libpetri 0.3.2 → 0.3.4

package/dist/verification/index.d.ts

@@ -388,6 +388,7 @@ declare class SmtVerifier {
     private _initialMarking;
     private _property;
     private readonly _environmentPlaces;
+    private readonly _sinkPlaces;
     private _environmentMode;
     private _timeoutMs;
     private constructor();
@@ -397,6 +398,11 @@ declare class SmtVerifier {
     property(property: SmtProperty): this;
     environmentPlaces(...places: EnvironmentPlace<any>[]): this;
     environmentMode(mode: EnvironmentAnalysisMode): this;
+    /**
+     * Declares expected sink (terminal) places for deadlock-freedom analysis.
+     * Markings where any sink place has a token are not considered deadlocks.
+     */
+    sinkPlaces(...places: Place<any>[]): this;
     timeout(ms: number): this;
     /**
      * Runs the verification pipeline.
@@ -484,7 +490,7 @@ interface EncodingResult {
  * - Reachable(M') :- Reachable(M) AND enabled(M,t) AND fire(M,M',t) — transition rules
  * - Error() :- Reachable(M) AND property_violation(M) — safety property
  */
-declare function encode(ctx: Z3Context, fp: Z3Fixedpoint, flatNet: FlatNet, initialMarking: MarkingState, property: SmtProperty, invariants: readonly PInvariant[]): EncodingResult;
+declare function encode(ctx: Z3Context, fp: Z3Fixedpoint, flatNet: FlatNet, initialMarking: MarkingState, property: SmtProperty, invariants: readonly PInvariant[], sinkPlaces?: ReadonlySet<Place<any>>): EncodingResult;
 
 /**
  * Result of counterexample decoding.

package/dist/verification/index.js

@@ -698,7 +698,7 @@ async function createSpacerRunner(timeoutMs) {
 }
 
 // src/verification/z3/smt-encoder.ts
-function encode(ctx, fp, flatNet, initialMarking, property, invariants) {
+function encode(ctx, fp, flatNet, initialMarking, property, invariants, sinkPlaces = /* @__PURE__ */ new Set()) {
   const P = flatNet.places.length;
   const Int = ctx.Int;
   const Bool_ = ctx.Bool;
@@ -720,7 +720,7 @@ function encode(ctx, fp, flatNet, initialMarking, property, invariants) {
     const ft = flatNet.transitions[t];
     encodeTransitionRule(ctx, fp, reachable, ft, flatNet, invariants, P);
   }
-  encodeErrorRule(ctx, fp, reachable, error, flatNet, property, P);
+  encodeErrorRule(ctx, fp, reachable, error, flatNet, property, sinkPlaces, P);
   return {
     errorExpr: error.call(),
     reachableDecl: reachable
@@ -791,24 +791,36 @@ function encodeFire(ctx, ft, _flatNet, mVars, mPrimeVars, P) {
   }
   return result;
 }
-function encodeErrorRule(ctx, fp, reachable, error, flatNet, property, P) {
+function encodeErrorRule(ctx, fp, reachable, error, flatNet, property, sinkPlaces, P) {
   const Int = ctx.Int;
   const mVars = [];
   for (let i = 0; i < P; i++) {
     mVars.push(Int.const(`em${i}`));
   }
   const reachBody = reachable.call(...mVars);
-  const violation = encodePropertyViolation(ctx, flatNet, property, mVars, P);
+  const violation = encodePropertyViolation(ctx, flatNet, property, sinkPlaces, mVars, P);
   const head = error.call();
   const body = ctx.And(reachBody, violation);
   const rule = ctx.Implies(body, head);
   const qRule = ctx.ForAll(mVars, rule);
   fp.addRule(qRule, `error_${property.type}`);
 }
-function encodePropertyViolation(ctx, flatNet, property, mVars, P) {
+function encodePropertyViolation(ctx, flatNet, property, sinkPlaces, mVars, P) {
   switch (property.type) {
-    case "deadlock-free":
-      return encodeDeadlock(ctx, flatNet, mVars, P);
+    case "deadlock-free": {
+      const deadlock = encodeDeadlock(ctx, flatNet, mVars, P);
+      if (sinkPlaces.size > 0) {
+        let notAtSink = ctx.Bool.val(true);
+        for (const sink of sinkPlaces) {
+          const idx = flatNetIndexOf(flatNet, sink);
+          if (idx >= 0) {
+            notAtSink = ctx.And(notAtSink, mVars[idx].eq(0));
+          }
+        }
+        return ctx.And(deadlock, notAtSink);
+      }
+      return deadlock;
+    }
     case "mutual-exclusion": {
       const idx1 = flatNetIndexOf(flatNet, property.p1);
       const idx2 = flatNetIndexOf(flatNet, property.p2);
@@ -926,6 +938,7 @@ var SmtVerifier = class _SmtVerifier {
   _initialMarking = MarkingState.empty();
   _property = deadlockFree();
   _environmentPlaces = /* @__PURE__ */ new Set();
+  _sinkPlaces = /* @__PURE__ */ new Set();
   _environmentMode = unbounded();
   _timeoutMs = 6e4;
   static forNet(net) {
@@ -953,6 +966,14 @@ var SmtVerifier = class _SmtVerifier {
     this._environmentMode = mode;
     return this;
   }
+  /**
+   * Declares expected sink (terminal) places for deadlock-freedom analysis.
+   * Markings where any sink place has a token are not considered deadlocks.
+   */
+  sinkPlaces(...places) {
+    for (const p of places) this._sinkPlaces.add(p);
+    return this;
+  }
   timeout(ms) {
     this._timeoutMs = ms;
     return this;
@@ -965,7 +986,8 @@ var SmtVerifier = class _SmtVerifier {
     const report = [];
     report.push("=== IC3/PDR SAFETY VERIFICATION ===\n");
     report.push(`Net: ${this.net.name}`);
-    report.push(`Property: ${propertyDescription(this._property)}`);
+    const propDesc = this._sinkPlaces.size === 0 ? propertyDescription(this._property) : `${propertyDescription(this._property)} (sinks: ${[...this._sinkPlaces].map((p) => p.name).join(", ")})`;
+    report.push(`Property: ${propDesc}`);
     report.push(`Timeout: ${(this._timeoutMs / 1e3).toFixed(0)}s
 `);
     report.push("Phase 1: Flattening net...");
@@ -992,7 +1014,7 @@ var SmtVerifier = class _SmtVerifier {
     }
     report.push(`  Result: ${structResultStr}
 `);
-    if (this._property.type === "deadlock-free" && structResult.type === "no-potential-deadlock") {
+    if (this._property.type === "deadlock-free" && this._sinkPlaces.size === 0 && structResult.type === "no-potential-deadlock") {
       report.push("=== RESULT ===\n");
       report.push("PROVEN (structural): Deadlock-freedom verified by Commoner's theorem.");
       report.push("  All siphons contain initially marked traps.");
@@ -1038,7 +1060,7 @@ var SmtVerifier = class _SmtVerifier {
       );
     }
     try {
-      const encoding = encode(runner.ctx, runner.fp, flatNet, this._initialMarking, this._property, invariants);
+      const encoding = encode(runner.ctx, runner.fp, flatNet, this._initialMarking, this._property, invariants, this._sinkPlaces);
       const queryResult = await runner.query(encoding.errorExpr, encoding.reachableDecl);
       switch (queryResult.type) {
         case "proven": {
@@ -1063,7 +1085,7 @@ var SmtVerifier = class _SmtVerifier {
             report.push("");
           }
           report.push("=== RESULT ===\n");
-          report.push(`PROVEN (IC3/PDR): ${propertyDescription(this._property)}`);
+          report.push(`PROVEN (IC3/PDR): ${propDesc}`);
           report.push("  Z3 Spacer proved no reachable state violates the property.");
           report.push("  NOTE: Verification ignores timing constraints and JS guards.");
           report.push("  An untimed proof is STRONGER than a timed one (timing only restricts behavior).");
@@ -1086,7 +1108,7 @@ var SmtVerifier = class _SmtVerifier {
           report.push("  Status: SAT (counterexample found)\n");
           const decoded = decode(runner.ctx, queryResult.answer, flatNet);
           report.push("=== RESULT ===\n");
-          report.push(`VIOLATED: ${propertyDescription(this._property)}`);
+          report.push(`VIOLATED: ${propDesc}`);
           if (decoded.trace.length > 0) {
             report.push(`  Counterexample trace (${decoded.trace.length} states):`);
             for (let i = 0; i < decoded.trace.length; i++) {
@@ -1114,7 +1136,7 @@ var SmtVerifier = class _SmtVerifier {
           report.push(`  Status: UNKNOWN (${queryResult.reason})
 `);
           report.push("=== RESULT ===\n");
-          report.push(`UNKNOWN: Could not determine ${propertyDescription(this._property)}`);
+          report.push(`UNKNOWN: Could not determine ${propDesc}`);
           report.push(`  Reason: ${queryResult.reason}`);
           return buildResult(
             { type: "unknown", reason: queryResult.reason },

package/dist/verification/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/verification/marking-state.ts","../../src/verification/encoding/flat-transition.ts","../../src/verification/encoding/flat-net.ts","../../src/verification/encoding/incidence-matrix.ts","../../src/verification/encoding/net-flattener.ts","../../src/verification/invariant/p-invariant.ts","../../src/verification/invariant/p-invariant-computer.ts","../../src/verification/invariant/structural-check.ts","../../src/verification/smt-property.ts","../../src/verification/smt-verification-result.ts","../../src/verification/z3/spacer-runner.ts","../../src/verification/z3/smt-encoder.ts","../../src/verification/z3/counterexample-decoder.ts","../../src/verification/smt-verifier.ts"],"sourcesContent":["import type { Place } from '../core/place.js';\n\n/** @internal Symbol key restricting construction to the builder and factory methods. */\nconst MARKING_STATE_KEY = Symbol('MarkingState.internal');\n\n/**\n * Immutable snapshot of a Petri net marking for state space analysis.\n *\n * Maps places (by name) to integer token counts. Only stores places with count > 0.\n * Used for invariant computation and structural verification, not runtime execution.\n */\nexport class MarkingState {\n  private readonly tokenCounts: ReadonlyMap<string, number>;\n  private readonly placesByName: ReadonlyMap<string, Place<any>>;\n\n  /** @internal Use {@link MarkingState.builder} or {@link MarkingState.empty} to create instances. */\n  constructor(key: symbol, tokenCounts: Map<string, number>, placesByName: Map<string, Place<any>>) {\n    if (key !== MARKING_STATE_KEY) throw new Error('Use MarkingState.builder() to create instances');\n    this.tokenCounts = tokenCounts;\n    this.placesByName = placesByName;\n  }\n\n  /** Returns the token count for a place (0 if absent). */\n  tokens(place: Place<any>): number {\n    return this.tokenCounts.get(place.name) ?? 0;\n  }\n\n  /** Checks if a place has at least one token. */\n  hasTokens(place: Place<any>): boolean {\n    return this.tokens(place) > 0;\n  }\n\n  /** Checks if any of the given places has tokens. */\n  hasTokensInAny(places: Iterable<Place<any>>): boolean {\n    for (const p of places) {\n      if (this.hasTokens(p)) return true;\n    }\n    return false;\n  }\n\n  /** Returns all places with tokens > 0. */\n  placesWithTokens(): Place<any>[] {\n    return [...this.placesByName.values()];\n  }\n\n  /** Returns the total number of tokens. */\n  totalTokens(): number {\n    let sum = 0;\n    for (const count of this.tokenCounts.values()) sum += count;\n    return sum;\n  }\n\n  /** Checks if no tokens exist anywhere. */\n  isEmpty(): boolean {\n    return this.tokenCounts.size === 0;\n  }\n\n  toString(): string {\n    if (this.tokenCounts.size === 0) return '{}';\n    const entries = [...this.tokenCounts.entries()]\n      .sort(([a], [b]) => a.localeCompare(b))\n      .map(([name, count]) => `${name}:${count}`);\n    return `{${entries.join(', ')}}`;\n  }\n\n  static empty(): MarkingState {\n    return new MarkingState(MARKING_STATE_KEY, new Map(), new Map());\n  }\n\n  static builder(): MarkingStateBuilder {\n    return new MarkingStateBuilder();\n  }\n}\n\nexport class MarkingStateBuilder {\n  private readonly tokenCounts = new Map<string, number>();\n  private readonly placesByName = new Map<string, Place<any>>();\n\n  /** Sets the token count for a place. */\n  tokens(place: Place<any>, count: number): this {\n    if (count < 0) throw new Error(`Token count cannot be negative: ${count}`);\n    if (count > 0) {\n      this.tokenCounts.set(place.name, count);\n      this.placesByName.set(place.name, place);\n    } else {\n      this.tokenCounts.delete(place.name);\n      this.placesByName.delete(place.name);\n    }\n    return this;\n  }\n\n  /** Adds tokens to a place. */\n  addTokens(place: Place<any>, count: number): this {\n    if (count < 0) throw new Error(`Token count cannot be negative: ${count}`);\n    if (count > 0) {\n      const current = this.tokenCounts.get(place.name) ?? 0;\n      this.tokenCounts.set(place.name, current + count);\n      this.placesByName.set(place.name, place);\n    }\n    return this;\n  }\n\n  build(): MarkingState {\n    return new MarkingState(MARKING_STATE_KEY, new Map(this.tokenCounts), new Map(this.placesByName));\n  }\n}\n","import type { Transition } from '../../core/transition.js';\n\n/**\n * A flattened transition with pre/post vectors for SMT encoding.\n *\n * Each Transition with XOR outputs is expanded into multiple FlatTransitions\n * (one per branch). Non-XOR transitions map 1:1.\n */\nexport interface FlatTransition {\n  /** Display name (e.g. \"Search_b0\", \"Search_b1\"). */\n  readonly name: string;\n  /** The original transition. */\n  readonly source: Transition;\n  /** Which XOR branch (-1 if no XOR). */\n  readonly branchIndex: number;\n  /** Tokens consumed per place (indexed by place index). */\n  readonly preVector: readonly number[];\n  /** Tokens produced per place (indexed by place index). */\n  readonly postVector: readonly number[];\n  /** Place indices where inhibitor arcs block firing. */\n  readonly inhibitorPlaces: readonly number[];\n  /** Place indices requiring a token without consuming. */\n  readonly readPlaces: readonly number[];\n  /** Place indices set to 0 on firing. */\n  readonly resetPlaces: readonly number[];\n  /** True at index i means place i uses All/AtLeast semantics. */\n  readonly consumeAll: readonly boolean[];\n}\n\nexport function flatTransition(\n  name: string,\n  source: Transition,\n  branchIndex: number,\n  preVector: number[],\n  postVector: number[],\n  inhibitorPlaces: number[],\n  readPlaces: number[],\n  resetPlaces: number[],\n  consumeAll: boolean[],\n): FlatTransition {\n  return {\n    name,\n    source,\n    branchIndex,\n    preVector,\n    postVector,\n    inhibitorPlaces,\n    readPlaces,\n    resetPlaces,\n    consumeAll,\n  };\n}\n","import type { Place } from '../../core/place.js';\nimport type { FlatTransition } from './flat-transition.js';\n\n/**\n * A flattened Petri net with indexed places and XOR-expanded transitions.\n *\n * Intermediate representation between the high-level PetriNet and Z3 CHC encoding.\n */\nexport interface FlatNet {\n  /** Ordered list of places (index = position). */\n  readonly places: readonly Place<any>[];\n  /** Reverse lookup: place name -> index. */\n  readonly placeIndex: ReadonlyMap<string, number>;\n  /** XOR-expanded flat transitions. */\n  readonly transitions: readonly FlatTransition[];\n  /** For bounded environment places: place name -> max tokens. */\n  readonly environmentBounds: ReadonlyMap<string, number>;\n}\n\nexport function flatNetPlaceCount(net: FlatNet): number {\n  return net.places.length;\n}\n\nexport function flatNetTransitionCount(net: FlatNet): number {\n  return net.transitions.length;\n}\n\nexport function flatNetIndexOf(net: FlatNet, place: Place<any>): number {\n  return net.placeIndex.get(place.name) ?? -1;\n}\n","import type { FlatNet } from './flat-net.js';\n\n/**\n * Incidence matrix for a flattened Petri net.\n *\n * The incidence matrix C is defined as C[t][p] = post[t][p] - pre[t][p].\n * It captures the net effect of each transition on each place.\n *\n * P-invariants are solutions to y^T * C = 0, found via null space\n * computation on C^T.\n */\nexport class IncidenceMatrix {\n  private readonly _pre: readonly (readonly number[])[];\n  private readonly _post: readonly (readonly number[])[];\n  private readonly _incidence: readonly (readonly number[])[];\n  private readonly _numTransitions: number;\n  private readonly _numPlaces: number;\n\n  private constructor(\n    pre: number[][],\n    post: number[][],\n    incidence: number[][],\n    numTransitions: number,\n    numPlaces: number,\n  ) {\n    this._pre = pre;\n    this._post = post;\n    this._incidence = incidence;\n    this._numTransitions = numTransitions;\n    this._numPlaces = numPlaces;\n  }\n\n  /**\n   * Computes the incidence matrix from a FlatNet.\n   */\n  static from(flatNet: FlatNet): IncidenceMatrix {\n    const T = flatNet.transitions.length;\n    const P = flatNet.places.length;\n\n    const pre: number[][] = [];\n    const post: number[][] = [];\n    const incidence: number[][] = [];\n\n    for (let t = 0; t < T; t++) {\n      const ft = flatNet.transitions[t]!;\n      const preRow = new Array<number>(P);\n      const postRow = new Array<number>(P);\n      const incRow = new Array<number>(P);\n\n      for (let p = 0; p < P; p++) {\n        preRow[p] = ft.preVector[p]!;\n        postRow[p] = ft.postVector[p]!;\n        incRow[p] = postRow[p]! - preRow[p]!;\n      }\n\n      pre.push(preRow);\n      post.push(postRow);\n      incidence.push(incRow);\n    }\n\n    return new IncidenceMatrix(pre, post, incidence, T, P);\n  }\n\n  /**\n   * Returns C^T (transpose of incidence matrix), dimensions [P][T].\n   * Used for P-invariant computation: null space of C^T gives P-invariants.