smt package
This commit is contained in:
Artur Meski
4
smt/__init__.py
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4
smt/__init__.py
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from smt.smt_checker import SmtChecker
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from smt.smt_checker_distrib_rs import SmtCheckerDistribRS
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from smt.smt_checker_pgrs import SmtCheckerPGRS
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from smt.smt_checker_rsc import SmtCheckerRSC
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530
smt/smt_checker.py
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530
smt/smt_checker.py
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"""
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SMT-based Model Checking Module for RS
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"""
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from z3 import *
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from time import time
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from sys import stdout
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class SmtChecker(object):
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def __init__(self, rs):
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##############################################################
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# Encoded RS
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##############################################################
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rs.sanity_check()
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self.reaction_system = rs
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##############################################################
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# SMT variables
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##############################################################
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self.v = []
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self.v_init = []
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#self.vSucc = []
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#self.vSuccInit = []
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self.v_ctx = []
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self.next_level_to_encode = 0
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##############################################################
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# SMT solver instance
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##############################################################
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self.solver = Solver()
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#def smtVar(self, level, entityID, primed=False):
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# return "?"
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def prepare_context_variables(self):
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"""Encodes all the context variables"""
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level = self.next_level_to_encode
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variables = []
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for entity in self.reaction_system.background_set:
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variables.append(Bool("C"+str(level)+"_"+entity))
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self.v_ctx.append(variables)
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def prepare_state_variables(self):
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"""Encodes all the state variables (including successors)"""
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level = self.next_level_to_encode
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variables = []
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#variablesSucc = []
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for entity in self.reaction_system.background_set:
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variables.append(Bool("L"+str(level)+"_"+entity))
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#variablesSucc.append(Bool("R"+str(level)+"_"+entity))
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self.v.append(variables)
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#self.vSucc.append(variablesSucc)
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self.v_init.append(Bool("L"+str(level)+"_Init"))
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#self.vSuccInit.append(Bool("R"+str(level)+"_Init"))
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def prepare_all_variables(self):
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"""Encodes all the variables"""
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self.prepare_state_variables()
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self.prepare_context_variables()
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self.next_level_to_encode += 1
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def enc_init_state(self, level):
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"""Encodes the initial state at the given level"""
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init_state_enc = self.v_init[level]
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for v in self.v[level]:
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init_state_enc = simplify(And(init_state_enc, Not(v)))
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return init_state_enc
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def enc_init_contexts(self, level):
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"""Encodes the initial contexts set at the given level"""
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init_contexts_set_enc = False # Or
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for ctx in self.reaction_system.init_contexts:
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single_ctx_enc = True # And
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not_ctx_entities = list(range(0, len(self.reaction_system.background_set)))
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for entity in ctx:
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single_ctx_enc = simplify(And(single_ctx_enc, self.v_ctx[level][entity]))
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not_ctx_entities.remove(entity)
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for entity in not_ctx_entities:
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single_ctx_enc = simplify(And(single_ctx_enc, Not(self.v_ctx[level][entity])))
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init_contexts_set_enc = simplify(Or(init_contexts_set_enc, single_ctx_enc))
