Index

A

abort() (in module ppmd.mpi) AccessType (class in ppmd.access) add() (ppmd.opt.Code method) (ppmd.state_modifier.StateModifier method) add_cflag() (ppmd.lib.compiler.Compiler method) add_item() (ppmd.utility.high_method.Schedule method) add_line() (ppmd.opt.Code method) add_onto() (ppmd.coulomb.octal.EntryData method) ALegendrePolynomialGen (class in ppmd.coulomb.sph_harm) ALegendrePolynomialGenEphemeral (class in ppmd.coulomb.sph_harm) all_reduce() (in module ppmd.mpi) AllocMem (class in ppmd.mpi), [1]

AllToAll (class in ppmd.pairloop.alltoall) AllToAllNS (class in ppmd.pairloop.alltoall) AllToAllNSOMP (class in ppmd.pairloop.alltoall_omp) alpha (ppmd.coulomb.ewald.EwaldOrthoganal attribute) analyse() (in module ppmd.kernel) apply() (ppmd.domain.BoundaryTypePeriodic method) apply_lr_mtl() (ppmd.coulomb.fmm_pbc.LongRangeMTL method) Array (class in ppmd.host) array (ppmd.mpi.AllocMem attribute), [1] as_func() (ppmd.state.BaseMDState method) av_time() (ppmd.modules.code_timer.LoopTimer property) available_free_memory() (in module ppmd.host)

B

BaseDomainHalo (class in ppmd.domain) BaseMDState (class in ppmd.state) BasePotential (class in ppmd.utility.potential.c_potential) BCType (class in ppmd.coulomb.mm_lm_common) binary() (ppmd.lib.compiler.Compiler property) boundary() (ppmd.domain.BaseDomainHalo property) boundary_cells (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) boundary_outer() (ppmd.domain.BaseDomainHalo property)

boundary_starts (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) BoundaryTypePeriodic (class in ppmd.domain) broadcast_data_from() (ppmd.data.particle_dat.ParticleDat method) (ppmd.state.BaseMDState method) Buckingham (class in ppmd.utility.potential.c_potential) BuckinghamSymmetric (class in ppmd.utility.potential.c_potential) build_lib() (in module ppmd.lib.build) build_static_libs() (in module ppmd.cuda.cuda_build)

C

c_flags() (ppmd.lib.compiler.Compiler property) cart_comm (ppmd.coulomb.octal.cube_owner_map attribute) cartcomm_dims_xyz() (in module ppmd.mpi) cartcomm_get_move_send_recv_ranks() (in module ppmd.mpi) cartcomm_periods_xyz() (in module ppmd.mpi) cartcomm_shift() (in module ppmd.mpi) cartcomm_top_xyz() (in module ppmd.mpi) CartesianHaloSix (class in ppmd.halo) cell_array() (ppmd.cell.CellList property) (ppmd.domain.BaseDomainHalo property) cell_contents_count() (ppmd.cell.CellList property) cell_count() (ppmd.domain.BaseDomainHalo property) cell_decompose() (ppmd.domain.BaseDomainHalo method) (ppmd.state.BaseMDState method) cell_edge_lengths() (ppmd.domain.BaseDomainHalo property) cell_list() (ppmd.cell.CellList property) cell_reverse_lookup() (ppmd.cell.CellList property) cell_width() (ppmd.cell.CellList property) CellByCellOMP (class in ppmd.pairloop.cellbycell_omp) CellList (class in ppmd.cell) CellSlice (class in ppmd.halo) (class in ppmd.pygcl.halo_exchange_3d) check() (in module ppmd.mpi) (ppmd.cell.CellList method) check_consistency() (ppmd.state_modifier.StateModifier method) check_lib_rebuild() (ppmd.pairloop.neighbourlist_27cell.NeighbourListNonN3 method) check_npart_total() (ppmd.state.BaseMDState method) check_position_consistency() (ppmd.state.BaseMDState method) check_pythonhashseed() (in module ppmd.mpi) cleanup() (ppmd.utility.high_method.DrawParticles method) close() (ppmd.pio.pfprint method) cmplx_mul() (in module ppmd.coulomb.sph_harm) Code (class in ppmd.opt) code() (ppmd.kernel.Kernel property) comm (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) comment (ppmd.utility.xyz.XYZ attribute) compile_flag() (ppmd.lib.compiler.Compiler property) Compiler (class in ppmd.lib.compiler) compute_alpha() (in module ppmd.coulomb.ewald) compute_f() (ppmd.coulomb.fmm_pbc.FMMPbc method) compute_g() (ppmd.coulomb.fmm_pbc.FMMPbc method) compute_grid_ownership() (ppmd.coulomb.octal.cube_owner_map static method) compute_interaction_lists() (in module ppmd.coulomb.fmm_interaction_lists) (in module ppmd.coulomb.octal) compute_interaction_offsets() (in module ppmd.coulomb.octal)

