Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y A a (seamm_md_analysis.transport.GreenKuboFit attribute) a_err (seamm_md_analysis.transport.GreenKuboFit attribute) abort() (seamm_md_analysis.h5md.H5MDWriter method) acf_err() (in module seamm_md_analysis.correlate) add_component_traces() (in module seamm_md_analysis.plots) add_helfand_trace() (in module seamm_md_analysis.plots) add_msd_trace() (in module seamm_md_analysis.plots) agree (seamm_md_analysis.stats.ComponentCheck attribute) AMU_PER_A3_IN_G_PER_ML (in module seamm_md_analysis.state) ANISOTROPIC_FIXES (in module seamm_md_analysis.state) attrs (seamm_md_analysis.io.TimeSeries attribute) autocorrelation_functions() (in module seamm_md_analysis.correlate) average_window (seamm_md_analysis.io.TimeSeries attribute) axb() (in module seamm_md_analysis.transport) B block_average() (in module seamm_md_analysis.stats) box() (seamm_md_analysis.io.MDData method) box_appender() (seamm_md_analysis.h5md.H5MDWriter method) bulk_modulus (seamm_md_analysis.state.State attribute) bulk_modulus() (in module seamm_md_analysis.state) C ccf_err() (in module seamm_md_analysis.correlate) ccovf() (in module seamm_md_analysis.correlate) cell() (seamm_md_analysis.io.MDData method) cell_dipole() (in module seamm_md_analysis.electric) cell_widths() (in module seamm_md_analysis.step_support) charges() (seamm_md_analysis.io.MDData method) check() (in module seamm_md_analysis.requirements) check_md_flowchart() (in module seamm_md_analysis.step_support) chi2 (seamm_md_analysis.stats.ComponentCheck attribute) ci95 (seamm_md_analysis.stats.Estimate property) classify_molecules() (in module seamm_md_analysis.electric) close() (seamm_md_analysis.h5md.H5MDWriter method) (seamm_md_analysis.io.MDData method) collective_helfand_moments() (in module seamm_md_analysis.transport) collective_msd() (in module seamm_md_analysis.electric) component_check() (in module seamm_md_analysis.stats) component_helfand_moments() (in module seamm_md_analysis.transport) ComponentCheck (class in seamm_md_analysis.stats) conductivity_from_msd() (in module seamm_md_analysis.electric) creator (seamm_md_analysis.io.MDData property) D data (seamm_md_analysis.requirements.Provides attribute) density (seamm_md_analysis.state.RunState attribute) (seamm_md_analysis.state.State attribute) describe_error() (seamm_md_analysis.stats.Estimate method) detect_equilibration() (in module seamm_md_analysis.stats) dielectric_constant() (in module seamm_md_analysis.electric) dipole_correlation() (in module seamm_md_analysis.electric) dof (seamm_md_analysis.stats.ComponentCheck attribute) dt (seamm_md_analysis.io.TimeSeries property) dynamics (seamm_md_analysis.requirements.Requirements attribute) E E (in module seamm_md_analysis.electric) each_iteration (in module seamm_md_analysis.step_support) effective_correlation_functions() (in module seamm_md_analysis.transport) ensemble (seamm_md_analysis.state.RunState attribute) (seamm_md_analysis.state.State attribute) EPS0 (in module seamm_md_analysis.electric) equilibrium_density (seamm_md_analysis.state.State attribute) Estimate (class in seamm_md_analysis.stats) exp_1() (in module seamm_md_analysis.transport) exp_2() (in module seamm_md_analysis.transport) F first (seamm_md_analysis.io.MDData property) fit_green_kubo_integral() (in module seamm_md_analysis.transport) fit_helfand_moment() (in module seamm_md_analysis.transport) fit_slope() (in module seamm_md_analysis.transport) flux_correlation_matrices() (in module seamm_md_analysis.transport) flux_helfand_matrices() (in module seamm_md_analysis.transport) fmt_err() (in module seamm_md_analysis.stats) formatted() (seamm_md_analysis.stats.Estimate method) from_samples() (seamm_md_analysis.stats.Estimate class method) G GreenKuboFit (class in seamm_md_analysis.transport) H H5MDWriter (class in seamm_md_analysis.h5md) has_observable() (seamm_md_analysis.io.MDData method) has_particles() (seamm_md_analysis.io.MDData method) helfand_slope() (in module seamm_md_analysis.transport) I ids() (seamm_md_analysis.io.MDData method) Interval (class in seamm_md_analysis.requirements) interval() (seamm_md_analysis.requirements.Provides method) ion_charge_scale (seamm_md_analysis.io.MDData property) is_cubic() (in module seamm_md_analysis.state) isotropic_average() (in module seamm_md_analysis.stats) isotropy() (in module seamm_md_analysis.state) iter_dump_frames() (in module seamm_md_analysis.legacy) iter_frames() (seamm_md_analysis.io.MDData method) iter_vector_frames() (in module seamm_md_analysis.legacy) K KB (in module seamm_md_analysis.electric) KB_ATM_A3 (in module seamm_md_analysis.state) kind (seamm_md_analysis.io.TimeSeries attribute) L lammps_box_to_cell() (in module seamm_md_analysis.legacy) LinearFit (class in seamm_md_analysis.transport) M masses() (seamm_md_analysis.io.MDData method) max_steps (seamm_md_analysis.requirements.Need attribute) max_time (seamm_md_analysis.requirements.Need attribute) md_inputs() (in module seamm_md_analysis.step_support) md_run_sources (in module seamm_md_analysis.io) md_substeps() (in module seamm_md_analysis.step_support) MDData (class in seamm_md_analysis.io) mean_and_stderr() (in module seamm_md_analysis.stats) mean_and_stderr_correlated() (in module seamm_md_analysis.stats) module seamm_md_analysis seamm_md_analysis.correlate seamm_md_analysis.electric seamm_md_analysis.h5md seamm_md_analysis.io seamm_md_analysis.legacy seamm_md_analysis.plots seamm_md_analysis.requirements seamm_md_analysis.state seamm_md_analysis.stats seamm_md_analysis.step_support seamm_md_analysis.transport seamm_md_analysis.units molecule_extents() (in module seamm_md_analysis.step_support) moving_average() (in module seamm_md_analysis.correlate) msd_by_species() (in module seamm_md_analysis.transport) multicomponent_correlation_functions() (in module seamm_md_analysis.transport) multicomponent_helfand_moments() (in module seamm_md_analysis.transport) N n (seamm_md_analysis.stats.Estimate attribute) n_frames() (seamm_md_analysis.io.MDData method) name (seamm_md_analysis.io.TimeSeries attribute) names (seamm_md_analysis.requirements.Need attribute) Need (class in seamm_md_analysis.requirements) needs (seamm_md_analysis.requirements.Requirements attribute) nernst_einstein() (in module seamm_md_analysis.electric) NOT_CANONICAL (in module seamm_md_analysis.step_support) notes (seamm_md_analysis.state.State attribute) npt_reference() (in module seamm_md_analysis.step_support) O observable() (seamm_md_analysis.h5md.H5MDWriter method) (seamm_md_analysis.io.MDData method) observables() (seamm_md_analysis.io.MDData method) open_md() (in module seamm_md_analysis.io) P p (seamm_md_analysis.stats.ComponentCheck attribute) parameters (seamm_md_analysis.io.MDData property) parameters() (seamm_md_analysis.h5md.H5MDWriter method) particle_appender() (seamm_md_analysis.h5md.H5MDWriter method) particle_groups() (seamm_md_analysis.io.MDData method) particle_series() (seamm_md_analysis.io.MDData method) particles() (seamm_md_analysis.h5md.H5MDWriter method) periodic (seamm_md_analysis.io.MDData property) (seamm_md_analysis.requirements.Requirements attribute) plot_components() (in module seamm_md_analysis.plots) plot_correlation_functions() (in module seamm_md_analysis.plots) plot_GK_integrals() (in module seamm_md_analysis.plots) plot_helfand_moments() (in module seamm_md_analysis.plots) plot_helfand_slopes() (in module seamm_md_analysis.plots) preceding_viscosity() (in module seamm_md_analysis.step_support) pressure (seamm_md_analysis.state.RunState attribute) (seamm_md_analysis.state.State attribute) print_details() (in module seamm_md_analysis.step_support) provenance (seamm_md_analysis.io.MDData property) provenance() (seamm_md_analysis.h5md.H5MDWriter method) Provides (class in seamm_md_analysis.requirements) publish_viscosity() (in module seamm_md_analysis.step_support) R read_dump_trajectory() (in module seamm_md_analysis.legacy) read_files (in module seamm_md_analysis.step_support) read_trajectory() (in module seamm_md_analysis.legacy) read_vector_trajectory() (in module seamm_md_analysis.legacy) report_state() (in module seamm_md_analysis.step_support) request_sampling() (in module seamm_md_analysis.step_support) Requirements (class in seamm_md_analysis.requirements) run_own_md (in module seamm_md_analysis.step_support) run_state() (in module