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#print("initContextSetEnc: " + repr(initContextsSetEnc))
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return init_contexts_set_enc
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def enc_not_allowed_contexts(self, level):
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"""Encodes all the context entities that are not allowed in the context sets"""
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bg_set = set(range(0,len(self.reaction_system.background_set)))
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ctx_ent_set = set(self.reaction_system.context_entities)
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not_ctx_ent_set = bg_set.difference(ctx_ent_set)
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enc = True
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for entity in not_ctx_ent_set:
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enc = simplify(And(enc, Not(self.v_ctx[level][entity])))
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return 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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rcts_for_prod_entity = self.reaction_system.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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#encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
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# And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
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enc_rct_prod = False
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for ri_pair in rcts_for_prod_entity: # reactants-inhibitors pair
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enc_reactants = True
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enc_inhibitors = True
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for reactant in ri_pair[0]:
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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 ri_pair[1]:
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enc_inhibitors = simplify(And(enc_inhibitors,
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Not(Or(self.v[level][inhibitor], self.v_ctx[level][inhibitor]))))
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enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
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#print("encEnabledness(" + repr(prodEntity) + "): " + repr(simplify(And(encInitEnab, encRctProd))))
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#return simplify(And(encInitEnab, encRctProd))
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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 enc_ent_prod
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def enc_transition_relation(self, level):
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"""Encodes the transition relation"""
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unused_entities = list(range(0,len(self.reaction_system.background_set)))
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enc_trans = True
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for prod_entity in self.reaction_system.get_reactions_by_product():
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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, Not(self.v_init[level+1])))
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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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if level == 0:
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enc_init_enab = self.enc_init_contexts(level)
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else: # level > 0:
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enc_init_enab = self.enc_not_allowed_contexts(level)
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#encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
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# And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
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enc_trans = simplify(And(enc_trans, enc_init_enab))
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return enc_trans
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def enc_state(self, level, state):
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"""Encodes the state at the given level"""
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enc = Not(self.v_init[level])
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state_ids = self.reaction_system.get_state_ids(state)
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for entity in state_ids:
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enc = And(enc, self.v[level][entity])
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not_in_state = set(range(0, len(self.reaction_system.background_set)))
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not_in_state = not_in_state.difference(set(state_ids))
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for entity in not_in_state:
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enc = And(enc, Not(self.v[level][entity]))
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return enc
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def decode_witness(self, max_level):
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m = self.solver.model()
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for level in range(0,max_level+1):
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print("\n[Level=" + repr(level) + "]")
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if repr(m[self.v_init[level]]) == "True":
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print("** Initial state")
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print("State:\n{"),
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for var_id in range(0, len(self.v[level])):
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if repr(m[self.v[level][var_id]]) == "True":
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print("\t" + self.reaction_system.get_entity_name(var_id)),
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print("}")
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if level != max_level:
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print("Context set:"),
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print("{"),
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for var_id in range(0, len(self.v[level])):
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if repr(m[self.v_ctx[level][var_id]]) == "True":
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print("\t" + self.reaction_system.get_entity_name(var_id)),
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print("}")