compute_interaction_plookup() (in module ppmd.coulomb.octal) compute_interaction_radius() (in module ppmd.coulomb.octal) compute_interaction_tlookup() (in module ppmd.coulomb.octal) compute_local_size_offset() (in module ppmd.coulomb.octal) compute_map_product_contribs() (ppmd.coulomb.octal.cube_owner_map static method) compute_map_product_owners() (ppmd.coulomb.octal.cube_owner_map static method) compute_rc_nc_cutoff() (in module ppmd.coulomb.ewald) Constant (class in ppmd.kernel) contrib_mpi (ppmd.coulomb.octal.cube_owner_map attribute) contrib_starts (ppmd.coulomb.octal.cube_owner_map attribute) convert_offset_tuples() (in module ppmd.cell) copy() (ppmd.data.particle_dat.ParticleDat method) count() (ppmd.utility.high_method.Schedule property) Cpp11MT19937 (class in ppmd.modules.mt19937) cpu_time() (ppmd.modules.code_timer.LoopTimer property) create() (ppmd.cell.CellList method) create_cartcomm() (in module ppmd.mpi) create_halo_pairs_slice_halo() (in module ppmd.halo) (in module ppmd.pygcl.halo_exchange_3d) ctype() (ppmd.data.global_array.GlobalArrayClassic property) (ppmd.host.Array property) (ppmd.host.Matrix property) ctypes_data() (ppmd.host.Array property) (ppmd.host.Matrix property) (ppmd.host.ThreadSpace property) ctypes_data_access() (ppmd.data.global_array.GlobalArrayClassic method) (ppmd.data.particle_dat.ParticleDat method) (ppmd.host.Array method) (ppmd.host.Matrix method) ctypes_data_post() (ppmd.data.global_array.GlobalArrayClassic method) (ppmd.data.particle_dat.ParticleDat method) (ppmd.host.Array method) (ppmd.host.Matrix method) ctypes_data_read() (ppmd.data.global_array.GlobalArrayClassic property) ctypes_data_write() (ppmd.data.global_array.GlobalArrayClassic property) ctypes_value() (ppmd.data.scalar_array.ScalarArray property) cube_count (ppmd.coulomb.octal.cube_owner_map attribute) cube_owner_map (class in ppmd.coulomb.octal) cube_side_count (ppmd.coulomb.octal.cube_owner_map attribute) cube_to_mpi (ppmd.coulomb.octal.cube_owner_map attribute) cube_to_send (ppmd.coulomb.octal.cube_owner_map attribute) cube_tuple_to_lin_xyz() (in module ppmd.coulomb.octal) cube_tuple_to_lin_zyx() (in module ppmd.coulomb.octal) cubic_lattice() (in module ppmd.utility.lattice) cuda_flop_rate_mtl() (ppmd.coulomb.fmm.PyFMM method)

D

data() (ppmd.data.particle_dat.ParticleDat property) (ppmd.host.Matrix property) DatArgStore (class in ppmd.access) datdict() (ppmd.utility.potential.c_potential.Buckingham method) (ppmd.utility.potential.c_potential.LennardJonesCounter method) (ppmd.utility.potential.c_potential.LennardJonesShifted method) (ppmd.utility.potential.c_potential.NULL static method) dbg_flags() (ppmd.lib.compiler.Compiler property) decomposition (in module ppmd.mpi) determine_update_status() (ppmd.method.ListUpdateController method) dim (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) dims() (ppmd.domain.BaseDomainHalo property) DipoleCorrector (class in ppmd.coulomb.fmm_pbc) domain() (ppmd.cell.CellList property) (ppmd.state.BaseMDState property) dot_vec_multipole() (ppmd.coulomb.sph_harm.MultipoleDotVecCreator method) draw() (ppmd.utility.high_method.DrawParticles method)

DrawParticles (class in ppmd.utility.high_method) DSLArrayAccess (class in ppmd.modules.dsl_array_access) DSLCellListIter (class in ppmd.modules.dsl_cell_list_loop) DSLGlobalArrayAccess (class in ppmd.modules.dsl_array_access) DSLKernelSymSub (class in ppmd.modules.dsl_kernel_symbols) DSLPartitionTempSpace (class in ppmd.modules.dsl_cell_gather_scatter) DSLRecordLocal() (in module ppmd.modules.dsl_record_local) DSLSeqComp (class in ppmd.modules.dsl_seq_comp) DSLSeqGather() (in module ppmd.modules.dsl_cell_gather_scatter) DSLStrideComp (class in ppmd.modules.dsl_stride_comp) DSLStrideGather() (in module ppmd.modules.dsl_cell_gather_scatter) DSLStrideScatter() (in module ppmd.modules.dsl_cell_gather_scatter) DSLStructComp (class in ppmd.modules.dsl_struct_comp) dtype (ppmd.coulomb.fmm.PyFMM attribute) dtype() (ppmd.host.Array property) (ppmd.host.Matrix property) DtypeToCtype (class in ppmd.lib.common) dump_profile() (in module ppmd.opt)

E

end() (ppmd.host.Array property) EnergyStore (class in ppmd.utility.high_method) EntryData (class in ppmd.coulomb.octal) enum() (in module ppmd.mpi) eps_m() (in module ppmd.coulomb.wigner) evaluate() (ppmd.utility.high_method.RadialDistributionPeriodicNVE method) (ppmd.utility.high_method.VelocityAutoCorrelation method) evaluate_contributions() (ppmd.coulomb.ewald.EwaldOrthoganal method) evaluate_potential_field() (ppmd.coulomb.ewald_half.EwaldOrthoganalHalf method) evaluate_self_interactions() (ppmd.coulomb.ewald.EwaldOrthoganal method) EwaldOrthoganal (class in ppmd.coulomb.ewald) EwaldOrthoganalHalf (class in ppmd.coulomb.ewald_half) EwaldOrthogonal (in module ppmd.coulomb.ewald) EwaldOrthogonalHalf (in module ppmd.coulomb.ewald_half) exchange() (ppmd.pygcl.halo_exchange_3d.HaloExchange3D method) exchange_cell_counts() (ppmd.halo.CartesianHaloSix method) execute() (ppmd.loop.particle_loop.ParticleLoop method) (ppmd.loop.particle_loop_omp.ParticleLoopOMP method) (ppmd.pairloop.alltoall.AllToAllNS method) (ppmd.pairloop.alltoall_omp.AllToAllNSOMP method) (ppmd.pairloop.cellbycell_omp.CellByCellOMP method) (ppmd.pairloop.neighbourlist.PairLoopNeighbourList method) (ppmd.pairloop.neighbourlist.PairLoopNeighbourListNS method) (ppmd.pairloop.neighbourlist_omp.PairLoopNeighbourListNSOMP method) (ppmd.pairloop.sub_cellbycell_omp.SubCellByCellOMP method) (ppmd.utility.high_method.KineticEnergyTracker method) (ppmd.utility.high_method.PotentialEnergyTracker method)

execute_boundary_conditions() (ppmd.method.ListUpdateController method) extent() (ppmd.domain.BaseDomainHalo property) extent_internal() (ppmd.domain.BaseDomainHalo property) extern_numpy_ptr() (in module ppmd.coulomb.fmm) extract_forces_energy_real() (ppmd.coulomb.ewald.EwaldOrthoganal method) extract_forces_energy_reciprocal() (ppmd.coulomb.ewald.EwaldOrthoganal method) extract_from() (ppmd.coulomb.octal.EntryData method)

