Index

A

A() (kbkit.kbi.thermodynamics.KBThermo method) activity_metadata (kbkit.kbi.thermodynamics.KBThermo property) ActivityCoefficientResult (class in kbkit.schema.activity_metadata) ActivityMetadata (class in kbkit.schema.activity_metadata)

add_kbi() (kbkit.kbi.integrator.KBIntegrator method) add_kbi_value() (kbkit.kbi.integrator.KBIntegrator method) add_lkbi() (kbkit.kbi.integrator.KBIntegrator method) add_lkbi_fit() (kbkit.kbi.integrator.KBIntegrator method) available_properties() (kbkit.io.energy.EnergyParser method)

B

B() (kbkit.kbi.thermodynamics.KBThermo method)

box_volume (kbkit.io.topology.TopologyParser property) by_types (kbkit.schema.activity_metadata.ActivityMetadata property)

C

calculator (kbkit.api.pipeline.Pipeline property) compute_geometric_extrapolation() (kbkit.kbi.integrator.KBIntegrator method) compute_hr() (kbkit.kbi.integrator.KBIntegrator method)

compute_kbi() (kbkit.kbi.integrator.KBIntegrator method) compute_running_kbi() (kbkit.kbi.integrator.KBIntegrator method) configurational_enthalpy() (kbkit.io.energy.EnergyParser method)

D

data (kbkit.io.energy.EnergyParser property) DEFAULT_UNITS (kbkit.io.energy.EnergyParser attribute) delta_ij (kbkit.kbi.thermodynamics.KBThermo property)

det_H() (kbkit.kbi.thermodynamics.KBThermo method) dlngamma_dxi() (kbkit.kbi.thermodynamics.KBThermo method) dmu_dxi() (kbkit.kbi.thermodynamics.KBThermo method)

E

electrolyte_basis (kbkit.systems.collection.SystemCollection property) electrolyte_kbi() (kbkit.kbi.calculator.KBICalculator method) electrolyte_molecules (kbkit.systems.collection.SystemCollection property) electrolyte_x (kbkit.systems.collection.SystemCollection property) electron_count (kbkit.io.topology.TopologyParser property)

energy (kbkit.systems.properties.SystemProperties property) EnergyFormat (class in kbkit.io.energy) EnergyParser (class in kbkit.io.energy) excess_property() (kbkit.systems.collection.SystemCollection method) extract_molecules() (kbkit.io.rdf.RdfParser static method) extract_molecules_from_top() (kbkit.io.topology.TopologyParser static method)

F

FLUCT_PROPS (kbkit.io.energy.EnergyParser attribute) fn (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute)

from_collection() (kbkit.visualization.timeseries.TimeseriesPlotter class method) from_rdf() (kbkit.kbi.integrator.KBIntegrator class method)

G

g_ex() (kbkit.kbi.thermodynamics.KBThermo method) g_id() (kbkit.kbi.thermodynamics.KBThermo method) g_mix() (kbkit.kbi.thermodynamics.KBThermo method) Gamma() (kbkit.kbi.thermodynamics.KBThermo method) geometric_extrapolation_result (kbkit.kbi.integrator.KBIntegrator property) geometric_weight() (kbkit.kbi.integrator.KBIntegrator method) get() (kbkit.io.energy.EnergyParser method) (kbkit.schema.activity_metadata.ActivityMetadata method) (kbkit.systems.collection.SystemCollection method) (kbkit.systems.properties.SystemProperties method)

get_mol_index() (kbkit.systems.collection.SystemCollection method) get_units() (kbkit.systems.collection.SystemCollection method) gr_vdv (kbkit.kbi.integrator.KBIntegrator property) GROMACS (kbkit.io.energy.EnergyFormat attribute) (kbkit.io.topology.TopologyFormat attribute) GROMACS_UNITS (kbkit.io.energy.EnergyParser attribute)

H

H() (kbkit.kbi.thermodynamics.KBThermo method) h_mix() (kbkit.kbi.thermodynamics.KBThermo method) has_all_required_pures() (kbkit.systems.collection.SystemCollection method) has_fn (kbkit.schema.activity_metadata.ActivityCoefficientResult property)

has_rdf() (kbkit.schema.system_metadata.SystemMetadata method) heat_capacity_cp() (kbkit.io.energy.EnergyParser method) heat_capacity_cv() (kbkit.io.energy.EnergyParser method) hr (kbkit.kbi.integrator.KBIntegrator property)