\n   */\n  transposedIncidence(): number[][] {\n    const ct: number[][] = [];\n    for (let p = 0; p < this._numPlaces; p++) {\n      const row = new Array<number>(this._numTransitions);\n      for (let t = 0; t < this._numTransitions; t++) {\n        row[t] = this._incidence[t]![p]!;\n      }\n      ct.push(row);\n    }\n    return ct;\n  }\n\n  /** Returns the pre-matrix (tokens consumed). T×P. */\n  pre(): readonly (readonly number[])[] { return this._pre; }\n\n  /** Returns the post-matrix (tokens produced). T×P. */\n  post(): readonly (readonly number[])[] { return this._post; }\n\n  /** Returns the incidence matrix C[t][p] = post - pre. T×P. */\n  incidence(): readonly (readonly number[])[] { return this._incidence; }\n\n  numTransitions(): number { return this._numTransitions; }\n  numPlaces(): number { return this._numPlaces; }\n}\n","/**\n * @module net-flattener\n *\n * Flattens a PetriNet into integer-indexed pre/post vectors for SMT encoding.\n *\n * **XOR expansion**: Transitions with XOR output specs are expanded into multiple\n * flat transitions — one per deterministic branch. Each branch produces tokens to\n * exactly one XOR child's places. This converts non-deterministic output routing\n * into separate transitions that the SMT solver can reason about independently.\n *\n * **Vector construction**: For each flat transition, builds:\n * - `preVector[p]`: tokens consumed from place p (input cardinality)\n * - `postVector[p]`: tokens produced to place p (from the selected branch)\n * - `consumeAll[p]`: true for `all`/`at-least` inputs (consume everything)\n * - Index arrays for inhibitor, read, and reset arcs\n *\n * Places are sorted by name for stable, deterministic indexing across runs.\n */\nimport type { PetriNet } from '../../core/petri-net.js';\nimport type { Place, EnvironmentPlace } from '../../core/place.js';\nimport type { Out } from '../../core/out.js';\nimport type { FlatNet } from './flat-net.js';\nimport { flatTransition } from './flat-transition.js';\nimport { enumerateBranches, allPlaces as outAllPlaces } from '../../core/out.js';\n\n/**\n * How to treat environment places during analysis.\n */\nexport type EnvironmentAnalysisMode =\n  | { readonly type: 'unbounded' }\n  | { readonly type: 'bounded'; readonly maxTokens: number };\n\nexport function unbounded(): EnvironmentAnalysisMode {\n  return { type: 'unbounded' };\n}\n\nexport function bounded(maxTokens: number): EnvironmentAnalysisMode {\n  return { type: 'bounded', maxTokens };\n}\n\n/**\n * Flattens a PetriNet into a FlatNet suitable for SMT encoding.\n *\n * Flattening involves:\n * 1. Assigning each place a stable integer index (sorted by name)\n * 2. Expanding XOR outputs into separate flat transitions (one per branch)\n * 3. Building pre/post vectors from input/output specs\n * 4. Recording inhibitor, read, and reset arcs\n * 5. Setting environment bounds for bounded analysis mode\n */\nexport function flatten(\n  net: PetriNet,\n  environmentPlaces: Set<EnvironmentPlace<any>> = new Set(),\n  environmentMode: EnvironmentAnalysisMode = unbounded(),\n): FlatNet {\n  // 1. Collect ALL places\n  const allPlacesSet = new Map<string, Place<any>>();\n  for (const p of net.places) {\n    allPlacesSet.set(p.name, p);\n  }\n  for (const t of net.transitions) {\n    for (const inSpec of t.inputSpecs) {\n      allPlacesSet.set(inSpec.place.name, inSpec.place);\n    }\n    if (t.outputSpec !== null) {\n      for (const p of outAllPlaces(t.outputSpec)) {\n        allPlacesSet.set(p.name, p);\n      }\n    }\n    for (const arc of t.inhibitors) allPlacesSet.set(arc.place.name, arc.place);\n    for (const arc of t.reads) allPlacesSet.set(arc.place.name, arc.place);\n    for (const arc of t.resets) allPlacesSet.set(arc.place.name, arc.place);\n  }\n\n  // Sort by name for stable indexing\n  const places = [...allPlacesSet.values()].sort((a, b) => a.name.localeCompare(b.name));\n\n  const placeIndex = new Map<string, number>();\n  for (let i = 0; i < places.length; i++) {\n    placeIndex.set(places[i]!.name, i);\n  }\n\n  // 2. Compute environment bounds\n  const environmentBounds = new Map<string, number>();\n  if (environmentMode.type === 'bounded') {\n    for (const ep of environmentPlaces) {\n      environmentBounds.set(ep.place.name, environmentMode.maxTokens);\n    }\n  }\n\n  // 3. Expand transitions\n  const n = places.length;\n  const flatTransitions = [];\n\n  for (const transition of net.transitions) {\n    const branches = enumerateOutputBranches(transition);\n\n    for (let branchIdx = 0; branchIdx < branches.length; branchIdx++) {\n      const branchPlaces = branches[branchIdx]!;\n      const name = branches.length > 1\n        ? `${transition.name}_b${branchIdx}`\n        : transition.name;\n\n      // Build pre-vector and consumeAll flags\n      const preVector = new Array<number>(n).fill(0);\n      const consumeAll = new Array<boolean>(n).fill(false);\n\n      for (const inSpec of transition.inputSpecs) {\n        const idx = placeIndex.get(inSpec.place.name);\n        if (idx === undefined) continue;\n\n        switch (inSpec.type) {\n          case 'one':\n            preVector[idx] = 1;\n            break;\n          case 'exactly':\n            preVector[idx] = inSpec.count;\n            break;\n          case 'all':\n            preVector[idx] = 1;\n            consumeAll[idx] = true;\n            break;\n          case 'at-least':\n            preVector[idx] = inSpec.minimum;\n            consumeAll[idx] = true;\n            break;\n        }\n      }\n\n      // Build post-vector from branch output places\n      const postVector = new Array<number>(n).fill(0);\n      for (const p of branchPlaces) {\n        const idx = placeIndex.get(p.name);\n        if (idx !== undefined) {\n          postVector[idx] = 1;\n        }\n      }\n\n      // Inhibitor places\n      const inhibitorPlaces = transition.inhibitors\n        .map(arc => placeIndex.get(arc.place.name))\n        .filter((idx): idx is number => idx !== undefined);\n\n      // Read places\n      const readPlaces = transition.reads\n        .map(arc => placeIndex.get(arc.place.name))\n        .filter((idx): idx is number => idx !== undefined);\n\n      // Reset places\n      const resetPlaces = transition.resets\n        .map(arc => placeIndex.get(arc.place.name))\n        .filter((idx): idx is number => idx !== undefined);\n\n      flatTransitions.push(flatTransition(\n        name,\n        transition,\n        branches.length > 1 ? branchIdx : -1,\n        preVector,\n        postVector,\n        inhibitorPlaces,\n        readPlaces,\n        resetPlaces,\n        consumeAll,\n      ));\n    }\n  }\n\n  return {\n    places,\n    placeIndex,\n    transitions: flatTransitions,\n    environmentBounds,\n  };\n}\n\nfunction enumerateOutputBranches(t: { outputSpec: Out | null }): ReadonlySet<Place<any>>[] {\n  if (t.outputSpec !== null) {\n    return enumerateBranches(t.outputSpec) as ReadonlySet<Place<any>>[];\n  }\n  // No outputs (sink transition)\n  return [new Set()];\n}\n","/**\n * A P-invariant (place invariant) of a Petri net.\n *\n * A P-invariant is a vector y such that y^T * C = 0, where C is the\n * incidence matrix. This means that for any reachable marking M:\n * sum(y_i * M_i) = constant, where constant = sum(y_i * M0_i).\n *\n * P-invariants provide structural bounds on places and are used as\n * strengthening lemmas for the IC3/PDR engine.\n */\nexport interface PInvariant {\n  /** Weight vector (one entry per place index). */\n  readonly weights: readonly number[];\n  /** The invariant value sum(y_i * M0_i). */\n  readonly constant: number;\n  /** Set of place indices where weight != 0. */\n  readonly support: ReadonlySet<number>;\n}\n\nexport function pInvariant(weights: number[], constant: number, support: Set<number>): PInvariant {\n  return { weights, constant, support };\n}\n\nexport function pInvariantToString(inv: PInvariant): string {\n  const parts: string[] = [];\n  for (const i of inv.support) {\n    if (inv.weights[i] !== 1) {\n      parts.push(`${inv.weights[i]}*p${i}`);\n    } else {\n      parts.push(`p${i}`);\n    }\n  }\n  return `PInvariant[${parts.join(' + ')} = ${inv.constant}]`;\n}\n","/**\n * @module p-invariant-computer\n *\n * Computes P-invariants of a Petri net via integer Gaussian elimination (Farkas' algorithm).\n *\n * **Algorithm**: A P-invariant is a non-negative integer vector y such that y^T · C = 0\n * (where C is the incidence matrix). This expresses a conservation law: the weighted\n * token sum Σ(y_i · M[i]) is constant across all reachable markings.\n *\n * **Farkas variant**: Constructs the augmented matrix [C^T | I_P] and row-reduces\n * the C^T portion to zero using integer elimination (no floating point). Rows where\n * the C^T part becomes all-zero yield invariant vectors from the identity part.\n * Row normalization by GCD keeps values small during elimination.\n *\n * **Integer Gaussian elimination**: Each elimination step multiplies rows by pivot\n * coefficients (a·row - b·pivotRow) to avoid fractions. This preserves integer\n * arithmetic throughout, critical for exact invariant computation.\n *\n * Invariants are used to strengthen SMT queries (added as constraints on M').\n */\nimport type { FlatNet } from '../encoding/flat-net.js';\nimport type { IncidenceMatrix } from '../encoding/incidence-matrix.js';\nimport type { MarkingState } from '../marking-state.js';\nimport type { PInvariant } from './p-invariant.js';\nimport { pInvariant } from './p-invariant.js';\n\n/**\n * Computes P-invariants of a Petri net via integer Gaussian elimination.\n *\n * P-invariants are non-negative integer vectors y where y^T * C = 0.\n * They express conservation laws: the weighted token sum is constant\n * across all reachable markings.\n *\n * Algorithm: compute the null space of C^T using integer row reduction\n * with an augmented identity matrix (Farkas' algorithm variant).\n */\nexport function computePInvariants(\n  matrix: IncidenceMatrix,\n  flatNet: FlatNet,\n  initialMarking: MarkingState,\n): PInvariant[] {\n  const P = matrix.numPlaces();\n  const T = matrix.numTransitions();\n\n  if (P === 0 || T === 0) return [];\n\n  // We want to find y such that y^T * C = 0, i.e., C^T * y = 0\n  // Start with augmented matrix [C^T | I_P]\n  // Row-reduce C^T part to zero; the I_P part gives the invariant vectors.\n  const ct = matrix.transposedIncidence(); // P × T\n\n  // Augmented matrix: P rows, T + P columns\n  // Use regular numbers (safe for nets with < ~50 places/transitions)\n  const cols = T + P;\n  const augmented: number[][] = [];\n  for (let i = 0; i < P; i++) {\n    const row = new Array<number>(cols).fill(0);\n    for (let j = 0; j < T; j++) {\n      row[j] = ct[i]![j]!;\n    }\n    row[T + i] = 1; // identity part\n    augmented.push(row);\n  }\n\n  // Integer Gaussian elimination on the C^T part (columns 0..T-1)\n  let pivotRow = 0;\n  for (let col = 0; col < T && pivotRow < P; col++) {\n    // Find pivot (non-zero entry in this column)\n    let pivot = -1;\n    for (let row = pivotRow; row < P; row++) {\n      if (augmented[row]![col] !== 0) {\n        pivot = row;\n        break;\n      }\n    }\n    if (pivot === -1) continue; // free variable\n\n    // Swap pivot row\n    if (pivot !== pivotRow) {\n      const tmp = augmented[pivotRow]!;\n      augmented[pivotRow] = augmented[pivot]!;\n      augmented[pivot] = tmp;\n    }\n\n    // Eliminate this column in all other rows\n    for (let row = 0; row < P; row++) {\n      if (row === pivotRow || augmented[row]![col] === 0) continue;\n\n      const a = augmented[pivotRow]![col]!;\n      const b = augmented[row]![col]!;\n\n      // row = a*row - b*pivotRow (keeps integers, eliminates col)\n      for (let c = 0; c < cols; c++) {\n        augmented[row]![c] = a * augmented[row]![c]! - b * augmented[pivotRow]![c]!;\n      }\n\n      // Normalize by GCD to keep values small\n      normalizeRow(augmented[row]!, cols);\n    }\n\n    pivotRow++;\n  }\n\n  // Extract invariants: rows where C^T part is all zeros\n  const invariants: PInvariant[] = [];\n  for (let row = 0; row < P; row++) {\n    let isZero = true;\n    for (let col = 0; col < T; col++) {\n      if (augmented[row]![col] !== 0) {\n        isZero = false;\n        break;\n      }\n    }\n    if (!isZero) continue;\n\n    // Extract the weight vector from the identity part\n    const weights = new Array<number>(P);\n    let allNonNegative = true;\n    let hasPositive = false;\n\n    for (let i = 0; i < P; i++) {\n      weights[i] = augmented[row]![T + i]!;\n      if (weights[i]! < 0) {\n        allNonNegative = false;\n        break;\n      }\n      if (weights[i]! > 0) hasPositive = true;\n    }\n\n    // We want semi-positive invariants (all weights >= 0, at least one > 0)\n    if (!allNonNegative) {\n      // Try negating\n      let allNonPositive = true;\n      for (let i = 0; i < P; i++) {\n        if (augmented[row]![T + i]! > 0) {\n          allNonPositive = false;\n          break;\n        }\n      }\n      if (allNonPositive) {\n        for (let i = 0; i < P; i++) {\n          weights[i] = -augmented[row]![T + i]!;\n        }\n        hasPositive = true;\n        allNonNegative = true;\n      }\n    }\n\n    if (!allNonNegative || !hasPositive) continue;\n\n    // Normalize: divide by GCD of weights\n    let g = 0;\n    for (const w of weights) {\n      if (w > 0) g = gcd(g, w);\n    }\n    if (g > 1) {\n      for (let i = 0; i < P; i++) {\n        weights[i] = weights[i]! / g;\n      }\n    }\n\n    // Compute support and constant\n    const support = new Set<number>();\n    let constant = 0;\n    for (let i = 0; i < P; i++) {\n      if (weights[i] !== 0) {\n        support.add(i);\n        const place = flatNet.places[i]!;\n        constant += weights[i]! * initialMarking.tokens(place);\n      }\n    }\n\n    invariants.push(pInvariant(weights, constant, support));\n  }\n\n  return invariants;\n}\n\n/**\n * Checks if every place is covered by at least one P-invariant.\n * If true, the net is structurally bounded.\n */\nexport function isCoveredByInvariants(invariants: readonly PInvariant[], numPlaces: number): boolean {\n  const covered = new Array<boolean>(numPlaces).fill(false);\n  for (const inv of invariants) {\n    for (const idx of inv.support) {\n      if (idx < numPlaces) covered[idx] = true;\n    }\n  }\n  return covered.every(c => c);\n}\n\nfunction normalizeRow(row: number[], cols: number): void {\n  let g = 0;\n  for (let c = 0; c < cols; c++) {\n    if (row[c] !== 0) {\n      g = gcd(g, Math.abs(row[c]!));\n    }\n  }\n  if (g > 1) {\n    for (let c = 0; c < cols; c++) {\n      row[c] = row[c]! / g;\n    }\n  }\n}\n\nfunction gcd(a: number, b: number): number {\n  while (b !== 0) {\n    const t = b;\n    b = a % b;\n    a = t;\n  }\n  return a;\n}\n","/**\n * @module structural-check\n *\n * Structural deadlock pre-check using siphon/trap analysis (Commoner's theorem).\n *\n * **Commoner's theorem**: A Petri net is deadlock-free if every siphon contains\n * an initially marked trap.\n *\n * **Siphon**: A set of places S where every transition that outputs to S also\n * inputs from S. Key property: once all places in a siphon become empty,\n * they can never be re-marked. An empty siphon can cause deadlock.\n *\n * **Trap**: A set of places S where every transition that inputs from S also\n * outputs to S. Key property: once any place in a trap is marked,\n * the trap remains marked forever.\n *\n * **Algorithm**: For each place, compute the minimal siphon containing it via\n * fixed-point expansion. For each siphon, find the maximal trap within it\n * (fixed-point contraction). If every siphon contains an initially-marked\n * trap, deadlock-freedom is proven structurally — no SMT query needed.\n *\n * Limited to nets with ≤50 places to bound enumeration cost.\n */\nimport type { FlatNet } from '../encoding/flat-net.js';\nimport type { MarkingState } from '../marking-state.js';\n\nconst MAX_PLACES_FOR_SIPHON_ANALYSIS = 50;\n\n/**\n * Result of structural deadlock check using siphon/trap analysis.\n */\nexport type StructuralCheckResult =\n  | { readonly type: 'no-potential-deadlock' }\n  | { readonly type: 'potential-deadlock'; readonly siphon: ReadonlySet<number> }\n  | { readonly type: 'inconclusive'; readonly reason: string };\n\n/**\n * Structural deadlock pre-check using siphon/trap analysis.\n *\n * Commoner's theorem: a Petri net is deadlock-free if every siphon\n * contains a marked trap.\n *\n * A siphon is a set of places S such that every transition with\n * an output in S also has an input in S. Once empty, a siphon stays empty.\n *\n * A trap is a set of places S such that every transition with\n * an input in S also has an output in S. Once marked, a trap stays marked.\n */\nexport function structuralCheck(flatNet: FlatNet, initialMarking: MarkingState): StructuralCheckResult {\n  const P = flatNet.places.length;\n\n  if (P === 0) {\n    return { type: 'no-potential-deadlock' };\n  }\n\n  if (P > MAX_PLACES_FOR_SIPHON_ANALYSIS) {\n    return { type: 'inconclusive', reason: `Net has ${P} places, siphon enumeration skipped` };\n  }\n\n  const siphons = findMinimalSiphons(flatNet);\n\n  if (siphons.length === 0) {\n    return { type: 'no-potential-deadlock' };\n  }\n\n  for (const siphon of siphons) {\n    const trap = findMaximalTrapIn(flatNet, siphon);\n\n    if (trap.size === 0 || !isMarked(trap, flatNet, initialMarking)) {\n      return { type: 'potential-deadlock', siphon };\n    }\n  }\n\n  return { type: 'no-potential-deadlock' };\n}\n\n/**\n * Finds minimal siphons by checking all non-empty subsets of deadlock-enabling places.