seamm_md_analysis

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