa (C++ function)
- pele::RadialGaussian (C++ class)
- pele::RadialGaussian::RadialGaussian (C++ function)
- pele::RadialGaussianCOM (C++ class)
- pele::RadialGaussianCOM::RadialGaussianCOM (C++ function)
- pele::RBPotentialWrapper (C++ class)
- pele::RBPotentialWrapper::get_energy (C++ function)
- pele::RBPotentialWrapper::get_energy_gradient (C++ function)
- pele::RBPotentialWrapper::RBPotentialWrapper (C++ function)
- pele::RBTopology (C++ class)
- pele::RBTopology::add_site (C++ function)
- pele::RBTopology::align_all_angle_axis_vectors (C++ function)
- pele::RBTopology::align_angle_axis_vectors (C++ function)
- pele::RBTopology::align_path (C++ function)
- pele::RBTopology::assign_atom_indices (C++ function)
- pele::RBTopology::distance_squared (C++ function)
- pele::RBTopology::distance_squared_grad (C++ function)
- pele::RBTopology::get_coords_adaptor (C++ function)
- pele::RBTopology::get_sites (C++ function)
- pele::RBTopology::get_zero_modes (C++ function)
- pele::RBTopology::natoms_total (C++ function)
- pele::RBTopology::nrigid (C++ function)
- pele::RBTopology::number_of_non_rigid_atoms (C++ function)
- pele::RBTopology::RBTopology (C++ function)
- pele::RBTopology::to_atomistic (C++ function)
- pele::RBTopology::transform_gradient (C++ function)
- pele::reset_energies (C++ function)
- pele::reset_user_data (C++ function)
- pele::RigidFragment (C++ class)
- pele::RigidFragment::add_symmetry_rotation (C++ function)
- pele::RigidFragment::distance_squared (C++ function)
- pele::RigidFragment::distance_squared_grad (C++ function)
- pele::RigidFragment::get_atom_indices (C++ function)
- pele::RigidFragment::get_smallest_rij (C++ function)
- pele::RigidFragment::get_symmetry_rotations (C++ function)
- pele::RigidFragment::natoms (C++ function)
- pele::RigidFragment::RigidFragment (C++ function)
- pele::RigidFragment::set_atom_indices (C++ function)
- pele::RigidFragment::to_atomistic (C++ function)
- pele::RigidFragment::transform_grad (C++ function), [1]
- pele::RosenBrock (C++ class)
- pele::RosenBrock::get_energy (C++ function)
- pele::RosenBrock::get_energy_gradient (C++ function)
- pele::RosenBrock::RosenBrock (C++ function)
- pele::RosenBrock::~RosenBrock (C++ function)
- pele::rot_mat_derivatives (C++ function)
- pele::rot_mat_derivatives_small_theta (C++ function)
- pele::rot_mat_to_aa (C++ function)
- pele::rot_mat_to_quaternion (C++ function)
- pele::rotate_aa (C++ function)
- pele::Saddle (C++ class)
- pele::Saddle::get_energy (C++ function)
- pele::Saddle::get_energy_gradient (C++ function)
- pele::Saddle::Saddle (C++ function)
- pele::Saddle::~Saddle (C++ function)
- pele::scalar_t (C++ type)
- pele::sf_HS_WCA_interaction (C++ class)
- pele::sf_HS_WCA_interaction::energy (C++ function)
- pele::sf_HS_WCA_interaction::energy_gradient (C++ function)
- pele::sf_HS_WCA_interaction::energy_gradient_hessian (C++ function)
- pele::sf_HS_WCA_interaction::evaluate_pair_potential (C++ function)
- pele::sf_HS_WCA_interaction::sf_HS_WCA_interaction (C++ function)
- pele::SimplePairwiseNeighborList (C++ class)
- pele::SimplePairwiseNeighborList::add_energy_gradient (C++ function)
- pele::SimplePairwiseNeighborList::get_energy (C++ function)
- pele::SimplePairwiseNeighborList::get_energy_gradient (C++ function)
- pele::SimplePairwiseNeighborList::SimplePairwiseNeighborList (C++ function), [1]
- pele::SimplePairwiseNeighborList::~SimplePairwiseNeighborList (C++ function)
- pele::SimplePairwisePotential (C++ class)
- pele::SimplePairwisePotential::add_energy_gradient (C++ function), [1], [2]
- pele::SimplePairwisePotential::add_energy_gradient_hessian (C++ function), [1]
- pele::SimplePairwisePotential::add_hessian (C++ function)
- pele::SimplePairwisePotential::compute_norm (C++ function)
- pele::SimplePairwisePotential::exact_gradient (C++ member)
- pele::SimplePairwisePotential::exact_gradient_initialized (C++ member)
- pele::SimplePairwisePotential::exact_sum (C++ member)
- pele::SimplePairwisePotential::get_energy (C++ function)
- pele::SimplePairwisePotential::get_energy_change (C++ function)
- pele::SimplePairwisePotential::get_energy_gradient (C++ function), [1], [2]
- pele::SimplePairwisePotential::get_energy_gradient_hessian (C++ function)
- pele::SimplePairwisePotential::get_energy_gradient_hessian_rattlers (C++ function)
- pele::SimplePairwisePotential::get_hessian (C++ function)
- pele::SimplePairwisePotential::get_interaction_energy_gradient (C++ function)
- pele::SimplePairwisePotential::get_interaction_energy_gradient_hessian (C++ function)
- pele::SimplePairwisePotential::get_ndim (C++ function)
- pele::SimplePairwisePotential::get_neighbors (C++ function)
