package kappa-library
Public internals of the Kappa tool suite. Use this package to use kappa as a lib
Install
Dune Dependency
Authors
Maintainers
Sources
v4.1.3.tar.gz
md5=1c9a8a0d79f085757817f90834e166f5
sha512=13ac40442940ba6e72d7dc5bf952e67443872f7bff63e9c76a3a699a6904c88696047fe04519b7ec6546371642f6ee7b0983117be302694aca15500b0df40de3
doc/src/kappa-library.runtime/generic_rule_interpreter.ml.html
Source file generic_rule_interpreter.ml
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(******************************************************************************) (* _ __ * The Kappa Language *) (* | |/ / * Copyright 2010-2020 CNRS - Harvard Medical School - INRIA - IRIF *) (* | ' / *********************************************************************) (* | . \ * This file is distributed under the terms of the *) (* |_|\_\ * GNU Lesser General Public License Version 3 *) (******************************************************************************) type precomputed = { unary_patterns: Pattern.Set.t; always_outdated: Operator.DepSet.t; } module Make (Instances : Instances_sig.S) = struct type event_predicate = int option -> Matching.t -> Instantiation.concrete Instantiation.test list -> Instantiation.concrete Instantiation.action list -> bool type imperative_fields = { precomputed: precomputed; instances: Instances.t; variables_cache: Nbr.t array; variables_overwrite: Primitives.alg_expr option array; tokens: Nbr.t array; activities: Random_tree.tree; (* pair numbers are regular rule, odd unary instances *) random_state: Random.State.t; story_machinery: (string (*obs name*) * Pattern.id array * Instantiation.abstract Instantiation.test list list) list Pattern.ObsMap.t (*currently tracked ccs *) option; species: (string (*filename*) * Pattern.id array (*with only one pattern*) * Instantiation.abstract Instantiation.test list list) list Pattern.ObsMap.t; changed_connectivity: (int, unit) Hashtbl.t; (* set of ccs that have changed *) } type instance = bool * int * (Kappa_terms.Matching.t * int list * Kappa_site_graphs.Edges.path option) option type t = { mutable outdated: bool; (* Without rectangular approximation *) matchings_of_rule: (Matching.t * int list) list Mods.IntMap.t; unary_candidates: (* rule_id -> list of matchings *) (Matching.t * int list * Edges.path option) list Mods.IntMap.t; (* rule -> cc -> number_instances (activity per cc) *) nb_rectangular_instances_by_cc: ValMap.t Mods.IntMap.t; edges: Edges.t; imp: imperative_fields; outdated_elements: Operator.DepSet.t; events_to_block: event_predicate option; } let get_edges st = st.edges let sum_instances_numbers ?rule_id insts l = List.fold_left (fun ac x -> ac + Instances.number_of_instances ?rule_id insts x) 0 l type result = Clash | Corrected | Blocked | Success of t let raw_get_alg env overwr i = match overwr.(i) with | None -> Model.get_alg env i | Some expr -> expr let value_bool counter state expr = let () = assert (not state.outdated) in Expr_interpreter.value_bool counter ~get_alg:(fun i -> Alg_expr.CONST state.imp.variables_cache.(i)) ~get_mix:(fun patterns -> Nbr.I (sum_instances_numbers state.imp.instances patterns)) ~get_tok:(fun i -> state.imp.tokens.(i)) expr let value_alg counter state alg = let () = assert (not state.outdated) in Expr_interpreter.value_alg counter ~get_alg:(fun i -> Alg_expr.CONST state.imp.variables_cache.(i)) ~get_mix:(fun patterns -> Nbr.I (sum_instances_numbers state.imp.instances patterns)) ~get_tok:(fun i -> state.imp.tokens.(i)) alg let recompute env counter state i = state.imp.variables_cache.(i) <- value_alg counter state (raw_get_alg env state.imp.variables_overwrite i) let activity state = Random_tree.total state.imp.activities let get_activity rule state = Random_tree.find rule state.imp.activities let set_activity rule v state = Random_tree.add rule v state.imp.activities let pick_rule rt state = fst (Random_tree.random rt state.imp.activities) let initial_activity ~outputs env counter state = Model.fold_rules (fun i () rule -> if Array.length rule.Primitives.connected_components = 0 then ( match Nbr.to_float @@ value_alg counter state (fst rule.Primitives.rate) with | None -> outputs (Data.Warning ( Some (snd rule.Primitives.rate), fun f -> let noCounters = false in Format.fprintf f "Problematic rule rate replaced by 0"; Kappa_printer.elementary_rule ~env ~noCounters f rule )) | Some rate -> set_activity (2 * i) rate state )) () env let empty ~outputs ~with_trace random_state env counter = let activity_tree = Random_tree.create (2 * Model.nb_rules env) in let unary_patterns = Model.unary_patterns env in let always_outdated = let deps_in_t, deps_in_e, _, _ = Model.all_dependencies env in Operator.DepSet.union deps_in_t deps_in_e in let with_connected_components = not (Pattern.Set.is_empty unary_patterns) in let variables_overwrite = Array.make (Model.nb_algs env) None in let variables_cache = Array.make (Model.nb_algs env) Nbr.zero in let cand = { imp = { activities = activity_tree; precomputed = { unary_patterns; always_outdated }; instances = Instances.empty env; variables_overwrite; variables_cache; tokens = Array.make (Model.nb_tokens env) Nbr.zero; random_state; story_machinery = (if with_trace then Some (Pattern.Env.new_obs_map (Model.domain