F

factor() (in module ppmd.domain) FarFieldDirect (class in ppmd.coulomb.direct) fcc() (in module ppmd.utility.lattice) filter_on_domain_boundary() (ppmd.state.BaseMDState method) finalise() (ppmd.utility.high_method.ParticleTracker method) flop_rate_mtl() (ppmd.coulomb.fmm.PyFMM method)

FMMLocal (class in ppmd.coulomb.fmm_local) FMMPbc (class in ppmd.coulomb.fmm_pbc) free() (ppmd.coulomb.fmm.PyFMM method) (ppmd.coulomb.octal.OctalGridLevel method) (ppmd.coulomb.octal.OctalTree method) FREE_SPACE (ppmd.coulomb.mm_lm_common.BCType attribute) FreeSpaceDirect (class in ppmd.coulomb.direct)

G

gather_data_on() (ppmd.data.particle_dat.ParticleDat method) (ppmd.state.BaseMDState method) gather_matrix() (in module ppmd.pairloop.neighbourlist) get_args() (ppmd.access.StaticArgStore method) get_boundary_cell_contents_count() (ppmd.halo.CartesianHaloSix method) get_boundary_cell_groups() (ppmd.halo.CartesianHaloSix method) get_boundary_cells() (ppmd.domain.BaseDomainHalo method) get_cart_rank_offset() (in module ppmd.pygcl.halo_exchange_3d) get_cell_to_particle_map() (ppmd.state.BaseMDState method) get_control_value() (in module ppmd.utility.dl_monte) (in module ppmd.utility.dl_poly) get_cpp_arguments() (ppmd.modules.code_timer.LoopTimer method) get_cpp_arguments_ast() (ppmd.modules.code_timer.LoopTimer method) (ppmd.modules.module.Module method) (ppmd.modules.mt19937.Cpp11MT19937 method) get_cpp_headers() (ppmd.modules.code_timer.LoopTimer method) get_cpp_headers_ast() (ppmd.modules.code_timer.LoopTimer method) (ppmd.modules.module.Module method) (ppmd.modules.mt19937.Cpp11MT19937 method) get_cpp_post_loop_code() (ppmd.modules.code_timer.LoopTimer method) get_cpp_post_loop_code_ast() (ppmd.modules.code_timer.LoopTimer method) (ppmd.modules.module.Module method) (ppmd.modules.mt19937.Cpp11MT19937 method) get_cpp_pre_loop_code() (ppmd.modules.code_timer.LoopTimer method) get_cpp_pre_loop_code_ast() (ppmd.modules.code_timer.LoopTimer method) (ppmd.modules.module.Module method) (ppmd.modules.mt19937.Cpp11MT19937 method) get_data_map() (ppmd.utility.potential.c_potential.Buckingham method) (ppmd.utility.potential.c_potential.LennardJonesShifted method) (ppmd.utility.potential.c_potential.VLennardJonesNoU method) (ppmd.utility.potential.sym_potential.SymbolicPotential method) get_denominator_sym() (ppmd.coulomb.sph_harm.SphCoeffGen method) get_dir_counts() (ppmd.halo.CartesianHaloSix method) get_domain_decomp() (in module ppmd.domain) get_e_sym() (ppmd.coulomb.sph_harm.SphExpGen method) get_field_value() (in module ppmd.utility.dl_poly)

get_halo_cell_groups() (ppmd.halo.CartesianHaloSix method) get_kinetic_energy_array() (ppmd.utility.high_method.KineticEnergyTracker method) get_line() (ppmd.coulomb.sph_harm.PRadiusModifier method) get_neighbour_list() (ppmd.pairloop.list_controller.NListController method) get_npart_local_func() (ppmd.state.BaseMDState method) get_numerator_sym() (ppmd.coulomb.sph_harm.SphCoeffGen method) get_offsets() (ppmd.pairloop.sub_cell.SubCell method) get_p_sym() (ppmd.coulomb.sph_harm.ALegendrePolynomialGen method) (ppmd.coulomb.sph_harm.ALegendrePolynomialGenEphemeral method) (ppmd.coulomb.sph_harm.PRadiusModifier method) get_pointer() (ppmd.pairloop.state_handler.StateHandler method) get_position_dat() (ppmd.state.BaseMDState method) get_position_shifts() (ppmd.halo.CartesianHaloSix method) get_potential_energy_array() (ppmd.utility.high_method.PotentialEnergyTracker method) get_python_parameters() (ppmd.modules.code_timer.LoopTimer method) (ppmd.modules.module.Module method) (ppmd.modules.mt19937.Cpp11MT19937 method) get_radius_sym() (ppmd.coulomb.sph_harm.PRadiusModifier method) (ppmd.coulomb.sph_harm.SphGen method) (ppmd.coulomb.sph_harm.SphGenEphemeral method) get_recv_ranks() (ppmd.halo.CartesianHaloSix method) get_send_ranks() (ppmd.halo.CartesianHaloSix method) get_setup_parameters() (ppmd.cell.CellList method) get_shift() (ppmd.domain.BaseDomainHalo method) get_timer_accuracy() (in module ppmd.opt) get_y_sym() (ppmd.coulomb.sph_harm.SphGen method) (ppmd.coulomb.sph_harm.SphGenEphemeral method) global_to_local (ppmd.coulomb.octal.OctalGridLevel attribute) global_to_local_halo (ppmd.coulomb.octal.OctalGridLevel attribute) global_to_local_parent (ppmd.coulomb.octal.OctalGridLevel attribute) GlobalArray (class in ppmd.data.global_array) GlobalArrayClassic (class in ppmd.data.global_array) GlobalArrayShared (class in ppmd.data.global_array) GlobalDataMover (class in ppmd.data.data_movement) green() (in module ppmd.coulomb.fmm) (in module ppmd.coulomb.fmm_pbc) grid_cube_size (ppmd.coulomb.octal.OctalGridLevel attribute)