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def check_reachability(self, state, print_witness=True, print_time=False):
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"""Main testing function"""
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if print_time:
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start = time()
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self.prepare_all_variables()
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self.solver.add(self.enc_init_state(0))
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current_level = 0
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while True:
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#print("Level: " + str(current_level))
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print("\rLevel: " + str(current_level)),
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stdout.flush()
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self.prepare_all_variables()
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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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result = self.solver.check()
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print(result)
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if result == sat:
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print("\nSAT")
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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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self.solver.add(self.enc_transition_relation(current_level))
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current_level += 1
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if print_time:
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stop = time()
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print("Time: " + repr(stop-start))
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#
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# class SmtCheckerPGRS(object):
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#
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# def __init__(self, rs):
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#
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# ##############################################################
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# # Encoded RS
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# ##############################################################
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# rs.sanity_check()
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# self.reaction_system = rs
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#
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# ##############################################################
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# # SMT variables
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# ##############################################################
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# self.v = []
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# self.v_init = []
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#
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# #self.vSucc = []
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# #self.vSuccInit = []
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#
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# self.v_ctx = []
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#
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# self.next_level_to_encode = 0
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#
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# ##############################################################
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# # SMT solver instance
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# ##############################################################
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# self.solver = Solver()
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#
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# #def smtVar(self, level, entityID, primed=False):
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# # return "?"
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#
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# def prepare_context_variables(self):
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# """Encodes all the context variables"""
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#
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# level = self.next_level_to_encode
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#
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# variables = []
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# for entity in self.reaction_system.background_set:
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# variables.append(Bool("C"+str(level)+"_"+entity))
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#
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# self.v_ctx.append(variables)
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#
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# def prepare_state_variables(self):
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# """Encodes all the state variables (including successors)"""
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#
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# level = self.next_level_to_encode
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#
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# variables = []
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# #variablesSucc = []
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# for entity in self.reaction_system.background_set:
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# variables.append(Bool("L"+str(level)+"_"+entity))
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# #variablesSucc.append(Bool("R"+str(level)+"_"+entity))
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#
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# self.v.append(variables)
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# #self.vSucc.append(variablesSucc)
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#
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# self.v_init.append(Bool("L"+str(level)+"_Init"))
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# #self.vSuccInit.append(Bool("R"+str(level)+"_Init"))
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#
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# def prepare_all_variables(self):
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# """Encodes all the variables"""
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#