\n * Uses a fixed-point approach: start from each place and grow the siphon.\n */\nexport function findMinimalSiphons(flatNet: FlatNet): ReadonlySet<number>[] {\n  const P = flatNet.places.length;\n  const siphons: Set<number>[] = [];\n\n  // Pre-compute: for each place, which transitions have it as output?\n  const placeAsOutput: number[][] = [];\n  for (let p = 0; p < P; p++) {\n    placeAsOutput.push([]);\n  }\n\n  for (let t = 0; t < flatNet.transitions.length; t++) {\n    const ft = flatNet.transitions[t]!;\n    for (let p = 0; p < P; p++) {\n      if (ft.postVector[p]! > 0) {\n        placeAsOutput[p]!.push(t);\n      }\n    }\n  }\n\n  for (let startPlace = 0; startPlace < P; startPlace++) {\n    const siphon = computeSiphonContaining(startPlace, flatNet, placeAsOutput);\n    if (siphon !== null && siphon.size > 0) {\n      let isMinimal = true;\n      const toRemove: number[] = [];\n      for (let i = 0; i < siphons.length; i++) {\n        const existing = siphons[i]!;\n        if (setsEqual(existing, siphon)) {\n          isMinimal = false;\n          break;\n        }\n        if (isSubsetOf(existing, siphon)) {\n          isMinimal = false;\n          break;\n        }\n        if (isSubsetOf(siphon, existing)) {\n          toRemove.push(i);\n        }\n      }\n      for (let i = toRemove.length - 1; i >= 0; i--) {\n        siphons.splice(toRemove[i]!, 1);\n      }\n      if (isMinimal) {\n        siphons.push(siphon);\n      }\n    }\n  }\n\n  return siphons;\n}\n\nfunction computeSiphonContaining(\n  startPlace: number,\n  flatNet: FlatNet,\n  placeAsOutput: number[][],\n): Set<number> | null {\n  const siphon = new Set<number>();\n  siphon.add(startPlace);\n\n  let changed = true;\n  while (changed) {\n    changed = false;\n    const snapshot = [...siphon];\n\n    for (const p of snapshot) {\n      for (const t of placeAsOutput[p]!) {\n        const ft = flatNet.transitions[t]!;\n\n        let hasInputInSiphon = false;\n        for (let q = 0; q < flatNet.places.length; q++) {\n          if (ft.preVector[q]! > 0 && siphon.has(q)) {\n            hasInputInSiphon = true;\n            break;\n          }\n        }\n\n        if (!hasInputInSiphon) {\n          let added = false;\n          for (let q = 0; q < flatNet.places.length; q++) {\n            if (ft.preVector[q]! > 0) {\n              if (!siphon.has(q)) {\n                siphon.add(q);\n                changed = true;\n              }\n              added = true;\n              break;\n            }\n          }\n          if (!added) {\n            return null;\n          }\n        }\n      }\n    }\n  }\n\n  return siphon;\n}\n\n/**\n * Finds the maximal trap within a given set of places.\n * Uses fixed-point: start with the full set and remove places that violate the trap condition.\n */\nexport function findMaximalTrapIn(flatNet: FlatNet, places: ReadonlySet<number>): ReadonlySet<number> {\n  const trap = new Set(places);\n\n  let changed = true;\n  while (changed) {\n    changed = false;\n    const toRemove: number[] = [];\n\n    for (const p of trap) {\n      let satisfies = true;\n      for (let t = 0; t < flatNet.transitions.length; t++) {\n        const ft = flatNet.transitions[t]!;\n        if (ft.preVector[p]! > 0) {\n          let outputsToTrap = false;\n          for (const q of trap) {\n            if (ft.postVector[q]! > 0) {\n              outputsToTrap = true;\n              break;\n            }\n          }\n          if (!outputsToTrap) {\n            satisfies = false;\n            break;\n          }\n        }\n      }\n      if (!satisfies) {\n        toRemove.push(p);\n      }\n    }\n\n    if (toRemove.length > 0) {\n      for (const p of toRemove) trap.delete(p);\n      changed = true;\n    }\n  }\n\n  return trap;\n}\n\nfunction isMarked(placeIndices: ReadonlySet<number>, flatNet: FlatNet, marking: MarkingState): boolean {\n  for (const idx of placeIndices) {\n    const place = flatNet.places[idx]!;\n    if (marking.tokens(place) > 0) return true;\n  }\n  return false;\n}\n\nfunction setsEqual(a: ReadonlySet<number>, b: ReadonlySet<number>): boolean {\n  if (a.size !== b.size) return false;\n  for (const v of a) {\n    if (!b.has(v)) return false;\n  }\n  return true;\n}\n\nfunction isSubsetOf(sub: ReadonlySet<number>, sup: ReadonlySet<number>): boolean {\n  if (sub.size > sup.size) return false;\n  for (const v of sub) {\n    if (!sup.has(v)) return false;\n  }\n  return true;\n}\n","import type { Place } from '../core/place.js';\n\n/**\n * Safety properties that can be verified via IC3/PDR.\n *\n * Each property is encoded as an error condition: if a reachable state\n * violates the property, Spacer finds a counterexample. If no violation\n * is reachable, the property is proven.\n */\nexport type SmtProperty = DeadlockFree | MutualExclusion | PlaceBound | Unreachable;\n\n/** Deadlock-freedom: no reachable marking has all transitions disabled. */\nexport interface DeadlockFree {\n  readonly type: 'deadlock-free';\n}\n\n/** Mutual exclusion: two places never have tokens simultaneously. */\nexport interface MutualExclusion {\n  readonly type: 'mutual-exclusion';\n  readonly p1: Place<any>;\n  readonly p2: Place<any>;\n}\n\n/** Place bound: a place never exceeds a given token count. */\nexport interface PlaceBound {\n  readonly type: 'place-bound';\n  readonly place: Place<any>;\n  readonly bound: number;\n}\n\n/** Unreachability: the given places never all have tokens simultaneously. */\nexport interface Unreachable {\n  readonly type: 'unreachable';\n  readonly places: ReadonlySet<Place<any>>;\n}\n\n// Factory functions\n\nexport function deadlockFree(): DeadlockFree {\n  return { type: 'deadlock-free' };\n}\n\nexport function mutualExclusion(p1: Place<any>, p2: Place<any>): MutualExclusion {\n  return { type: 'mutual-exclusion', p1, p2 };\n}\n\nexport function placeBound(place: Place<any>, bound: number): PlaceBound {\n  return { type: 'place-bound', place, bound };\n}\n\nexport function unreachable(places: ReadonlySet<Place<any>>): Unreachable {\n  return { type: 'unreachable', places: new Set(places) };\n}\n\n/** Human-readable description of a property. */\nexport function propertyDescription(prop: SmtProperty): string {\n  switch (prop.type) {\n    case 'deadlock-free':\n      return 'Deadlock-freedom';\n    case 'mutual-exclusion':\n      return `Mutual exclusion of ${prop.p1.name} and ${prop.p2.name}`;\n    case 'place-bound':\n      return `Place ${prop.place.name} bounded by ${prop.bound}`;\n    case 'unreachable':\n      return `Unreachability of marking with tokens in {${[...prop.places].map(p => p.name).join(', ')}}`;\n  }\n}\n","import type { MarkingState } from './marking-state.js';\nimport type { PInvariant } from './invariant/p-invariant.js';\n\n/**\n * Verification verdict.\n */\nexport type Verdict = Proven | Violated | Unknown;\n\n/** Property proven safe. No reachable state violates it. */\nexport interface Proven {\n  readonly type: 'proven';\n  readonly method: string;\n  readonly inductiveInvariant: string | null;\n}\n\n/** Property violated. A counterexample trace is available. */\nexport interface Violated {\n  readonly type: 'violated';\n}\n\n/** Could not determine. */\nexport interface Unknown {\n  readonly type: 'unknown';\n  readonly reason: string;\n}\n\n/**\n * Solver statistics.\n */\nexport interface SmtStatistics {\n  readonly places: number;\n  readonly transitions: number;\n  readonly invariantsFound: number;\n  readonly structuralResult: string;\n}\n\n/**\n * Result of SMT-based verification.\n */\nexport interface SmtVerificationResult {\n  readonly verdict: Verdict;\n  readonly report: string;\n  readonly invariants: readonly PInvariant[];\n  readonly discoveredInvariants: readonly string[];\n  readonly counterexampleTrace: readonly MarkingState[];\n  readonly counterexampleTransitions: readonly string[];\n  readonly elapsedMs: number;\n  readonly statistics: SmtStatistics;\n}\n\nexport function isProven(result: SmtVerificationResult): boolean {\n  return result.verdict.type === 'proven';\n}\n\nexport function isViolated(result: SmtVerificationResult): boolean {\n  return result.verdict.type === 'violated';\n}\n","import { init } from 'z3-solver';\nimport type { Bool, Expr, FuncDecl } from 'z3-solver';\n\n/**\n * Result of a Spacer query.\n */\nexport type QueryResult = QueryProven | QueryViolated | QueryUnknown;\n\n/** Property proven: no reachable error state (UNSAT). */\nexport interface QueryProven {\n  readonly type: 'proven';\n  readonly invariantFormula: string | null;\n  readonly levelInvariants: readonly string[];\n}\n\n/** Counterexample found (SAT). The answer is the derivation tree. */\nexport interface QueryViolated {\n  readonly type: 'violated';\n  readonly answer: Expr | null;\n}\n\n/** Solver could not determine (timeout, resource limit). */\nexport interface QueryUnknown {\n  readonly type: 'unknown';\n  readonly reason: string;\n}\n\n/**\n * The Z3 context and helpers returned by SpacerRunner.create().\n * Exposes the context object for building expressions.\n */\nexport interface SpacerContext {\n  /** The Z3 high-level context for building expressions. */\n  readonly ctx: ReturnType<Awaited<ReturnType<typeof init>>['Context']>;\n  /** The Z3 Fixedpoint solver instance (Spacer engine). Z3 types are complex; using any. */\n  readonly fp: any;\n\n  /** Queries whether the error state is reachable. */\n  query(errorExpr: Bool, reachableDecl?: FuncDecl): Promise<QueryResult>;\n\n  /** Releases Z3 resources. */\n  dispose(): void;\n}\n\n// Use a type alias for the Z3 context to avoid the deep inference\ntype Z3Context = ReturnType<Awaited<ReturnType<typeof init>>['Context']>;\n\n/**\n * Creates a Spacer runner with the given timeout.\n *\n * Uses Z3's Spacer engine (CHC solver based on IC3/PDR) to prove or\n * disprove safety properties.\n */\nexport async function createSpacerRunner(timeoutMs: number): Promise<SpacerContext> {\n  const { Context } = await init();\n  const ctx = new Context('main') as Z3Context;\n  const fp = new (ctx as any).Fixedpoint() as any;\n\n  // Configure Spacer engine\n  fp.set('engine', 'spacer');\n  fp.set('spacer.global', true);\n  fp.set('spacer.use_bg_invs', true);\n  if (timeoutMs > 0) {\n    fp.set('timeout', Math.min(timeoutMs, 2147483647));\n  }\n\n  async function query(errorExpr: Bool, reachableDecl?: FuncDecl): Promise<QueryResult> {\n    try {\n      const status = await fp.query(errorExpr);\n\n      if (status === 'unsat') {\n        let invariantFormula: string | null = null;\n        const levelInvariants: string[] = [];\n\n        try {\n          const answer = fp.getAnswer();\n          if (answer != null) {\n            invariantFormula = answer.toString();\n          }\n        } catch {\n          // Some configurations don't produce answers\n        }\n\n        if (reachableDecl != null) {\n          try {\n            const levels = fp.getNumLevels(reachableDecl);\n            for (let i = 0; i < levels; i++) {\n              const cover = fp.getCoverDelta(i, reachableDecl);\n              if (cover != null && !(ctx as any).isTrue(cover)) {\n                levelInvariants.push(`Level ${i}: ${cover.toString()}`);\n              }\n            }\n          } catch {\n            // Level queries may not be available\n          }\n        }\n\n        return { type: 'proven', invariantFormula, levelInvariants };\n      }\n\n      if (status === 'sat') {\n        let answer: Expr | null = null;\n        try {\n          answer = fp.getAnswer();\n        } catch {\n          // Some configurations don't produce answers\n        }\n        return { type: 'violated', answer };\n      }\n\n      // unknown\n      return { type: 'unknown', reason: fp.getReasonUnknown() };\n    } catch (e: any) {\n      return { type: 'unknown', reason: `Z3 exception: ${e.message ?? e}` };\n    }\n  }\n\n  function dispose(): void {\n    try {\n      fp.release();\n    } catch {\n      // ignore\n    }\n  }\n\n  return {\n    ctx,\n    fp,\n    query,\n    dispose,\n  } as SpacerContext;\n}\n","/**\n * @module smt-encoder\n *\n * Encodes a flattened Petri net as Constrained Horn Clauses (CHC) for Z3's Spacer engine.\n *\n * **CHC encoding strategy**: The net's state space is modeled as integer vectors\n * (one variable per place = token count). Three rule types:\n *\n * 1. **Init**: `Reachable(M0)` — the initial marking is reachable\n * 2. **Transition**: `Reachable(M') :- Reachable(M) ∧ enabled(M,t) ∧ fire(M,M',t)` —\n *    one rule per flat transition (XOR branches are separate transitions)\n * 3. **Error**: `Error() :- Reachable(M) ∧ violation(M)` — safety property violation\n *\n * Transition rules include: non-negativity constraints on M', P-invariant strengthening\n * clauses, and environment bounds for bounded analysis.\n *\n * Z3 types are complex and partially untyped; the ctx/fp parameters use `any`.\n */\nimport type { Arith, Bool, FuncDecl } from 'z3-solver';\nimport type { FlatNet } from '../encoding/flat-net.js';\nimport type { FlatTransition } from '../encoding/flat-transition.js';\nimport type { MarkingState } from '../marking-state.js';\nimport type { SmtProperty } from '../smt-property.js';\nimport type { PInvariant } from '../invariant/p-invariant.js';\nimport { flatNetIndexOf } from '../encoding/flat-net.js';\n\n/** Z3 high-level context. Typed as `any` because z3-solver's TS types are incomplete. */\ntype Z3Context = any;\n/** Z3 Fixedpoint solver instance. Typed as `any` because z3-solver's TS types are incomplete. */\ntype Z3Fixedpoint = any;\n\n/**\n * Result of CHC encoding.\n */\nexport interface EncodingResult {\n  readonly errorExpr: Bool;\n  readonly reachableDecl: FuncDecl;\n}\n\n/**\n * Encodes a flattened Petri net as Constrained Horn Clauses (CHC) for Z3's Spacer engine.\n *\n * CHC rules:\n * - Reachable(M0) — initial state is reachable\n * - Reachable(M') :- Reachable(M) AND enabled(M,t) AND fire(M,M',t) — transition rules\n * - Error() :- Reachable(M) AND property_violation(M) — safety property\n */\nexport function encode(\n  ctx: Z3Context,\n  fp: Z3Fixedpoint,\n  flatNet: FlatNet,\n  initialMarking: MarkingState,\n  property: SmtProperty,\n  invariants: readonly PInvariant[],\n): EncodingResult {\n  const P = flatNet.places.length;\n  const Int = ctx.Int;\n  const Bool_ = ctx.Bool;\n\n  // Create sorts array for function declaration\n  const intSort = Int.sort();\n  const boolSort = Bool_.sort();\n  const markingSorts: any[] = new Array(P).fill(intSort);\n\n  // Create the Reachable relation: (Int, Int, ...) -> Bool\n  const reachable: FuncDecl = ctx.Function.declare('Reachable', ...markingSorts, boolSort);\n  fp.registerRelation(reachable);\n\n  // Create the Error relation: () -> Bool\n  const error: FuncDecl = ctx.Function.declare('Error', boolSort);\n  fp.registerRelation(error);\n\n  // === Rule 1: Initial state ===\n  // Reachable(m0_0, m0_1, ..., m0_{P-1})\n  const m0Args: Arith[] = [];\n  for (let i = 0; i < P; i++) {\n    const tokens = initialMarking.tokens(flatNet.places[i]!);\n    m0Args.push(Int.val(tokens));\n  }\n  const initFact = (reachable as any).call(...m0Args) as Bool;\n  fp.addRule(initFact, 'init');\n\n  // === Rule 2: Transition rules ===\n  for (let t = 0; t < flatNet.transitions.length; t++) {\n    const ft = flatNet.transitions[t]!;\n    encodeTransitionRule(ctx, fp, reachable, ft, flatNet, invariants, P);\n  }\n\n  // === Rule 3: Error rule (property violation) ===\n  encodeErrorRule(ctx, fp, reachable, error, flatNet, property, P);\n\n  return {\n    errorExpr: (error as any).call() as Bool,\n    reachableDecl: reachable,\n  };\n}\n\nfunction encodeTransitionRule(\n  ctx: Z3Context,\n  fp: Z3Fixedpoint,\n  reachable: FuncDecl,\n  ft: FlatTransition,\n  flatNet: FlatNet,\n  invariants: readonly PInvariant[],\n  P: number,\n): void {\n  const Int = ctx.Int;\n\n  // Create named variables for current and next marking\n  const mVars: Arith[] = [];\n  const mPrimeVars: Arith[] = [];\n  for (let i = 0; i < P; i++) {\n    mVars.push(Int.const(`m${i}`));\n    mPrimeVars.push(Int.const(`mp${i}`));\n  }\n\n  // Body: Reachable(M) AND enabled(M,t) AND fire(M,M',t) AND non-negativity(M') AND invariants(M') AND env bounds(M')\n  const reachBody = (reachable as any).call(...mVars) as Bool;\n  const enabled = encodeEnabled(ctx, ft, flatNet, mVars, P);\n  const fireRelation = encodeFire(ctx, ft, flatNet, mVars, mPrimeVars, P);\n\n  // Non-negativity of M'\n  let nonNeg: Bool = ctx.Bool.val(true);\n  for (let i = 0; i < P; i++) {\n    nonNeg = ctx.And(nonNeg, mPrimeVars[i]!.ge(0));\n  }\n\n  // P-invariant constraints on M'\n  const invConstraints = encodeInvariantConstraints(ctx, invariants, mPrimeVars, P);\n\n  // Environment bounds on M'\n  let envBounds: Bool = ctx.Bool.val(true);\n  