Index

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) 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)

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) charges() (seamm_md_analysis.io.MDData method) check() (in module seamm_md_analysis.requirements) check_md_flowchart() (in module seamm_md_analysis.step_support)

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_helfand_moments() (in module seamm_md_analysis.transport) conductivity_from_msd() (in module seamm_md_analysis.electric) creator (seamm_md_analysis.io.MDData property)

D

data (seamm_md_analysis.requirements.Provides attribute) detect_equilibration() (in module seamm_md_analysis.stats)

dielectric_constant() (in module seamm_md_analysis.electric) dipole_correlation() (in module seamm_md_analysis.electric) dt (seamm_md_analysis.io.TimeSeries property)

E

E (in module seamm_md_analysis.electric) EPS0 (in module seamm_md_analysis.electric)

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) fmt_err() (in module seamm_md_analysis.stats)

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)

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)

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.stats seamm_md_analysis.step_support seamm_md_analysis.transport seamm_md_analysis.units

moving_average() (in module seamm_md_analysis.correlate) msd_by_species() (in module seamm_md_analysis.transport)

N

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)

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

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) 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) 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)

S

sample_time (seamm_md_analysis.requirements.Need attribute) 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.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) slope (seamm_md_analysis.transport.LinearFit 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) statistical_inefficiency() (in module seamm_md_analysis.stats) stderr (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)

T

tau (seamm_md_analysis.transport.GreenKuboFit attribute) tau_err (seamm_md_analysis.transport.GreenKuboFit 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) 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)

universe() (seamm_md_analysis.io.MDData method)

V

value (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)

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)