Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y _ __getitem__() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) __init__() (amep.base.BaseDatabase method) (amep.base.BaseEvalData method) (amep.base.BaseEvaluation method) (amep.base.BaseField method) (amep.base.BaseFrame method) (amep.base.BaseFunction method) (amep.base.BaseReader method) (amep.base.BaseTrajectory method) (amep.evaluate.ClusterGrowth method) (amep.evaluate.ClusterSizeDist method) (amep.evaluate.Dist method) (amep.evaluate.EkinRot method) (amep.evaluate.EkinTot method) (amep.evaluate.EkinTrans method) (amep.evaluate.Function method) (amep.evaluate.HexOrderCor method) (amep.evaluate.LDdist method) (amep.evaluate.MSD method) (amep.evaluate.OACF method) (amep.evaluate.PCF2d method) (amep.evaluate.PCFangle method) (amep.evaluate.PosOrderCor method) (amep.evaluate.Psi6dist method) (amep.evaluate.RDF method) (amep.evaluate.SF2d method) (amep.evaluate.SFiso method) (amep.evaluate.SpatialVelCor method) (amep.evaluate.Tconf method) (amep.evaluate.TimeCor method) (amep.evaluate.Tkin method) (amep.evaluate.Tkin4 method) (amep.evaluate.Tosc method) (amep.evaluate.VACF method) (amep.evaluate.VelDist method) (amep.functions.ExGaussian method) (amep.functions.Fit method) (amep.functions.Gaussian method) (amep.functions.Gaussian2d method) (amep.functions.MaxwellBoltzmann method) (amep.functions.NormalizedGaussian method) (amep.functions.SkewGaussian method) (amep.reader.ContinuumReader method) (amep.reader.GROMACSReader method) (amep.reader.H5amepReader method) (amep.reader.HOOMDReader method) (amep.reader.LammpsReader method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) A acf() (in module amep.timecor) add() (amep.base.BaseDatabase method) add_author_info() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) add_colorbar() (in module amep.plot) add_data() (amep.base.BaseFrame method) add_field_info() (amep.trajectory.FieldTrajectory method) add_inset() (in module amep.plot) add_param() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) add_particle_info() (amep.trajectory.ParticleTrajectory method) add_script() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) add_software_info() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) amep.base module, [1] amep.cluster module, [1] amep.continuum module, [1] amep.evaluate module, [1] amep.functions module, [1] amep.load module, [1] amep.order module, [1] amep.pbc module, [1] amep.plot module, [1] amep.reader module, [1] amep.spatialcor module, [1] amep.statistics module, [1] amep.thermo module, [1] amep.timecor module, [1] amep.trajectory module, [1] amep.utils module, [1] amep_plot_defaults() (in module amep.plot) angmom() (amep.base.BaseFrame method) animate() (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) animate_trajectory() (in module amep.plot) args (amep.evaluate.TimeCor property) authors (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) average_func() (in module amep.utils) avg (amep.evaluate.ClusterGrowth property) (amep.evaluate.ClusterSizeDist property) (amep.evaluate.EkinRot property) (amep.evaluate.EkinTot property) (amep.evaluate.EkinTrans property) (amep.evaluate.Function property) (amep.evaluate.HexOrderCor property) (amep.evaluate.LDdist property) (amep.evaluate.MSD property) (amep.evaluate.OACF property) (amep.evaluate.PCF2d property) (amep.evaluate.PCFangle property) (amep.evaluate.PosOrderCor property) (amep.evaluate.Psi6dist property) (amep.evaluate.RDF property) (amep.evaluate.SF2d property) (amep.evaluate.SFiso property) (amep.evaluate.SpatialVelCor property) (amep.evaluate.Tconf property) (amep.evaluate.Tkin property) (amep.evaluate.Tkin4 property) (amep.evaluate.Tosc property) (amep.evaluate.VACF property) B BaseDatabase (class in amep.base) BaseEvalData (class in amep.base) BaseEvaluation (class in amep.base) BaseField (class in amep.base) BaseFrame (class in amep.base) BaseFunction (class in amep.base) BaseReader (class in amep.base) BaseTrajectory (class in amep.base) binder_cumulant() (in module amep.statistics) box (amep.base.BaseField property) (amep.base.BaseFrame property) box() (in module amep.plot) box_boundary() (in module