H

halo() (ppmd.access.AccessType property) halo_aware (ppmd.data.scalar_array.ScalarArray attribute) halo_cells (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) halo_exchange() (ppmd.coulomb.octal.OctalGridLevel method) (ppmd.data.particle_dat.ParticleDat method) halo_exchange_level() (ppmd.coulomb.octal.OctalDataTree method) halo_start (ppmd.data.particle_dat.ParticleDat attribute) halo_start_reset() (ppmd.data.particle_dat.ParticleDat method) halo_start_set() (ppmd.data.particle_dat.ParticleDat method) halo_start_shift() (ppmd.data.particle_dat.ParticleDat method)

halo_starts (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) halo_version_id (ppmd.cell.CellList attribute) HaloExchange3D (class in ppmd.pygcl.halo_exchange_3d) halos() (ppmd.domain.BaseDomainHalo property) hash() (ppmd.lib.compiler.Compiler property) Header (class in ppmd.kernel) header (ppmd.modules.dsl_seq_comp.DSLSeqComp attribute) (ppmd.modules.dsl_stride_comp.DSLStrideComp attribute) (ppmd.modules.dsl_struct_comp.DSLStructComp attribute) headers() (ppmd.kernel.Kernel property) hexdigest() (ppmd.kernel.Kernel method)

I

identity_element (ppmd.data.global_array.GlobalArrayClassic attribute) im_lm() (ppmd.coulomb.fmm.PyFMM method) (ppmd.coulomb.fmm_pbc.FMMPbc method) INC (in module ppmd.access) inc_version() (ppmd.host.Array method) (ppmd.host.Matrix method) INC_ZERO (in module ppmd.access) increment_step_count() (ppmd.method.ListUpdateController method) incremented() (ppmd.access.AccessType property) index() (ppmd.kernel.Reduction property) instance_id (ppmd.cell.CellList attribute)

integrate() (ppmd.utility.high_method.IntegratorVelocityVerlet method) (ppmd.utility.high_method.VelocityVerlet method) integrate_thermostat() (ppmd.utility.high_method.VelocityVerletAnderson method) IntegratorRange (class in ppmd.method) IntegratorVelocityVerlet (class in ppmd.utility.high_method) internal_to_ev() (in module ppmd.coulomb.fmm) (ppmd.coulomb.ewald.EwaldOrthoganal static method) (ppmd.coulomb.fmm.PyFMM static method) invalidate_lists() (ppmd.state.BaseMDState method) items() (ppmd.access.DatArgStore method) (ppmd.access.StaticArgStore method)

K

Kernel (class in ppmd.kernel) kernel() (ppmd.utility.potential.c_potential.Buckingham property) (ppmd.utility.potential.c_potential.BuckinghamSymmetric property) (ppmd.utility.potential.c_potential.LennardJones property) (ppmd.utility.potential.c_potential.LennardJonesCounter property) (ppmd.utility.potential.c_potential.LennardJonesShifted property) (ppmd.utility.potential.c_potential.NoVLennardJones property) (ppmd.utility.potential.c_potential.NULL property) (ppmd.utility.potential.c_potential.TestPotential1 property) (ppmd.utility.potential.c_potential.TestPotential2 property) (ppmd.utility.potential.c_potential.TestPotential3 property) (ppmd.utility.potential.c_potential.TestPotential4 property) (ppmd.utility.potential.c_potential.TestPotential4p property) (ppmd.utility.potential.c_potential.VLennardJones property) (ppmd.utility.potential.c_potential.VLennardJones2 property) (ppmd.utility.potential.c_potential.VLennardJonesNoU property) (ppmd.utility.potential.sym_potential.SymbolicPotential property) kernel_arg (ppmd.modules.dsl_array_access.DSLArrayAccess attribute) (ppmd.modules.dsl_array_access.DSLGlobalArrayAccess attribute)

kernel_arg_decl (ppmd.modules.dsl_array_access.DSLArrayAccess attribute) (ppmd.modules.dsl_array_access.DSLGlobalArrayAccess attribute) (ppmd.modules.dsl_seq_comp.DSLSeqComp attribute) (ppmd.modules.dsl_stride_comp.DSLStrideComp attribute) (ppmd.modules.dsl_struct_comp.DSLStructComp attribute) kernel_create_arg (ppmd.modules.dsl_seq_comp.DSLSeqComp attribute) (ppmd.modules.dsl_struct_comp.DSLStructComp attribute) kernel_create_i_arg (ppmd.modules.dsl_array_access.DSLGlobalArrayAccess attribute) (ppmd.modules.dsl_stride_comp.DSLStrideComp attribute) kernel_create_i_scatter (ppmd.modules.dsl_array_access.DSLArrayAccess attribute) (ppmd.modules.dsl_array_access.DSLGlobalArrayAccess attribute) (ppmd.modules.dsl_stride_comp.DSLStrideComp attribute) kernel_create_j_arg (ppmd.modules.dsl_array_access.DSLArrayAccess attribute) (ppmd.modules.dsl_array_access.DSLGlobalArrayAccess attribute) (ppmd.modules.dsl_stride_comp.DSLStrideComp attribute) KineticEnergyTracker (class in ppmd.utility.high_method) kmax (ppmd.coulomb.ewald.EwaldOrthoganal attribute)