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# self.prepare_state_variables()
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# self.prepare_context_variables()
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# self.next_level_to_encode += 1
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#
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# def enc_init_state(self, level):
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# """Encodes the initial state at the given level"""
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#
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# init_state_enc = self.v_init[level]
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#
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# for v in self.v[level]:
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# init_state_enc = simplify(And(init_state_enc, Not(v)))
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#
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# return init_state_enc
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#
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# def enc_init_contexts(self, level):
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# """Encodes the initial contexts set at the given level"""
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#
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# init_contexts_set_enc = False # Or
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#
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# for ctx in self.reaction_system.init_contexts:
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# single_ctx_enc = True # And
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#
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# not_ctx_entities = list(range(0, len(self.reaction_system.background_set)))
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# for entity in ctx:
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# single_ctx_enc = simplify(And(single_ctx_enc, self.v_ctx[level][entity]))
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# not_ctx_entities.remove(entity)
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#
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# for entity in not_ctx_entities:
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# single_ctx_enc = simplify(And(single_ctx_enc, Not(self.v_ctx[level][entity])))
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#
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# init_contexts_set_enc = simplify(Or(init_contexts_set_enc, single_ctx_enc))
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#
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# #print("initContextSetEnc: " + repr(initContextsSetEnc))
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# return init_contexts_set_enc
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#
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# def enc_not_allowed_contexts(self, level):
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# """Encodes all the context entities that are not allowed in the context sets"""
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#
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# bg_set = set(range(0,len(self.reaction_system.background_set)))
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# ctx_ent_set = set(self.reaction_system.context_entities)
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#
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# not_ctx_ent_set = bg_set.difference(ctx_ent_set)
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#
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# enc = True
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# for entity in not_ctx_ent_set:
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# enc = simplify(And(enc, Not(self.v_ctx[level][entity])))
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#
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# return enc
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#
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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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#
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# rcts_for_prod_entity = self.reaction_system.get_reactions_by_product()[prod_entity]
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#
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# if rcts_for_prod_entity == []:
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# return False
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#
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# #encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
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# # And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
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#
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# enc_rct_prod = False
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# for ri_pair in rcts_for_prod_entity: # reactants-inhibitors pair
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# enc_reactants = True
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# enc_inhibitors = True
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# for reactant in ri_pair[0]:
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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 ri_pair[1]:
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# enc_inhibitors = simplify(And(enc_inhibitors,
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# Not(Or(self.v[level][inhibitor], self.v_ctx[level][inhibitor]))))
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#
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# enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
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#
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# #print("encEnabledness(" + repr(prodEntity) + "): " + repr(simplify(And(encInitEnab, encRctProd))))
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# #return simplify(And(encInitEnab, encRctProd))
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# return enc_rct_prod
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#
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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 enc_ent_prod
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#
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# def enc_transition_relation(self, level):
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# """Encodes the transition relation"""
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#
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# unused_entities = list(range(0,len(self.reaction_system.background_set)))
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#