env) (fun _ -> [])) else None); species = Pattern.Env.new_obs_map (Model.domain env) (fun _ -> []); changed_connectivity = Hashtbl.create 32; }; outdated = false; matchings_of_rule = Mods.IntMap.empty; unary_candidates = Mods.IntMap.empty; nb_rectangular_instances_by_cc = Mods.IntMap.empty; edges = Edges.empty ~with_connected_components; outdated_elements = always_outdated; events_to_block = None; } in let () = Tools.iteri (recompute env counter cand) (Model.nb_algs env) in let () = initial_activity ~outputs env counter cand in cand let concrete_actions_for_incomplete_inj ~debug_mode rule matching = let abstract_actions = rule.Primitives.instantiations.Instantiation.actions in let inj = matching, Mods.IntMap.empty in List_util.map_option (Instantiation.try_concretize_action ~debug_mode inj) abstract_actions let concrete_tests ~debug_mode rule matching = let abstract_tests = rule.Primitives.instantiations.Instantiation.tests |> List.concat in let inj = matching, Mods.IntMap.empty in List.map (Instantiation.concretize_test ~debug_mode inj) abstract_tests let is_blocked ~debug_mode state ?rule_id rule matching = match state.events_to_block with | None -> false | Some to_block -> let actions = concrete_actions_for_incomplete_inj ~debug_mode rule matching in let tests = concrete_tests ~debug_mode rule matching in to_block rule_id matching tests actions let set_events_to_block predicate state = { state with events_to_block = predicate; matchings_of_rule = Mods.IntMap.empty; unary_candidates = Mods.IntMap.empty; } let instance_to_matching ~debug_mode domain edges instance patterns = Tools.array_fold_lefti (fun i matching root -> match matching with | None -> None | Some matching -> Matching.reconstruct ~debug_mode domain edges matching i patterns.(i) root) (Some Matching.empty) instance let all_injections ~debug_mode ?excp ?unary_rate ?rule_id state_insts domain edges patterna = let out = Instances.fold_instances ?excp ?rule_id state_insts patterna ~init:[] (fun instance acc -> match instance_to_matching ~debug_mode domain edges instance patterna with | None -> acc | Some matching -> let rev_roots = Array.fold_left (fun t h -> h :: t) [] instance in (matching, rev_roots) :: acc) in match unary_rate with | None -> out | Some (_, None) -> List.filter (function | _, [ r1; r2 ] -> not (Edges.in_same_connected_component r1 r2 edges) | _, _ -> false) out | Some (_, (Some _ as max_distance)) -> List.filter (fun (inj, _) -> let nodes = Matching.elements_with_types domain patterna inj in None = Edges.are_connected ?max_distance edges nodes.(0) nodes.(1)) out let pop_exact_matchings matchings_of_rule rule = snd (Mods.IntMap.pop rule matchings_of_rule) let pick_a_rule_instance ~debug_mode state random_state domain edges ?rule_id rule = let from_patterns () = let pats = rule.Primitives.connected_components in Instances.fold_picked_instance ?rule_id state.imp.instances random_state pats ~init:(Matching.empty, [], None) (fun id pattern root (inj, rev_roots, _) -> match Matching.reconstruct ~debug_mode domain edges inj id pattern root with | None -> None | Some inj' -> Some (inj', root :: rev_roots, None)) in match rule_id with | None -> from_patterns () | Some id -> (match Mods.IntMap.find_option id state.matchings_of_rule with | Some [] -> None | Some l -> let a, b = List_util.random random_state l in Some (a, b, None) | None -> from_patterns ()) let adjust_rule_instances ~debug_mode ~rule_id ?unary_rate state domain edges ccs rule = let matches = all_injections ~debug_mode ?unary_rate ~rule_id state.imp.instances domain edges ccs in let matches = if state.events_to_block = None then matches else matches |> List.filter (fun (matching, _) -> not (is_blocked ~debug_mode state ~rule_id rule matching)) in ( List.length matches, { state with matchings_of_rule = Mods.IntMap.add rule_id matches state.matchings_of_rule; } ) (* With rectangular approximation *) let compute_unary_number instances (nb_rectangular_instances_by_cc, unary_candidates) modified_ccs rule rule_id = let pat1 = rule.Primitives.connected_components.(0) in let pat2 = rule.Primitives.connected_components.(1) in let number_of_unary_instances_in_cc = Instances.number_of_unary_instances_in_cc ~rule_id instances (pat1, pat2) in let old_pack = Mods.IntMap.find_default ValMap.empty rule_id nb_rectangular_instances_by_cc in let new_pack = Hashtbl.fold (fun cc () i_inst -> let new_v = number_of_unary_instances_in_cc cc in if new_v = 0 then ValMap.remove cc i_inst else ValMap.add cc new_v i_inst) modified_ccs old_pack in let va = ValMap.total new_pack in let nb_rectangular_instances_by_cc' = if va = 0L then Mods.IntMap.remove rule_id nb_rectangular_instances_by_cc else Mods.IntMap.add rule_id new_pack nb_rectangular_instances_by_cc in let _, unary_candidates' = (* Invalidates the cache *) Mods.IntMap.pop rule_id unary_candidates in va, (nb_rectangular_instances_by_cc', unary_candidates') let pick_a_unary_rule_instance ~debug_mode state random_state domain edges ~rule_id rule = match Mods.IntMap.find_option rule_id state.unary_candidates with | Some l -> let inj, roots, path = List_util.random random_state l in Some (inj, roots, path) | None -> let pat1 = rule.Primitives.connected_components.(0) in let pat2 = rule.Primitives.connected_components.