rxn_network

• rxn_network.core
  • Composition
    • Composition.reduced_formula
• rxn_network.costs
  • rxn_network.costs.base
    • Calculator
      • Calculator.calculate()
      • Calculator.calculate_many()
      • Calculator.decorate()
      • Calculator.decorate_many()
    • CostFunction
      • CostFunction.evaluate()
  • rxn_network.costs.calculators
    • ChempotDistanceCalculator
      • ChempotDistanceCalculator.calculate()
      • ChempotDistanceCalculator.from_entries()
    • PrimaryCompetitionCalculator
      • PrimaryCompetitionCalculator.calculate()
    • SecondaryCompetitionCalculator
      • SecondaryCompetitionCalculator.calculate()
    • SecondaryCompetitionWithEhullCalculator
      • SecondaryCompetitionWithEhullCalculator.calculate()
    • SecondaryCompetitionMaxCalculator
      • SecondaryCompetitionMaxCalculator.calculate()
    • SecondaryCompetitionAreaCalculator
      • SecondaryCompetitionAreaCalculator.calculate()
  • rxn_network.costs.functions
    • Softplus
      • Softplus.evaluate()
    • WeightedSum
      • WeightedSum.evaluate()
  • rxn_network.costs.pareto
    • get_pareto_front()
    • is_pareto_efficient()
• rxn_network.data
  • load_experimental_data()
  • make_float_keys()
• rxn_network.entries
  • rxn_network.entries.corrections
    • CarbonateCorrection
      • CarbonateCorrection.num_ions
      • CarbonateCorrection.carbonate_correction
    • CarbonDioxideAtmosphericCorrection
      • CarbonDioxideAtmosphericCorrection.get_dmu()
      • CarbonDioxideAtmosphericCorrection.temp
      • CarbonDioxideAtmosphericCorrection.pco2
  • rxn_network.entries.entry_set
    • normal()
    • GibbsEntrySet
      • GibbsEntrySet.add()
      • GibbsEntrySet.update()
      • GibbsEntrySet.discard()
      • GibbsEntrySet.pd_dict
      • GibbsEntrySet.get_subset_in_chemsys()
      • GibbsEntrySet.filter_by_stability()
      • GibbsEntrySet.build_indices()
      • GibbsEntrySet.get_min_entry_by_formula()
      • GibbsEntrySet.get_stabilized_entry()
      • GibbsEntrySet.get_entries_with_new_temperature()
      • GibbsEntrySet.get_entries_with_jitter()
      • GibbsEntrySet.get_interpolated_entry()
      • GibbsEntrySet.get_e_above_hull()
      • GibbsEntrySet.from_pd()
      • GibbsEntrySet.copy()
      • GibbsEntrySet.as_dict()
      • GibbsEntrySet.from_computed_entries()
      • GibbsEntrySet.entries_list
      • GibbsEntrySet.min_entries_by_formula
      • GibbsEntrySet.temperature
      • GibbsEntrySet.chemsys
      • GibbsEntrySet.get_adjusted_entry()
  • rxn_network.entries.experimental
    • ExperimentalReferenceEntry
      • ExperimentalReferenceEntry.get_new_temperature()
      • ExperimentalReferenceEntry.to_grand_entry()
      • ExperimentalReferenceEntry.temperature
      • ExperimentalReferenceEntry.is_experimental
      • ExperimentalReferenceEntry.is_element
      • ExperimentalReferenceEntry.unique_id
      • ExperimentalReferenceEntry.as_dict()
      • ExperimentalReferenceEntry.from_dict()
  • rxn_network.entries.freed
    • FREEDReferenceEntry
  • rxn_network.entries.gibbs
    • GibbsComputedEntry
      • GibbsComputedEntry.get_new_temperature()
      • GibbsComputedEntry.gibbs_adjustment()
      • GibbsComputedEntry.to_grand_entry()
      • GibbsComputedEntry.copy()
      • GibbsComputedEntry.from_structure()
      • GibbsComputedEntry.is_experimental
      • GibbsComputedEntry.unique_id
      • GibbsComputedEntry.as_dict()
      • GibbsComputedEntry.from_dict()
  • rxn_network.entries.interpolated
    • InterpolatedEntry
      • InterpolatedEntry.to_grand_entry()
      • InterpolatedEntry.get_new_temperature()
      • InterpolatedEntry.unique_id
