Namespace pele

PELE IMPLEMENTATION OF Class ATLJ POTENTIAL IN C++.

Detailed Description

A faster steepest descent implementation in pele.

Should include line search methods for use in various optimizers refer to Nocedal and Wright Chapter 3 for information.

Interface from pele array to Eigen.

preferably should be header only,

generally slow but works on ill conditioned problems

Classes

• Struct BaseInteraction

• Template Struct cartesian_distance

• Template Struct Factorial

• Template Struct Factorial< 0 >

• Struct frenkel_interaction

• Struct harmonic_interaction

• Template Struct HS_halfint_pairwise_power_interaction

• Struct HS_WCA_interaction

• Template Struct InverseHalfIntPower_interaction

• Template Struct InverseHalfIntPowerHS_interaction

• Template Struct InverseIntPower_interaction

• Template Struct InverseIntPowerHS_interaction

• Struct InversePower_interaction

• Struct InversePowerHS_interaction

• Struct InversePowerStillinger_cut_interaction

• Struct InversePowerStillinger_interaction

• Struct InversePowerStillingerQuadCutInteraction

• Template Struct InversePowerStillingerQuadCutInteractionInt

• Struct lj_interaction

• Struct lj_interaction_cut_smooth

• Template Struct meta_dist

• Template Struct meta_dist< 1 >

• Template Struct meta_image

• Template Struct meta_image< 1 >

• Template Struct meta_leesedwards_distance

• Template Struct meta_leesedwards_distance< 2 >

• Template Struct meta_leesedwards_image

• Template Struct meta_leesedwards_image< 2 >

• Template Struct meta_periodic_distance

• Template Struct meta_periodic_distance< 1 >

• Template Struct meta_pow

• Template Struct meta_pow< T, 0 >

• Template Struct meta_pow< T, 10 >

• Template Struct meta_pow< T, 12 >

• Template Struct meta_pow< T, 4 >

• Template Struct meta_pow< T, 6 >

• Template Struct meta_pow< T, 8 >

• Template Struct meta_pow< T, 9 >

• Struct morse_interaction

• Struct UserData_

• Struct WCA_interaction

• Class AbstractStopCriterion

• Template Class Array

• Class ATLJ

• Template Class AtomListPotential

• Class BacktrackingLineSearch

• Template Class BaseAccumulator

• Class BaseHarmonic

• Class BasePotential

• Class BaseRadialGaussian

• Class BerthierDistribution3d

• Class BracketingLineSearch

• Template Class CartesianDistanceWrapper

• Template Class CellListPotential

• Template Class CellLists

• Template Class CellListsContainer

• Template Class CellListsLoop

• Template Class combination_generator

• Class CombinedPotential

• Class CoordsAdaptor

• Class CosineGradientDescent

• Class CVODEBDFOptimizer

• Template Class DistanceData

• Class DistanceInterface

• Class Edge

• Template Class EnergyAccumulator

• Template Class EnergyAccumulatorExact

• Template Class EnergyGradientAccumulator

• Template Class EnergyGradientAccumulatorExact

• Template Class EnergyGradientHessianAccumulator

• Template Class EnergyGradientHessianAccumulatorExact

• Template Class EnergyHessianAccumulator

• Class ExtendedMixedOptimizer

• Class ExtendedPotential

• Class FlatHarmonic

• Class Frenkel

• Class FrenkelPeriodic

• Template Class FrenkelPeriodicCellLists

• Class FrozenCoordsConverter

• Class FrozenPotentialWrapper

• Class GaussianPot

• Class GenericMixedDescent

• Class GradientDescent

• Class GradientOptimizer

• Class GradientStopCriterion

• Class Graph

• Class Harmonic

• Class HarmonicAtomList

• Class HarmonicCOM

• Class HarmonicNeighborList

• Template Class HS_WCA

• Template Class HS_WCACellLists

• Template Class HS_WCALeesEdwards

• Template Class HS_WCALeesEdwardsCellLists

• Template Class HS_WCANeighborList

• Template Class HS_WCAPeriodic

• Template Class HS_WCAPeriodicCellLists

• Template Class HSHalfIntPairwisePower

• Template Class HSHalfIntPairwisePowerPeriodic

• Template Class HSHalfIntPairwisePowerPeriodicCellLists

• Template Class InverseHalfIntPower

• Template Class InverseHalfIntPowerHS

• Template Class InverseHalfIntPowerHSPeriodic

• Template Class InverseHalfIntPowerHSPeriodicCellLists

• Template Class InverseHalfIntPowerPeriodic

• Template Class InverseHalfIntPowerPeriodicCellLists

• Template Class InverseIntPower

• Template Class InverseIntPowerHS

• Template Class InverseIntPowerHSPeriodic

• Template Class InverseIntPowerHSPeriodicCellLists

• Template Class InverseIntPowerPeriodic

• Template Class InverseIntPowerPeriodicCellLists

• Template Class InversePower

• Template Class InversePowerHS

• Template Class InversePowerHSPeriodic

• Template Class InversePowerHSPeriodicCellLists

• Template Class InversePowerPeriodic

• Template Class InversePowerPeriodicCellLists

• Template Class InversePowerStillinger

• Template Class InversePowerStillingerCut

• Template Class InversePowerStillingerCutPeriodic

• Template Class InversePowerStillingerCutPeriodicCellLists

• Template Class InversePowerStillingerCutQuad

• Template Class InversePowerStillingerCutQuadInt

• Template Class InversePowerStillingerCutQuadIntPeriodic

• Template Class InversePowerStillingerCutQuadIntPeriodicCellLists

• Template Class InversePowerStillingerCutQuadPeriodic