amep.plot) C center (amep.base.BaseField property) (amep.base.BaseFrame property) center_of_mass() (in module amep.cluster) check_path() (in module amep.base) cluster_properties() (in module amep.continuum) ClusterGrowth (class in amep.evaluate) ClusterSizeDist (class in amep.evaluate) colored_line() (in module amep.plot) compute_parallel() (in module amep.utils) ContinuumReader (class in amep.reader) coords() (amep.base.BaseFrame method) coords_to_density() (in module amep.continuum) create_video() (in module amep.plot) D data() (amep.base.BaseField method) (amep.base.BaseFrame method) delete() (amep.base.BaseDatabase method) delete_author_info() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) delete_field_info() (amep.trajectory.FieldTrajectory method) delete_param() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) delete_particle_info() (amep.trajectory.ParticleTrajectory method) delete_script() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) delete_software_info() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) density() (amep.base.BaseFrame method) detect2peaks() (in module amep.utils) dim (amep.base.BaseField property) (amep.base.BaseFrame property) (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) dimension() (in module amep.utils) direction (amep.evaluate.OACF property) (amep.evaluate.VACF property) Dist (class in amep.evaluate) distance_matrix() (in module amep.pbc) distance_matrix_parallel() (in module amep.pbc) distances() (in module amep.pbc) distribution() (in module amep.statistics) domain_length() (in module amep.utils) dr2_wca() (in module amep.utils) dr_wca() (in module amep.utils) draw_arrow() (in module amep.plot) draw_box() (in module amep.plot) dt (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) E EkinRot (class in amep.evaluate) EkinTot (class in amep.evaluate) EkinTrans (class in amep.evaluate) envelope() (in module amep.utils) errors (amep.base.BaseFunction property) (amep.functions.ExGaussian property) (amep.functions.Fit property) (amep.functions.Gaussian property) (amep.functions.Gaussian2d property) (amep.functions.MaxwellBoltzmann property) (amep.functions.NormalizedGaussian property) (amep.functions.SkewGaussian property) evaluation() (in module amep.load) ExGaussian (class in amep.functions) F f() (amep.functions.ExGaussian method) (amep.functions.Gaussian method) (amep.functions.Gaussian2d method) (amep.functions.MaxwellBoltzmann method) (amep.functions.NormalizedGaussian method) (amep.functions.SkewGaussian method) field() (in module amep.plot) FieldTrajectory (class in amep.trajectory) FileError filename (amep.base.BaseReader property) (amep.reader.ContinuumReader property) (amep.reader.GROMACSReader property) (amep.reader.H5amepReader property) (amep.reader.HOOMDReader property) (amep.reader.LammpsReader property) find_pairs() (in module amep.pbc) Fit (class in amep.functions) fit() (amep.base.BaseFunction method) (amep.functions.ExGaussian method) (amep.functions.Fit method) (amep.functions.Gaussian method) (amep.functions.Gaussian2d method) (amep.functions.MaxwellBoltzmann method) (amep.functions.NormalizedGaussian method) (amep.functions.SkewGaussian method) fold() (in module amep.pbc) forces() (amep.base.BaseFrame method) format_axis() (in module amep.plot) frames (amep.evaluate.ClusterGrowth property) (amep.evaluate.ClusterSizeDist property) (amep.evaluate.Dist property) (amep.evaluate.EkinRot property) (amep.evaluate.EkinTot property) (amep.evaluate.EkinTrans property) (amep.evaluate.Function property) (amep.evaluate.HexOrderCor property) (amep.evaluate.LDdist property) (amep.evaluate.MSD property) (amep.evaluate.OACF property) (amep.evaluate.PCF2d property) (amep.evaluate.PCFangle property) (amep.evaluate.Psi6dist property) (amep.evaluate.RDF property) (amep.evaluate.SF2d property) (amep.evaluate.SFiso property) (amep.evaluate.SpatialVelCor property) (amep.evaluate.Tconf property) (amep.evaluate.TimeCor property) (amep.evaluate.Tkin property) (amep.evaluate.Tkin4 property) (amep.evaluate.Tosc property) (amep.evaluate.VACF property) (amep.evaluate.VelDist property) Function (class in amep.evaluate) G Gaussian (class in