L

L (ppmd.coulomb.fmm.PyFMM attribute) l_flags() (ppmd.lib.compiler.Compiler property) labels (ppmd.utility.xyz.XYZ attribute) LennardJones (class in ppmd.utility.potential.c_potential) LennardJonesCounter (class in ppmd.utility.potential.c_potential) LennardJonesShifted (class in ppmd.utility.potential.c_potential) lib_from_file_source() (in module ppmd.lib.build) ListUpdateController (class in ppmd.method)

load_config() (in module ppmd.config.config) (in module ppmd.cuda.cuda_config) load_last_profiles() (in module ppmd.opt) load_profiles() (in module ppmd.opt) local_grid_cube_size (ppmd.coulomb.octal.OctalGridLevel attribute) local_grid_offset (ppmd.coulomb.octal.OctalGridLevel attribute) LocalExpEval (class in ppmd.coulomb.sph_harm) LongRangeMTL (class in ppmd.coulomb.fmm_pbc) LoopTimer (class in ppmd.modules.code_timer)

M

mark_halos_old() (ppmd.data.particle_dat.ParticleDat method) Matrix (class in ppmd.host) max() (ppmd.data.particle_dat.ParticleDat method) (ppmd.data.scalar_array.ScalarArray property) max_cell_contents_count() (ppmd.cell.CellList property) (ppmd.plain_cell_list.PlainCellList property) max_npart (ppmd.data.particle_dat.ParticleDat attribute) mean() (ppmd.data.scalar_array.ScalarArray property) min() (ppmd.data.scalar_array.ScalarArray property) MM_LM_Common (class in ppmd.coulomb.mm_lm_common) mode() (ppmd.access.AccessType property) modify() (ppmd.state.BaseMDState method) modify_view() (ppmd.data.particle_dat.ParticleDat method) module ppmd ppmd.access ppmd.cell ppmd.config ppmd.config.config ppmd.coulomb ppmd.coulomb.cached ppmd.coulomb.direct ppmd.coulomb.ewald ppmd.coulomb.ewald_half ppmd.coulomb.fmm ppmd.coulomb.fmm_interaction_lists ppmd.coulomb.fmm_local ppmd.coulomb.fmm_pbc ppmd.coulomb.lm ppmd.coulomb.mm ppmd.coulomb.mm_lm_common ppmd.coulomb.octal ppmd.coulomb.sph_harm ppmd.coulomb.wigner ppmd.cuda ppmd.cuda.cuda_build ppmd.cuda.cuda_config ppmd.data ppmd.data.data_movement ppmd.data.global_array ppmd.data.particle_dat ppmd.data.scalar_array ppmd.domain ppmd.halo ppmd.host ppmd.kernel ppmd.lib ppmd.lib.build ppmd.lib.common ppmd.lib.compiler ppmd.loop ppmd.loop.particle_loop ppmd.loop.particle_loop_omp ppmd.method ppmd.modules ppmd.modules.code_timer ppmd.modules.dsl_array_access ppmd.modules.dsl_cell_gather_scatter ppmd.modules.dsl_cell_list_loop ppmd.modules.dsl_kernel_symbols ppmd.modules.dsl_record_local ppmd.modules.dsl_seq_comp ppmd.modules.dsl_stride_comp ppmd.modules.dsl_struct_comp ppmd.modules.module ppmd.modules.mt19937 ppmd.mpi ppmd.opt ppmd.pairloop ppmd.pairloop.alltoall ppmd.pairloop.alltoall_omp ppmd.pairloop.base ppmd.pairloop.cellbycell_omp ppmd.pairloop.list_controller ppmd.pairloop.neighbour_matrix_omp ppmd.pairloop.neighbour_matrix_omp_sub ppmd.pairloop.neighbourlist ppmd.pairloop.neighbourlist_14cell ppmd.pairloop.neighbourlist_27cell ppmd.pairloop.neighbourlist_omp ppmd.pairloop.state_handler ppmd.pairloop.sub_cell ppmd.pairloop.sub_cellbycell_omp ppmd.pio ppmd.plain_cell_list ppmd.pygcl ppmd.pygcl.halo_exchange_3d ppmd.runtime ppmd.state ppmd.state_modifier ppmd.utility ppmd.utility.dl_monte ppmd.utility.dl_poly ppmd.utility.high_method ppmd.utility.lattice ppmd.utility.potential ppmd.utility.potential.c_potential ppmd.utility.potential.sym_potential ppmd.utility.sanitise ppmd.utility.xyz

Module (class in ppmd.modules.module) move_to_neighbour() (ppmd.state.BaseMDState method) mpi_decompose() (ppmd.domain.BaseDomainHalo method) multipole_exp() (ppmd.coulomb.sph_harm.MultipoleExpCreator method) MultipoleDotVecCreator (class in ppmd.coulomb.sph_harm) MultipoleExpCreator (class in ppmd.coulomb.sph_harm)

N

name (ppmd.data.particle_dat.ParticleDat attribute) (ppmd.data.scalar_array.ScalarArray attribute) name() (ppmd.kernel.Kernel property) (ppmd.lib.compiler.Compiler property) ncol() (ppmd.host.Matrix property) ncomp (ppmd.data.particle_dat.ParticleDat attribute) ncomp() (ppmd.data.global_array.GlobalArray property) (ppmd.data.global_array.GlobalArrayClassic property) (ppmd.host.Array property) NEAREST (ppmd.coulomb.mm_lm_common.BCType attribute) NearestDirect (class in ppmd.coulomb.direct) NeighbourListNonN3 (class in ppmd.pairloop.neighbourlist_27cell) NeighbourListOMP (class in ppmd.pairloop.neighbour_matrix_omp) NeighbourListOMPSub (class in ppmd.pairloop.neighbour_matrix_omp_sub) NeighbourListv2 (class in ppmd.pairloop.neighbourlist_14cell) nested_iterator() (in module ppmd.utility.lattice) next() (ppmd.method.IntegratorRange method)