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# enc_trans = True
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#
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# for prod_entity in self.reaction_system.get_reactions_by_product():
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# unused_entities.remove(prod_entity)
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#
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# enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity)))
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#
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# enc_trans = simplify(And(enc_trans, Not(self.v_init[level+1])))
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#
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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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#
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# if level == 0:
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# enc_init_enab = self.enc_init_contexts(level)
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# else: # level > 0:
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# enc_init_enab = self.enc_not_allowed_contexts(level)
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#
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# #encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
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# # And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
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#
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# enc_trans = simplify(And(enc_trans, enc_init_enab))
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#
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# return enc_trans
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#
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# def enc_state(self, level, state):
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# """Encodes the state at the given level"""
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#
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# enc = Not(self.v_init[level])
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#
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||||
# state_ids = self.reaction_system.get_state_ids(state)
|
||||
#
|
||||
# for entity in state_ids:
|
||||
# enc = And(enc, self.v[level][entity])
|
||||
#
|
||||
# not_in_state = set(range(0, len(self.reaction_system.background_set)))
|
||||
# not_in_state = not_in_state.difference(set(state_ids))
|
||||
#
|
||||
# for entity in not_in_state:
|
||||
# enc = And(enc, Not(self.v[level][entity]))
|
||||
#
|
||||
# return enc
|
||||
#
|
||||
# def decode_witness(self, max_level):
|
||||
#
|
||||
# m = self.solver.model()
|
||||
#
|
||||
# for level in range(0,max_level+1):
|
||||
#
|
||||
# print("\n[Level=" + repr(level) + "]")
|
||||
#
|
||||
# if repr(m[self.v_init[level]]) == "True":
|
||||
# print("** Initial state")
|
||||
#
|
||||
# print("State:\n{"),
|
||||
# for var_id in range(0, len(self.v[level])):
|
||||
# if repr(m[self.v[level][var_id]]) == "True":
|
||||
# print("\t" + self.reaction_system.get_entity_name(var_id)),
|
||||
# print("}")
|
||||
#
|
||||
# if level != max_level:
|
||||
# print("Context set:"),
|
||||
# print("{"),
|
||||
# for var_id in range(0, len(self.v[level])):
|
||||
# if repr(m[self.v_ctx[level][var_id]]) == "True":
|
||||
# print("\t" + self.reaction_system.get_entity_name(var_id)),
|
||||
# print("}")
|
||||
#
|
||||
#
|
||||
# def check_reachability(self, state, print_witness=True, print_time=False):
|
||||
# """Main testing function"""
|
||||
#
|
||||
# if print_time:
|
||||
# start = time()
|
||||
#
|
||||
# self.prepare_all_variables()
|
||||
# self.solver.add(self.enc_init_state(0))
|
||||
# current_level = 0
|
||||
#
|
||||
# while True:
|
||||
# #print("Level: " + str(current_level))
|
||||
# print("\rLevel: " + str(current_level)),
|
||||
# stdout.flush()
|
||||
#
|
||||
# self.prepare_all_variables()
|
||||
#
|
||||
# # reachability test:
|
||||
# self.solver.push()
|
||||
# self.solver.add(self.enc_state(current_level,state))
|
||||
#
|
||||
# result = self.solver.check()
|
||||
# print(result)
|
||||
# if result == sat:
|
||||
# print("\nSAT")
|
||||
# if print_witness:
|
||||
# self.decode_witness(current_level)
|
||||
# break
|
||||
# else:
|
||||
# self.solver.pop()
|
||||
#
|
||||
# self.solver.add(self.enc_transition_relation(current_level))
|
||||
#
|
||||
# current_level += 1
|
||||
#
|
||||
# if print_time:
|
||||
# stop = time()
|
||||
# print("Time: " + repr(stop-start))
|
||||
432
smt/smt_checker_distrib_rs.py
Normal file
432
smt/smt_checker_distrib_rs.py
Normal file
@@ -0,0 +1,432 @@
|
||||
"""
|
||||
SMT-based Model Checking Module for RS with Context Automaton
|
||||
"""
|
||||
|
||||
from z3 import *
|
||||
from time import time,sleep
|
||||
from sys import stdout
|
||||
import resource
|
||||
|
||||
# def simplify(x):
|
||||
# return x
|
||||
|
||||
class SmtCheckerDistribRS(object):
|
||||
|
||||
def __init__(self, drs, debug_level=1):
|
||||
|
||||
print("[i] Initialising the SMT module")
|
||||
|
||||
drs.sanity_check()
|
||||
|
||||
self.solver = Solver()
|
||||
|
||||
self.debug_level = debug_level
|
||||
self.drs = drs
|
||||
self.n_components = self.drs.components_count
|
||||
|
||||
# encoding variables
|
||||
self.v = [] # level -> component -> variables
|
||||
self.v_ctx = []
|
||||
self.v_act = [] # indicators of which component is active
|
||||
self.ca_state = []
|
||||
|
||||
self.level_to_encode = 0
|
||||
|
||||
def prepare_all_variables(self):
|
||||
"""Encodes the required variables"""
|
||||
|
||||
self.prepare_state_variables()
|
||||
self.prepare_context_variables()
|
||||
self.prepare_activity_variables()
|
||||
|
||||
self.level_to_encode += 1 # prepare for the next invocation
|
||||
|
||||
def prepare_context_variables(self):
|
||||
"""Encodes the context variables"""
|
||||
|
||||
level = self.level_to_encode
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Preparing context variables for level=" + str(level))
|
||||
|
||||
level_variables = []
|
||||
|
||||
for i in range(self.n_components):
|
||||
|
||||
comp_variables = []
|
||||
|
||||
for entity in self.drs.background_set:
|
||||
comp_variables.append(Bool("Ctx"+str(level)+"V"+str(i)+"_"+entity))
|
||||
|
||||
level_variables.append(comp_variables)
|
||||
|
||||
self.v_ctx.append(level_variables)
|
||||
|
||||
def prepare_activity_variables(self):
|
||||
"""Encodes the activity variables"""
|
||||
|
||||
level = self.level_to_encode
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Preparing activity variables for level=" + str(level))
|
||||
|
||||
level_variables = []
|
||||
|
||||
for i in range(self.n_components):
|
||||
# L - level, A - activity indicator
|
