Implementation of reachability testing for RSC using SMT. Intitially tested version. No known issues.
This commit is contained in:
Artur Meski
160
smtcheckerrsc.py
160
smtcheckerrsc.py
@@ -69,47 +69,42 @@ class SmtCheckerRSC(object):
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return init_state_enc
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def enc_enabledness(self, level, prod_entity):
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"""Encodes the enabledness condition for a given level and a given entity"""
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def enc_produced_concentration(self, level, prod_entity):
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"""Encodes the produced concentrations for the given level and entity"""
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rcts_for_prod_entity = self.rs.get_reactions_by_product()[prod_entity]
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if rcts_for_prod_entity == []:
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return False
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#
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# TODO:
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#
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# czy potrzebujemy get_reactions_by_product?
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# czy może wystarczy jak zakodujemy reakcje jako trójki?
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#
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# ... na pewno musi być informacja o produkowanym stężeniu
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#
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return simplify(self.v[level+1][prod_entity] == 0)
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enc_rct_prod = False
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for reactants,inhibitors in rcts_for_prod_entity:
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for reactants,inhibitors,products in rcts_for_prod_entity:
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enc_reactants = True
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enc_inhibitors = True
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for reactant in reactants:
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# enc_products -- below
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for reactant,concentration in reactants:
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][reactant], self.v_ctx[level][reactant])))
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for inhibitor in inhibitors:
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Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
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for inhibitor,concentration in inhibitors:
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enc_inhibitors = simplify(And(enc_inhibitors,
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And(self.v[level][inhibitor], self.v_ctx[level][inhibitor])))
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And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
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enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
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enc_products = self.v[level+1][products[0][0]] == products[0][1]
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enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors, enc_products)))
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return enc_rct_prod
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def enc_entity_production(self, level, prod_entity):
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"""Encodes the production of a given entity from a given level at level+1"""
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enc_enab_cond = self.enc_enabledness(level, prod_entity)
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enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
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And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
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return simplify(enc_ent_prod)
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# def enc_entity_production(self, level, prod_entity):
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# """Encodes the production of a given entity from a given level at level+1"""
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#
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# enc_enab_cond = self.enc_enabledness(level, prod_entity)
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#
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# enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
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# And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
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#
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# return simplify(enc_ent_prod)
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def enc_transition_relation(self, level):
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return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
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@@ -121,13 +116,15 @@ class SmtCheckerRSC(object):
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enc_trans = True
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for prod_entity in self.rs.get_reactions_by_product():
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reactions = self.rs.get_reactions_by_product()
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for prod_entity in reactions:
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unused_entities.remove(prod_entity)
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enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity)))
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enc_trans = simplify(And(enc_trans, self.enc_produced_concentration(level, prod_entity)))
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for prod_entity in unused_entities:
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enc_trans = simplify(And(enc_trans, Not(self.v[level+1][prod_entity])))
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enc_trans = simplify(And(enc_trans, self.v[level+1][prod_entity] == 0))
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return enc_trans
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@@ -141,15 +138,17 @@ class SmtCheckerRSC(object):
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dst_enc = self.ca_state[level+1] == dst
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all_ent = set(range(len(self.rs.background_set)))
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incl_ctx = ctx
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incl_ctx = set([e for e,c in ctx])
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excl_ctx = all_ent - incl_ctx
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ctx_enc = True
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for c in incl_ctx:
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ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][c]))
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for c in excl_ctx:
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ctx_enc = simplify(And(ctx_enc, Not(self.v_ctx[level][c])))
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for e,c in ctx:
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ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][e] == c))
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for e in excl_ctx:
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ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][e] == 0))
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cur_trans = simplify(And(src_enc, ctx_enc, dst_enc))
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enc_trans = simplify(Or(enc_trans, cur_trans))
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@@ -202,19 +201,27 @@ class SmtCheckerRSC(object):
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print(" State: {", end=""),
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for var_id in range(len(self.v[level])):
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if repr(m[self.v[level][var_id]]) == "True":
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print(" " + self.rs.get_entity_name(var_id), end="")
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var_rep = repr(m[self.v[level][var_id]])
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if not var_rep.isdigit():
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raise RuntimeError("unexpected: representation is not a positive integer")
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if int(var_rep) > 0:
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print(" " + self.rs.get_entity_name(var_id) + "=" + var_rep, end="")
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# print(" " + repr(m[self.v[level][var_id]]), end="")
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print(" }")
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if level != max_level:
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print(" Context set: ", end="")
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print("{", end="")
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for var_id in range(len(self.v[level])):
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if repr(m[self.v_ctx[level][var_id]]) == "True":
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print(" " + self.rs.get_entity_name(var_id), end="")
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var_rep = repr(m[self.v_ctx[level][var_id]])
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if not var_rep.isdigit():
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raise RuntimeError("unexpected: representation is not a positive integer")
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if int(var_rep) > 0:
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print(" " + self.rs.get_entity_name(var_id) + "=" + var_rep, end="")
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print(" }")
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def check_reachability(self, state, print_witness=True, print_time=False):
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def check_reachability(self, state, exact_state=False, print_witness=True,
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print_time=False, print_mem=False, max_level=100):
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"""Main testing function"""
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if print_time:
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@@ -224,33 +231,50 @@ class SmtCheckerRSC(object):
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self.solver.add(self.enc_init_state(0))
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current_level = 0
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print(self.enc_exact_state(current_level,state))
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# print(self.enc_exact_state(current_level,state))
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#
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# print(self.enc_produced_concentration(current_level, 1))
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# while True:
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# print("\r[i] Level: " + str(current_level), end="")
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# stdout.flush()
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#
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# self.prepare_all_variables()
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#
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# # reachability test:
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# self.solver.push()
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# self.solver.add(self.enc_state(current_level,state))
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#
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# result = self.solver.check()
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# if result == sat:
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# print("\n[+] SAT at level=" + str(current_level))
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# if print_witness:
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# self.decode_witness(current_level)
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# break
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# else:
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# self.solver.pop()
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#
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# self.solver.add(self.enc_transition_relation(current_level))
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#
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# current_level += 1
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#
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# if print_time:
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# stop = time()
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# print()
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# print("[i] Time: " + repr(stop-start))
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self.prepare_all_variables()
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print(And(self.enc_transition_relation(current_level), self.enc_init_state(0)))
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while True:
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self.prepare_all_variables()
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print("-----[ Working at level=" + str(current_level) + " ]-----")
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stdout.flush()
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# reachability test:
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print("[i] Adding the reachability test...")
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self.solver.push()
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if exact_state:
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self.solver.add(self.enc_exact_state(current_level,state))
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else:
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self.solver.add(self.enc_min_state(current_level,state))
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result = self.solver.check()
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if result == sat:
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print("\n[+] SAT at level=" + str(current_level))
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if print_witness:
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self.decode_witness(current_level)
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break
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else:
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self.solver.pop()
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print("[i] Unrolling the transition relation")
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self.solver.add(self.enc_transition_relation(current_level))
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print("-----[ level=" + str(current_level) + " done ]")
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current_level += 1
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if current_level > max_level:
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print("Stopping at level=" + str(max_level))
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break
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if print_time:
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stop = time()
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print()
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print("[i] Time: " + repr(stop-start))
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