for (const [name, bound] of flatNet.environmentBounds) {\n    const idx = flatNet.placeIndex.get(name);\n    if (idx != null) {\n      envBounds = ctx.And(envBounds, mPrimeVars[idx]!.le(bound));\n    }\n  }\n\n  // Body conjunction\n  const body = ctx.And(reachBody, enabled, fireRelation, nonNeg, invConstraints, envBounds);\n\n  // Head: Reachable(M')\n  const head = (reachable as any).call(...mPrimeVars) as Bool;\n\n  // Rule: forall M, M'. body => head\n  const allVars = [...mVars, ...mPrimeVars];\n  const rule = ctx.Implies(body, head);\n  const qRule = ctx.ForAll(allVars, rule);\n\n  fp.addRule(qRule, `t_${ft.name}`);\n}\n\nfunction encodeEnabled(\n  ctx: Z3Context,\n  ft: FlatTransition,\n  _flatNet: FlatNet,\n  mVars: Arith[],\n  P: number,\n): Bool {\n  let result: Bool = ctx.Bool.val(true);\n\n  // Input requirements: M[p] >= pre[p]\n  for (let p = 0; p < P; p++) {\n    if (ft.preVector[p]! > 0) {\n      result = ctx.And(result, mVars[p]!.ge(ft.preVector[p]!));\n    }\n  }\n\n  // Read arcs: M[p] >= 1\n  for (const p of ft.readPlaces) {\n    result = ctx.And(result, mVars[p]!.ge(1));\n  }\n\n  // Inhibitor arcs: M[p] == 0\n  for (const p of ft.inhibitorPlaces) {\n    result = ctx.And(result, mVars[p]!.eq(0));\n  }\n\n  // Non-negativity of current marking\n  for (let p = 0; p < P; p++) {\n    result = ctx.And(result, mVars[p]!.ge(0));\n  }\n\n  return result;\n}\n\nfunction encodeFire(\n  ctx: Z3Context,\n  ft: FlatTransition,\n  _flatNet: FlatNet,\n  mVars: Arith[],\n  mPrimeVars: Arith[],\n  P: number,\n): Bool {\n  let result: Bool = ctx.Bool.val(true);\n\n  for (let p = 0; p < P; p++) {\n    const isReset = ft.resetPlaces.includes(p);\n\n    if (isReset || ft.consumeAll[p]) {\n      // Reset/consumeAll: M'[p] = post[p]\n      result = ctx.And(result, mPrimeVars[p]!.eq(ft.postVector[p]!));\n    } else {\n      // Standard: M'[p] = M[p] - pre[p] + post[p]\n      const delta = ft.postVector[p]! - ft.preVector[p]!;\n      if (delta === 0) {\n        result = ctx.And(result, mPrimeVars[p]!.eq(mVars[p]!));\n      } else {\n        result = ctx.And(result, mPrimeVars[p]!.eq(mVars[p]!.add(delta)));\n      }\n    }\n  }\n\n  return result;\n}\n\nfunction encodeErrorRule(\n  ctx: Z3Context,\n  fp: Z3Fixedpoint,\n  reachable: FuncDecl,\n  error: FuncDecl,\n  flatNet: FlatNet,\n  property: SmtProperty,\n  P: number,\n): void {\n  const Int = ctx.Int;\n\n  // Create variables for the error rule\n  const mVars: Arith[] = [];\n  for (let i = 0; i < P; i++) {\n    mVars.push(Int.const(`em${i}`));\n  }\n\n  const reachBody = (reachable as any).call(...mVars) as Bool;\n  const violation = encodePropertyViolation(ctx, flatNet, property, mVars, P);\n\n  const head = (error as any).call() as Bool;\n  const body = ctx.And(reachBody, violation);\n  const rule = ctx.Implies(body, head);\n  const qRule = ctx.ForAll(mVars, rule);\n\n  fp.addRule(qRule, `error_${property.type}`);\n}\n\nfunction encodePropertyViolation(\n  ctx: Z3Context,\n  flatNet: FlatNet,\n  property: SmtProperty,\n  mVars: Arith[],\n  P: number,\n): Bool {\n  switch (property.type) {\n    case 'deadlock-free':\n      return encodeDeadlock(ctx, flatNet, mVars, P);\n\n    case 'mutual-exclusion': {\n      const idx1 = flatNetIndexOf(flatNet, property.p1);\n      const idx2 = flatNetIndexOf(flatNet, property.p2);\n      if (idx1 < 0) throw new Error(`MutualExclusion references unknown place: ${property.p1.name}`);\n      if (idx2 < 0) throw new Error(`MutualExclusion references unknown place: ${property.p2.name}`);\n      return ctx.And(mVars[idx1]!.ge(1), mVars[idx2]!.ge(1));\n    }\n\n    case 'place-bound': {\n      const idx = flatNetIndexOf(flatNet, property.place);\n      if (idx < 0) throw new Error(`PlaceBound references unknown place: ${property.place.name}`);\n      return mVars[idx]!.gt(property.bound);\n    }\n\n    case 'unreachable': {\n      let allMarked: Bool = ctx.Bool.val(true);\n      for (const place of property.places) {\n        const idx = flatNetIndexOf(flatNet, place);\n        if (idx >= 0) {\n          allMarked = ctx.And(allMarked, mVars[idx]!.ge(1));\n        }\n      }\n      return allMarked;\n    }\n  }\n}\n\n/** Encodes the deadlock condition: no transition is enabled. */\nfunction encodeDeadlock(\n  ctx: Z3Context,\n  flatNet: FlatNet,\n  mVars: Arith[],\n  P: number,\n): Bool {\n  let deadlock: Bool = ctx.Bool.val(true);\n\n  for (const ft of flatNet.transitions) {\n    const enabled = encodeEnabled(ctx, ft, flatNet, mVars, P);\n    deadlock = ctx.And(deadlock, ctx.Not(enabled));\n  }\n\n  return deadlock;\n}\n\nfunction encodeInvariantConstraints(\n  ctx: Z3Context,\n  invariants: readonly PInvariant[],\n  mVars: Arith[],\n  P: number,\n): Bool {\n  let result: Bool = ctx.Bool.val(true);\n\n  for (const inv of invariants) {\n    // sum(y_i * M[i]) == constant\n    let sum: Arith = ctx.Int.val(0);\n    for (const idx of inv.support) {\n      if (idx < P) {\n        sum = sum.add(mVars[idx]!.mul(inv.weights[idx]!));\n      }\n    }\n    result = ctx.And(result, sum.eq(inv.constant));\n  }\n\n  return result;\n}\n","import type { Expr } from 'z3-solver';\nimport { MarkingState } from '../marking-state.js';\nimport type { FlatNet } from '../encoding/flat-net.js';\n\n/**\n * Result of counterexample decoding.\n */\nexport interface DecodedTrace {\n  readonly trace: readonly MarkingState[];\n  readonly transitions: readonly string[];\n}\n\n/**\n * Decodes Z3 Spacer counterexample answers into Petri net marking traces.\n *\n * When Spacer finds a counterexample (property violation), it produces\n * a derivation tree showing how the error state is reachable. This function\n * extracts the marking at each step to produce a human-readable trace.\n */\nexport function decode(ctx: any, answer: Expr | null, flatNet: FlatNet): DecodedTrace {\n  const trace: MarkingState[] = [];\n  const transitions: string[] = [];\n\n  if (answer == null) {\n    return { trace, transitions };\n  }\n\n  try {\n    extractTrace(ctx, answer, flatNet, trace, transitions);\n  } catch {\n    // Z3 answer format varies; gracefully degrade\n  }\n\n  return { trace, transitions };\n}\n\n/**\n * Recursively traverses the Z3 proof tree to extract marking states.\n */\nfunction extractTrace(\n  ctx: any,\n  expr: any,\n  flatNet: FlatNet,\n  trace: MarkingState[],\n  transitions: string[],\n): void {\n  if (expr == null) return;\n\n  // Check if this is a function application\n  if (!ctx.isApp(expr)) return;\n\n  let name: string;\n  try {\n    const decl = expr.decl();\n    name = String(decl.name());\n  } catch {\n    return;\n  }\n\n  // Check if this is a Reachable application with integer arguments\n  const P = flatNet.places.length;\n  if (name === 'Reachable') {\n    const numArgs = expr.numArgs();\n    if (numArgs === P) {\n      const marking = extractMarking(ctx, expr, flatNet);\n      if (marking != null) {\n        trace.push(marking);\n      }\n    }\n  }\n\n  // Recurse into children to find the derivation chain\n  try {\n    const numArgs = expr.numArgs();\n    for (let i = 0; i < numArgs; i++) {\n      const child = expr.arg(i);\n      extractTrace(ctx, child, flatNet, trace, transitions);\n    }\n  } catch {\n    // Not all expressions support arg()\n  }\n\n  // Try to extract transition name from rule application\n  if (name.startsWith('t_')) {\n    transitions.push(name.substring(2));\n  }\n}\n\n/**\n * Extracts a MarkingState from a Reachable(...) application.\n */\nfunction extractMarking(ctx: any, reachableApp: any, flatNet: FlatNet): MarkingState | null {\n  const P = flatNet.places.length;\n  if (reachableApp.numArgs() !== P) return null;\n\n  const builder = MarkingState.builder();\n  for (let i = 0; i < P; i++) {\n    const arg = reachableApp.arg(i);\n    if (ctx.isIntVal(arg)) {\n      const tokens = Number(arg.value());\n      if (tokens > 0) {\n        builder.tokens(flatNet.places[i]!, tokens);\n      }\n    } else {\n      // Non-concrete value in counterexample\n      return null;\n    }\n  }\n  return builder.build();\n}\n","import type { PetriNet } from '../core/petri-net.js';\nimport type { EnvironmentPlace } from '../core/place.js';\nimport { MarkingState, MarkingStateBuilder } from './marking-state.js';\nimport type { SmtProperty } from './smt-property.js';\nimport { deadlockFree, propertyDescription } from './smt-property.js';\nimport type { SmtVerificationResult, SmtStatistics, Verdict } from './smt-verification-result.js';\nimport type { PInvariant } from './invariant/p-invariant.js';\nimport type { FlatNet } from './encoding/flat-net.js';\nimport { flatten, type EnvironmentAnalysisMode, unbounded } from './encoding/net-flattener.js';\nimport { IncidenceMatrix } from './encoding/incidence-matrix.js';\nimport { computePInvariants, isCoveredByInvariants } from './invariant/p-invariant-computer.js';\nimport { structuralCheck } from './invariant/structural-check.js';\nimport { createSpacerRunner } from './z3/spacer-runner.js';\nimport { encode } from './z3/smt-encoder.js';\nimport { decode } from './z3/counterexample-decoder.js';\n\n/**\n * IC3/PDR-based safety verifier for Petri nets using Z3's Spacer engine.\n *\n * Proves safety properties (especially deadlock-freedom) without\n * enumerating all reachable states. IC3 constructs inductive invariants\n * incrementally, which works well for bounded nets.\n *\n * Key design decisions:\n * - Operates on the marking projection (integer vectors) — no timing\n * - An untimed deadlock-freedom proof is stronger than needed\n *   (timing can only restrict behavior)\n * - Guards are ignored — over-approximation is sound for safety properties\n * - If a counterexample is found, it may be spurious in timed/guarded\n *   semantics — the report notes this\n *\n * Verification Pipeline:\n * 1. Flatten — expand XOR, index places, build pre/post vectors\n * 2. Structural pre-check — siphon/trap analysis (may prove early)\n * 3. P-invariants — compute conservation laws for strengthening\n * 4. SMT encode + query — IC3/PDR via Z3 Spacer\n * 5. Decode result — proof or counterexample trace\n */\nexport class SmtVerifier {\n  private _initialMarking: MarkingState = MarkingState.empty();\n  private _property: SmtProperty = deadlockFree();\n  private readonly _environmentPlaces = new Set<EnvironmentPlace<any>>();\n  private _environmentMode: EnvironmentAnalysisMode = unbounded();\n  private _timeoutMs: number = 60_000;\n\n  private constructor(private readonly net: PetriNet) {}\n\n  static forNet(net: PetriNet): SmtVerifier {\n    return new SmtVerifier(net);\n  }\n\n  initialMarking(marking: MarkingState): this;\n  initialMarking(configurator: (builder: MarkingStateBuilder) => void): this;\n  initialMarking(arg: MarkingState | ((builder: MarkingStateBuilder) => void)): this {\n    if (arg instanceof MarkingState) {\n      this._initialMarking = arg;\n    } else {\n      const builder = MarkingState.builder();\n      arg(builder);\n      this._initialMarking = builder.build();\n    }\n    return this;\n  }\n\n  property(property: SmtProperty): this {\n    this._property = property;\n    return this;\n  }\n\n  environmentPlaces(...places: EnvironmentPlace<any>[]): this {\n    for (const p of places) this._environmentPlaces.add(p);\n    return this;\n  }\n\n  environmentMode(mode: EnvironmentAnalysisMode): this {\n    this._environmentMode = mode;\n    return this;\n  }\n\n  timeout(ms: number): this {\n    this._timeoutMs = ms;\n    return this;\n  }\n\n  /**\n   * Runs the verification pipeline.\n   */\n  async verify(): Promise<SmtVerificationResult> {\n    const start = performance.now();\n    const report: string[] = [];\n    report.push('=== IC3/PDR SAFETY VERIFICATION ===\\n');\n    report.push(`Net: ${this.net.name}`);\n    report.push(`Property: ${propertyDescription(this._property)}`);\n    report.push(`Timeout: ${(this._timeoutMs / 1000).toFixed(0)}s\\n`);\n\n    // Phase 1: Flatten\n    report.push('Phase 1: Flattening net...');\n    const flatNet = flatten(this.net, this._environmentPlaces, this._environmentMode);\n    report.push(`  Places: ${flatNet.places.length}`);\n    report.push(`  Transitions (expanded): ${flatNet.transitions.length}`);\n    if (flatNet.environmentBounds.size > 0) {\n      report.push(`  Environment bounds: ${flatNet.environmentBounds.size} places`);\n    }\n    report.push('');\n\n    // Phase 2: Structural pre-check\n    report.push('Phase 2: Structural pre-check (siphon/trap)...');\n    const structResult = structuralCheck(flatNet, this._initialMarking);\n    let structResultStr: string;\n    switch (structResult.type) {\n      case 'no-potential-deadlock':\n        structResultStr = 'no potential deadlock';\n        break;\n      case 'potential-deadlock':\n        structResultStr = `potential deadlock (siphon: {${[...structResult.siphon].join(',')}})`;\n        break;\n      case 'inconclusive':\n        structResultStr = `inconclusive (${structResult.reason})`;\n        break;\n    }\n    report.push(`  Result: ${structResultStr}\\n`);\n\n    // If structural check proves deadlock-freedom for DeadlockFree property\n    if (\n      this._property.type === 'deadlock-free' &&\n      structResult.type === 'no-potential-deadlock'\n    ) {\n      report.push('=== RESULT ===\\n');\n      report.push('PROVEN (structural): Deadlock-freedom verified by Commoner\\'s theorem.');\n      report.push('  All siphons contain initially marked traps.');\n      return buildResult(\n        { type: 'proven', method: 'structural', inductiveInvariant: null },\n        report.join('\\n'), [], [], [], [],\n        performance.now() - start,\n        { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: 0, structuralResult: structResultStr },\n      );\n    }\n\n    // Phase 3: P-invariants\n    report.push('Phase 3: Computing P-invariants...');\n    const matrix = IncidenceMatrix.from(flatNet);\n    const invariants = computePInvariants(matrix, flatNet, this._initialMarking);\n    report.push(`  Found: ${invariants.length} P-invariant(s)`);\n    const structurallyBounded = isCoveredByInvariants(invariants, flatNet.places.length);\n    report.push(`  Structurally bounded: ${structurallyBounded ? 'YES' : 'NO'}`);\n    for (const inv of invariants) {\n      report.push(`  ${formatInvariant(inv, flatNet)}`);\n    }\n    report.push('');\n\n    // Phase 4: SMT encode + query via Spacer\n    report.push('Phase 4: IC3/PDR verification via Z3 Spacer...');\n\n    let runner;\n    try {\n      runner = await createSpacerRunner(this._timeoutMs);\n    } catch (e: any) {\n      report.push(`  ERROR: ${e.message ?? e}\\n`);\n      report.push('=== RESULT ===\\n');\n      report.push(`UNKNOWN: Z3 initialization error: ${e.message ?? e}`);\n      return buildResult(\n        { type: 'unknown', reason: `Z3 init error: ${e.message ?? e}` },\n        report.join('\\n'), invariants, [], [], [],\n        performance.now() - start,\n        { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n      );\n    }\n\n    try {\n      const encoding = encode(runner.ctx, runner.fp, flatNet, this._initialMarking, this._property, invariants);\n      const queryResult = await runner.query(encoding.errorExpr, encoding.reachableDecl);\n\n      switch (queryResult.type) {\n        case 'proven': {\n          report.push('  Status: UNSAT (property holds)\\n');\n\n          // Decode IC3-synthesized invariants with place name substitution\n          const discoveredInvariants: string[] = [];\n          if (queryResult.invariantFormula != null) {\n            discoveredInvariants.push(substituteNames(queryResult.invariantFormula, flatNet));\n          }\n          for (const level of queryResult.levelInvariants) {\n            discoveredInvariants.push(substituteNames(level, flatNet));\n          }\n\n          // Phase 5: Inductive invariant\n          if (discoveredInvariants.length > 0) {\n            report.push('Phase 5: Inductive invariant (discovered by IC3)');\n            report.push(`  Spacer synthesized: ${discoveredInvariants[0]}`);\n            report.push('  This formula is INDUCTIVE: preserved by all transitions.');\n            if (discoveredInvariants.length > 1) {\n              report.push('  Per-level clauses:');\n              for (let i = 1; i < discoveredInvariants.length; i++) {\n                report.push(`    ${discoveredInvariants[i]}`);\n              }\n            }\n            report.push('');\n          }\n\n          report.push('=== RESULT ===\\n');\n          report.push(`PROVEN (IC3/PDR): ${propertyDescription(this._property)}`);\n          report.push('  Z3 Spacer proved no reachable state violates the property.');\n          report.push('  NOTE: Verification ignores timing constraints and JS guards.');\n          report.push('  An untimed proof is STRONGER than a timed one (timing only restricts behavior).');\n\n          return buildResult(\n            {\n              type: 'proven',\n              method: 'IC3/PDR',\n              inductiveInvariant: queryResult.invariantFormula != null\n                ? substituteNames(queryResult.invariantFormula, flatNet)\n                : null,\n            },\n            report.join('\\n'), invariants, discoveredInvariants, [], [],\n            