I

i0() (kbkit.kbi.thermodynamics.KBThermo method) i0_kappa() (kbkit.kbi.thermodynamics.KBThermo method) i0_p() (kbkit.kbi.thermodynamics.KBThermo method) i0_x() (kbkit.kbi.thermodynamics.KBThermo method)

i0_xp() (kbkit.kbi.thermodynamics.KBThermo method) ideal_property() (kbkit.systems.collection.SystemCollection method) is_pure() (kbkit.schema.system_metadata.SystemMetadata method) isothermal_compressibility() (kbkit.io.energy.EnergyParser method) (kbkit.kbi.thermodynamics.KBThermo method)

K

kbi (kbkit.kbi.integrator.KBIntegrator property) kbi() (kbkit.kbi.calculator.KBICalculator method) (kbkit.kbi.thermodynamics.KBThermo method) kbi_plotter (kbkit.api.pipeline.Pipeline property) kbi_plotter() (kbkit.kbi.calculator.KBICalculator method) kbi_res (kbkit.api.pipeline.Pipeline property) KBIAnalysisPlotter (class in kbkit.visualization.kbi) KBICalculator (class in kbkit.kbi.calculator) KBIntegrator (class in kbkit.kbi.integrator) kbkit.api.pipeline module kbkit.io.energy module kbkit.io.rdf module kbkit.io.topology module kbkit.kbi.calculator module kbkit.kbi.integrator module

kbkit.kbi.thermodynamics module kbkit.schema.activity_metadata module kbkit.schema.property_result module kbkit.schema.system_metadata module kbkit.systems.collection module kbkit.systems.properties module kbkit.visualization.kbi module kbkit.visualization.thermo module kbkit.visualization.timeseries module KBThermo (class in kbkit.kbi.thermodynamics) kind (kbkit.schema.system_metadata.SystemMetadata attribute)

L

LAMMPS (kbkit.io.energy.EnergyFormat attribute) (kbkit.io.topology.TopologyFormat attribute) LAMMPS_to_GMX (kbkit.io.energy.EnergyParser attribute)

LAMMPS_UNITS (kbkit.io.energy.EnergyParser attribute) lngamma() (kbkit.kbi.thermodynamics.KBThermo method) load() (kbkit.systems.collection.SystemCollection class method)

M

M() (kbkit.kbi.thermodynamics.KBThermo method) make_figures() (kbkit.api.pipeline.Pipeline method) (kbkit.visualization.thermo.ThermoPlotter method) metadata (kbkit.schema.property_result.PropertyResult attribute) mixtures (kbkit.systems.collection.SystemCollection property) module kbkit.api.pipeline kbkit.io.energy kbkit.io.rdf kbkit.io.topology kbkit.kbi.calculator kbkit.kbi.integrator kbkit.kbi.thermodynamics kbkit.schema.activity_metadata kbkit.schema.property_result kbkit.schema.system_metadata kbkit.systems.collection kbkit.systems.properties kbkit.visualization.kbi kbkit.visualization.thermo kbkit.visualization.timeseries

mol (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) molar_enthalpy() (kbkit.io.energy.EnergyParser method) molar_volume() (kbkit.io.energy.EnergyParser method) (kbkit.kbi.thermodynamics.KBThermo method) molecule_count (kbkit.io.topology.TopologyParser property) molecules (kbkit.io.topology.TopologyParser property) (kbkit.systems.collection.SystemCollection property)

N

n_i (kbkit.systems.collection.SystemCollection property) n_sys (kbkit.systems.collection.SystemCollection property)

name (kbkit.schema.property_result.PropertyResult attribute) (kbkit.schema.system_metadata.SystemMetadata attribute) nu (kbkit.systems.collection.SystemCollection property)

P

path (kbkit.schema.system_metadata.SystemMetadata attribute) Pipeline (class in kbkit.api.pipeline) plot() (kbkit.visualization.thermo.ThermoPlotter method) (kbkit.visualization.timeseries.TimeseriesPlotter method) plot_activity_coef_deriv_fits() (kbkit.visualization.thermo.ThermoPlotter method) plot_binary_mixing() (kbkit.visualization.thermo.ThermoPlotter method) plot_composition() (kbkit.visualization.kbi.KBIAnalysisPlotter method) plot_kbi() (kbkit.kbi.integrator.KBIntegrator method) plot_kbi_compare() (kbkit.kbi.integrator.KBIntegrator method) plot_kbi_compare_extrapolation() (kbkit.kbi.integrator.KBIntegrator method) plot_kbi_extrapolation() (kbkit.kbi.integrator.KBIntegrator method)

plot_property() (kbkit.visualization.thermo.ThermoPlotter method) plot_property_ternary() (kbkit.visualization.thermo.ThermoPlotter method) plot_rkbis() (kbkit.visualization.kbi.KBIAnalysisPlotter method) plot_ternary() (kbkit.visualization.thermo.ThermoPlotter method) plotRDF() (kbkit.io.rdf.RdfParser method) plotter() (kbkit.kbi.thermodynamics.KBThermo method) property_type (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) (kbkit.schema.property_result.PropertyResult attribute) PropertyResult (class in kbkit.schema.property_result) props (kbkit.schema.system_metadata.SystemMetadata attribute) pure_property() (kbkit.systems.collection.SystemCollection method) pures (kbkit.systems.collection.SystemCollection property)