      • InterpolatedEntry.is_experimental
  • rxn_network.entries.nist
    • NISTReferenceEntry
  • rxn_network.entries.utils
    • process_entries()
    • initialize_entry()
    • get_entries()
    • get_all_entries_in_chemsys()
    • parse_criteria()
• rxn_network.enumerators
  • rxn_network.enumerators.base
    • Enumerator
      • Enumerator.enumerate()
  • rxn_network.enumerators.basic
    • BasicEnumerator
      • BasicEnumerator.enumerate()
      • BasicEnumerator.stabilize
      • BasicEnumerator.build_pd
      • BasicEnumerator.build_grand_pd
    • BasicOpenEnumerator
  • rxn_network.enumerators.minimize
    • MinimizeGibbsEnumerator
    • MinimizeGrandPotentialEnumerator
  • rxn_network.enumerators.utils
    • get_computed_rxn()
    • react_interface()
    • get_elems_set()
    • get_total_chemsys_str()
    • group_by_chemsys()
    • stabilize_entries()
    • run_enumerators()
• rxn_network.flows
  • SynthesisPlanningFlowMaker
    • SynthesisPlanningFlowMaker.make()
  • NetworkFlowMaker
    • NetworkFlowMaker.make()
• rxn_network.jobs
  • rxn_network.jobs.core
    • GetEntrySetMaker
      • GetEntrySetMaker.make()
    • ReactionEnumerationMaker
      • ReactionEnumerationMaker.make()
    • CalculateCompetitionMaker
      • CalculateCompetitionMaker.make()
    • NetworkMaker
      • NetworkMaker.make()
    • PathwaySolverMaker
      • PathwaySolverMaker.make()
  • rxn_network.jobs.schema
    • EntrySetDocument
      • EntrySetDocument.task_label
      • EntrySetDocument.last_updated
      • EntrySetDocument.entries
      • EntrySetDocument.e_above_hull
      • EntrySetDocument.include_polymorphs
      • EntrySetDocument.formulas_to_include
      • EntrySetDocument.model_computed_fields
    • EnumeratorTaskDocument
      • EnumeratorTaskDocument.task_label
      • EnumeratorTaskDocument.last_updated
      • EnumeratorTaskDocument.rxns
      • EnumeratorTaskDocument.targets
      • EnumeratorTaskDocument.elements
      • EnumeratorTaskDocument.chemsys
      • EnumeratorTaskDocument.added_elements
      • EnumeratorTaskDocument.added_chemsys
      • EnumeratorTaskDocument.enumerators
      • EnumeratorTaskDocument.model_computed_fields
    • CompetitionTaskDocument
      • CompetitionTaskDocument.task_label
      • CompetitionTaskDocument.last_updated
      • CompetitionTaskDocument.rxns
      • CompetitionTaskDocument.target_formula
      • CompetitionTaskDocument.open_elem
      • CompetitionTaskDocument.chempot
      • CompetitionTaskDocument.added_elements
      • CompetitionTaskDocument.added_chemsys
      • CompetitionTaskDocument.calculate_competition
      • CompetitionTaskDocument.calculate_chempot_distances
      • CompetitionTaskDocument.temp
      • CompetitionTaskDocument.batch_size
      • CompetitionTaskDocument.cpd_kwargs
      • CompetitionTaskDocument.model_computed_fields
    • NetworkTaskDocument
      • NetworkTaskDocument.task_label
      • NetworkTaskDocument.last_updated
      • NetworkTaskDocument.network
      • NetworkTaskDocument.paths
      • NetworkTaskDocument.k
      • NetworkTaskDocument.precursors
      • NetworkTaskDocument.targets
      • NetworkTaskDocument.model_computed_fields
    • PathwaySolverTaskDocument
      • PathwaySolverTaskDocument.task_label
      • PathwaySolverTaskDocument.last_updated
      • PathwaySolverTaskDocument.solver
      • PathwaySolverTaskDocument.balanced_paths
      • PathwaySolverTaskDocument.precursors
      • PathwaySolverTaskDocument.targets
      • PathwaySolverTaskDocument.net_rxn
      • PathwaySolverTaskDocument.max_num_combos
      • PathwaySolverTaskDocument.find_intermediate_rxns
      • PathwaySolverTaskDocument.intermediate_rxn_energy_cutoff