(1) in let pick_unary_instance_in_cc = Instances.pick_unary_instance_in_cc ~rule_id state.imp.instances random_state (pat1, pat2) in let cc_id = ValMap.random random_state (Mods.IntMap.find_default ValMap.empty rule_id state.nb_rectangular_instances_by_cc) in let root1, root2 = pick_unary_instance_in_cc cc_id in let () = if debug_mode then Format.printf "@[On roots:@ %i@ %i@]@." root1 root2 in let pattern1 = rule.Primitives.connected_components.(0) in let pattern2 = rule.Primitives.connected_components.(1) in let inj1 = Matching.reconstruct ~debug_mode domain edges Matching.empty 0 pattern1 root1 in (match inj1 with | None -> None | Some inj -> (match Matching.reconstruct ~debug_mode domain edges inj 1 pattern2 root2 with | None -> None | Some inj_out -> Some (inj_out, [ root2; root1 ], None))) let adjust_unary_rule_instances ~debug_mode ~rule_id ?max_distance state domain graph pats rule = let pattern1 = pats.(0) in let pattern2 = pats.(1) in let cands, len = Instances.fold_unary_instances ~rule_id state.imp.instances (pattern1, pattern2) ~init:([], 0) (fun (root1, root2) ((list, len) as out) -> let inj1 = Matching.reconstruct ~debug_mode domain graph Matching.empty 0 pattern1 root1 in match inj1 with | None -> out | Some inj -> (match Matching.reconstruct ~debug_mode domain graph inj 1 pattern2 root2 with | None -> out | Some inj' -> (match max_distance with | None -> (inj', [ root2; root1 ], None) :: list, succ len | Some _ -> let nodes = Matching.elements_with_types domain pats inj' in (match Edges.are_connected ?max_distance graph nodes.(0) nodes.(1) with | None -> out | Some _ as p -> if is_blocked ~debug_mode state ~rule_id rule inj' then out else (inj', [ root2; root1 ], p) :: list, succ len)))) in let unary_candidates = if len = 0 then Mods.IntMap.remove rule_id state.unary_candidates else Mods.IntMap.add rule_id cands state.unary_candidates in len, { state with unary_candidates } let print env f state = let sigs = Model.signatures env in Format.fprintf f "@[<v>%a@,%a@]" (Pp.list Pp.space (fun f (i, mix) -> Format.fprintf f "%%init: %i @[<h>%a@]" i User_graph.print_cc mix)) (Edges.build_user_snapshot ~debug_mode:false ~raw:false sigs state.edges) (Pp.array Pp.space (fun i f el -> Format.fprintf f "%%init: %a %a" Nbr.print el (Model.print_token ~env) i)) state.imp.tokens let debug_print f state = Format.fprintf f "@[<v>%a@,%a@,%a@]" Edges.debug_print state.edges (Pp.array Pp.space (fun i f el -> Format.fprintf f "%a token_%i" Nbr.print el i)) state.imp.tokens Instances.debug_print state.imp.instances type stats = { mixture_stats: Edges.stats } let stats state = { mixture_stats = Edges.stats state.edges } let print_stats f state = Format.fprintf f "%i agents" (stats state).mixture_stats.Edges.nb_agents let new_place free_id (inj_nodes, inj_fresh) = function | Matching.Agent.Existing _ -> failwith "Rule_interpreter.new_place" | Matching.Agent.Fresh (_, id) -> inj_nodes, Mods.IntMap.add id free_id inj_fresh let apply_negative_transformation ?mod_connectivity_store instances (side_effects, edges) = function | Primitives.Transformation.Agent (id, _) -> let edges' = Edges.remove_agent id edges in side_effects, edges' | Primitives.Transformation.Freed ((id, _), s) -> (*(n,s)-bottom*) let edges' = Edges.remove_free id s edges in side_effects, edges' | Primitives.Transformation.Linked (((id, _), s), ((id', _), s')) -> let edges', cc_modif = Edges.remove_link id s id' s' edges in let () = Instances.break_apart_cc instances edges' ?mod_connectivity_store cc_modif in side_effects, edges' | Primitives.Transformation.NegativeWhatEver (((id, _), s) as n) -> (match List.partition (fun x -> x = n) side_effects with | _ :: _, side_effects' -> side_effects', edges | [], _ -> (match Edges.link_destination id s edges with | None -> side_effects, Edges.remove_free id s edges | Some (((id', _) as nc'), s') -> let edges', cc_modif = Edges.remove_link id s id' s' edges in let () = Instances.break_apart_cc instances edges' ?mod_connectivity_store cc_modif in (nc', s') :: side_effects, edges')) | Primitives.Transformation.PositiveInternalized _ -> raise (ExceptionDefn.Internal_Error (Loc.annot_with_dummy "PositiveInternalized in negative update")) | Primitives.Transformation.NegativeInternalized ((id, _), s) -> let _, edges' = Edges.remove_internal id s edges in side_effects, edges' let apply_positive_transformation ~debug_mode sigs ?mod_connectivity_store instances (inj2graph, side_effects, edges) = function | Primitives.Transformation.Agent n -> let nc, inj2graph', edges' = let ty = Matching.Agent.get_type n in let id, edges' = Edges.add_agent sigs ty edges in (id, ty), new_place id inj2graph n, edges' in (inj2graph', side_effects, edges'), Primitives.Transformation.Agent nc | Primitives.Transformation.Freed (n, s) -> (*(n,s)-bottom*) let ((id, _) as nc) = Matching.Agent.concretize ~debug_mode inj2graph n in (*(A,23)*) let edges' = Edges.add_free id s edges in let side_effects' = List_util.smart_filter (fun x -> x <> (nc, s)) side_effects in (inj2graph, side_effects', edges'), Primitives.Transformation.Freed (nc, s) | Primitives.Transformation.Linked ((n, s), (n', s')) -> let nc = Matching.Agent.concretize ~debug_mode inj2graph n in let nc' = Matching.Agent.concretize ~debug_mode inj2graph n' in let edges', modif_cc = Edges.add_link nc s nc' s' edges in let side_effects' = List_util.smart_filter (fun x -> x <> (nc, s) && x <> (nc', s')) side_effects in let () = Instances.merge_cc instances ?mod_connectivity_store modif_cc in ( (inj2graph, side_effects', edges'), Primitives.Transformation.Linked ((nc, s), (nc', s')) ) | Primitives.Transformation.NegativeWhatEver _ -> raise (ExceptionDefn.Internal_Error (Loc.annot_with_dummy "NegativeWhatEver in positive update")) | Primitives.Transformation.PositiveInternalized (n, s, i) -> let ((id, _) as nc) = Matching.Agent.concretize ~debug_mode inj2graph n in let edges' = Edges.add_internal id s i edges in ( (inj2graph, side_effects, edges'), Primitives.Transformation.PositiveInternalized (nc, s, i) ) | Primitives.Transformation.NegativeInternalized _ -> raise (ExceptionDefn.Internal_Error (Loc.annot_with_dummy "NegativeInternalized in positive update")) let apply_concrete_positive_transformation sigs ?mod_connectivity_store instances edges = function | Primitives.Transformation.Agent (id, ty) -> let _, edges' = Edges.add_agent ~id sigs ty edges in edges' | Primitives.Transformation.Freed ((id, _), s) -> (*(n,s)-bottom*) let edges' = Edges.add_free id s edges in edges' | Primitives.Transformation.Linked ((nc, s), (nc', s')) -> let edges', modif_cc = Edges.add_link nc s nc' s' edges in let () = Instances.merge_cc instances ?mod_connectivity_store modif_cc in edges' | Primitives.Transformation.NegativeWhatEver _ -> raise (ExceptionDefn.Internal_Error (Loc.annot_with_dummy "NegativeWhatEver in positive update")) | Primitives.Transformation.PositiveInternalized ((id, _), s, i) -> let edges' = Edges.add_internal id s i edges in edges' | Primitives.Transformation.NegativeInternalized _ -> raise (ExceptionDefn.Internal_Error (Loc.annot_with_dummy "NegativeInternalized in positive update")) let obs_from_transformation ~debug_mode domain edges acc = function | Primitives.Transformation.Agent nc -> Matching.observables_from_agent domain edges acc nc | Primitives.Transformation.Freed (nc, s) -> (*(n,s)-bottom*) Matching.observables_from_free ~debug_mode domain edges acc nc s | Primitives.Transformation.Linked ((nc, s), (nc', s')) -> Matching.observables_from_link ~debug_mode domain edges acc nc s nc' s' | Primitives.Transformation.PositiveInternalized (nc, s, i) -> Matching.observables_from_internal ~debug_mode domain edges acc nc s i | Primitives.Transformation.NegativeInternalized (((id, _) as nc), s) -> let i = Edges.get_internal id s edges in Matching.observables_from_internal ~debug_mode domain edges acc nc s i | Primitives.Transformation.NegativeWhatEver (((id, _) as nc), s) -> (match Edges.link_destination id s edges with | None -> Matching.observables_from_free ~debug_mode domain edges acc nc s | Some (nc', s') -> Matching.observables_from_link ~debug_mode domain edges acc nc s nc' s') let obs_from_transformations ~debug_mode domain edges trans = List.fold_left (obs_from_transformation ~debug_mode domain edges) (([], Operator.DepSet.empty), Matching.empty_cache) trans |> fst let path_tests path tests = let known_agents = List.fold_left (List.fold_left (fun acc -> function | Instantiation.Is_Here (id, _) -> Mods.IntSet.add id acc | Instantiation.Is_Bound_to _ | Instantiation.Is_Bound _ | Instantiation.Has_Internal _ | Instantiation.Has_Binding_type _ | Instantiation.Is_Free _ -> acc)) Mods.IntSet.empty tests in let pretests = List_util.map_option (fun (x, y) -> if List.for_all (List.for_all (function | Instantiation.Is_Bound_to (a, b) -> x <> a && x <> b && y <> a && y <> b | Instantiation.Has_Internal _ | Instantiation.Is_Free _ | Instantiation.Is_Bound _ | Instantiation.Has_Binding_type _ | Instantiation.Is_Here _ -> true)) tests then Some (Instantiation.Is_Bound_to (x, y)) else None) path in let _, path_tests = List.fold_left (fun (ag, te) ((((id, _) as a), _), (((id', _) as a'), _)) -> let ag', te' = if Mods.IntSet.mem id ag then ag, te else Mods.IntSet.add id ag, Instantiation.Is_Here a :: te in if Mods.IntSet.mem id' ag' then ag', te' else Mods.IntSet.add id' ag', Instantiation.Is_Here a' :: te') (known_agents, pretests) path in path_tests let step_of_event counter = function | Trace.INIT _, e -> Trace.Init e.Instantiation.actions | Trace.RULE r, x -> Trace.Rule (r, x, Counter.next_step_simulation_info counter) | Trace.PERT p, x -> Trace.Pert (p, x, Counter.current_simulation_info counter) let store_event ~debug_mode counter inj2graph new_tracked_obs_instances event_kind ?path extra_side_effects rule outputs = function | None -> () | Some _ -> let cevent = Instantiation.concretize_event ~debug_mode inj2graph rule.Primitives.instantiations in let full_concrete_event = { Instantiation.tests = cevent.Instantiation.tests; Instantiation.actions = cevent.Instantiation.actions; Instantiation.side_effects_src = cevent.Instantiation.side_effects_src; Instantiation.side_effects_dst = List.rev_append extra_side_effects cevent.Instantiation.side_effects_dst; Instantiation.connectivity_tests = (match path with | None -> [] | Some None -> assert false | Some (Some path) -> path_tests path cevent.Instantiation.tests); } in let () = outputs (Data.TraceStep (step_of_event counter (event_kind, full_concrete_event))) in