seamm_md_analysis.state) RunState (class in seamm_md_analysis.state) S sample_time (seamm_md_analysis.requirements.Need attribute) schur_complement() (in module seamm_md_analysis.transport) seamm_md_analysis module seamm_md_analysis.correlate module seamm_md_analysis.electric module seamm_md_analysis.h5md module seamm_md_analysis.io module seamm_md_analysis.legacy module seamm_md_analysis.plots module seamm_md_analysis.requirements module seamm_md_analysis.state module seamm_md_analysis.stats module seamm_md_analysis.step_support module seamm_md_analysis.transport module seamm_md_analysis.units module select_md_runs() (in module seamm_md_analysis.io) SHEAR_COMPONENTS (in module seamm_md_analysis.transport) shear_labels (in module seamm_md_analysis.plots) shear_stress_components() (in module seamm_md_analysis.transport) size_warnings() (in module seamm_md_analysis.step_support) slope (seamm_md_analysis.transport.LinearFit attribute) source (seamm_md_analysis.stats.Estimate attribute) source_choices (in module seamm_md_analysis.step_support) source_parameters() (in module seamm_md_analysis.step_support) species() (seamm_md_analysis.io.MDData method) species_helfand_moments() (in module seamm_md_analysis.transport) squared_displacement_sums() (in module seamm_md_analysis.transport) standard_observables (in module seamm_md_analysis.h5md) State (class in seamm_md_analysis.state) state_data() (in module seamm_md_analysis.step_support) state_of_runs() (in module seamm_md_analysis.step_support) STATE_PARAMETERS (in module seamm_md_analysis.step_support) STATE_REPORTED (in module seamm_md_analysis.step_support) state_results (in module seamm_md_analysis.step_support) state_table() (in module seamm_md_analysis.state) statistical_inefficiency() (in module seamm_md_analysis.stats) stderr (seamm_md_analysis.stats.Estimate attribute) (seamm_md_analysis.transport.GreenKuboFit attribute) (seamm_md_analysis.transport.LinearFit attribute) step (seamm_md_analysis.requirements.Provides attribute) steps (seamm_md_analysis.io.TimeSeries attribute) (seamm_md_analysis.requirements.Interval attribute) STOCHASTIC (in module seamm_md_analysis.step_support) summarize_state() (in module seamm_md_analysis.state) T t_factor() (in module seamm_md_analysis.stats) target_pressure (seamm_md_analysis.state.RunState attribute) (seamm_md_analysis.state.State attribute) tau (seamm_md_analysis.transport.GreenKuboFit attribute) tau_err (seamm_md_analysis.transport.GreenKuboFit attribute) temperature (seamm_md_analysis.state.RunState attribute) (seamm_md_analysis.state.State attribute) TENSOR_COMPONENTS (in module seamm_md_analysis.correlate) tensor_correlation_functions() (in module seamm_md_analysis.correlate) tensor_labels (in module seamm_md_analysis.plots) text (seamm_md_analysis.stats.ComponentCheck attribute) time (seamm_md_analysis.requirements.Interval attribute) time_units (seamm_md_analysis.io.TimeSeries attribute) times (seamm_md_analysis.io.TimeSeries attribute) TimeSeries (class in seamm_md_analysis.io) timestep (seamm_md_analysis.requirements.Provides attribute) to() (seamm_md_analysis.io.TimeSeries method) to_h5md() (in module seamm_md_analysis.units) to_pint() (in module seamm_md_analysis.units) U units (seamm_md_analysis.io.TimeSeries attribute) (seamm_md_analysis.stats.Estimate attribute) universe() (seamm_md_analysis.io.MDData method) V value (seamm_md_analysis.stats.Estimate attribute) (seamm_md_analysis.transport.GreenKuboFit attribute) values (seamm_md_analysis.io.TimeSeries attribute) vector_labels (in module seamm_md_analysis.plots) viscosity_variable (in module seamm_md_analysis.step_support) volume (seamm_md_analysis.state.RunState attribute) (seamm_md_analysis.state.State attribute) W why (seamm_md_analysis.requirements.Need attribute) windowed_displacement_products() (in module seamm_md_analysis.transport) X xs (seamm_md_analysis.transport.GreenKuboFit attribute) (seamm_md_analysis.transport.LinearFit attribute) Y yeh_hummer_correction() (in module seamm_md_analysis.transport) YEH_HUMMER_XI (in module seamm_md_analysis.transport) ys (seamm_md_analysis.transport.GreenKuboFit attribute) (seamm_md_analysis.transport.LinearFit attribute)