performance.now() - start,\n            { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n          );\n        }\n\n        case 'violated': {\n          report.push('  Status: SAT (counterexample found)\\n');\n\n          const decoded = decode(runner.ctx, queryResult.answer, flatNet);\n\n          report.push('=== RESULT ===\\n');\n          report.push(`VIOLATED: ${propertyDescription(this._property)}`);\n          if (decoded.trace.length > 0) {\n            report.push(`  Counterexample trace (${decoded.trace.length} states):`);\n            for (let i = 0; i < decoded.trace.length; i++) {\n              report.push(`    ${i}: ${decoded.trace[i]}`);\n            }\n          }\n          if (decoded.transitions.length > 0) {\n            report.push(`  Firing sequence: ${decoded.transitions.join(' -> ')}`);\n          }\n          report.push('\\n  WARNING: This counterexample is in UNTIMED semantics.');\n          report.push('  It may be spurious if timing constraints prevent this sequence.');\n          report.push('  JS guards are also ignored in this analysis.');\n\n          return buildResult(\n            { type: 'violated' },\n            report.join('\\n'), invariants, [], decoded.trace as MarkingState[], decoded.transitions as string[],\n            performance.now() - start,\n            { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n          );\n        }\n\n        case 'unknown': {\n          report.push(`  Status: UNKNOWN (${queryResult.reason})\\n`);\n          report.push('=== RESULT ===\\n');\n          report.push(`UNKNOWN: Could not determine ${propertyDescription(this._property)}`);\n          report.push(`  Reason: ${queryResult.reason}`);\n\n          return buildResult(\n            { type: 'unknown', reason: queryResult.reason },\n            report.join('\\n'), invariants, [], [], [],\n            performance.now() - start,\n            { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n          );\n        }\n      }\n    } catch (e: any) {\n      report.push(`  ERROR: ${e.message ?? e}\\n`);\n      report.push('=== RESULT ===\\n');\n      report.push(`UNKNOWN: Z3 solver error: ${e.message ?? e}`);\n\n      return buildResult(\n        { type: 'unknown', reason: `Z3 error: ${e.message ?? e}` },\n        report.join('\\n'), invariants, [], [], [],\n        performance.now() - start,\n        { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n      );\n    } finally {\n      runner.dispose();\n    }\n  }\n}\n\n/**\n * Substitutes Z3 variable names (m0, m1, ...) with place names in a formula string.\n */\nfunction substituteNames(formula: string, flatNet: FlatNet): string {\n  // Replace from highest index first to avoid m1 matching inside m10\n  for (let i = flatNet.places.length - 1; i >= 0; i--) {\n    formula = formula.replace(new RegExp(`\\\\bm${i}\\\\b`, 'g'), flatNet.places[i]!.name);\n  }\n  return formula;\n}\n\nfunction formatInvariant(inv: PInvariant, flatNet: FlatNet): string {\n  const parts: string[] = [];\n  for (const idx of inv.support) {\n    if (inv.weights[idx] !== 1) {\n      parts.push(`${inv.weights[idx]}*${flatNet.places[idx]!.name}`);\n    } else {\n      parts.push(flatNet.places[idx]!.name);\n    }\n  }\n  return `${parts.join(' + ')} = ${inv.constant}`;\n}\n\nfunction buildResult(\n  verdict: Verdict,\n  report: string,\n  invariants: readonly PInvariant[],\n  discoveredInvariants: readonly string[],\n  trace: readonly MarkingState[],\n  transitions: readonly string[],\n  elapsedMs: number,\n  statistics: SmtStatistics,\n): SmtVerificationResult {\n  return { verdict, report, invariants, discoveredInvariants, counterexampleTrace: trace, counterexampleTransitions: transitions, elapsedMs, statistics 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+{"version":3,"sources":["../../src/verification/marking-state.ts","../../src/verification/encoding/flat-transition.ts","../../src/verification/encoding/flat-net.ts","../../src/verification/encoding/incidence-matrix.ts","../../src/verification/encoding/net-flattener.ts","../../src/verification/invariant/p-invariant.ts","../../src/verification/invariant/p-invariant-computer.ts","../../src/verification/invariant/structural-check.ts","../../src/verification/smt-property.ts","../../src/verification/smt-verification-result.ts","../../src/verification/z3/spacer-runner.ts","../../src/verification/z3/smt-encoder.ts","../../src/verification/z3/counterexample-decoder.ts","../../src/verification/smt-verifier.ts"],"sourcesContent":["import type { Place } from '../core/place.js';\n\n/** @internal Symbol key restricting construction to the builder and factory methods. */\nconst MARKING_STATE_KEY = Symbol('MarkingState.internal');\n\n/**\n * Immutable snapshot of a Petri net marking for state space analysis.\n *\n * Maps places (by name) to integer token counts. Only stores places with count > 0.\n * Used for invariant computation and structural verification, not runtime execution.\n */\nexport class MarkingState {\n  private readonly tokenCounts: ReadonlyMap<string, number>;\n  private readonly placesByName: ReadonlyMap<string, Place<any>>;\n\n  /** @internal Use {@link MarkingState.builder} or {@link MarkingState.empty} to create instances. */\n  constructor(key: symbol, tokenCounts: Map<string, number>, placesByName: Map<string, Place<any>>) {\n    if (key !== MARKING_STATE_KEY) throw new Error('Use MarkingState.builder() to create instances');\n    this.tokenCounts = tokenCounts;\n    this.placesByName = placesByName;\n  }\n\n  /** Returns the token count for a place (0 if absent). */\n  tokens(place: Place<any>): number {\n    return this.tokenCounts.get(place.name) ?? 0;\n  }\n\n  /** Checks if a place has at least one token. */\n  hasTokens(place: Place<any>): boolean {\n    return this.tokens(place) > 0;\n  }\n\n  /** Checks if any of the given places has tokens. */\n  hasTokensInAny(places: Iterable<Place<any>>): boolean {\n    for (const p of places) {\n      if (this.hasTokens(p)) return true;\n    }\n    return false;\n  }\n\n  /** Returns all places with tokens > 0. */\n  placesWithTokens(): Place<any>[] {\n    return [...this.placesByName.values()];\n  }\n\n  /** Returns the total number of tokens. */\n  totalTokens(): number {\n    let sum = 0;\n    for (const count of this.tokenCounts.values()) sum += count;\n    return sum;\n  }\n\n  /** Checks if no tokens exist anywhere. */\n  isEmpty(): boolean {\n    return this.tokenCounts.size === 0;\n  }\n\n  toString(): string {\n    if (this.tokenCounts.size === 0) return '{}';\n    const entries = [...this.tokenCounts.entries()]\n      .sort(([a], [b]) => a.localeCompare(b))\n      .map(([name, count]) => `${name}:${count}`);\n    return `{${entries.join(', ')}}`;\n  }\n\n  static empty(): MarkingState {\n    return new MarkingState(MARKING_STATE_KEY, new Map(), new Map());\n  }\n\n  static builder(): MarkingStateBuilder {\n    return new MarkingStateBuilder();\n  }\n}\n\nexport class MarkingStateBuilder {\n  private readonly tokenCounts = new Map<string, number>();\n  private readonly placesByName = new Map<string, Place<any>>();\n\n  /** Sets the token count for a place. */\n  tokens(place: Place<any>, count: number): this {\n    if (count < 0) throw new Error(`Token count cannot be negative: ${count}`);\n    if (count > 0) {\n      this.tokenCounts.set(place.name, count);\n      this.placesByName.set(place.name, place);\n    } else {\n      this.tokenCounts.delete(place.name);\n      this.placesByName.delete(place.name);\n    }\n    return this;\n  }\n\n  /** Adds tokens to a place. */\n  addTokens(place: Place<any>, count: number): this {\n    if (count < 0) throw new Error(`Token count cannot be negative: ${count}`);\n    if (count > 0) {\n      const current = this.tokenCounts.get(place.name) ?? 0;\n      this.tokenCounts.set(place.name, current + count);\n      this.placesByName.set(place.name, place);\n    }\n    return this;\n  }\n\n  build(): MarkingState {\n    return new MarkingState(MARKING_STATE_KEY, new Map(this.tokenCounts), new Map(this.placesByName));\n  }\n}\n","import type { Transition } from '../../core/transition.js';\n\n/**\n * A flattened transition with pre/post vectors for SMT encoding.\n *\n * Each Transition with XOR outputs is expanded into multiple FlatTransitions\n * (one per branch). Non-XOR transitions map 1:1.\n */\nexport interface FlatTransition {\n  /** Display name (e.g. \"Search_b0\", \"Search_b1\"). */\n  readonly name: string;\n  /** The original transition. */\n  readonly source: Transition;\n  /** Which XOR branch (-1 if no XOR). */\n  readonly branchIndex: number;\n  /** Tokens consumed per place (indexed by place index). */\n  readonly preVector: readonly number[];\n  /** Tokens produced per place (indexed by place index). */\n  readonly postVector: readonly number[];\n  /** Place indices where inhibitor arcs block firing. */\n  readonly inhibitorPlaces: readonly number[];\n  /** Place indices requiring a token without consuming. */\n  readonly readPlaces: readonly number[];\n  /** Place indices set to 0 on firing. */\n  readonly resetPlaces: readonly number[];\n  /** True at index i means place i uses All/AtLeast semantics. */\n  readonly consumeAll: readonly boolean[];\n}\n\nexport function flatTransition(\n  name: string,\n  source: Transition,\n  branchIndex: number,\n  preVector: number[],\n  postVector: number[],\n  inhibitorPlaces: number[],\n  readPlaces: number[],\n  resetPlaces: number[],\n  consumeAll: boolean[],\n): FlatTransition {\n  return {\n    name,\n    source,\n    branchIndex,\n    preVector,\n    postVector,\n    inhibitorPlaces,\n    readPlaces,\n    resetPlaces,\n    consumeAll,\n  };\n}\n","import type { Place } from '../../core/place.js';\nimport type { FlatTransition } from './flat-transition.js';\n\n/**\n * A flattened Petri net with indexed places and XOR-expanded transitions.\n *\n * Intermediate representation between the high-level PetriNet and Z3 CHC encoding.\n */\nexport interface FlatNet {\n  /** Ordered list of places (index = position). */\n  readonly places: readonly Place<any>[];\n  /** Reverse lookup: place name -> index. */\n  readonly placeIndex: ReadonlyMap<string, number>;\n  /** XOR-expanded flat transitions. */\n  readonly transitions: readonly FlatTransition[];\n  /** For bounded environment places: place name -> max tokens. */\n  readonly environmentBounds: ReadonlyMap<string, number>;\n}\n\nexport function flatNetPlaceCount(net: FlatNet): number {\n  return net.places.length;\n}\n\nexport function flatNetTransitionCount(net: FlatNet): number {\n  return net.transitions.length;\n}\n\nexport function flatNetIndexOf(net: FlatNet, place: Place<any>): number {\n  return net.placeIndex.get(place.name) ?? -1;\n}\n","import type { FlatNet } from './flat-net.js';\n\n/**\n * Incidence matrix for a flattened Petri net.\n *\n * The incidence matrix C is defined as C[t][p] = post[t][p] - pre[t][p].\n * It captures the net effect of each transition on each place.\n *\n * P-invariants are solutions to y^T * C = 0, found via null space\n * computation on C^T.\n */\nexport class IncidenceMatrix {\n  private readonly _pre: readonly (readonly number[])[];\n  private readonly _post: readonly (readonly number[])[];\n  private readonly _incidence: readonly (readonly number[])[];\n  private readonly _numTransitions: number;\n  private readonly _numPlaces: number;\n\n  private constructor(\n    pre: number[][],\n    post: number[][],\n    incidence: number[][],\n    numTransitions: number,\n    numPlaces: number,\n  ) {\n    this._pre = pre;\n    this._post = post;\n    this._incidence = incidence;\n    this._numTransitions = numTransitions;\n    this._numPlaces = numPlaces;\n  }\n\n  /**\n   * Computes the incidence matrix from a FlatNet.\n   */\n  static from(flatNet: FlatNet): IncidenceMatrix {\n    const T = flatNet.transitions.length;\n    const P = flatNet.places.length;\n\n    const pre: number[][] = [];\n    const post: number[][] = [];\n    const incidence: number[][] = [];\n\n    for (let t = 0; t < T; t++) {\n      const ft = flatNet.transitions[t]!;\n      const preRow = new Array<number>(P);\n      const postRow = new Array<number>(P);\n      const incRow = new Array<number>(P);\n\n      for (let p = 0; p < P; p++) {\n        preRow[p] = ft.preVector[p]!;\n        postRow[p] = ft.postVector[p]!;\n        incRow[p] = postRow[p]! - preRow[p]!;\n      }\n\n      pre.push(preRow);\n      post.push(postRow);\n      incidence.push(incRow);\n    }\n\n    return new IncidenceMatrix(pre, post, incidence, T, P);\n  }\n\n  /**\n   * Returns C^T (transpose of incidence matrix), dimensions [P][T].\n   * Used for P-invariant computation: null space of C^T gives P-invariants.\n   */\n  transposedIncidence(): number[][] {\n    const ct: number[][] = [];\n    for (let p = 0; p < this._numPlaces; p++) {\n      const row = new Array<number>(this._numTransitions);\n      for (let t = 0; t < this._numTransitions; t++) {\n        row[t] = this._incidence[t]![p]!;\n      }\n      ct.push(row);\n    }\n    return ct;\n  }\n\n  /** Returns the pre-matrix (tokens consumed). T×P. */\n  pre(): readonly (readonly number[])[] { return this._pre; }\n\n  /** Returns the post-matrix (tokens produced). T×P. */\n  post(): readonly (readonly number[])[] { return this._post; }\n\n  /** Returns the incidence matrix C[t][p] = post - pre. T×P. */\n  incidence(): readonly (readonly number[])[] { return this._incidence; }\n\n  numTransitions(): number { return this._numTransitions; }\n  numPlaces(): number { return this._numPlaces; }\n}\n","/**\n * @module net-flattener\n *\n * Flattens a PetriNet into integer-indexed pre/post vectors for SMT encoding.\n *\n * **XOR expansion**: Transitions with XOR output specs are expanded into multiple\n * flat transitions — one per deterministic branch. Each branch produces tokens to\n * exactly one XOR child's places. This converts non-deterministic output routing\n * into separate transitions that the SMT solver can reason about independently.\n *\n * **Vector construction**: For each flat transition, builds:\n * - `preVector[p]`: tokens consumed from place p (input cardinality)\n * - `postVector[p]`: tokens produced to place p (from the selected branch)\n * - `consumeAll[p]`: true for `all`/`at-least` inputs (consume everything)\n * - Index arrays for inhibitor, read, and reset arcs\n *\n * Places are sorted by name for stable, deterministic indexing across runs.\n */\nimport type { PetriNet } from '../../core/petri-net.js';\nimport type { Place, EnvironmentPlace } from '../../core/place.js';\nimport type { Out } from '../../core/out.js';\nimport type { FlatNet } from './flat-net.js';\nimport { flatTransition } from './flat-transition.js';\nimport { enumerateBranches, allPlaces as outAllPlaces } from '../../core/out.js';\n\n/**\n * How to treat environment places during analysis.\n */\nexport type EnvironmentAnalysisMode =\n  | { readonly type: 'unbounded' }\n  | { readonly type: 'bounded'; readonly maxTokens: number };\n\nexport function unbounded(): EnvironmentAnalysisMode {\n  return { type: 'unbounded' };\n}\n\nexport function bounded(maxTokens: number): EnvironmentAnalysisMode {\n  return { type: 'bounded', maxTokens };\n}\n\n/**\n * Flattens a PetriNet into a FlatNet suitable for SMT encoding.\n *\n * Flattening involves:\n * 1. Assigning each place a stable integer index (sorted by name)\n * 2. Expanding XOR outputs into separate flat transitions (one per branch)\n * 3. Building pre/post vectors from input/output specs\n * 4. Recording inhibitor, read, and reset arcs\n * 5. Setting environment bounds for bounded analysis mode\n */\nexport function flatten(\n  net: PetriNet,\n  environmentPlaces: Set<EnvironmentPlace<any>> = new Set(),\n  environmentMode: EnvironmentAnalysisMode = unbounded(),\n): FlatNet {\n  // 1. Collect ALL places\n  const allPlacesSet = new Map<string, Place<any>>();\n  for (const p of net.places) {\n    allPlacesSet.set(p.name, p);\n  }\n  for (const t of net.transitions) {\n    for (const inSpec of t.inputSpecs) {\n      allPlacesSet.set(inSpec.place.name, inSpec.place);\n    }\n    if (t.outputSpec !