nlist_controller (in module ppmd.pairloop.list_controller) NListController (class in ppmd.pairloop.list_controller) norm_linf() (ppmd.data.particle_dat.ParticleDat method) norm_vec() (ppmd.utility.high_method.DrawParticles method) NoVLennardJones (class in ppmd.utility.potential.c_potential) npart() (ppmd.state.BaseMDState property) npart_local (ppmd.data.particle_dat.ParticleDat attribute) npart_local() (ppmd.state.BaseMDState property) npart_local_halo (ppmd.data.particle_dat.ParticleDat attribute) npart_total() (ppmd.data.particle_dat.ParticleDat property) nrow() (ppmd.host.Matrix property) NULL (class in ppmd.utility.potential.c_potential) (in module ppmd.access) null_matrix() (in module ppmd.host) num_atoms (ppmd.utility.xyz.XYZ attribute) num_cells() (ppmd.coulomb.octal.OctalDataTree method) num_particles() (ppmd.cell.CellList property) numpy_to_xyz() (in module ppmd.utility.xyz)

O

OctalDataTree (class in ppmd.coulomb.octal) OctalGridLevel (class in ppmd.coulomb.octal) OctalTree (class in ppmd.coulomb.octal) offset() (ppmd.cell.CellList property)

op (ppmd.data.global_array.GlobalArrayClassic attribute) operator() (ppmd.kernel.Reduction property) opt_flags() (ppmd.lib.compiler.Compiler property) owners (ppmd.coulomb.octal.OctalGridLevel attribute)

P

PairLoopNeighbourList (class in ppmd.pairloop.neighbourlist) PairLoopNeighbourListNS (class in ppmd.pairloop.neighbourlist) PairLoopNeighbourListNSOMP (class in ppmd.pairloop.neighbourlist_omp) parent_local_size (ppmd.coulomb.octal.OctalGridLevel attribute) ParticleDat (class in ppmd.data.particle_dat) ParticleDatModifier (class in ppmd.data.data_movement) ParticleLoop (class in ppmd.loop.particle_loop) ParticleLoopOMP (class in ppmd.loop.particle_loop_omp) ParticleTracker (class in ppmd.utility.high_method) pause() (ppmd.opt.SynchronizedTimer method) (ppmd.opt.Timer method) PBC (ppmd.coulomb.mm_lm_common.BCType attribute) PBCDirect (class in ppmd.coulomb.direct) PercentagePrinter (class in ppmd.utility.high_method) pfactor() (in module ppmd.domain) pfprint (class in ppmd.pio) PlainCellList (class in ppmd.plain_cell_list) plot() (ppmd.utility.high_method.EnergyStore method) (ppmd.utility.high_method.RadialDistributionPeriodicNVE method) (ppmd.utility.high_method.VelocityAutoCorrelation method) pointer() (ppmd.kernel.Reduction property) pointer_offset() (in module ppmd.host) PositionDat (class in ppmd.data.particle_dat) positions (ppmd.utility.xyz.XYZ attribute) post_execute() (ppmd.pairloop.state_handler.StateHandler method) post_halo_exchange() (ppmd.cell.CellList method) post_update() (ppmd.method.ListUpdateController method) PotentialEnergyTracker (class in ppmd.utility.high_method) ppmd module ppmd.access module ppmd.cell module ppmd.config module ppmd.config.config module ppmd.coulomb module ppmd.coulomb.cached module ppmd.coulomb.direct module ppmd.coulomb.ewald module ppmd.coulomb.ewald_half module ppmd.coulomb.fmm module ppmd.coulomb.fmm_interaction_lists module ppmd.coulomb.fmm_local module ppmd.coulomb.fmm_pbc module ppmd.coulomb.lm module ppmd.coulomb.mm module ppmd.coulomb.mm_lm_common module ppmd.coulomb.octal module ppmd.coulomb.sph_harm module ppmd.coulomb.wigner module ppmd.cuda module ppmd.cuda.cuda_build module ppmd.cuda.cuda_config module ppmd.data module ppmd.data.data_movement module ppmd.data.global_array module ppmd.data.particle_dat module ppmd.data.scalar_array module ppmd.domain module ppmd.halo module ppmd.host module ppmd.kernel module ppmd.lib module ppmd.lib.build module ppmd.lib.common module ppmd.lib.compiler module ppmd.loop module ppmd.loop.particle_loop module ppmd.loop.particle_loop_omp module ppmd.method module ppmd.modules module