• Template Class InversePowerStillingerCutQuadPeriodicCellLists

• Template Class InversePowerStillingerPeriodic

• Class LAMMPSPotential

• Template Class LatticeNeighbors

• Class LBFGS

• Class LBFGSParam

• Template Class leesedwards_distance

• Template Class LeesEdwardsDistanceWrapper

• Class LineSearch

• Class LJ

• Class LJCut

• Class LJCutAtomList

• Class LJCutPeriodic

• Class LJCutPeriodicAtomList

• Template Class LJCutPeriodicCellLists

• Class LJNeighborList

• Class LJPeriodic

• Class LowestEigPotential

• Template Class MatrixAdapter

• Template Class MatrixNM

• Template Class MeanFieldPSpinSpherical

• Class MeasureAngleAxisCluster

• Class MixedDescentEndOnly

• Class MODIFIED_FIRE

• Class MoreThuente

• Class Morse

• Template Class NeighborAccumulator

• Class Newton

• Class NewtonStopCriterion

• Class NewtonWithExtendedPotential

• Class NGT

• Class NocedalWrightLineSearch

• Class Node

• Class NonAdditiveCutoffCalculator

• Class ODEBasedOptimizer

• Class OldLineSearch

• Class Optimizer

• Class Orthogonalize

• Class OrthogonalizeTranslational

• Template Class OverlapAccumulator

• Class PairwisePotentialInterface

• Template Class periodic_distance

• Template Class PeriodicDistanceWrapper

• Class PoweredCosineSum

• Class PythonPotential

• Class RadialGaussian

• Class RadialGaussianCOM

• Class RBPotentialWrapper

• Class RBTopology

• Class RigidFragment

• Class RosenBrock

• Class Saddle

• Template Class sf_HS_WCA_interaction

• Template Class SimplePairwiseNeighborList

• Template Class SimplePairwisePotential

• Class Steepest_Descent

• Class StepnormStopCriterion

• Class TransformAACluster

• Class TransformPolicy

• Template Class VecN

• Class WCA

• Class WCA2D

• Class WCAAtomList

• Class WCANeighborList

• Class WCAPeriodic

• Class WCAPeriodic2D

• Class XCube

Enums

• Enum HessianType

• Enum LINE_SEARCH_TERMINATION_CONDITION

• Enum StopCriterionType

Functions

• Function pele::aa_to_quaternion

• Function pele::aa_to_rot_mat

• Function pele::accumulate_energies_omp

• Template Function pele::accumulate_gradient

• Template Function pele::accumulate_hessian

• Function pele::add_symmetry_offset

• Function pele::add_translation_offset_2d

• Function pele::check_sundials_retval

• Function pele::compare_degree

• Function pele::cross_shifted

• Function pele::dot(Array<double> const&, Array<double> const&)

• Template Function pele::dot(VecN<N, dtype> const&, VecN<N, dtype> const&)

• Template Function pele::dot(MatrixNM<N, L, dtype> const&, MatrixNM<L, M, dtype> const&)

• Template Function pele::dot(MatrixNM<N, M, dtype> const&, pele::VecN<M, dtype> const&)

• Function pele::eig_eq_pele

• Function pele::eig_eq_pele_data

• Function pele::eig_mat_eq_pele

• Function pele::f(double, N_Vector, N_Vector, void *)

• Function pele::f(sunrealtype, N_Vector, N_Vector, void *)

• Function pele::generate_2d_symmetries

• Function pele::generate_3d_symmetries

• Function pele::generate_bidisperse_radii

• Function pele::generate_random_coordinates

• Function pele::get_box_length

• Function pele::get_ncellx_scale

• Function pele::get_symmetries

• Template Function pele::hacky_mat_mul

• Template Function pele::identity

• Template Function pele::init_distance_datas

• Function pele::init_energies

• Function pele::Jac

• Template Function pele::make_combination_generator

• Function pele::N_Vector_eq_pele

• Template Function pele::neg_half_int_pow

• Template Function pele::neg_int_pow

• Function pele::norm(Array<double> const&)

• Template Function pele::norm(VecN<N, dtype> const&)

• Template Function pele::operator*

• Template Function pele::operator<<(std::ostream&, const Array<dtype>&)

• Function pele::operator<<(std::ostream&, std::shared_ptr<Graph>)

• Template Function pele::operator<<(std::ostream&, const pele::MatrixAdapter<dtype>&)

• Template Function pele::operator<<(std::ostream&, const MatrixNM<N, M, dtype>&)

• Template Function pele::operator<<(std::ostream&, const VecN<N, dtype>&)

• Function pele::origin_in_hull_2d

• Function pele::pele_eq_eig

• Function pele::pele_eq_eig_data

• Function pele::pele_eq_N_Vector

• Template Function pele::pos_half_int_pow

• Template Function pele::pos_int_pow

• Function pele::pressure_tensor

• Function pele::print_matrix

• Template Function pele::print_vector

• Function pele::quaternion_multiply

• Function pele::quaternion_to_aa

• Function pele::reset_energies

• Function pele::reset_user_data

• Function pele::rot_mat_derivatives

• Function pele::rot_mat_derivatives_small_theta

• Function pele::rot_mat_to_aa

• Function pele::rot_mat_to_quaternion

• Function pele::rotate_aa

• Function pele::sort_circle

• Template Function pele::sort_indexes

• Template Function pele::transpose

• Function pele::zero_modes_translational

Typedefs

• Typedef pele::cell_t

• Typedef pele::color_type

• Typedef pele::edge_ptr

• Typedef pele::node_id

• Typedef pele::node_ptr

• Typedef pele::scalar_t

• Typedef pele::UserData

• Typedef pele::vector_t

Variables

• Variable pele::digits