== null) {\n      for (const p of outAllPlaces(t.outputSpec)) {\n        allPlacesSet.set(p.name, p);\n      }\n    }\n    for (const arc of t.inhibitors) allPlacesSet.set(arc.place.name, arc.place);\n    for (const arc of t.reads) allPlacesSet.set(arc.place.name, arc.place);\n    for (const arc of t.resets) allPlacesSet.set(arc.place.name, arc.place);\n  }\n\n  // Sort by name for stable indexing\n  const places = [...allPlacesSet.values()].sort((a, b) => a.name.localeCompare(b.name));\n\n  const placeIndex = new Map<string, number>();\n  for (let i = 0; i < places.length; i++) {\n    placeIndex.set(places[i]!.name, i);\n  }\n\n  // 2. Compute environment bounds\n  const environmentBounds = new Map<string, number>();\n  if (environmentMode.type === 'bounded') {\n    for (const ep of environmentPlaces) {\n      environmentBounds.set(ep.place.name, environmentMode.maxTokens);\n    }\n  }\n\n  // 3. Expand transitions\n  const n = places.length;\n  const flatTransitions = [];\n\n  for (const transition of net.transitions) {\n    const branches = enumerateOutputBranches(transition);\n\n    for (let branchIdx = 0; branchIdx < branches.length; branchIdx++) {\n      const branchPlaces = branches[branchIdx]!;\n      const name = branches.length > 1\n        ? `${transition.name}_b${branchIdx}`\n        : transition.name;\n\n      // Build pre-vector and consumeAll flags\n      const preVector = new Array<number>(n).fill(0);\n      const consumeAll = new Array<boolean>(n).fill(false);\n\n      for (const inSpec of transition.inputSpecs) {\n        const idx = placeIndex.get(inSpec.place.name);\n        if (idx === undefined) continue;\n\n        switch (inSpec.type) {\n          case 'one':\n            preVector[idx] = 1;\n            break;\n          case 'exactly':\n            preVector[idx] = inSpec.count;\n            break;\n          case 'all':\n            preVector[idx] = 1;\n            consumeAll[idx] = true;\n            break;\n          case 'at-least':\n            preVector[idx] = inSpec.minimum;\n            consumeAll[idx] = true;\n            break;\n        }\n      }\n\n      // Build post-vector from branch output places\n      const postVector = new Array<number>(n).fill(0);\n      for (const p of branchPlaces) {\n        const idx = placeIndex.get(p.name);\n        if (idx !== undefined) {\n          postVector[idx] = 1;\n        }\n      }\n\n      // Inhibitor places\n      const inhibitorPlaces = transition.inhibitors\n        .map(arc => placeIndex.get(arc.place.name))\n        .filter((idx): idx is number => idx !== undefined);\n\n      // Read places\n      const readPlaces = transition.reads\n        .map(arc => placeIndex.get(arc.place.name))\n        .filter((idx): idx is number => idx !== undefined);\n\n      // Reset places\n      const resetPlaces = transition.resets\n        .map(arc => placeIndex.get(arc.place.name))\n        .filter((idx): idx is number => idx !== undefined);\n\n      flatTransitions.push(flatTransition(\n        name,\n        transition,\n        branches.length > 1 ? branchIdx : -1,\n        preVector,\n        postVector,\n        inhibitorPlaces,\n        readPlaces,\n        resetPlaces,\n        consumeAll,\n      ));\n    }\n  }\n\n  return {\n    places,\n    placeIndex,\n    transitions: flatTransitions,\n    environmentBounds,\n  };\n}\n\nfunction enumerateOutputBranches(t: { outputSpec: Out | null }): ReadonlySet<Place<any>>[] {\n  if (t.outputSpec !== null) {\n    return enumerateBranches(t.outputSpec) as ReadonlySet<Place<any>>[];\n  }\n  // No outputs (sink transition)\n  return [new Set()];\n}\n","/**\n * A P-invariant (place invariant) of a Petri net.\n *\n * A P-invariant is a vector y such that y^T * C = 0, where C is the\n * incidence matrix. This means that for any reachable marking M:\n * sum(y_i * M_i) = constant, where constant = sum(y_i * M0_i).\n *\n * P-invariants provide structural bounds on places and are used as\n * strengthening lemmas for the IC3/PDR engine.\n */\nexport interface PInvariant {\n  /** Weight vector (one entry per place index). */\n  readonly weights: readonly number[];\n  /** The invariant value sum(y_i * M0_i). */\n  readonly constant: number;\n  /** Set of place indices where weight != 0. */\n  readonly support: ReadonlySet<number>;\n}\n\nexport function pInvariant(weights: number[], constant: number, support: Set<number>): PInvariant {\n  return { weights, constant, support };\n}\n\nexport function pInvariantToString(inv: PInvariant): string {\n  const parts: string[] = [];\n  for (const i of inv.support) {\n    if (inv.weights[i] !== 1) {\n      parts.push(`${inv.weights[i]}*p${i}`);\n    } else {\n      parts.push(`p${i}`);\n    }\n  }\n  return `PInvariant[${parts.join(' + ')} = ${inv.constant}]`;\n}\n","/**\n * @module p-invariant-computer\n *\n * Computes P-invariants of a Petri net via integer Gaussian elimination (Farkas' algorithm).\n *\n * **Algorithm**: A P-invariant is a non-negative integer vector y such that y^T · C = 0\n * (where C is the incidence matrix). This expresses a conservation law: the weighted\n * token sum Σ(y_i · M[i]) is constant across all reachable markings.\n *\n * **Farkas variant**: Constructs the augmented matrix [C^T | I_P] and row-reduces\n * the C^T portion to zero using integer elimination (no floating point). Rows where\n * the C^T part becomes all-zero yield invariant vectors from the identity part.\n * Row normalization by GCD keeps values small during elimination.\n *\n * **Integer Gaussian elimination**: Each elimination step multiplies rows by pivot\n * coefficients (a·row - b·pivotRow) to avoid fractions. This preserves integer\n * arithmetic throughout, critical for exact invariant computation.\n *\n * Invariants are used to strengthen SMT queries (added as constraints on M').\n */\nimport type { FlatNet } from '../encoding/flat-net.js';\nimport type { IncidenceMatrix } from '../encoding/incidence-matrix.js';\nimport type { MarkingState } from '../marking-state.js';\nimport type { PInvariant } from './p-invariant.js';\nimport { pInvariant } from './p-invariant.js';\n\n/**\n * Computes P-invariants of a Petri net via integer Gaussian elimination.\n *\n * P-invariants are non-negative integer vectors y where y^T * C = 0.\n * They express conservation laws: the weighted token sum is constant\n * across all reachable markings.\n *\n * Algorithm: compute the null space of C^T using integer row reduction\n * with an augmented identity matrix (Farkas' algorithm variant).\n */\nexport function computePInvariants(\n  matrix: IncidenceMatrix,\n  flatNet: FlatNet,\n  initialMarking: MarkingState,\n): PInvariant[] {\n  const P = matrix.numPlaces();\n  const T = matrix.numTransitions();\n\n  if (P === 0 || T === 0) return [];\n\n  // We want to find y such that y^T * C = 0, i.e., C^T * y = 0\n  // Start with augmented matrix [C^T | I_P]\n  // Row-reduce C^T part to zero; the I_P part gives the invariant vectors.\n  const ct = matrix.transposedIncidence(); // P × T\n\n  // Augmented matrix: P rows, T + P columns\n  // Use regular numbers (safe for nets with < ~50 places/transitions)\n  const cols = T + P;\n  const augmented: number[][] = [];\n  for (let i = 0; i < P; i++) {\n    const row = new Array<number>(cols).fill(0);\n    for (let j = 0; j < T; j++) {\n      row[j] = ct[i]![j]!;\n    }\n    row[T + i] = 1; // identity part\n    augmented.push(row);\n  }\n\n  // Integer Gaussian elimination on the C^T part (columns 0..T-1)\n  let pivotRow = 0;\n  for (let col = 0; col < T && pivotRow < P; col++) {\n    // Find pivot (non-zero entry in this column)\n    let pivot = -1;\n    for (let row = pivotRow; row < P; row++) {\n      if (augmented[row]![col] !== 0) {\n        pivot = row;\n        break;\n      }\n    }\n    if (pivot === -1) continue; // free variable\n\n    // Swap pivot row\n    if (pivot !== pivotRow) {\n      const tmp = augmented[pivotRow]!;\n      augmented[pivotRow] = augmented[pivot]!;\n      augmented[pivot] = tmp;\n    }\n\n    // Eliminate this column in all other rows\n    for (let row = 0; row < P; row++) {\n      if (row === pivotRow || augmented[row]![col] === 0) continue;\n\n      const a = augmented[pivotRow]![col]!;\n      const b = augmented[row]![col]!;\n\n      // row = a*row - b*pivotRow (keeps integers, eliminates col)\n      for (let c = 0; c < cols; c++) {\n        augmented[row]![c] = a * augmented[row]![c]! - b * augmented[pivotRow]![c]!;\n      }\n\n      // Normalize by GCD to keep values small\n      normalizeRow(augmented[row]!, cols);\n    }\n\n    pivotRow++;\n  }\n\n  // Extract invariants: rows where C^T part is all zeros\n  const invariants: PInvariant[] = [];\n  for (let row = 0; row < P; row++) {\n    let isZero = true;\n    for (let col = 0; col < T; col++) {\n      if (augmented[row]![col] !== 0) {\n        isZero = false;\n        break;\n      }\n    }\n    if (!isZero) continue;\n\n    // Extract the weight vector from the identity part\n    const weights = new Array<number>(P);\n    let allNonNegative = true;\n    let hasPositive = false;\n\n    for (let i = 0; i < P; i++) {\n      weights[i] = augmented[row]![T + i]!;\n      if (weights[i]! < 0) {\n        allNonNegative = false;\n        break;\n      }\n      if (weights[i]! > 0) hasPositive = true;\n    }\n\n    // We want semi-positive invariants (all weights >= 0, at least one > 0)\n    if (!allNonNegative) {\n      // Try negating\n      let allNonPositive = true;\n      for (let i = 0; i < P; i++) {\n        if (augmented[row]![T + i]! > 0) {\n          allNonPositive = false;\n          break;\n        }\n      }\n      if (allNonPositive) {\n        for (let i = 0; i < P; i++) {\n          weights[i] = -augmented[row]![T + i]!;\n        }\n        hasPositive = true;\n        allNonNegative = true;\n      }\n    }\n\n    if (!allNonNegative || !hasPositive) continue;\n\n    // Normalize: divide by GCD of weights\n    let g = 0;\n    for (const w of weights) {\n      if (w > 0) g = gcd(g, w);\n    }\n    if (g > 1) {\n      for (let i = 0; i < P; i++) {\n        weights[i] = weights[i]! / g;\n      }\n    }\n\n    // Compute support and constant\n    const support = new Set<number>();\n    let constant = 0;\n    for (let i = 0; i < P; i++) {\n      if (weights[i] !== 0) {\n        support.add(i);\n        const place = flatNet.places[i]!;\n        constant += weights[i]! * initialMarking.tokens(place);\n      }\n    }\n\n    invariants.push(pInvariant(weights, constant, support));\n  }\n\n  return invariants;\n}\n\n/**\n * Checks if every place is covered by at least one P-invariant.\n * If true, the net is structurally bounded.\n */\nexport function isCoveredByInvariants(invariants: readonly PInvariant[], numPlaces: number): boolean {\n  const covered = new Array<boolean>(numPlaces).fill(false);\n  for (const inv of invariants) {\n    for (const idx of inv.support) {\n      if (idx < numPlaces) covered[idx] = true;\n    }\n  }\n  return covered.every(c => c);\n}\n\nfunction normalizeRow(row: number[], cols: number): void {\n  let g = 0;\n  for (let c = 0; c < cols; c++) {\n    if (row[c] !== 0) {\n      g = gcd(g, Math.abs(row[c]!));\n    }\n  }\n  if (g > 1) {\n    for (let c = 0; c < cols; c++) {\n      row[c] = row[c]! / g;\n    }\n  }\n}\n\nfunction gcd(a: number, b: number): number {\n  while (b !== 0) {\n    const t = b;\n    b = a % b;\n    a = t;\n  }\n  return a;\n}\n","/**\n * @module structural-check\n *\n * Structural deadlock pre-check using siphon/trap analysis (Commoner's theorem).\n *\n * **Commoner's theorem**: A Petri net is deadlock-free if every siphon contains\n * an initially marked trap.\n *\n * **Siphon**: A set of places S where every transition that outputs to S also\n * inputs from S. Key property: once all places in a siphon become empty,\n * they can never be re-marked. An empty siphon can cause deadlock.\n *\n * **Trap**: A set of places S where every transition that inputs from S also\n * outputs to S. Key property: once any place in a trap is marked,\n * the trap remains marked forever.\n *\n * **Algorithm**: For each place, compute the minimal siphon containing it via\n * fixed-point expansion. For each siphon, find the maximal trap within it\n * (fixed-point contraction). If every siphon contains an initially-marked\n * trap, deadlock-freedom is proven structurally — no SMT query needed.\n *\n * Limited to nets with ≤50 places to bound enumeration cost.\n */\nimport type { FlatNet } from '../encoding/flat-net.js';\nimport type { MarkingState } from '../marking-state.js';\n\nconst MAX_PLACES_FOR_SIPHON_ANALYSIS = 50;\n\n/**\n * Result of structural deadlock check using siphon/trap analysis.\n */\nexport type StructuralCheckResult =\n  | { readonly type: 'no-potential-deadlock' }\n  | { readonly type: 'potential-deadlock'; readonly siphon: ReadonlySet<number> }\n  | { readonly type: 'inconclusive'; readonly reason: string };\n\n/**\n * Structural deadlock pre-check using siphon/trap analysis.\n *\n * Commoner's theorem: a Petri net is deadlock-free if every siphon\n * contains a marked trap.\n *\n * A siphon is a set of places S such that every transition with\n * an output in S also has an input in S. Once empty, a siphon stays empty.\n *\n * A trap is a set of places S such that every transition with\n * an input in S also has an output in S. Once marked, a trap stays marked.\n */\nexport function structuralCheck(flatNet: FlatNet, initialMarking: MarkingState): StructuralCheckResult {\n  const P = flatNet.places.length;\n\n  if (P === 0) {\n    return { type: 'no-potential-deadlock' };\n  }\n\n  if (P > MAX_PLACES_FOR_SIPHON_ANALYSIS) {\n    return { type: 'inconclusive', reason: `Net has ${P} places, siphon enumeration skipped` };\n  }\n\n  const siphons = findMinimalSiphons(flatNet);\n\n  if (siphons.length === 0) {\n    return { type: 'no-potential-deadlock' };\n  }\n\n  for (const siphon of siphons) {\n    const trap = findMaximalTrapIn(flatNet, siphon);\n\n    if (trap.size === 0 || !isMarked(trap, flatNet, initialMarking)) {\n      return { type: 'potential-deadlock', siphon };\n    }\n  }\n\n  return { type: 'no-potential-deadlock' };\n}\n\n/**\n * Finds minimal siphons by checking all non-empty subsets of deadlock-enabling places.\n * Uses a fixed-point approach: start from each place and grow the siphon.\n */\nexport function findMinimalSiphons(flatNet: FlatNet): ReadonlySet<number>[] {\n  const P = flatNet.places.length;\n  const siphons: Set<number>[] = [];\n\n  // Pre-compute: for each place, which transitions have it as output?\n  const placeAsOutput: number[][] = [];\n  for (let p = 0; p < P; p++) {\n    placeAsOutput.push([]);\n  }\n\n  for (let t = 0; t < flatNet.transitions.length; t++) {\n    const ft = flatNet.transitions[t]!;\n    for (let p = 0; p < P; p++) {\n      if (ft.postVector[p]! > 0) {\n        placeAsOutput[p]!.push(t);\n      }\n    }\n  }\n\n  for (let startPlace = 0; startPlace < P; startPlace++) {\n    const siphon = computeSiphonContaining(startPlace, flatNet, placeAsOutput);\n    if (siphon !== null && siphon.size > 0) {\n      let isMinimal = true;\n      const toRemove: number[] = [];\n      for (let i = 0; i < siphons.length; i++) {\n        const existing = siphons[i]!;\n        if (setsEqual(existing, siphon)) {\n          isMinimal = false;\n          break;\n        }\n        if (isSubsetOf(existing, siphon)) {\n          isMinimal = false;\n          break;\n        }\n        if (isSubsetOf(siphon, existing)) {\n          toRemove.push(i);\n        }\n      }\n      for (let i = toRemove.length - 1; i >= 0; i--) {\n        siphons.splice(toRemove[i]!, 1);\n      }\n      if (isMinimal) {\n        siphons.push(siphon);\n      }\n    }\n  }\n\n  return siphons;\n}\n\nfunction computeSiphonContaining(\n  startPlace: number,\n  flatNet: FlatNet,\n  placeAsOutput: number[][],\n): Set<number> | null {\n  const siphon = new Set<number>();\n  siphon.add(startPlace);\n\n  let changed = true;\n  while (changed) {\n    changed = false;\n    const snapshot = [...siphon];\n\n    for (const p of snapshot) {\n      for (const t of placeAsOutput[p]!) {\n        const ft = flatNet.transitions[t]!;\n\n        let hasInputInSiphon = false;\n        for (let q = 0; q < flatNet.places.length; q++) {\n          if (ft.preVector[q]! > 0 && siphon.has(q)) {\n            hasInputInSiphon = true;\n            break;\n          }\n        }\n\n        if (!hasInputInSiphon) {\n          let added = false;\n          for (let q = 0; q < flatNet.places.length; q++) {\n            if (ft.preVector[q]! > 0) {\n              if (!siphon.has(q)) {\n                siphon.add(q);\n                changed = true;\n              }\n              added = true;\n              break;\n            }\n          }\n          if (!added) {\n            return null;\n          }\n        }\n      }\n    }\n  }\n\n  return siphon;\n}\n\n/**\n * Finds the maximal trap within a given set of places.\n * Uses fixed-point: start with the full set and remove places that violate the trap condition.\n */\nexport function findMaximalTrapIn(flatNet: FlatNet, places: ReadonlySet<number>): ReadonlySet<number> {\n  const trap = new Set(places);\n\n  let changed = true;\n  while (changed) {\n    changed = false;\n    const toRemove: number[] = [];\n\n    for (const p of trap) {\n      let satisfies = true;\n      for (let t = 0; t < flatNet.transitions.length; t++) {\n        const ft = flatNet.transitions[t]!;\n        if (ft.preVector[p]! > 0) {\n          let outputsToTrap = false;\n          for (const q of trap) {\n            if (ft.postVector[q]! > 0) {\n              outputsToTrap = true;\n              break;\n            }\n          }\n          if (!outputsToTrap) {\n            satisfies = false;\n            break;\n          }\n        }\n      }\n      if (!satisfies) {\n        toRemove.push(p);\n      }\n    }\n\n    if (toRemove.length > 0) {\n      for (const p of toRemove) trap.delete(p);\n      changed = true;\n    }\n  }\n\n  return trap;\n}\n\nfunction isMarked(placeIndices: ReadonlySet<number>, flatNet: FlatNet, marking: MarkingState): boolean {\n  for (const idx of placeIndices) {\n    const place = flatNet.places[idx]!;\n    if (marking.tokens(place) > 0) return true;\n  }\n  return false;\n}\n\nfunction setsEqual(a: ReadonlySet<number>, b: ReadonlySet<number>): boolean {\n  if (a.size !