R

R() (kbkit.kbi.thermodynamics.KBThermo method) rdf_path (kbkit.schema.system_metadata.SystemMetadata attribute) RdfParser (class in kbkit.io.rdf) residue_counts (kbkit.systems.collection.SystemCollection property) residue_kbi() (kbkit.kbi.calculator.KBICalculator method) residue_molecules (kbkit.systems.collection.SystemCollection property) residue_x (kbkit.systems.collection.SystemCollection property)

results (kbkit.api.pipeline.Pipeline property) (kbkit.kbi.thermodynamics.KBThermo property) (kbkit.schema.activity_metadata.ActivityMetadata attribute) (kbkit.systems.collection.SystemCollection property) rho() (kbkit.kbi.thermodynamics.KBThermo method) rkbi (kbkit.kbi.integrator.KBIntegrator property) RT() (kbkit.kbi.thermodynamics.KBThermo method) running_kbi_map (kbkit.kbi.integrator.KBIntegrator property)

S

s0_e() (kbkit.kbi.thermodynamics.KBThermo method) s0_ij() (kbkit.kbi.thermodynamics.KBThermo method) s0_kappa() (kbkit.kbi.thermodynamics.KBThermo method) s0_kappa_e() (kbkit.kbi.thermodynamics.KBThermo method) s0_p() (kbkit.kbi.thermodynamics.KBThermo method) s0_p_e() (kbkit.kbi.thermodynamics.KBThermo method) s0_x() (kbkit.kbi.thermodynamics.KBThermo method) s0_x_e() (kbkit.kbi.thermodynamics.KBThermo method)

s0_xp() (kbkit.kbi.thermodynamics.KBThermo method) s0_xp_e() (kbkit.kbi.thermodynamics.KBThermo method) s_ex() (kbkit.kbi.thermodynamics.KBThermo method) s_mix() (kbkit.kbi.thermodynamics.KBThermo method) simulated_property() (kbkit.systems.collection.SystemCollection method) SystemCollection (class in kbkit.systems.collection) SystemMetadata (class in kbkit.schema.system_metadata) SystemProperties (class in kbkit.systems.properties) systems (kbkit.api.pipeline.Pipeline property)

T

temperature() (kbkit.kbi.thermodynamics.KBThermo method) thermo (kbkit.api.pipeline.Pipeline property) thermo_plotter (kbkit.api.pipeline.Pipeline property) ThermoPlotter (class in kbkit.visualization.thermo) timeseries_plotter() (kbkit.api.pipeline.Pipeline method) (kbkit.systems.collection.SystemCollection method) (kbkit.systems.properties.SystemProperties method)

TimeseriesPlotter (class in kbkit.visualization.timeseries) to() (kbkit.schema.property_result.PropertyResult method) TOP (kbkit.io.topology.TopologyFormat attribute) topology (kbkit.systems.properties.SystemProperties property) topology_properties (kbkit.systems.properties.SystemProperties property) TopologyFormat (class in kbkit.io.topology) TopologyParser (class in kbkit.io.topology) total_molecules (kbkit.io.topology.TopologyParser property)

U

u0_weight() (kbkit.kbi.integrator.KBIntegrator method) u1_weight() (kbkit.kbi.integrator.KBIntegrator method) u2_weight() (kbkit.kbi.integrator.KBIntegrator method)

units (kbkit.io.energy.EnergyParser property) (kbkit.schema.property_result.PropertyResult attribute) (kbkit.systems.collection.SystemCollection property)

V

v_bar() (kbkit.kbi.thermodynamics.KBThermo method)

value (kbkit.schema.property_result.PropertyResult attribute)

X

x (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) (kbkit.systems.collection.SystemCollection property)

x_eval (kbkit.schema.activity_metadata.ActivityCoefficientResult property)

Y

y (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute)

y_eval (kbkit.schema.activity_metadata.ActivityCoefficientResult property)

Z

z_bar (kbkit.kbi.thermodynamics.KBThermo property)

z_i (kbkit.kbi.thermodynamics.KBThermo property) z_i_diff (kbkit.kbi.thermodynamics.KBThermo property)