List.iter (fun (i, x) -> outputs (Data.TraceStep (Trace.Obs (i, x, Counter.next_story counter)))) new_tracked_obs_instances let get_species_obs ~debug_mode sigs edges obs acc tracked = List.fold_left (fun acc (pattern, (root, _)) -> try List.fold_left (fun acc (fn, patterns, _) -> if Array.fold_left (fun ok pid -> Pattern.compare_canonicals pid pattern = 0 || ok) false patterns then ( let spec = Edges.species ~debug_mode sigs root edges in (fn, patterns, spec) :: acc ) else acc) acc (Pattern.ObsMap.get tracked pattern) with Not_found -> acc) acc obs let store_obs ~debug_mode domain edges instances obs acc = function | None -> acc | Some tracked -> List.fold_left (fun acc (pattern, (root, _)) -> try List.fold_left (fun acc (ev, patterns, tests) -> List.fold_left (fun acc (inj, _) -> let tests' = List.map (List.map (Instantiation.concretize_test ~debug_mode (inj, Mods.IntMap.empty))) tests in (ev, tests') :: acc) acc (all_injections ~debug_mode instances ~excp:(pattern, root) domain edges patterns)) acc (Pattern.ObsMap.get tracked pattern) with Not_found -> acc) acc obs let update_edges ~debug_mode outputs counter domain inj_nodes state event_kind ?path rule sigs = let () = assert (not state.outdated) in let () = state.outdated <- true in let mod_connectivity_store = state.imp.changed_connectivity in (*Negative update*) let concrete_removed = List.map (Primitives.Transformation.concretize ~debug_mode (inj_nodes, Mods.IntMap.empty)) rule.Primitives.removed in let (del_obs, del_deps), _ = List.fold_left (obs_from_transformation ~debug_mode domain state.edges) (([], Operator.DepSet.empty), Matching.empty_cache) concrete_removed in let side_effects, edges_after_neg = List.fold_left (apply_negative_transformation ~mod_connectivity_store state.imp.instances) ([], state.edges) concrete_removed in let () = List.iter (fun (pat, (root, _)) -> Instances.update_roots state.imp.instances false state.imp.precomputed.unary_patterns edges_after_neg mod_connectivity_store pat root) del_obs in (*Positive update*) let (final_inj2graph, remaining_side_effects, edges'), concrete_inserted = List.fold_left (fun (x, p) h -> let x', h' = apply_positive_transformation ~debug_mode (Pattern.Env.signatures domain) ~mod_connectivity_store state.imp.instances x h in x', h' :: p) (((inj_nodes, Mods.IntMap.empty), side_effects, edges_after_neg), []) rule.Primitives.inserted in let edges'', concrete_inserted' = List.fold_left (fun (e, i) (((id, _) as nc), s) -> Edges.add_free id s e, Primitives.Transformation.Freed (nc, s) :: i) (edges', concrete_inserted) remaining_side_effects in let (new_obs, new_deps), _ = List.fold_left (obs_from_transformation ~debug_mode domain edges'') (([], Operator.DepSet.empty), Matching.empty_cache) concrete_inserted' in let () = List.iter (fun (pat, (root, _)) -> Instances.update_roots state.imp.instances true state.imp.precomputed.unary_patterns edges'' mod_connectivity_store pat root) new_obs in (*Store event*) let new_tracked_obs_instances = store_obs ~debug_mode domain edges'' state.imp.instances new_obs [] state.imp.story_machinery in let () = store_event ~debug_mode counter final_inj2graph new_tracked_obs_instances event_kind ?path remaining_side_effects rule outputs state.imp.story_machinery in (*Print species*) let species = get_species_obs ~debug_mode sigs edges'' new_obs [] state.imp.species in let () = List.iter (fun (file, _, mixture) -> outputs (Data.Species (file, Counter.current_time counter, mixture))) species in let rev_deps = Operator.DepSet.union state.outdated_elements (Operator.DepSet.union del_deps new_deps) in { outdated = false; imp = state.imp; matchings_of_rule = state.matchings_of_rule; unary_candidates = state.unary_candidates; nb_rectangular_instances_by_cc = state.nb_rectangular_instances_by_cc; edges = edges''; outdated_elements = rev_deps; events_to_block = state.events_to_block; } let update_edges_from_actions ~debug_mode ~outputs sigs counter domain state (actions, side_effect_dst) = let () = assert (not state.outdated) in let () = state.outdated <- true in let mod_connectivity_store = state.imp.changed_connectivity in (*Negative update*) let lnk_dst ((a, _), s) = Edges.link_destination a s state.edges in let concrete_removed = Primitives.Transformation.negative_transformations_of_actions sigs lnk_dst actions in let (del_obs, del_deps), _ = List.fold_left (obs_from_transformation ~debug_mode domain state.edges) (([], Operator.DepSet.empty), Matching.empty_cache) concrete_removed in let _side_effects, edges_after_neg = List.fold_left (apply_negative_transformation ~mod_connectivity_store state.imp.instances) ([], state.edges) concrete_removed in let () = List.iter (fun (pat, (root, _)) -> Instances.update_roots state.imp.instances false state.imp.precomputed.unary_patterns edges_after_neg mod_connectivity_store pat root) del_obs in (*Positive update*) let concrete_inserted = Primitives.Transformation.positive_transformations_of_actions sigs side_effect_dst actions in let edges' = List.fold_left (fun x h -> apply_concrete_positive_transformation (Pattern.Env.signatures domain) ~mod_connectivity_store state.imp.instances x h) edges_after_neg concrete_inserted in let (new_obs, new_deps), _ = List.fold_left (obs_from_transformation ~debug_mode domain edges') (([], Operator.DepSet.empty), Matching.empty_cache) concrete_inserted in let () = List.iter (fun (pat, (root, _)) -> Instances.update_roots state.imp.instances true state.imp.precomputed.unary_patterns edges' mod_connectivity_store pat root) new_obs in (*Print species*) let species = get_species_obs ~debug_mode sigs edges' new_obs [] state.imp.species in let () = List.iter (fun (file, _, mixture) -> outputs (Data.Species (file, Counter.current_time counter, mixture))) species in let rev_deps = Operator.DepSet.union state.outdated_elements (Operator.DepSet.union del_deps new_deps) in { outdated = false; imp = state.imp; matchings_of_rule = state.matchings_of_rule; nb_rectangular_instances_by_cc = state.nb_rectangular_instances_by_cc; unary_candidates = state.unary_candidates; edges = edges'; outdated_elements = rev_deps; events_to_block = state.events_to_block; } let max_dist_to_int counter state d = Nbr.to_int (value_alg counter state d) (* cc_va is the number of embeddings. It only has to be multiplied by the rate constant of the rule *) let store_activity ~debug_mode store env counter state id syntax_id rate cc_va = let () = if debug_mode then Format.printf "@[%sule %a has now %i instances.@]@." (if id mod 2 = 1 then "Unary r" else "R") (Model.print_rule ~noCounters:true ~env) (id / 2) cc_va in let act = match Nbr.to_float @@ value_alg counter state rate with | None -> if cc_va = 0 then 0. else infinity | Some rate -> rate *. float_of_int cc_va in let () = if act < 0. then ( let unary = id mod 2 = 1 in raise (ExceptionDefn.Malformed_Decl ( Format.asprintf "At t=%.2f %sctivity of rule %a has become negative (%f)" (Counter.current_time counter) (if unary then "Unary " else "") (Model.print_rule ~noCounters:debug_mode ~env) id act, Model.get_ast_rule_rate_pos ~unary env syntax_id )) ) in let old_act = get_activity id state in let () = set_activity id act state in store syntax_id old_act act let update_outdated_activities ~debug_mode store env counter state known_perts = let () = assert (not state.outdated) in let unary_rule_update modified_cc instances i pack rule = match rule.Primitives.unary_rate with | None -> pack | Some (unrate, _) -> let va, pack' = compute_unary_number instances pack modified_cc rule i in let () = store_activity ~debug_mode store env counter state ((2 * i) + 1) rule.Primitives.syntactic_rule (fst unrate) (Int64.to_int va) in pack' in let rec aux dep acc = Operator.DepSet.fold (fun dep ((exact_matchings, perts) as acc) -> match dep with | Operator.ALG j -> let () = recompute env counter state j in aux (Model.get_alg_reverse_dependencies env j) acc | Operator.MODIF p -> exact_matchings, p :: perts | Operator.RULE i -> let rule = Model.get_rule env i in let pattern_va = Instances.number_of_instances ~rule_id:i state.imp.instances rule.Primitives.connected_components in let () = store_activity ~debug_mode store env counter state (2 * i) rule.Primitives.syntactic_rule (fst rule.Primitives.rate) pattern_va in pop_exact_matchings exact_matchings i, perts) dep acc in let matchings_of_rule, perts = aux state.outdated_elements (state.matchings_of_rule, known_perts) in let nb_rectangular_instances_by_cc, unary_candidates = if Hashtbl.length state.imp.changed_connectivity = 0 then state.nb_rectangular_instances_by_cc, state.unary_candidates else ( let out = Model.fold_rules (unary_rule_update state.imp.changed_connectivity state.imp.instances) (state.nb_rectangular_instances_by_cc, state.unary_candidates) env in let () = Hashtbl.reset state.imp.changed_connectivity in out ) in ( { outdated = false; imp = state.imp; edges = state.edges; events_to_block = state.events_to_block; matchings_of_rule; nb_rectangular_instances_by_cc; unary_candidates; outdated_elements = state.imp.precomputed.always_outdated; }, perts ) let overwrite_var i counter state expr = let () = state.imp.variables_overwrite.(i) <- Some (Alg_expr.CONST (value_alg counter state expr)) in { state with outdated_elements = Operator.DepSet.add (Operator.ALG i) state.outdated_elements; } let update_tokens env counter state injected = let injected' = List.rev_map (fun ((expr, _), i) -> value_alg counter state expr, i) injected in { state with outdated_elements = List.fold_left (fun rdeps (va, i) -> let () = state.imp.tokens.(i) <- Nbr.add state.imp.tokens.(i) va in let deps' = Model.get_token_reverse_dependencies env i in if Operator.DepSet.is_empty deps' then rdeps else Operator.DepSet.union rdeps deps') state.outdated_elements injected'; } let transform_by_a_rule ~debug_mode outputs env counter state event_kind ?path rule ?rule_id inj = if is_blocked ~debug_mode state ?rule_id rule inj then Blocked else ( let state = update_tokens env counter state rule.Primitives.delta_tokens in let state = update_edges ~debug_mode outputs counter (Model.domain env) inj state event_kind ?path rule (Model.signatures env) in Success state ) let apply_given_unary_instance ~debug_mode ~outputs ~rule_id env counter state event_kind rule = function | None -> Clash | Some (inj, _rev_roots, path) -> let () = assert (not state.outdated) in let state' = { state with outdated_elements = Operator.DepSet.add (Operator.RULE rule_id) state.outdated_elements; } in (match path with | Some _ -> transform_by_a_rule ~debug_mode outputs env counter state' event_kind ~path rule ~rule_id inj | None -> let max_distance = match rule.Primitives.unary_rate with | None -> None | Some (_, dist_opt) -> (match dist_opt with | None -> None | Some d -> Some (max_dist_to_int counter state' d)) in let domain = Model.domain env in let nodes = Matching.elements_with_types domain rule.Primitives.connected_components inj in if max_distance = None && state.imp.story_machinery = None then if Edges.in_same_connected_component (fst (List.hd nodes.