ppmd.modules.code_timer module ppmd.modules.dsl_array_access module ppmd.modules.dsl_cell_gather_scatter module ppmd.modules.dsl_cell_list_loop module ppmd.modules.dsl_kernel_symbols module ppmd.modules.dsl_record_local module ppmd.modules.dsl_seq_comp module ppmd.modules.dsl_stride_comp module ppmd.modules.dsl_struct_comp module ppmd.modules.module module ppmd.modules.mt19937 module ppmd.mpi module ppmd.opt module ppmd.pairloop module ppmd.pairloop.alltoall module ppmd.pairloop.alltoall_omp module ppmd.pairloop.base module ppmd.pairloop.cellbycell_omp module ppmd.pairloop.list_controller module ppmd.pairloop.neighbour_matrix_omp module ppmd.pairloop.neighbour_matrix_omp_sub module ppmd.pairloop.neighbourlist module ppmd.pairloop.neighbourlist_14cell module ppmd.pairloop.neighbourlist_27cell module ppmd.pairloop.neighbourlist_omp module ppmd.pairloop.state_handler module ppmd.pairloop.sub_cell module ppmd.pairloop.sub_cellbycell_omp module ppmd.pio module ppmd.plain_cell_list module ppmd.pygcl module ppmd.pygcl.halo_exchange_3d module ppmd.runtime module ppmd.state module ppmd.state_modifier module ppmd.utility module ppmd.utility.dl_monte module ppmd.utility.dl_poly module ppmd.utility.high_method module ppmd.utility.lattice module ppmd.utility.potential module ppmd.utility.potential.c_potential module ppmd.utility.potential.sym_potential module ppmd.utility.sanitise module ppmd.utility.xyz module pprint() (in module ppmd.pio) (ppmd.pio.pfprint method) PRadiusModifier (class in ppmd.coulomb.sph_harm) pre_execute() (ppmd.pairloop.state_handler.StateHandler method) pre_update() (ppmd.method.ListUpdateController method) prepare_halo_sort() (ppmd.cell.CellList method) print_profile() (in module ppmd.opt) print_str_on_0() (in module ppmd.mpi) PROFILE (in module ppmd.opt) pwrite() (ppmd.pio.pfprint method) py_compute_phi_local() (ppmd.coulomb.sph_harm.LocalExpEval method) py_dot_vec() (ppmd.coulomb.sph_harm.MultipoleDotVecCreator method) py_local_exp() (in module ppmd.coulomb.sph_harm) py_multipole_exp() (in module ppmd.coulomb.sph_harm) (ppmd.coulomb.sph_harm.MultipoleExpCreator method) PyFMM (class in ppmd.coulomb.fmm) PyLM (class in ppmd.coulomb.lm) PyMM (class in ppmd.coulomb.mm)

R

R_y() (in module ppmd.coulomb.wigner) R_z() (in module ppmd.coulomb.wigner) R_z_vec() (in module ppmd.coulomb.wigner) R_zy() (in module ppmd.coulomb.wigner) R_zyz() (in module ppmd.coulomb.wigner) R_zyz_given_y() (in module ppmd.coulomb.wigner) RadialDistributionPeriodicNVE (class in ppmd.utility.high_method) radius_cell_decompose() (in module ppmd.cell) RadiusSquared (class in ppmd.utility.potential.sym_potential) raw_write() (ppmd.utility.high_method.RadialDistributionPeriodicNVE method) rc() (ppmd.utility.potential.c_potential.LennardJonesShifted property) (ppmd.utility.potential.c_potential.NULL property) re_lm() (ppmd.coulomb.fmm.PyFMM method) (ppmd.coulomb.fmm_pbc.FMMPbc method) READ (in module ppmd.access) read() (ppmd.access.AccessType property) read_control() (in module ppmd.utility.dl_monte) (in module ppmd.utility.dl_poly) read_domain_extent() (in module ppmd.utility.dl_poly) read_field() (in module ppmd.utility.dl_poly) read_forces() (in module ppmd.utility.dl_poly) read_ids() (in module ppmd.utility.dl_poly) read_positions() (in module ppmd.utility.dl_monte) (in module ppmd.utility.dl_poly) read_symbols() (in module ppmd.utility.dl_poly) read_velocities() (in module ppmd.utility.dl_poly) real_cutoff (ppmd.coulomb.ewald.EwaldOrthoganal attribute) realloc() (ppmd.host.Array method) (ppmd.host.Matrix method)

rebuild_cell_to_particle_maps() (ppmd.state.BaseMDState method) recip_cutoff (ppmd.coulomb.ewald.EwaldOrthoganal attribute) recip_vectors (ppmd.coulomb.ewald.EwaldOrthoganal attribute) recv_ranks (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) red() (in module ppmd.coulomb.fmm) (in module ppmd.coulomb.fmm_pbc) Reduction (class in ppmd.kernel) reduction_variable_lookup() (ppmd.kernel.Kernel method) remove() (ppmd.state_modifier.StateModifier method) remove_by_slot() (ppmd.state.BaseMDState method) replace() (ppmd.kernel.Constant method) reset() (ppmd.opt.Timer method) (ppmd.utility.high_method.RadialDistributionPeriodicNVE method) reset_callbacks() (ppmd.cell.CellList method) resize() (ppmd.data.particle_dat.ParticleDat method) (ppmd.data.scalar_array.ScalarArray method) Restrict() (in module ppmd.loop.particle_loop) (in module ppmd.loop.particle_loop_omp) (in module ppmd.pairloop.base) restrict_keyword() (ppmd.lib.compiler.Compiler property) rn() (ppmd.utility.potential.c_potential.NULL property) rprint() (in module ppmd.pio) RW (in module ppmd.access) Ry_set() (in module ppmd.coulomb.wigner) Rzyz_set() (in module ppmd.coulomb.wigner) Rzyz_set_2() (in module ppmd.coulomb.wigner) Rzyz_set_orig() (in module ppmd.coulomb.wigner)

S

ScalarArray (class in ppmd.data.scalar_array) scale() (ppmd.data.scalar_array.ScalarArray method) scatter_data_from() (ppmd.state.BaseMDState method) scatter_matrix() (in module ppmd.pairloop.neighbourlist) Schedule (class in ppmd.utility.high_method) schedule() (ppmd.utility.high_method.Schedule property) send_parent_to_halo() (in module ppmd.coulomb.octal) send_plain_to_parent() (in module ppmd.coulomb.octal) send_ranks (ppmd.pygcl.halo_exchange_3d.HaloExchange3D attribute) set() (ppmd.data.global_array.GlobalArrayClassic method) set_extent() (ppmd.domain.BaseDomainHalo method) set_state() (ppmd.domain.BoundaryTypePeriodic method) set_timestep() (ppmd.method.ListUpdateController method) set_v0() (ppmd.utility.high_method.VelocityAutoCorrelation method) setup() (ppmd.pairloop.neighbourlist_14cell.NeighbourListv2 method) (ppmd.pairloop.neighbourlist_27cell.NeighbourListNonN3 method) setup_callback_on_update() (ppmd.cell.CellList method) setup_pre_update() (ppmd.cell.CellList method) setup_update_tracking() (ppmd.cell.CellList method) shared_lib_flag() (ppmd.lib.compiler.Compiler property) shell_iterator() (in module ppmd.coulomb.octal) shell_width (ppmd.coulomb.ewald.EwaldOrthoganal attribute) simple_lib_creator() (in module ppmd.cuda.cuda_build) (in module ppmd.lib.build) size (ppmd.data.global_array.GlobalArrayClassic attribute) size() (ppmd.host.Array property) (ppmd.host.Matrix property) sort() (ppmd.cell.CellList method) (ppmd.plain_cell_list.PlainCellList method)