      • PathwaySolverTaskDocument.use_basic_enumerator
      • PathwaySolverTaskDocument.use_minimize_enumerator
      • PathwaySolverTaskDocument.filter_interdependent
      • PathwaySolverTaskDocument.model_computed_fields
  • rxn_network.jobs.utils
    • get_added_elem_data()
• rxn_network.network
  • rxn_network.network.base
    • Network
      • Network.build()
      • Network.find_pathways()
      • Network.set_precursors()
      • Network.set_target()
      • Network.as_dict()
      • Network.from_dict()
      • Network.precursors
      • Network.target
      • Network.graph
      • Network.chemsys
    • Graph
      • Graph.as_dict()
      • Graph.from_dict()
  • rxn_network.network.entry
    • NetworkEntryType
    • NetworkEntry
      • NetworkEntry.entries
      • NetworkEntry.elements
      • NetworkEntry.chemsys
      • NetworkEntry.dim
      • NetworkEntry.description
      • NetworkEntry.as_dict()
      • NetworkEntry.from_dict()
    • DummyEntry
  • rxn_network.network.network
    • ReactionNetwork
      • ReactionNetwork.build()
      • ReactionNetwork.find_pathways()
      • ReactionNetwork.set_precursors()
      • ReactionNetwork.set_target()
    • get_rxn_nodes_and_edges()
    • get_loopback_edges()
    • get_edge_weight()
    • yens_ksp()
  • rxn_network.network.visualize
    • plot_network()
• rxn_network.pathways
  • rxn_network.pathways.balanced
    • BalancedPathway
      • BalancedPathway.get_comp_matrix()
      • BalancedPathway.get_coeff_vector_for_rxn()
      • BalancedPathway.contains_interdependent_rxns()
      • BalancedPathway.balance()
      • BalancedPathway.average_cost
  • rxn_network.pathways.base
    • Pathway
      • Pathway.entries
      • Pathway.all_reactants
      • Pathway.all_products
      • Pathway.compositions
      • Pathway.reactants
      • Pathway.products
      • Pathway.intermediates
      • Pathway.energy
      • Pathway.energy_per_atom
  • rxn_network.pathways.basic
    • BasicPathway
      • BasicPathway.reactions
      • BasicPathway.total_cost
      • BasicPathway.is_experimental
  • rxn_network.pathways.pathway_set
    • PathwaySet
      • PathwaySet.paths
      • PathwaySet.from_paths()
  • rxn_network.pathways.plotting
    • PathwayPlotter
      • PathwayPlotter.plot_pathway()
      • PathwayPlotter.plot_energy_cascade()
      • PathwayPlotter.elems
      • PathwayPlotter.num_atoms_df
      • PathwayPlotter.formulas
      • PathwayPlotter.df
      • PathwayPlotter.compositions
  • rxn_network.pathways.solver
    • Solver
      • Solver.pathways
      • Solver.reactions
      • Solver.costs
      • Solver.num_rxns
      • Solver.num_entries
    • PathwaySolver
      • PathwaySolver.solve()
      • PathwaySolver.entries
• rxn_network.reactions
  • rxn_network.reactions.base
    • Reaction
      • Reaction.reactants
      • Reaction.products
      • Reaction.coefficients
      • Reaction.energy
      • Reaction.compositions
      • Reaction.elements
  • rxn_network.reactions.basic
    • BasicReaction
      • BasicReaction.balance()
      • BasicReaction.normalize_to()
      • BasicReaction.normalize_to_element()
      • BasicReaction.get_el_amount()
      • BasicReaction.get_coeff()
      • BasicReaction.normalized_repr_and_factor()
      • BasicReaction.copy()
      • BasicReaction.reverse()
      • BasicReaction.is_separable()
      • BasicReaction.reactant_atomic_fractions
      • BasicReaction.product_atomic_fractions
      • BasicReaction.reactant_molar_fractions
      • BasicReaction.product_molar_fractions
      • BasicReaction.from_string()
      • BasicReaction.from_formulas()
      • BasicReaction.reactants