amep.functions) gaussian() (in module amep.functions) Gaussian2d (class in amep.functions) gaussian2d() (in module amep.functions) generate() (amep.base.BaseFunction method) (amep.functions.ExGaussian method) (amep.functions.Fit method) (amep.functions.Gaussian method) (amep.functions.Gaussian2d method) (amep.functions.MaxwellBoltzmann method) (amep.functions.NormalizedGaussian method) (amep.functions.SkewGaussian method) geometric_center() (in module amep.cluster) get_author_info() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) get_class_logger() (in module amep.base) get_field_info() (amep.trajectory.FieldTrajectory method) get_module_logger() (in module amep.base) get_particle_info() (amep.trajectory.ParticleTrajectory method) get_script() (amep.base.BaseTrajectory method) (amep.trajectory.FieldTrajectory method) (amep.trajectory.ParticleTrajectory method) gkde() (in module amep.continuum) grid (amep.base.BaseField property) GROMACSReader (class in amep.reader) group_jobs() (in module amep.utils) gyration_tensor() (in module amep.cluster) H H5amepReader (class in amep.reader) hde() (in module amep.continuum) HexOrderCor (class in amep.evaluate) histogram2d() (in module amep.statistics) HOOMDReader (class in amep.reader) I identify() (in module amep.cluster) identify_clusters() (in module amep.continuum) ids() (amep.base.BaseFrame method) in_box() (in module amep.utils) in_circle() (in module amep.utils) indices (amep.evaluate.ClusterGrowth property) (amep.evaluate.ClusterSizeDist property) (amep.evaluate.Dist property) (amep.evaluate.EkinRot property) (amep.evaluate.EkinTot property) (amep.evaluate.EkinTrans property) (amep.evaluate.Function property) (amep.evaluate.HexOrderCor property) (amep.evaluate.LDdist property) (amep.evaluate.MSD property) (amep.evaluate.OACF property) (amep.evaluate.PCF2d property) (amep.evaluate.PCFangle property) (amep.evaluate.Psi6dist property) (amep.evaluate.RDF property) (amep.evaluate.SF2d property) (amep.evaluate.SFiso property) (amep.evaluate.SpatialVelCor property) (amep.evaluate.Tconf property) (amep.evaluate.TimeCor property) (amep.evaluate.Tkin property) (amep.evaluate.Tkin4 property) (amep.evaluate.Tosc property) (amep.evaluate.VACF property) (amep.evaluate.VelDist property) inertia_tensor() (in module amep.cluster) info (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) isf() (in module amep.timecor) K k0 (amep.evaluate.PosOrderCor property) k_nearest_neighbors() (in module amep.order) kdtree() (in module amep.pbc) keys (amep.base.BaseField property) (amep.base.BaseFrame property) keys() (amep.base.BaseEvaluation method) (amep.evaluate.ClusterGrowth method) (amep.evaluate.ClusterSizeDist method) (amep.evaluate.Dist method) (amep.evaluate.EkinRot method) (amep.evaluate.EkinTot method) (amep.evaluate.EkinTrans method) (amep.evaluate.Function method) (amep.evaluate.HexOrderCor method) (amep.evaluate.LDdist method) (amep.evaluate.MSD method) (amep.evaluate.OACF method) (amep.evaluate.PCF2d method) (amep.evaluate.PCFangle method) (amep.evaluate.PosOrderCor method) (amep.evaluate.Psi6dist method) (amep.evaluate.RDF method) (amep.evaluate.SF2d method) (amep.evaluate.SFiso method) (amep.evaluate.SpatialVelCor method) (amep.evaluate.Tconf method) (amep.evaluate.TimeCor method) (amep.evaluate.Tkin method) (amep.evaluate.Tkin4 method) (amep.evaluate.VACF method) (amep.evaluate.VelDist method) kintemp() (in module amep.thermo) kpeaks() (in module amep.utils) L LammpsReader (class in amep.reader) ld (amep.evaluate.LDdist property) LDdist (class in amep.evaluate) linear_extension() (in module amep.cluster) linear_mappable() (in module amep.plot) local_mass_density() (in module amep.order) local_number_density() (in module amep.order) local_packing_fraction() (in module amep.order) log_indices() (in module amep.utils) M mass() (amep.base.BaseFrame method) masses() (in module amep.cluster) matplotlib_plot_defaults() (in module amep.plot) MaxwellBoltzmann (class in amep.functions) mesh_to_coords() (in module amep.utils) mirror_points() (in module amep.pbc) module