SphCoeffGen (class in ppmd.coulomb.sph_harm) spherical() (in module ppmd.coulomb.direct) (in module ppmd.coulomb.fmm_pbc) SphExpGen (class in ppmd.coulomb.sph_harm) SphGen (class in ppmd.coulomb.sph_harm) SphGenEphemeral (class in ppmd.coulomb.sph_harm) SphShellSum (class in ppmd.coulomb.fmm_pbc) SphSymbol (in module ppmd.coulomb.sph_harm) start() (ppmd.opt.SynchronizedTimer method) (ppmd.opt.Timer method) State (class in ppmd.state) StateHandler (class in ppmd.pairloop.state_handler) StateModifier (class in ppmd.state_modifier) StateModifierContext (class in ppmd.state_modifier) static_args() (ppmd.kernel.Kernel property) StaticArgStore (class in ppmd.access) stop() (ppmd.opt.SynchronizedTimer method) (ppmd.opt.Timer method) str_to_bool() (in module ppmd.config.config) string() (ppmd.opt.Code property) sub_sym() (ppmd.modules.dsl_kernel_symbols.DSLKernelSymSub method) SubCell (class in ppmd.pairloop.sub_cell) SubCellByCellOMP (class in ppmd.pairloop.sub_cellbycell_omp) SubCellList (class in ppmd.pairloop.sub_cell) sum() (ppmd.data.scalar_array.ScalarArray property) sum_npart_local() (ppmd.state.BaseMDState method) SymbolicPotential (class in ppmd.utility.potential.sym_potential) sync_view_to_data() (ppmd.data.particle_dat.ParticleDat method) SynchronizedTimer (class in ppmd.opt)

T

test_evaluate_python_lr() (ppmd.coulomb.ewald.EwaldOrthoganal method) test_evaluate_python_self() (ppmd.coulomb.ewald.EwaldOrthoganal method) test_evaluate_python_sr() (ppmd.coulomb.ewald.EwaldOrthoganal method) TestPotential1 (class in ppmd.utility.potential.c_potential) TestPotential2 (class in ppmd.utility.potential.c_potential) TestPotential3 (class in ppmd.utility.potential.c_potential) TestPotential4 (class in ppmd.utility.potential.c_potential) TestPotential4p (class in ppmd.utility.potential.c_potential) ThreadSpace (class in ppmd.host)

tick() (ppmd.utility.high_method.PercentagePrinter method) (ppmd.utility.high_method.Schedule method) time() (ppmd.modules.code_timer.LoopTimer property) (ppmd.opt.Timer method) Timer (class in ppmd.opt) timer1() (ppmd.utility.high_method.VelocityVerlet property) timer2() (ppmd.utility.high_method.VelocityVerlet property) total_num_particles() (ppmd.cell.CellList property) trigger_update() (ppmd.cell.CellList method) TypedDat (class in ppmd.data.particle_dat)

U

update() (ppmd.pairloop.neighbour_matrix_omp.NeighbourListOMP method) (ppmd.pairloop.neighbour_matrix_omp_sub.NeighbourListOMPSub method) (ppmd.pairloop.neighbourlist_14cell.NeighbourListv2 method) (ppmd.pairloop.neighbourlist_27cell.NeighbourListNonN3 method) (ppmd.utility.high_method.EnergyStore method)

update_if_required() (ppmd.pairloop.neighbour_matrix_omp.NeighbourListOMP method) (ppmd.pairloop.neighbourlist_27cell.NeighbourListNonN3 method)

V

values() (ppmd.access.DatArgStore method) variable() (ppmd.kernel.Reduction property) VelocityAutoCorrelation (class in ppmd.utility.high_method) VelocityVerlet (class in ppmd.utility.high_method) VelocityVerletAnderson (class in ppmd.utility.high_method) version() (ppmd.host.Array property) (ppmd.host.Matrix property)

version_id (ppmd.cell.CellList attribute) (ppmd.pairloop.neighbourlist_14cell.NeighbourListv2 attribute) (ppmd.pairloop.neighbourlist_27cell.NeighbourListNonN3 attribute) view() (ppmd.data.particle_dat.ParticleDat property) VLennardJones (class in ppmd.utility.potential.c_potential) VLennardJones2 (class in ppmd.utility.potential.c_potential) VLennardJonesNoU (class in ppmd.utility.potential.c_potential) volume() (ppmd.domain.BaseDomainHalo property)

W

wigner_d() (in module ppmd.coulomb.wigner) wigner_d_rec() (in module ppmd.coulomb.wigner) wrap_positions() (in module ppmd.utility.sanitise) WRITE (in module ppmd.access)

write() (ppmd.access.AccessType property) (ppmd.utility.high_method.ParticleTracker method) (ppmd.utility.high_method.WriteTrajectoryXYZ method) write_header() (in module ppmd.lib.build) WriteTrajectoryXYZ (class in ppmd.utility.high_method)

X

XYZ (class in ppmd.utility.xyz)

Y

yellow() (in module ppmd.coulomb.fmm) (in module ppmd.coulomb.fmm_pbc)

Z

zero() (ppmd.coulomb.octal.EntryData method) (ppmd.coulomb.octal.OctalDataTree method) (ppmd.data.particle_dat.ParticleDat method) (ppmd.host.Array method) (ppmd.host.Matrix method)