||||
level_variables.append(Bool("L"+str(level)+"A"+str(i)))
|
||||
|
||||
self.v_act.append(level_variables)
|
||||
|
||||
def prepare_state_variables(self):
|
||||
"""Encodes all the state variables"""
|
||||
|
||||
level = self.level_to_encode
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Preparing state variables for level=" + str(level))
|
||||
|
||||
level_variables = [] # level vars
|
||||
|
||||
for i in range(self.n_components):
|
||||
|
||||
comp_variables = []
|
||||
|
||||
for entity in self.drs.background_set:
|
||||
# L - level, V - component
|
||||
comp_variables.append(Bool("L"+str(level)+"V"+str(i)+"_"+entity))
|
||||
|
||||
level_variables.append(comp_variables)
|
||||
|
||||
self.v.append(level_variables)
|
||||
|
||||
# single state variable for CA
|
||||
self.ca_state.append(Int("CA"+str(level)+"_state"))
|
||||
|
||||
def enc_init_state(self, level):
|
||||
"""Encodes the initial state at the given level"""
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Encoding the initial state for level=" + str(level))
|
||||
|
||||
rs_init_state_enc = True
|
||||
|
||||
for i in range(self.n_components):
|
||||
for v in self.v[level][i]:
|
||||
rs_init_state_enc = simplify(And(rs_init_state_enc, Not(v))) # the initial state is empty
|
||||
|
||||
ca_init_state_enc = self.ca_state[level] == self.drs.get_init_state_id()
|
||||
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
|
||||
|
||||
# print ("init_state_enc:\n", init_state_enc)
|
||||
|
||||
return init_state_enc
|
||||
|
||||
def enc_enabledness(self, level, prod_entity, component_id):
|
||||
"""Encodes the enabledness condition for a given level and a given entity"""
|
||||
|
||||
rcts_for_prod_entity = self.drs.get_reactions_by_product(component_id)[prod_entity]
|
||||
|
||||
if rcts_for_prod_entity == []:
|
||||
return False
|
||||
|
||||
enc_rct_prod = False
|
||||
for reactants,inhibitors in rcts_for_prod_entity:
|
||||
|
||||
|
||||
enc_reactants = True
|
||||
for reactant in reactants:
|
||||
|
||||
enc_active_reactants = False
|
||||
for i in range(self.n_components):
|
||||
enc_active_reactants = simplify(Or(enc_active_reactants,
|
||||
And( Or(self.v[level][i][reactant], self.v_ctx[level][i][reactant]), self.v_act[level][i] )))
|
||||
|
||||
enc_reactants = And(enc_reactants, enc_active_reactants)
|
||||
|
||||
|
||||
enc_inhibitors = True
|
||||
for inhibitor in inhibitors:
|
||||
|
||||
enc_active_inhibitors = True
|
||||
for i in range(self.n_components):
|
||||
enc_active_inhibitors = simplify(And(enc_active_inhibitors,
|
||||
And(
|
||||
Or( And(Not(self.v[level][i][inhibitor]), Not(self.v_ctx[level][i][inhibitor])), Not(self.v_act[level][i]) )
|
||||
)))
|
||||
|
||||
enc_inhibitors = simplify(And(enc_inhibitors, enc_active_inhibitors))
|
||||
|
||||
# print("--> enc_inhibitors\n", enc_inhibitors)
|
||||
enc_rct_prod = Or(enc_rct_prod, And(enc_reactants, enc_inhibitors))
|
||||
|
||||
# print("enc_rct_prod:\n", enc_rct_prod)
|
||||
|
||||
enc_rct_prod = simplify(enc_rct_prod)
|
||||
|
||||
return enc_rct_prod
|
||||
|
||||
def enc_entity_production(self, level, prod_entity, component_id):
|
||||
"""Encodes the production of a given entity at level+1 from a given level"""
|
||||
|
||||
enc_enab_cond = self.enc_enabledness(level, prod_entity, component_id)
|
||||
|
||||
enc_base_ent_prod = simplify(Or(And(enc_enab_cond, self.v[level+1][component_id][prod_entity]),
|
||||
And(Not(enc_enab_cond), Not(self.v[level+1][component_id][prod_entity]))))
|
||||
|
||||
enc_active_ent_prod = simplify(And(self.v_act[level][component_id], enc_base_ent_prod))
|
||||
enc_inactive_ent_prod = simplify(And(
|
||||
Not(self.v_act[level][component_id]),
|
||||
self.v[level][component_id][prod_entity] == self.v[level+1][component_id][prod_entity]))
|
||||
|
||||
enc_ent_prod = Or(enc_active_ent_prod, enc_inactive_ent_prod)
|
||||
|
||||
# print("enc_ent_prod:\n", enc_ent_prod)
|
||||
|
||||
return simplify(enc_ent_prod)
|
||||
|
||||
def enc_rs_trans(self, level):
|
||||
"""Encodes the transition relation"""
|
||||
|
||||
enc_trans = True
|
||||
|
||||
for component_id in range(self.n_components):
|
||||
|
||||
print("\rEncoding for reactions: %d/%d" % (component_id,self.n_components-1), flush=True, end="")
|
||||
|
||||
unused_entities = list(range(len(self.drs.background_set)))
|
||||
|
||||
for prod_entity in self.drs.get_reactions_by_product(component_id):
|
||||
unused_entities.remove(prod_entity)
|
||||
|
||||
enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity, component_id)))
|
||||
|
||||
for prod_entity in unused_entities:
|
||||
enc_trans = simplify(And(enc_trans, Not(self.v[level+1][component_id][prod_entity])))
|
||||
|
||||
print()
|
||||
# print("enc_rs_trans:\n", enc_trans)
|
||||
|
||||
enc_trans = simplify(enc_trans)
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_automaton_trans(self, level):
|
||||
"""Encodes the transition relation for the context automaton"""
|
||||
|
||||
enc_trans = False
|
||||
|
||||
i = 0
|
||||
for src,(components,ctx_set),dst in self.drs.transitions:
|
||||
src_enc = self.ca_state[level] == src
|
||||
dst_enc = self.ca_state[level+1] == dst
|
||||
|
||||
print("\rEncoding for context automaton: %d/%d" % (i,len(self.drs.transitions)-1), flush=True, end="")
|
||||
|
||||
i = i + 1
|
||||
|
||||
# contexts {
|
||||
ctx_set_enc = True
|
||||
for comp_id in range(self.n_components):
|
||||
|
||||
all_ent = set(range(len(self.drs.background_set)))
|
||||
incl_ctx = ctx_set[comp_id]
|
||||
excl_ctx = all_ent - incl_ctx
|
||||
|
||||
ctx_enc = True
|
||||
|
||||
for c in incl_ctx:
|
||||
ctx_enc = And(ctx_enc, self.v_ctx[level][comp_id][c])
|
||||
for c in excl_ctx:
|
||||
ctx_enc = And(ctx_enc, Not(self.v_ctx[level][comp_id][c]))
|
||||
|
||||
ctx_set_enc = And(ctx_set_enc, ctx_enc)
|
||||
# } contexts
|
||||
|
||||
# active components {
|
||||
all_active = set(range(self.n_components))
|
||||
incl_comp = components
|
||||
excl_comp = all_active - incl_comp
|
||||
|
||||
active_components_enc = True
|
||||
for comp_id in incl_comp:
|
||||
active_components_enc = And(active_components_enc, self.v_act[level][comp_id])
|
||||
for comp_id in excl_comp:
|
||||
active_components_enc = And(active_components_enc, Not(self.v_act[level][comp_id]))
|
||||
# } active components
|
||||
|
||||
cur_trans = And(src_enc, ctx_set_enc, active_components_enc, dst_enc)
|
||||
|
||||
enc_trans = Or(enc_trans, cur_trans)
|
||||
|
||||
print()
|
||||
|
||||
enc_trans = simplify(enc_trans)
|
||||
|
||||
# print("enc_automaton_trans:\n", enc_trans)
|
||||
return enc_trans
|
||||
|
||||
def enc_transition_relation(self, level):
|
||||
|
||||
rs_enc = self.enc_rs_trans(level)
|
||||
aut_enc = self.enc_automaton_trans(level)
|
||||
|
||||
print("Conjunction...", flush=True, end="")
|
||||
|
||||
c = simplify(And(rs_enc, aut_enc))
|
||||
|
||||
print("done.")