== b.size) return false;\n  for (const v of a) {\n    if (!b.has(v)) return false;\n  }\n  return true;\n}\n\nfunction isSubsetOf(sub: ReadonlySet<number>, sup: ReadonlySet<number>): boolean {\n  if (sub.size > sup.size) return false;\n  for (const v of sub) {\n    if (!sup.has(v)) return false;\n  }\n  return true;\n}\n","import type { Place } from '../core/place.js';\n\n/**\n * Safety properties that can be verified via IC3/PDR.\n *\n * Each property is encoded as an error condition: if a reachable state\n * violates the property, Spacer finds a counterexample. If no violation\n * is reachable, the property is proven.\n */\nexport type SmtProperty = DeadlockFree | MutualExclusion | PlaceBound | Unreachable;\n\n/** Deadlock-freedom: no reachable marking has all transitions disabled. */\nexport interface DeadlockFree {\n  readonly type: 'deadlock-free';\n}\n\n/** Mutual exclusion: two places never have tokens simultaneously. */\nexport interface MutualExclusion {\n  readonly type: 'mutual-exclusion';\n  readonly p1: Place<any>;\n  readonly p2: Place<any>;\n}\n\n/** Place bound: a place never exceeds a given token count. */\nexport interface PlaceBound {\n  readonly type: 'place-bound';\n  readonly place: Place<any>;\n  readonly bound: number;\n}\n\n/** Unreachability: the given places never all have tokens simultaneously. */\nexport interface Unreachable {\n  readonly type: 'unreachable';\n  readonly places: ReadonlySet<Place<any>>;\n}\n\n// Factory functions\n\nexport function deadlockFree(): DeadlockFree {\n  return { type: 'deadlock-free' };\n}\n\nexport function mutualExclusion(p1: Place<any>, p2: Place<any>): MutualExclusion {\n  return { type: 'mutual-exclusion', p1, p2 };\n}\n\nexport function placeBound(place: Place<any>, bound: number): PlaceBound {\n  return { type: 'place-bound', place, bound };\n}\n\nexport function unreachable(places: ReadonlySet<Place<any>>): Unreachable {\n  return { type: 'unreachable', places: new Set(places) };\n}\n\n/** Human-readable description of a property. */\nexport function propertyDescription(prop: SmtProperty): string {\n  switch (prop.type) {\n    case 'deadlock-free':\n      return 'Deadlock-freedom';\n    case 'mutual-exclusion':\n      return `Mutual exclusion of ${prop.p1.name} and ${prop.p2.name}`;\n    case 'place-bound':\n      return `Place ${prop.place.name} bounded by ${prop.bound}`;\n    case 'unreachable':\n      return `Unreachability of marking with tokens in {${[...prop.places].map(p => p.name).join(', ')}}`;\n  }\n}\n","import type { MarkingState } from './marking-state.js';\nimport type { PInvariant } from './invariant/p-invariant.js';\n\n/**\n * Verification verdict.\n */\nexport type Verdict = Proven | Violated | Unknown;\n\n/** Property proven safe. No reachable state violates it. */\nexport interface Proven {\n  readonly type: 'proven';\n  readonly method: string;\n  readonly inductiveInvariant: string | null;\n}\n\n/** Property violated. A counterexample trace is available. */\nexport interface Violated {\n  readonly type: 'violated';\n}\n\n/** Could not determine. */\nexport interface Unknown {\n  readonly type: 'unknown';\n  readonly reason: string;\n}\n\n/**\n * Solver statistics.\n */\nexport interface SmtStatistics {\n  readonly places: number;\n  readonly transitions: number;\n  readonly invariantsFound: number;\n  readonly structuralResult: string;\n}\n\n/**\n * Result of SMT-based verification.\n */\nexport interface SmtVerificationResult {\n  readonly verdict: Verdict;\n  readonly report: string;\n  readonly invariants: readonly PInvariant[];\n  readonly discoveredInvariants: readonly string[];\n  readonly counterexampleTrace: readonly MarkingState[];\n  readonly counterexampleTransitions: readonly string[];\n  readonly elapsedMs: number;\n  readonly statistics: SmtStatistics;\n}\n\nexport function isProven(result: SmtVerificationResult): boolean {\n  return result.verdict.type === 'proven';\n}\n\nexport function isViolated(result: SmtVerificationResult): boolean {\n  return result.verdict.type === 'violated';\n}\n","import { init } from 'z3-solver';\nimport type { Bool, Expr, FuncDecl } from 'z3-solver';\n\n/**\n * Result of a Spacer query.\n */\nexport type QueryResult = QueryProven | QueryViolated | QueryUnknown;\n\n/** Property proven: no reachable error state (UNSAT). */\nexport interface QueryProven {\n  readonly type: 'proven';\n  readonly invariantFormula: string | null;\n  readonly levelInvariants: readonly string[];\n}\n\n/** Counterexample found (SAT). The answer is the derivation tree. */\nexport interface QueryViolated {\n  readonly type: 'violated';\n  readonly answer: Expr | null;\n}\n\n/** Solver could not determine (timeout, resource limit). */\nexport interface QueryUnknown {\n  readonly type: 'unknown';\n  readonly reason: string;\n}\n\n/**\n * The Z3 context and helpers returned by SpacerRunner.create().\n * Exposes the context object for building expressions.\n */\nexport interface SpacerContext {\n  /** The Z3 high-level context for building expressions. */\n  readonly ctx: ReturnType<Awaited<ReturnType<typeof init>>['Context']>;\n  /** The Z3 Fixedpoint solver instance (Spacer engine). Z3 types are complex; using any. */\n  readonly fp: any;\n\n  /** Queries whether the error state is reachable. */\n  query(errorExpr: Bool, reachableDecl?: FuncDecl): Promise<QueryResult>;\n\n  /** Releases Z3 resources. */\n  dispose(): void;\n}\n\n// Use a type alias for the Z3 context to avoid the deep inference\ntype Z3Context = ReturnType<Awaited<ReturnType<typeof init>>['Context']>;\n\n/**\n * Creates a Spacer runner with the given timeout.\n *\n * Uses Z3's Spacer engine (CHC solver based on IC3/PDR) to prove or\n * disprove safety properties.\n */\nexport async function createSpacerRunner(timeoutMs: number): Promise<SpacerContext> {\n  const { Context } = await init();\n  const ctx = new Context('main') as Z3Context;\n  const fp = new (ctx as any).Fixedpoint() as any;\n\n  // Configure Spacer engine\n  fp.set('engine', 'spacer');\n  fp.set('spacer.global', true);\n  fp.set('spacer.use_bg_invs', true);\n  if (timeoutMs > 0) {\n    fp.set('timeout', Math.min(timeoutMs, 2147483647));\n  }\n\n  async function query(errorExpr: Bool, reachableDecl?: FuncDecl): Promise<QueryResult> {\n    try {\n      const status = await fp.query(errorExpr);\n\n      if (status === 'unsat') {\n        let invariantFormula: string | null = null;\n        const levelInvariants: string[] = [];\n\n        try {\n          const answer = fp.getAnswer();\n          if (answer != null) {\n            invariantFormula = answer.toString();\n          }\n        } catch {\n          // Some configurations don't produce answers\n        }\n\n        if (reachableDecl != null) {\n          try {\n            const levels = fp.getNumLevels(reachableDecl);\n            for (let i = 0; i < levels; i++) {\n              const cover = fp.getCoverDelta(i, reachableDecl);\n              if (cover != null && !(ctx as any).isTrue(cover)) {\n                levelInvariants.push(`Level ${i}: ${cover.toString()}`);\n              }\n            }\n          } catch {\n            // Level queries may not be available\n          }\n        }\n\n        return { type: 'proven', invariantFormula, levelInvariants };\n      }\n\n      if (status === 'sat') {\n        let answer: Expr | null = null;\n        try {\n          answer = fp.getAnswer();\n        } catch {\n          // Some configurations don't produce answers\n        }\n        return { type: 'violated', answer };\n      }\n\n      // unknown\n      return { type: 'unknown', reason: fp.getReasonUnknown() };\n    } catch (e: any) {\n      return { type: 'unknown', reason: `Z3 exception: ${e.message ?? e}` };\n    }\n  }\n\n  function dispose(): void {\n    try {\n      fp.release();\n    } catch {\n      // ignore\n    }\n  }\n\n  return {\n    ctx,\n    fp,\n    query,\n    dispose,\n  } as SpacerContext;\n}\n","/**\n * @module smt-encoder\n *\n * Encodes a flattened Petri net as Constrained Horn Clauses (CHC) for Z3's Spacer engine.\n *\n * **CHC encoding strategy**: The net's state space is modeled as integer vectors\n * (one variable per place = token count). Three rule types:\n *\n * 1. **Init**: `Reachable(M0)` — the initial marking is reachable\n * 2. **Transition**: `Reachable(M') :- Reachable(M) ∧ enabled(M,t) ∧ fire(M,M',t)` —\n *    one rule per flat transition (XOR branches are separate transitions)\n * 3. **Error**: `Error() :- Reachable(M) ∧ violation(M)` — safety property violation\n *\n * Transition rules include: non-negativity constraints on M', P-invariant strengthening\n * clauses, and environment bounds for bounded analysis.\n *\n * Z3 types are complex and partially untyped; the ctx/fp parameters use `any`.\n */\nimport type { Arith, Bool, FuncDecl } from 'z3-solver';\nimport type { FlatNet } from '../encoding/flat-net.js';\nimport type { FlatTransition } from '../encoding/flat-transition.js';\nimport type { MarkingState } from '../marking-state.js';\nimport type { SmtProperty } from '../smt-property.js';\nimport type { PInvariant } from '../invariant/p-invariant.js';\nimport type { Place } from '../../core/place.js';\nimport { flatNetIndexOf } from '../encoding/flat-net.js';\n\n/** Z3 high-level context. Typed as `any` because z3-solver's TS types are incomplete. */\ntype Z3Context = any;\n/** Z3 Fixedpoint solver instance. Typed as `any` because z3-solver's TS types are incomplete. */\ntype Z3Fixedpoint = any;\n\n/**\n * Result of CHC encoding.\n */\nexport interface EncodingResult {\n  readonly errorExpr: Bool;\n  readonly reachableDecl: FuncDecl;\n}\n\n/**\n * Encodes a flattened Petri net as Constrained Horn Clauses (CHC) for Z3's Spacer engine.\n *\n * CHC rules:\n * - Reachable(M0) — initial state is reachable\n * - Reachable(M') :- Reachable(M) AND enabled(M,t) AND fire(M,M',t) — transition rules\n * - Error() :- Reachable(M) AND property_violation(M) — safety property\n */\nexport function encode(\n  ctx: Z3Context,\n  fp: Z3Fixedpoint,\n  flatNet: FlatNet,\n  initialMarking: MarkingState,\n  property: SmtProperty,\n  invariants: readonly PInvariant[],\n  sinkPlaces: ReadonlySet<Place<any>> = new Set(),\n): EncodingResult {\n  const P = flatNet.places.length;\n  const Int = ctx.Int;\n  const Bool_ = ctx.Bool;\n\n  // Create sorts array for function declaration\n  const intSort = Int.sort();\n  const boolSort = Bool_.sort();\n  const markingSorts: any[] = new Array(P).fill(intSort);\n\n  // Create the Reachable relation: (Int, Int, ...) -> Bool\n  const reachable: FuncDecl = ctx.Function.declare('Reachable', ...markingSorts, boolSort);\n  fp.registerRelation(reachable);\n\n  // Create the Error relation: () -> Bool\n  const error: FuncDecl = ctx.Function.declare('Error', boolSort);\n  fp.registerRelation(error);\n\n  // === Rule 1: Initial state ===\n  // Reachable(m0_0, m0_1, ..., m0_{P-1})\n  const m0Args: Arith[] = [];\n  for (let i = 0; i < P; i++) {\n    const tokens = initialMarking.tokens(flatNet.places[i]!);\n    m0Args.push(Int.val(tokens));\n  }\n  const initFact = (reachable as any).call(...m0Args) as Bool;\n  fp.addRule(initFact, 'init');\n\n  // === Rule 2: Transition rules ===\n  for (let t = 0; t < flatNet.transitions.length; t++) {\n    const ft = flatNet.transitions[t]!;\n    encodeTransitionRule(ctx, fp, reachable, ft, flatNet, invariants, P);\n  }\n\n  // === Rule 3: Error rule (property violation) ===\n  encodeErrorRule(ctx, fp, reachable, error, flatNet, property, sinkPlaces, P);\n\n  return {\n    errorExpr: (error as any).call() as Bool,\n    reachableDecl: reachable,\n  };\n}\n\nfunction encodeTransitionRule(\n  ctx: Z3Context,\n  fp: Z3Fixedpoint,\n  reachable: FuncDecl,\n  ft: FlatTransition,\n  flatNet: FlatNet,\n  invariants: readonly PInvariant[],\n  P: number,\n): void {\n  const Int = ctx.Int;\n\n  // Create named variables for current and next marking\n  const mVars: Arith[] = [];\n  const mPrimeVars: Arith[] = [];\n  for (let i = 0; i < P; i++) {\n    mVars.push(Int.const(`m${i}`));\n    mPrimeVars.push(Int.const(`mp${i}`));\n  }\n\n  // Body: Reachable(M) AND enabled(M,t) AND fire(M,M',t) AND non-negativity(M') AND invariants(M') AND env bounds(M')\n  const reachBody = (reachable as any).call(...mVars) as Bool;\n  const enabled = encodeEnabled(ctx, ft, flatNet, mVars, P);\n  const fireRelation = encodeFire(ctx, ft, flatNet, mVars, mPrimeVars, P);\n\n  // Non-negativity of M'\n  let nonNeg: Bool = ctx.Bool.val(true);\n  for (let i = 0; i < P; i++) {\n    nonNeg = ctx.And(nonNeg, mPrimeVars[i]!.ge(0));\n  }\n\n  // P-invariant constraints on M'\n  const invConstraints = encodeInvariantConstraints(ctx, invariants, mPrimeVars, P);\n\n  // Environment bounds on M'\n  let envBounds: Bool = ctx.Bool.val(true);\n  for (const [name, bound] of flatNet.environmentBounds) {\n    const idx = flatNet.placeIndex.get(name);\n    if (idx != null) {\n      envBounds = ctx.And(envBounds, mPrimeVars[idx]!.le(bound));\n    }\n  }\n\n  // Body conjunction\n  const body = ctx.And(reachBody, enabled, fireRelation, nonNeg, invConstraints, envBounds);\n\n  // Head: Reachable(M')\n  const head = (reachable as any).call(...mPrimeVars) as Bool;\n\n  // Rule: forall M, M'. body => head\n  const allVars = [...mVars, ...mPrimeVars];\n  const rule = ctx.Implies(body, head);\n  const qRule = ctx.ForAll(allVars, rule);\n\n  fp.addRule(qRule, `t_${ft.name}`);\n}\n\nfunction encodeEnabled(\n  ctx: Z3Context,\n  ft: FlatTransition,\n  _flatNet: FlatNet,\n  mVars: Arith[],\n  P: number,\n): Bool {\n  let result: Bool = ctx.Bool.val(true);\n\n  // Input requirements: M[p] >= pre[p]\n  for (let p = 0; p < P; p++) {\n    if (ft.preVector[p]! > 0) {\n      result = ctx.And(result, mVars[p]!.ge(ft.preVector[p]!));\n    }\n  }\n\n  // Read arcs: M[p] >= 1\n  for (const p of ft.readPlaces) {\n    result = ctx.And(result, mVars[p]!.ge(1));\n  }\n\n  // Inhibitor arcs: M[p] == 0\n  for (const p of ft.inhibitorPlaces) {\n    result = ctx.And(result, mVars[p]!.eq(0));\n  }\n\n  // Non-negativity of current marking\n  for (let p = 0; p < P; p++) {\n    result = ctx.And(result, mVars[p]!.ge(0));\n  }\n\n  return result;\n}\n\nfunction encodeFire(\n  ctx: Z3Context,\n  ft: FlatTransition,\n  _flatNet: FlatNet,\n  mVars: Arith[],\n  mPrimeVars: Arith[],\n  P: number,\n): Bool {\n  let result: Bool = ctx.Bool.val(true);\n\n  for (let p = 0; p < P; p++) {\n    const isReset = ft.resetPlaces.includes(p);\n\n    if (isReset || ft.consumeAll[p]) {\n      // Reset/consumeAll: M'[p] = post[p]\n      result = ctx.And(result, mPrimeVars[p]!.eq(ft.postVector[p]!));\n    } else {\n      // Standard: M'[p] = M[p] - pre[p] + post[p]\n      const delta = ft.postVector[p]! - ft.preVector[p]!;\n      if (delta === 0) {\n        result = ctx.And(result, mPrimeVars[p]!.eq(mVars[p]!));\n      } else {\n        result = ctx.And(result, mPrimeVars[p]!.eq(mVars[p]!.add(delta)));\n      }\n    }\n  }\n\n  return result;\n}\n\nfunction encodeErrorRule(\n  ctx: Z3Context,\n  fp: Z3Fixedpoint,\n  reachable: FuncDecl,\n  error: FuncDecl,\n  flatNet: FlatNet,\n  property: SmtProperty,\n  sinkPlaces: ReadonlySet<Place<any>>,\n  P: number,\n): void {\n  const Int = ctx.Int;\n\n  // Create variables for the error rule\n  const mVars: Arith[] = [];\n  for (let i = 0; i < P; i++) {\n    mVars.push(Int.const(`em${i}`));\n  }\n\n  const reachBody = (reachable as any).call(...mVars) as Bool;\n  const violation = encodePropertyViolation(ctx, flatNet, property, sinkPlaces, mVars, P);\n\n  const head = (error as any).call() as Bool;\n  const body = ctx.And(reachBody, violation);\n  const rule = ctx.Implies(body, head);\n  const qRule = ctx.ForAll(mVars, rule);\n\n  fp.addRule(qRule, `error_${property.type}`);\n}\n\nfunction encodePropertyViolation(\n  ctx: Z3Context,\n  flatNet: FlatNet,\n  property: SmtProperty,\n  sinkPlaces: ReadonlySet<Place<any>>,\n  mVars: Arith[],\n  P: number,\n): Bool {\n  switch (property.type) {\n    case 'deadlock-free': {\n      const deadlock = encodeDeadlock(ctx, flatNet, mVars, P);\n      if (sinkPlaces.size > 0) {\n        // Deadlock is only a violation if NOT at any expected sink place\n        let notAtSink: Bool = ctx.Bool.val(true);\n        for (const sink of sinkPlaces) {\n          const idx = flatNetIndexOf(flatNet, sink);\n          if (idx >= 0) {\n            notAtSink = ctx.And(notAtSink, mVars[idx]!.eq(0));\n          }\n        }\n        return ctx.And(deadlock, notAtSink);\n      }\n      return deadlock;\n    }\n\n    case 'mutual-exclusion': {\n      const idx1 = flatNetIndexOf(flatNet, property.p1);\n      const idx2 = flatNetIndexOf(flatNet, property.p2);\n      if (idx1 < 0) throw new Error(`MutualExclusion references unknown place: ${property.p1.name}`);\n      if (idx2 < 0) throw new Error(`MutualExclusion references unknown place: ${property.p2.name}`);\n      return ctx.And(mVars[idx1]!.ge(1), mVars[idx2]!.ge(1));\n    }\n\n    case 'place-bound': {\n      const idx = flatNetIndexOf(flatNet, property.place);\n      if (idx < 0) throw new Error(`PlaceBound references unknown place: ${property.place.name}`);\n      return mVars[idx]!.gt(property.bound);\n    }\n\n    case 'unreachable': {\n      let allMarked: Bool = ctx.Bool.val(true);\n      for (const place of property.places) {\n        const idx = flatNetIndexOf(flatNet, place);\n        if (idx >= 0) {\n          allMarked = ctx.And(allMarked, mVars[idx]!.ge(1));\n        }\n      }\n      return allMarked;\n    }\n  }\n}\n\n/** Encodes the deadlock condition: no transition is enabled. */\nfunction encodeDeadlock(\n  ctx: Z3Context,\n  flatNet: FlatNet,\n  mVars: Arith[],\n  P: number,\n): Bool {\n  let deadlock: Bool = ctx.Bool.val(true);\n\n  for (const ft of flatNet.transitions) {\n    const enabled = encodeEnabled(ctx, ft, flatNet, mVars, P);\n    deadlock = ctx.And(deadlock, ctx.Not(enabled));\n  }\n\n  return deadlock;\n}\n\nfunction encodeInvariantConstraints(\n  ctx: Z3Context,\n  invariants: readonly PInvariant[],\n  mVars: Arith[],\n  P: number,\n): Bool {\n  let result: Bool = ctx.Bool.val(true);\n\n  for (const inv of invariants) {\n    // sum(y_i * M[i]) == constant\n    let sum: Arith = ctx.Int.val(0);\n    for (const idx of inv.support) {\n      if (idx < P) {\n        sum = sum.add(mVars[idx]!.mul(inv.weights[idx]!));\n      }\n    }\n    result = ctx.And(result, sum.eq(inv.constant));\n  }\n\n  return result;\n}\n","import type { Expr } from 'z3-solver';\nimport { MarkingState } from '../marking-state.js';\nimport type { FlatNet } from '../encoding/flat-net.js';\n\n/**\n * Result of counterexample decoding.