      • BasicReaction.products
      • BasicReaction.compositions
      • BasicReaction.coefficients
      • BasicReaction.num_atoms
      • BasicReaction.energy
      • BasicReaction.energy_per_atom
      • BasicReaction.is_identity
      • BasicReaction.chemical_system
      • BasicReaction.normalized_repr
  • rxn_network.reactions.computed
    • ComputedReaction
      • ComputedReaction.balance()
      • ComputedReaction.get_new_temperature()
      • ComputedReaction.energy
      • ComputedReaction.energy_per_atom
      • ComputedReaction.energy_uncertainty
      • ComputedReaction.energy_uncertainty_per_atom
      • ComputedReaction.entries
      • ComputedReaction.copy()
      • ComputedReaction.reverse()
      • ComputedReaction.normalize_to()
      • ComputedReaction.normalize_to_element()
      • ComputedReaction.get_entry_idx_vector()
  • rxn_network.reactions.hull
    • InterfaceReactionHull
      • InterfaceReactionHull.plot()
      • InterfaceReactionHull.get_energy_above_hull()
      • InterfaceReactionHull.get_coordinate()
      • InterfaceReactionHull.get_hull_energy()
      • InterfaceReactionHull.get_reactions_by_coordinate()
      • InterfaceReactionHull.get_primary_competition()
      • InterfaceReactionHull.get_secondary_competition()
      • InterfaceReactionHull.get_secondary_competition_max_energy()
      • InterfaceReactionHull.get_secondary_competition_area()
      • InterfaceReactionHull.get_decomposition_energy()
      • InterfaceReactionHull.get_max_decomposition_energy()
      • InterfaceReactionHull.get_decomposition_area()
      • InterfaceReactionHull.get_coords_in_range()
      • InterfaceReactionHull.count()
      • InterfaceReactionHull.get_decomposition_energy_and_num_paths_recursive()
      • InterfaceReactionHull.hull_vertices
      • InterfaceReactionHull.stable_reactions
      • InterfaceReactionHull.unstable_reactions
  • rxn_network.reactions.open
    • OpenComputedReaction
      • OpenComputedReaction.balance()
      • OpenComputedReaction.get_new_temperature()
      • OpenComputedReaction.energy
      • OpenComputedReaction.elements
      • OpenComputedReaction.total_chemical_system
      • OpenComputedReaction.copy()
      • OpenComputedReaction.reverse()
      • OpenComputedReaction.reactant_atomic_fractions
      • OpenComputedReaction.product_atomic_fractions
      • OpenComputedReaction.from_computed_rxn()
      • OpenComputedReaction.as_dict()
      • OpenComputedReaction.from_dict()
  • rxn_network.reactions.plotting
    • plot_reaction_scatter()
    • pretty_df_layout()
    • filter_df_by_precursors()
  • rxn_network.reactions.reaction_set
    • ReactionSet
      • ReactionSet.get_rxns()
      • ReactionSet.from_rxns()
      • ReactionSet.to_dataframe()
      • ReactionSet.calculate_costs()
      • ReactionSet.add_rxns()
      • ReactionSet.add_rxn_set()
      • ReactionSet.get_rxns_by_reactants()
      • ReactionSet.get_rxns_by_product()
      • ReactionSet.filter_duplicates()
      • ReactionSet.set_chempot()
      • ReactionSet.set_new_temperature()
• rxn_network.thermo
  • rxn_network.thermo.chempot_diagram
    • ChemicalPotentialDiagram
      • ChemicalPotentialDiagram.shortest_domain_distance()
      • ChemicalPotentialDiagram.get_offset()
      • ChemicalPotentialDiagram.domains
      • ChemicalPotentialDiagram.metastable_domains
      • ChemicalPotentialDiagram.hs_int
  • rxn_network.thermo.utils
    • expand_pd()
• rxn_network.utils
  • rxn_network.utils.funcs
    • limited_powerset()
    • grouper()
    • get_project_root()
    • get_logger()
    • datetime_str()
  • rxn_network.utils.ray
    • initialize_ray()
    • to_iterator()