(0))) (fst (List.hd nodes.(1))) state.edges then transform_by_a_rule ~debug_mode outputs env counter state' event_kind ~path:None rule ~rule_id inj else Corrected else ( match Edges.are_connected ?max_distance state.edges nodes.(0) nodes.(1) with | None -> Corrected | Some _ as path -> transform_by_a_rule ~debug_mode outputs env counter state' event_kind ~path rule ~rule_id inj )) let apply_given_instance ~debug_mode ~outputs ?rule_id env counter state event_kind rule = function | None -> Clash | Some (inj, rev_roots, _path) -> let () = assert (not state.outdated) in let () = if debug_mode then ( let roots = Tools.array_rev_of_list rev_roots in Format.printf "@[On roots:@ @[%a@]@]@." (Pp.array Pp.space (fun _ -> Format.pp_print_int)) roots ) in (match rule.Primitives.unary_rate with | None -> transform_by_a_rule ~debug_mode outputs env counter state event_kind rule ?rule_id inj | Some (_, max_distance) -> (match max_distance with | None -> (match rev_roots with | [ root1; root0 ] -> if Edges.in_same_connected_component root0 root1 state.edges then Corrected else transform_by_a_rule ~debug_mode outputs env counter state event_kind rule ?rule_id inj | _ -> failwith "apply_given_rule unary rule without 2 patterns") | Some dist -> let domain = Model.domain env in let dist' = Some (max_dist_to_int counter state dist) in let nodes = Matching.elements_with_types domain rule.Primitives.connected_components inj in (match Edges.are_connected ?max_distance:dist' state.edges nodes.(0) nodes.(1) with | None -> transform_by_a_rule ~debug_mode outputs env counter state event_kind rule ?rule_id inj | Some _ -> Corrected))) let apply_given_rule ~debug_mode ~outputs ?rule_id env counter state event_kind rule = let domain = Model.domain env in let inst = pick_a_rule_instance ~debug_mode state state.imp.random_state domain state.edges ?rule_id rule in apply_given_instance ~debug_mode ~outputs ?rule_id env counter state event_kind rule inst let force_rule ~debug_mode ~outputs env counter state event_kind ?rule_id rule = match apply_given_rule ~debug_mode ~outputs ?rule_id env counter state event_kind rule with | Success out -> Some out | Corrected | Blocked | Clash -> let () = assert (not state.outdated) in let unary_rate = match rule.Primitives.unary_rate with | None -> None | Some (loc, dist_opt) -> (match dist_opt with | None -> Some (loc, None) | Some d -> Some (loc, Some (max_dist_to_int counter state d))) in (match all_injections ~debug_mode ?rule_id ?unary_rate state.imp.instances (Model.domain env) state.edges rule.Primitives.connected_components with | [] -> let () = outputs (Data.Warning ( None, fun f -> Format.fprintf f "At t=%f, %a does not apply (anymore)" (Counter.current_time counter) (Trace.print_event_kind ~env) event_kind )) in None | l -> let h, _ = List_util.random state.imp.random_state l in let out = transform_by_a_rule ~debug_mode outputs env counter state event_kind rule ?rule_id h in (match out with | Success out -> Some out | Blocked -> None | Clash | Corrected -> assert false)) let adjust_rule_instances ~debug_mode ~rule_id env counter state rule = let () = assert (not state.outdated) in let domain = Model.domain env in let unary_rate = match rule.Primitives.unary_rate with | None -> None | Some (loc, dist_opt) -> (match dist_opt with | None -> Some (loc, None) | Some d -> Some (loc, Some (max_dist_to_int counter state d))) in let act, state = adjust_rule_instances ~debug_mode ~rule_id ?unary_rate state domain state.edges rule.Primitives.connected_components rule in let () = store_activity ~debug_mode (fun _ _ _ -> ()) env counter state (2 * rule_id) rule.Primitives.syntactic_rule (fst rule.Primitives.rate) act in state (* Redefines `adjust_unary_rule_instances` *) let adjust_unary_rule_instances ~debug_mode ~rule_id env counter state rule = let () = assert (not state.outdated) in let domain = Model.domain env in let max_distance = Option_util.bind (fun (_, dist_opt) -> Option_util.map (max_dist_to_int counter state) dist_opt) rule.Primitives.unary_rate in let act, state = adjust_unary_rule_instances ~debug_mode ~rule_id ?max_distance state domain state.edges rule.Primitives.connected_components rule in let () = match rule.Primitives.unary_rate with | None -> assert false | Some (unrate, _) -> store_activity ~debug_mode (fun _ _ _ -> ()) env counter state ((2 * rule_id) + 1) rule.Primitives.syntactic_rule (fst unrate) act in state let incorporate_extra_pattern ~debug_mode domain state pattern = let () = assert (not state.outdated) in let () = Instances.incorporate_extra_pattern state.imp.instances pattern (Matching.roots_of ~debug_mode domain state.edges pattern) in { state with outdated = false } let snapshot ~debug_mode ~raw env counter