- pele::SimplePairwisePotential::get_neighbors_picky (C++ function)
- pele::SimplePairwisePotential::get_overlaps (C++ function)
- pele::SimplePairwisePotential::get_rij (C++ function)
- pele::SimplePairwisePotential::m_ndim (C++ member)
- pele::SimplePairwisePotential::m_radii_sca (C++ member)
- pele::SimplePairwisePotential::SimplePairwisePotential (C++ function), [1], [2]
- pele::SimplePairwisePotential::~SimplePairwisePotential (C++ function)
- pele::sort_circle (C++ function)
- pele::sort_indexes (C++ function)
- pele::Steepest_Descent (C++ class)
- pele::Steepest_Descent::Steepest_Descent (C++ function)
- pele::Steepest_Descent::~Steepest_Descent (C++ function)
- pele::StepnormStopCriterion (C++ class)
- pele::StepnormStopCriterion::StepnormStopCriterion (C++ function)
- pele::StepnormStopCriterion::stop_criterion_satisfied (C++ function)
- pele::StopCriterionType (C++ enum)
- pele::StopCriterionType::GRADIENT (C++ enumerator)
- pele::StopCriterionType::NEWTON (C++ enumerator)
- pele::StopCriterionType::STEPNORM (C++ enumerator)
- pele::TransformAACluster (C++ class)
- pele::TransformAACluster::m_topology (C++ member)
- pele::TransformAACluster::rotate (C++ function)
- pele::TransformAACluster::TransformAACluster (C++ function)
- pele::TransformAACluster::~TransformAACluster (C++ function)
- pele::TransformPolicy (C++ class)
- pele::TransformPolicy::rotate (C++ function)
- pele::TransformPolicy::~TransformPolicy (C++ function)
- pele::transpose (C++ function)
- pele::UserData (C++ type)
- pele::UserData_ (C++ struct)
- pele::UserData_::atol (C++ member)
- pele::UserData_::nfev (C++ member)
- pele::UserData_::nhev (C++ member)
- pele::UserData_::pot_ (C++ member)
- pele::UserData_::rtol (C++ member)
- pele::UserData_::stored_energy (C++ member)
- pele::UserData_::stored_grad (C++ member)
- pele::UserData_::stored_J (C++ member)
- pele::VecN (C++ class)
- pele::VecN::assign (C++ function), [1]
- pele::VecN::begin (C++ function), [1]
- pele::VecN::const_iterator (C++ type)
- pele::VecN::data (C++ function), [1]
- pele::VecN::end (C++ function), [1]
- pele::VecN::iterator (C++ type)
- pele::VecN::operator* (C++ function), [1]
- pele::VecN::operator*= (C++ function), [1]
- pele::VecN::operator+= (C++ function), [1]
- pele::VecN::operator- (C++ function)
- pele::VecN::operator-= (C++ function), [1]
- pele::VecN::operator/= (C++ function), [1]
- pele::VecN::operator= (C++ function)
- pele::VecN::operator[] (C++ function), [1]
- pele::VecN::prod (C++ function)
- pele::VecN::size (C++ function)
- pele::VecN::sum (C++ function)
- pele::VecN::VecN (C++ function), [1], [2], [3]
- pele::vector_t (C++ type)
- pele::WCA (C++ class)
- pele::WCA2D (C++ class)
- pele::WCA2D::WCA2D (C++ function)
- pele::WCA::WCA (C++ function)
- pele::WCA_interaction (C++ struct)
- pele::WCA_interaction::energy (C++ function)
- pele::WCA_interaction::energy_gradient (C++ function)
- pele::WCA_interaction::energy_gradient_hessian (C++ function)
- pele::WCA_interaction::WCA_interaction (C++ function)
- pele::WCAAtomList (C++ class)
- pele::WCAAtomList::WCAAtomList (C++ function), [1]
- pele::WCANeighborList (C++ class)
- pele::WCANeighborList::WCANeighborList (C++ function)
- pele::WCAPeriodic (C++ class)
- pele::WCAPeriodic2D (C++ class)
- pele::WCAPeriodic2D::WCAPeriodic2D (C++ function)
- pele::WCAPeriodic::WCAPeriodic (C++ function)
- pele::XCube (C++ class)
- pele::XCube::get_energy (C++ function)
- pele::XCube::get_energy_gradient (C++ function)
- pele::XCube::XCube (C++ function)
- pele::XCube::~XCube (C++ function)
- pele::zero_modes_translational (C++ function)
- periodic (pele.potentials.HS_WCA attribute)
- permute() (pele.angleaxis.TransformAngleAxisCluster method)
- pgorder (pele.storage.Minimum attribute)
- PI (C macro)
- plot() (pele.utils.benchmark.QuenchBenchmark method)
- PointGroupOrderCluster (class in pele.mindist)
- pop() (pele.optimize.Result method)
- popitem() (pele.optimize.Result method)
- populateBondConn() (pele.utils.amber.readAmberParam method)
- posAtoms (pele.utils.rbtools.CoordsAdapter attribute)
- posRigid (pele.utils.rbtools.CoordsAdapter attribute)
- PoweredCosineSum (class in pele.potentials)
- prepare() (pele.transition_states.NEBDriver method)
- PRINT_TO_FILE (C macro)
- printBondConn() (pele.utils.amber.readAmberParam method)
- printEvent() (pele.utils.histogram.PrintHistogram method)
- printHis() (pele.utils.histogram.PrintHistogram method)
- PrintHistogram (class in pele.utils.histogram)
- printState() (pele.transition_states.NEB method)
- printStep() (pele.basinhopping.BasinHopping method)
- properties() (pele.storage.Database method)
- PyInversePower (class in pele.potentials)
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