amep.base, [1] amep.cluster, [1] amep.continuum, [1] amep.evaluate, [1] amep.functions, [1] amep.load, [1] amep.order, [1] amep.pbc, [1] amep.plot, [1] amep.reader, [1] amep.spatialcor, [1] amep.statistics, [1] amep.thermo, [1] amep.timecor, [1] amep.trajectory, [1] amep.utils, [1] MSD (class in amep.evaluate) msd() (in module amep.timecor) msd_from_vacf() (in module amep.utils) N n() (amep.base.BaseFrame method) nearest_neighbors() (in module amep.order) new() (in module amep.plot) next_neighbors() (in module amep.order) nframes (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) nojump() (amep.trajectory.ParticleTrajectory method) nojump_coords() (amep.base.BaseFrame method) NormalizedGaussian (class in amep.functions) nth (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) O OACF (class in amep.evaluate) omegas() (amep.base.BaseFrame method) optimal_chunksize() (in module amep.utils) orientations() (amep.base.BaseFrame method) P params (amep.base.BaseFunction property) (amep.base.BaseTrajectory property) (amep.functions.ExGaussian property) (amep.functions.Fit property) (amep.functions.Gaussian property) (amep.functions.Gaussian2d property) (amep.functions.MaxwellBoltzmann property) (amep.functions.NormalizedGaussian property) (amep.functions.SkewGaussian property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) particles() (in module amep.plot) ParticleTrajectory (class in amep.trajectory) pbc_diff() (in module amep.pbc) pbc_diff_rect() (in module amep.pbc) pbc_points() (in module amep.pbc) PCF2d (class in amep.evaluate) pcf2d() (in module amep.spatialcor) pcf_angle() (in module amep.spatialcor) PCFangle (class in amep.evaluate) PosOrderCor (class in amep.evaluate) profile() (in module amep.utils) psi6 (amep.evaluate.Psi6dist property) Psi6dist (class in amep.evaluate) psi_k() (in module amep.order) ptype (amep.evaluate.MSD property) (amep.evaluate.OACF property) (amep.evaluate.TimeCor property) (amep.evaluate.VACF property) ptypes (amep.base.BaseFrame property) Q q (amep.evaluate.SFiso property) quaternion_conjugate() (in module amep.utils) quaternion_multiply() (in module amep.utils) quaternion_rotate() (in module amep.utils) qx (amep.evaluate.SF2d property) qy (amep.evaluate.SF2d property) R r (amep.evaluate.HexOrderCor property) (amep.evaluate.PCFangle property) (amep.evaluate.PosOrderCor property) (amep.evaluate.RDF property) (amep.evaluate.SpatialVelCor property) radius() (amep.base.BaseFrame method) radius_of_gyration() (in module amep.cluster) RDF (class in amep.evaluate) rdf() (in module amep.spatialcor) results (amep.base.BaseFunction property) (amep.functions.ExGaussian property) (amep.functions.Fit property) (amep.functions.Gaussian property) (amep.functions.Gaussian2d property) (amep.functions.MaxwellBoltzmann property) (amep.functions.NormalizedGaussian property) (amep.functions.SkewGaussian property) rfft() (in module amep.utils) rotate_coords() (in module amep.utils) rotation() (in module amep.utils) rotational_kinetic_energy() (in module amep.thermo) runningmean() (in module amep.utils) runningmean2d() (in module amep.utils) S save() (amep.base.BaseEvaluation method) (amep.evaluate.ClusterGrowth method) (amep.evaluate.ClusterSizeDist method) (amep.evaluate.Dist method) (amep.evaluate.EkinRot method) (amep.evaluate.EkinTot method) (amep.evaluate.EkinTrans method) (amep.evaluate.Function method) (amep.evaluate.HexOrderCor method) (amep.evaluate.LDdist method) (amep.evaluate.MSD method) (amep.evaluate.OACF method) (amep.evaluate.PCF2d method) (amep.evaluate.PCFangle method) (amep.evaluate.PosOrderCor method) (amep.evaluate.Psi6dist method) (amep.evaluate.RDF method) (amep.evaluate.SF2d method) (amep.evaluate.SFiso method) (amep.evaluate.SpatialVelCor method) (amep.evaluate.Tconf method) (amep.evaluate.TimeCor method) (amep.evaluate.Tkin method) (amep.evaluate.Tkin4 method) (amep.evaluate.VACF method) (amep.evaluate.VelDist method) savedir (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) scripts (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) segmented_mean() (in module amep.utils) segmented_mean2d() (in module amep.utils) set_locators() (in module amep.plot) SF2d (class in amep.evaluate) sf2d() (in module amep.continuum) (in module amep.spatialcor) SFiso (class in amep.evaluate) sfiso() (in module amep.spatialcor) sizes (amep.evaluate.ClusterSizeDist property) sizes() (in module amep.cluster) SkewGaussian (class in amep.functions) software (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) spatialcor() (in module amep.spatialcor) SpatialVelCor (class in amep.evaluate) spectrum() (in module amep.utils) sq_from_gr() (in module amep.utils) sq_from_sf2d() (in module amep.utils) start (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) step (amep.base.BaseField property) (amep.base.BaseFrame property) steps (amep.base.BaseReader property) (amep.base.BaseTrajectory property) (amep.reader.ContinuumReader property) (amep.reader.GROMACSReader property) (amep.reader.H5amepReader property) (amep.reader.HOOMDReader property) (amep.reader.LammpsReader property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) stop (amep.base.BaseTrajectory property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) style() (in module amep.plot) T Tconf (class in amep.evaluate) Tconf() (in module amep.thermo) theta (amep.evaluate.PCFangle property) time (amep.base.BaseField property) (amep.base.BaseFrame property) TimeCor (class in amep.evaluate) times (amep.base.BaseReader property) (amep.base.BaseTrajectory property) (amep.evaluate.ClusterGrowth property) (amep.evaluate.ClusterSizeDist property) (amep.evaluate.Dist property) (amep.evaluate.EkinRot property) (amep.evaluate.EkinTot property) (amep.evaluate.EkinTrans property) (amep.evaluate.Function property) (amep.evaluate.HexOrderCor property) (amep.evaluate.LDdist property) (amep.evaluate.MSD property) (amep.evaluate.OACF property) (amep.evaluate.PCF2d property) (amep.evaluate.PCFangle property) (amep.evaluate.Psi6dist property) (amep.evaluate.RDF property) (amep.evaluate.SF2d property) (amep.evaluate.SFiso property) (amep.evaluate.SpatialVelCor property) (amep.evaluate.Tconf property) (amep.evaluate.TimeCor property) (amep.evaluate.Tkin property) (amep.evaluate.Tkin4 property) (amep.evaluate.Tosc property) (amep.evaluate.VACF property) (amep.evaluate.VelDist property) (amep.reader.ContinuumReader property) (amep.reader.GROMACSReader property) (amep.reader.H5amepReader property) (amep.reader.HOOMDReader property) (amep.reader.LammpsReader property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) Tkin (class in amep.evaluate) Tkin() (in module amep.thermo) Tkin4 (class in amep.evaluate) Tkin4() (in module amep.thermo) to_latex() (in module amep.plot) torque() (amep.base.BaseFrame method) Tosc (class in amep.evaluate) Tosc() (in module amep.thermo) total_kinetic_energy() (in module amep.thermo) traj() (in module amep.load) traj_slice() (in module amep.utils) translational_kinetic_energy() (in module amep.thermo) type (amep.base.BaseTrajectory property) (amep.reader.H5amepReader property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) types() (amep.base.BaseFrame method) U unit_vector_2D() (in module amep.utils) unit_vector_3D() (in module amep.utils) unwrapped_coords() (amep.base.BaseFrame method) upper_triangle() (in module amep.utils) V v (amep.evaluate.VelDist property) v2 (amep.evaluate.VelDist property) v2dist (amep.evaluate.VelDist property) VACF (class in amep.evaluate) vdist (amep.evaluate.VelDist property) VelDist (class in amep.evaluate) velocities() (amep.base.BaseFrame method) version (amep.base.BaseTrajectory property) (amep.reader.H5amepReader property) (amep.trajectory.FieldTrajectory property) (amep.trajectory.ParticleTrajectory property) volume (amep.base.BaseField property) (amep.base.BaseFrame property) voronoi() (in module amep.order) (in module amep.plot) voronoi_density() (in module amep.order) vx (amep.evaluate.VelDist property) vxdist (amep.evaluate.VelDist property) vy (amep.evaluate.VelDist property) vydist (amep.evaluate.VelDist property) vz (amep.evaluate.VelDist property) vzdist (amep.evaluate.VelDist property) W wca() (in module amep.utils) weighted_runningmean() (in module amep.utils) weighted_runningmean2d() (in module amep.utils) X x (amep.evaluate.Dist property) (amep.evaluate.PCF2d property) xdist (amep.evaluate.Dist property) Y y (amep.evaluate.PCF2d property)