\n */\nexport interface DecodedTrace {\n  readonly trace: readonly MarkingState[];\n  readonly transitions: readonly string[];\n}\n\n/**\n * Decodes Z3 Spacer counterexample answers into Petri net marking traces.\n *\n * When Spacer finds a counterexample (property violation), it produces\n * a derivation tree showing how the error state is reachable. This function\n * extracts the marking at each step to produce a human-readable trace.\n */\nexport function decode(ctx: any, answer: Expr | null, flatNet: FlatNet): DecodedTrace {\n  const trace: MarkingState[] = [];\n  const transitions: string[] = [];\n\n  if (answer == null) {\n    return { trace, transitions };\n  }\n\n  try {\n    extractTrace(ctx, answer, flatNet, trace, transitions);\n  } catch {\n    // Z3 answer format varies; gracefully degrade\n  }\n\n  return { trace, transitions };\n}\n\n/**\n * Recursively traverses the Z3 proof tree to extract marking states.\n */\nfunction extractTrace(\n  ctx: any,\n  expr: any,\n  flatNet: FlatNet,\n  trace: MarkingState[],\n  transitions: string[],\n): void {\n  if (expr == null) return;\n\n  // Check if this is a function application\n  if (!ctx.isApp(expr)) return;\n\n  let name: string;\n  try {\n    const decl = expr.decl();\n    name = String(decl.name());\n  } catch {\n    return;\n  }\n\n  // Check if this is a Reachable application with integer arguments\n  const P = flatNet.places.length;\n  if (name === 'Reachable') {\n    const numArgs = expr.numArgs();\n    if (numArgs === P) {\n      const marking = extractMarking(ctx, expr, flatNet);\n      if (marking != null) {\n        trace.push(marking);\n      }\n    }\n  }\n\n  // Recurse into children to find the derivation chain\n  try {\n    const numArgs = expr.numArgs();\n    for (let i = 0; i < numArgs; i++) {\n      const child = expr.arg(i);\n      extractTrace(ctx, child, flatNet, trace, transitions);\n    }\n  } catch {\n    // Not all expressions support arg()\n  }\n\n  // Try to extract transition name from rule application\n  if (name.startsWith('t_')) {\n    transitions.push(name.substring(2));\n  }\n}\n\n/**\n * Extracts a MarkingState from a Reachable(...) application.\n */\nfunction extractMarking(ctx: any, reachableApp: any, flatNet: FlatNet): MarkingState | null {\n  const P = flatNet.places.length;\n  if (reachableApp.numArgs() !== P) return null;\n\n  const builder = MarkingState.builder();\n  for (let i = 0; i < P; i++) {\n    const arg = reachableApp.arg(i);\n    if (ctx.isIntVal(arg)) {\n      const tokens = Number(arg.value());\n      if (tokens > 0) {\n        builder.tokens(flatNet.places[i]!, tokens);\n      }\n    } else {\n      // Non-concrete value in counterexample\n      return null;\n    }\n  }\n  return builder.build();\n}\n","import type { PetriNet } from '../core/petri-net.js';\nimport type { EnvironmentPlace, Place } from '../core/place.js';\nimport { MarkingState, MarkingStateBuilder } from './marking-state.js';\nimport type { SmtProperty } from './smt-property.js';\nimport { deadlockFree, propertyDescription } from './smt-property.js';\nimport type { SmtVerificationResult, SmtStatistics, Verdict } from './smt-verification-result.js';\nimport type { PInvariant } from './invariant/p-invariant.js';\nimport type { FlatNet } from './encoding/flat-net.js';\nimport { flatten, type EnvironmentAnalysisMode, unbounded } from './encoding/net-flattener.js';\nimport { IncidenceMatrix } from './encoding/incidence-matrix.js';\nimport { computePInvariants, isCoveredByInvariants } from './invariant/p-invariant-computer.js';\nimport { structuralCheck } from './invariant/structural-check.js';\nimport { createSpacerRunner } from './z3/spacer-runner.js';\nimport { encode } from './z3/smt-encoder.js';\nimport { decode } from './z3/counterexample-decoder.js';\n\n/**\n * IC3/PDR-based safety verifier for Petri nets using Z3's Spacer engine.\n *\n * Proves safety properties (especially deadlock-freedom) without\n * enumerating all reachable states. IC3 constructs inductive invariants\n * incrementally, which works well for bounded nets.\n *\n * Key design decisions:\n * - Operates on the marking projection (integer vectors) — no timing\n * - An untimed deadlock-freedom proof is stronger than needed\n *   (timing can only restrict behavior)\n * - Guards are ignored — over-approximation is sound for safety properties\n * - If a counterexample is found, it may be spurious in timed/guarded\n *   semantics — the report notes this\n *\n * Verification Pipeline:\n * 1. Flatten — expand XOR, index places, build pre/post vectors\n * 2. Structural pre-check — siphon/trap analysis (may prove early)\n * 3. P-invariants — compute conservation laws for strengthening\n * 4. SMT encode + query — IC3/PDR via Z3 Spacer\n * 5. Decode result — proof or counterexample trace\n */\nexport class SmtVerifier {\n  private _initialMarking: MarkingState = MarkingState.empty();\n  private _property: SmtProperty = deadlockFree();\n  private readonly _environmentPlaces = new Set<EnvironmentPlace<any>>();\n  private readonly _sinkPlaces = new Set<Place<any>>();\n  private _environmentMode: EnvironmentAnalysisMode = unbounded();\n  private _timeoutMs: number = 60_000;\n\n  private constructor(private readonly net: PetriNet) {}\n\n  static forNet(net: PetriNet): SmtVerifier {\n    return new SmtVerifier(net);\n  }\n\n  initialMarking(marking: MarkingState): this;\n  initialMarking(configurator: (builder: MarkingStateBuilder) => void): this;\n  initialMarking(arg: MarkingState | ((builder: MarkingStateBuilder) => void)): this {\n    if (arg instanceof MarkingState) {\n      this._initialMarking = arg;\n    } else {\n      const builder = MarkingState.builder();\n      arg(builder);\n      this._initialMarking = builder.build();\n    }\n    return this;\n  }\n\n  property(property: SmtProperty): this {\n    this._property = property;\n    return this;\n  }\n\n  environmentPlaces(...places: EnvironmentPlace<any>[]): this {\n    for (const p of places) this._environmentPlaces.add(p);\n    return this;\n  }\n\n  environmentMode(mode: EnvironmentAnalysisMode): this {\n    this._environmentMode = mode;\n    return this;\n  }\n\n  /**\n   * Declares expected sink (terminal) places for deadlock-freedom analysis.\n   * Markings where any sink place has a token are not considered deadlocks.\n   */\n  sinkPlaces(...places: Place<any>[]): this {\n    for (const p of places) this._sinkPlaces.add(p);\n    return this;\n  }\n\n  timeout(ms: number): this {\n    this._timeoutMs = ms;\n    return this;\n  }\n\n  /**\n   * Runs the verification pipeline.\n   */\n  async verify(): Promise<SmtVerificationResult> {\n    const start = performance.now();\n    const report: string[] = [];\n    report.push('=== IC3/PDR SAFETY VERIFICATION ===\\n');\n    report.push(`Net: ${this.net.name}`);\n    const propDesc = this._sinkPlaces.size === 0\n      ? propertyDescription(this._property)\n      : `${propertyDescription(this._property)} (sinks: ${[...this._sinkPlaces].map(p => p.name).join(', ')})`;\n    report.push(`Property: ${propDesc}`);\n    report.push(`Timeout: ${(this._timeoutMs / 1000).toFixed(0)}s\\n`);\n\n    // Phase 1: Flatten\n    report.push('Phase 1: Flattening net...');\n    const flatNet = flatten(this.net, this._environmentPlaces, this._environmentMode);\n    report.push(`  Places: ${flatNet.places.length}`);\n    report.push(`  Transitions (expanded): ${flatNet.transitions.length}`);\n    if (flatNet.environmentBounds.size > 0) {\n      report.push(`  Environment bounds: ${flatNet.environmentBounds.size} places`);\n    }\n    report.push('');\n\n    // Phase 2: Structural pre-check\n    report.push('Phase 2: Structural pre-check (siphon/trap)...');\n    const structResult = structuralCheck(flatNet, this._initialMarking);\n    let structResultStr: string;\n    switch (structResult.type) {\n      case 'no-potential-deadlock':\n        structResultStr = 'no potential deadlock';\n        break;\n      case 'potential-deadlock':\n        structResultStr = `potential deadlock (siphon: {${[...structResult.siphon].join(',')}})`;\n        break;\n      case 'inconclusive':\n        structResultStr = `inconclusive (${structResult.reason})`;\n        break;\n    }\n    report.push(`  Result: ${structResultStr}\\n`);\n\n    // If structural check proves deadlock-freedom for DeadlockFree property\n    // (only valid when no sink places — structural check doesn't account for sinks)\n    if (\n      this._property.type === 'deadlock-free' &&\n      this._sinkPlaces.size === 0 &&\n      structResult.type === 'no-potential-deadlock'\n    ) {\n      report.push('=== RESULT ===\\n');\n      report.push('PROVEN (structural): Deadlock-freedom verified by Commoner\\'s theorem.');\n      report.push('  All siphons contain initially marked traps.');\n      return buildResult(\n        { type: 'proven', method: 'structural', inductiveInvariant: null },\n        report.join('\\n'), [], [], [], [],\n        performance.now() - start,\n        { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: 0, structuralResult: structResultStr },\n      );\n    }\n\n    // Phase 3: P-invariants\n    report.push('Phase 3: Computing P-invariants...');\n    const matrix = IncidenceMatrix.from(flatNet);\n    const invariants = computePInvariants(matrix, flatNet, this._initialMarking);\n    report.push(`  Found: ${invariants.length} P-invariant(s)`);\n    const structurallyBounded = isCoveredByInvariants(invariants, flatNet.places.length);\n    report.push(`  Structurally bounded: ${structurallyBounded ? 'YES' : 'NO'}`);\n    for (const inv of invariants) {\n      report.push(`  ${formatInvariant(inv, flatNet)}`);\n    }\n    report.push('');\n\n    // Phase 4: SMT encode + query via Spacer\n    report.push('Phase 4: IC3/PDR verification via Z3 Spacer...');\n\n    let runner;\n    try {\n      runner = await createSpacerRunner(this._timeoutMs);\n    } catch (e: any) {\n      report.push(`  ERROR: ${e.message ?? e}\\n`);\n      report.push('=== RESULT ===\\n');\n      report.push(`UNKNOWN: Z3 initialization error: ${e.message ?? e}`);\n      return buildResult(\n        { type: 'unknown', reason: `Z3 init error: ${e.message ?? e}` },\n        report.join('\\n'), invariants, [], [], [],\n        performance.now() - start,\n        { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n      );\n    }\n\n    try {\n      const encoding = encode(runner.ctx, runner.fp, flatNet, this._initialMarking, this._property, invariants, this._sinkPlaces);\n      const queryResult = await runner.query(encoding.errorExpr, encoding.reachableDecl);\n\n      switch (queryResult.type) {\n        case 'proven': {\n          report.push('  Status: UNSAT (property holds)\\n');\n\n          // Decode IC3-synthesized invariants with place name substitution\n          const discoveredInvariants: string[] = [];\n          if (queryResult.invariantFormula != null) {\n            discoveredInvariants.push(substituteNames(queryResult.invariantFormula, flatNet));\n          }\n          for (const level of queryResult.levelInvariants) {\n            discoveredInvariants.push(substituteNames(level, flatNet));\n          }\n\n          // Phase 5: Inductive invariant\n          if (discoveredInvariants.length > 0) {\n            report.push('Phase 5: Inductive invariant (discovered by IC3)');\n            report.push(`  Spacer synthesized: ${discoveredInvariants[0]}`);\n            report.push('  This formula is INDUCTIVE: preserved by all transitions.');\n            if (discoveredInvariants.length > 1) {\n              report.push('  Per-level clauses:');\n              for (let i = 1; i < discoveredInvariants.length; i++) {\n                report.push(`    ${discoveredInvariants[i]}`);\n              }\n            }\n            report.push('');\n          }\n\n          report.push('=== RESULT ===\\n');\n          report.push(`PROVEN (IC3/PDR): ${propDesc}`);\n          report.push('  Z3 Spacer proved no reachable state violates the property.');\n          report.push('  NOTE: Verification ignores timing constraints and JS guards.');\n          report.push('  An untimed proof is STRONGER than a timed one (timing only restricts behavior).');\n\n          return buildResult(\n            {\n              type: 'proven',\n              method: 'IC3/PDR',\n              inductiveInvariant: queryResult.invariantFormula != null\n                ? substituteNames(queryResult.invariantFormula, flatNet)\n                : null,\n            },\n            report.join('\\n'), invariants, discoveredInvariants, [], [],\n            performance.now() - start,\n            { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n          );\n        }\n\n        case 'violated': {\n          report.push('  Status: SAT (counterexample found)\\n');\n\n          const decoded = decode(runner.ctx, queryResult.answer, flatNet);\n\n          report.push('=== RESULT ===\\n');\n          report.push(`VIOLATED: ${propDesc}`);\n          if (decoded.trace.length > 0) {\n            report.push(`  Counterexample trace (${decoded.trace.length} states):`);\n            for (let i = 0; i < decoded.trace.length; i++) {\n              report.push(`    ${i}: ${decoded.trace[i]}`);\n            }\n          }\n          if (decoded.transitions.length > 0) {\n            report.push(`  Firing sequence: ${decoded.transitions.join(' -> ')}`);\n          }\n          report.push('\\n  WARNING: This counterexample is in UNTIMED semantics.');\n          report.push('  It may be spurious if timing constraints prevent this sequence.');\n          report.push('  JS guards are also ignored in this analysis.');\n\n          return buildResult(\n            { type: 'violated' },\n            report.join('\\n'), invariants, [], decoded.trace as MarkingState[], decoded.transitions as string[],\n            performance.now() - start,\n            { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n          );\n        }\n\n        case 'unknown': {\n          report.push(`  Status: UNKNOWN (${queryResult.reason})\\n`);\n          report.push('=== RESULT ===\\n');\n          report.push(`UNKNOWN: Could not determine ${propDesc}`);\n          report.push(`  Reason: ${queryResult.reason}`);\n\n          return buildResult(\n            { type: 'unknown', reason: queryResult.reason },\n            report.join('\\n'), invariants, [], [], [],\n            performance.now() - start,\n            { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n          );\n        }\n      }\n    } catch (e: any) {\n      report.push(`  ERROR: ${e.message ?? e}\\n`);\n      report.push('=== RESULT ===\\n');\n      report.push(`UNKNOWN: Z3 solver error: ${e.message ?? e}`);\n\n      return buildResult(\n        { type: 'unknown', reason: `Z3 error: ${e.message ?? e}` },\n        report.join('\\n'), invariants, [], [], [],\n        performance.now() - start,\n        { places: flatNet.places.length, transitions: flatNet.transitions.length, invariantsFound: invariants.length, structuralResult: structResultStr },\n      );\n    } finally {\n      runner.dispose();\n    }\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "libpetri",
-  "version": "0.3.2",
+  "version": "0.3.4",
   "description": "Coloured Time Petri Net engine — TypeScript port",
   "homepage": "https://libpetri.org",
   "repository": {
@@ -12,7 +12,9 @@
     "url": "https://github.com/debe/libpetri/issues"
   },
   "license": "Apache-2.0",
-  "files": ["dist"],
+  "files": [
+    "dist"
+  ],
   "type": "module",
   "exports": {
     ".": {