|
||||
|
||||
return c
|
||||
|
||||
def enc_state(self, level, global_state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
if len(global_state) != self.n_components:
|
||||
print("EEE: Wrong size of the global state! " + "(is " + str(len(global_state)) + ", should be " + str(self.n_components) + ")")
|
||||
exit(1)
|
||||
|
||||
enc = True
|
||||
|
||||
if self.debug_level > 2:
|
||||
print("[iii] Encoding exclusive/exact global state " + str(global_state) + " for level=" + str(level))
|
||||
|
||||
for i in range(self.n_components):
|
||||
local_state = global_state[i]
|
||||
|
||||
local_state_ids = self.drs.get_state_ids(local_state)
|
||||
|
||||
for entity in local_state_ids:
|
||||
enc = And(enc, self.v[level][i][entity])
|
||||
|
||||
not_in_state = self.drs.set_of_background_ids - set(local_state_ids)
|
||||
|
||||
for e_id in not_in_state:
|
||||
enc = simplify(And(enc, Not(self.v[level][i][e_id])))
|
||||
|
||||
simplify(enc)
|
||||
# print("state:\n", enc)
|
||||
return enc
|
||||
|
||||
def enc_inclusive_state(self, level, global_state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
if len(global_state) != self.n_components:
|
||||
print("EEE: Wrong size of the global state! " + "(is " + str(len(global_state)) + ", should be " + str(self.n_components) + ")")
|
||||
exit(1)
|
||||
|
||||
enc = True
|
||||
|
||||
if self.debug_level > 2:
|
||||
print("[iii] Encoding inclusive/general global state " + str(global_state) + " for level=" + str(level))
|
||||
|
||||
for i in range(self.n_components):
|
||||
local_state = global_state[i]
|
||||
|
||||
local_state_ids = self.drs.get_state_ids(local_state)
|
||||
|
||||
for entity in local_state_ids:
|
||||
enc = And(enc, self.v[level][i][entity])
|
||||
|
||||
simplify(enc)
|
||||
return enc
|
||||
|
||||
def decode_witness(self, max_level, print_model=False):
|
||||
|
||||
m = self.solver.model()
|
||||
|
||||
print("\nWitness:")
|
||||
|
||||
if print_model:
|
||||
print(m)
|
||||
|
||||
for level in range(max_level+1):
|
||||
|
||||
print("\n[Level=" + repr(level) + "]")
|
||||
|
||||
#print(m)
|
||||
#print(self.v[level][0][2])
|
||||
#print(m[self.v[level][0][2]])
|
||||
|
||||
print(" State: {", end=""),
|
||||
for c in range(self.n_components):
|
||||
print(" <", end="")
|
||||
for var_id in range(len(self.v[level][c])):
|
||||
if repr(m[self.v[level][c][var_id]]) == "True":
|
||||
print(" " + self.drs.get_entity_name(var_id), end="")
|
||||
print(" >", end="")
|
||||
print(" }")
|
||||
|
||||
if level != max_level:
|
||||
print(" Context set: ", end="")
|
||||
print("{", end="")
|
||||
for c in range(self.n_components):
|
||||
print(" <", end="")
|
||||
for var_id in range(len(self.v[level][c])):
|
||||
if repr(m[self.v_ctx[level][c][var_id]]) == "True":
|
||||
print(" " + self.drs.get_entity_name(var_id), end="")
|
||||
print(" >", end="")
|
||||
print(" }")
|
||||
|
||||
print(" Active components:", end="")
|
||||
for c in range(self.n_components):
|
||||
if repr(m[self.v_act[level][c]]) == "True":
|
||||
print(" " + str(c), end="")
|
||||
print()
|
||||
|
||||
|
||||
|
||||
def check_reachability(self, state, exclusive_state=False, print_witness=True, print_time=False, print_mem=False, max_level=100):
|
||||
"""Reachability checking"""
|
||||
|
||||
print("[i] Checking reachability...")
|
||||
|
||||
if print_time:
|
||||
start = time()
|
||||
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_init_state(0))
|
||||
current_level = 0
|
||||
|
||||
while True:
|
||||
|
||||
self.prepare_all_variables()
|
||||
|
||||
print("-----[ Working at level=" + str(current_level) + " ]-----")
|
||||
stdout.flush()
|
||||
|
||||
# reachability test:
|
||||
self.solver.push()
|
||||
print("[i] Adding the reachability test...")