state = { Data.snapshot_event = Counter.current_event counter; Data.snapshot_time = Counter.current_time counter; Data.snapshot_agents = Edges.build_user_snapshot ~debug_mode ~raw (Model.signatures env) state.edges; Data.snapshot_tokens = Array.mapi (fun i x -> Format.asprintf "%a" (Model.print_token ~env) i, x) state.imp.tokens; } let pick_an_instance ~debug_mode env state = let choice = pick_rule state.imp.random_state state in let rule_id = choice / 2 in let rule = Model.get_rule env rule_id in let domain = Model.domain env in ( choice mod 2 = 1, rule_id, if choice mod 2 = 1 then pick_a_unary_rule_instance ~debug_mode state state.imp.random_state domain state.edges ~rule_id rule else pick_a_rule_instance ~debug_mode state state.imp.random_state domain state.edges ~rule_id rule ) let is_correct_instance env graph (is_unary, rule_id, instance) = match instance with | None -> true | Some (_inj, inv_roots, path) -> let rule = Model.get_rule env rule_id in let pats = rule.Primitives.connected_components in Tools.array_fold_left2i (fun _ b cc r -> b && Instances.is_valid graph.imp.instances cc r) true pats (Tools.array_rev_of_list inv_roots) && ((not is_unary) || match path with | Some p -> Edges.is_valid_path p graph.edges | None -> (match inv_roots with | [ x; y ] -> Edges.in_same_connected_component x y graph.edges | _ -> assert false)) let apply_instance ~debug_mode ~outputs ?maxConsecutiveBlocked ~maxConsecutiveClash env counter graph (is_unary, rule_id, instance) = let cause = Trace.RULE rule_id in let rule = Model.get_rule env rule_id in let () = if debug_mode then Format.printf "@[<v>@[Applied@ %t%i:@]@ @[%a@]@]@." (fun f -> if is_unary then Format.fprintf f "unary@ ") rule_id (Kappa_printer.decompiled_rule ~noCounters:true ~full:true env) rule (*Rule_interpreter.print_dist env graph rule_id*) in let apply_given = if is_unary then apply_given_unary_instance ~debug_mode ~outputs ~rule_id else apply_given_instance ~debug_mode ~outputs ~rule_id in match apply_given env counter graph cause rule instance with | Success graph' -> let final_step = not (Counter.one_constructive_event ~rule_id counter) in Some rule.Primitives.syntactic_rule, final_step, graph' | (Clash | Corrected | Blocked) as out -> let continue = if out = Clash then Counter.one_clashing_instance_event ~rule_id counter else if out = Blocked then Counter.one_blocked_event counter else if is_unary then Counter.one_no_more_unary_event ~rule_id counter else Counter.one_no_more_binary_event ~rule_id counter in if Counter.consecutive_null_event ~rule_id counter < maxConsecutiveClash && match maxConsecutiveBlocked with | None -> true | Some n -> Counter.consecutive_blocked counter < n then None, not continue, graph else ( None, not continue, if is_unary then adjust_unary_rule_instances ~debug_mode ~rule_id env counter graph rule else adjust_rule_instances ~debug_mode ~rule_id env counter graph rule ) let aux_add_tracked patterns name tests state tpattern = let () = state.outdated <- true in let () = Array.iter (fun pattern -> let acc = Pattern.ObsMap.get tpattern pattern in Pattern.ObsMap.set tpattern pattern ((name, patterns, tests) :: acc)) patterns in { state with outdated = false } let add_tracked ~outputs patterns name tests state = let () = assert (not state.outdated) in match state.imp.story_machinery with | None -> let () = outputs (Data.Warning ( None, fun f -> Format.fprintf f "Observable %s should be tracked but the trace is not stored" name )) in state | Some tpattern -> aux_add_tracked patterns name tests state tpattern let remove_tracked patterns name state = let () = assert (not state.outdated) in match state.imp.story_machinery with | None -> state | Some tpattern -> (match name with | None -> let () = state.outdated <- true in let tester (_, el, _) = not @@ Tools.array_fold_lefti (fun i b x -> b && Pattern.is_equal_canonicals x el.(i)) true patterns in let () = Array.iter (fun pattern -> let acc = Pattern.ObsMap.get tpattern pattern in Pattern.ObsMap.set tpattern pattern (List.filter tester acc)) patterns in { state with outdated = false } | Some name -> let () = state.outdated <- true in let tester (n, _, _) = not (String.compare name n = 0) in let () = Pattern.ObsMap.iteri (fun cc_id plist -> Pattern.ObsMap.set tpattern cc_id (List.filter tester plist)) tpattern in { state with outdated = false }) let add_tracked_species patterns name tests state = aux_add_tracked patterns name tests state state.imp.species let remove_tracked_species name state = let () = state.outdated <- true in let tester (n, _, _) = not (String.compare name n = 0) in let () = Pattern.ObsMap.iteri (fun cc_id plist -> Pattern.ObsMap.set state.imp.species cc_id (List.filter tester plist)) state.imp.species in { state with outdated = false } let get_random_state state = state.imp.random_state let send_instances_message msg state = { state with imp = { state.imp with instances = Instances.receive_message msg state.imp.instances; }; } let add_outdated_dependencies new_deps state = let outdated_elements = Operator.DepSet.union new_deps state.outdated_elements in { state with outdated_elements } let debug_print_instances f st = Instances.debug_print f st.imp.instances end
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