|
||||
if exclusive_state == False:
|
||||
self.solver.add(self.enc_inclusive_state(current_level,state))
|
||||
else:
|
||||
self.solver.add(self.enc_state(current_level,state))
|
||||
|
||||
result = self.solver.check()
|
||||
if result == sat:
|
||||
print("\n[+] SAT at level=" + str(current_level))
|
||||
if print_witness:
|
||||
self.decode_witness(current_level)
|
||||
break
|
||||
else:
|
||||
self.solver.pop()
|
||||
|
||||
print("[i] Unrolling the transition relation")
|
||||
self.solver.add(self.enc_transition_relation(current_level))
|
||||
|
||||
print("-----[ level=" + str(current_level) + " done ]")
|
||||
current_level += 1
|
||||
|
||||
if current_level > max_level:
|
||||
print("Stopping at level=" + str(max_level))
|
||||
break
|
||||
|
||||
if print_time:
|
||||
stop = time()
|
||||
print()
|
||||
print("==== Time: " + repr(stop-start))
|
||||
|
||||
if print_mem:
|
||||
usage=resource.getrusage(resource.RUSAGE_SELF)
|
||||
print("MEM: usertime=%s systime=%s mem=%sMB" % (usage[0],usage[1], (resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024**2)))
|
||||
275
smt/smt_checker_pgrs.py
Normal file
275
smt/smt_checker_pgrs.py
Normal file
@@ -0,0 +1,275 @@
|
||||
"""
|
||||
SMT-based Model Checking Module for RS with Context Automaton
|
||||
"""
|
||||
|
||||
from z3 import *
|
||||
from time import time
|
||||
from sys import stdout
|
||||
import resource
|
||||
|
||||
class SmtCheckerPGRS(object):
|
||||
|
||||
def __init__(self, rsca):
|
||||
|
||||
rsca.sanity_check()
|
||||
|
||||
self.rs = rsca.rs
|
||||
self.ca = rsca.ca
|
||||
|
||||
self.v = []
|
||||
self.v_ctx = []
|
||||
self.ca_state = []
|
||||
self.next_level_to_encode = 0
|
||||
|
||||
self.solver = Solver()
|
||||
|
||||
self.verification_time = None
|
||||
|
||||
def prepare_all_variables(self):
|
||||
"""Encodes all the variables"""
|
||||
|
||||
self.prepare_state_variables()
|
||||
self.prepare_context_variables()
|
||||
self.next_level_to_encode += 1
|
||||
|
||||
def prepare_context_variables(self):
|
||||
"""Encodes all the context variables"""
|
||||
|
||||
level = self.next_level_to_encode
|
||||
|
||||
variables = []
|
||||
for entity in self.rs.background_set:
|
||||
variables.append(Bool("C"+str(level)+"_"+entity))
|
||||
|
||||
self.v_ctx.append(variables)
|
||||
|
||||
def prepare_state_variables(self):
|
||||
"""Encodes all the state variables"""
|
||||
|
||||
level = self.next_level_to_encode
|
||||
|
||||
variables = []
|
||||
for entity in self.rs.background_set:
|
||||
variables.append(Bool("L"+str(level)+"_"+entity))
|
||||
self.v.append(variables)
|
||||
|
||||
self.ca_state.append(Int("CA"+str(level)+"_state"))
|
||||
|
||||
def enc_init_state(self, level):
|
||||
"""Encodes the initial state at the given level"""
|
||||
|
||||
rs_init_state_enc = True
|
||||
|
||||
for v in self.v[level]:
|
||||
rs_init_state_enc = simplify(And(rs_init_state_enc, Not(v))) # the initial state is empty
|
||||
|
||||
ca_init_state_enc = self.ca_state[level] == self.ca.get_init_state_id()
|
||||
|
||||
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
|
||||
|
||||
return init_state_enc
|
||||
|
||||
def enc_enabledness(self, level, prod_entity):
|
||||
"""Encodes the enabledness condition for a given level and a given entity"""
|
||||
|
||||
rcts_for_prod_entity = self.rs.get_reactions_by_product()[prod_entity]
|
||||
|
||||
if rcts_for_prod_entity == []:
|
||||
return False
|
||||
|
||||
enc_rct_prod = False
|
||||
for reactants,inhibitors in rcts_for_prod_entity:
|
||||
enc_reactants = True
|
||||
enc_inhibitors = True
|
||||
for reactant in reactants:
|
||||
enc_reactants = simplify(And(enc_reactants,
|
||||
Or(self.v[level][reactant], self.v_ctx[level][reactant])))
|
||||
for inhibitor in inhibitors:
|
||||
enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
Not(Or(self.v[level][inhibitor], self.v_ctx[level][inhibitor]))))
|
||||
|
||||
enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
|
||||
|
||||
return enc_rct_prod
|
||||
|
||||
def enc_entity_production(self, level, prod_entity):
|
||||
"""Encodes the production of a given entity from a given level at level+1"""
|
||||
|
||||
enc_enab_cond = self.enc_enabledness(level, prod_entity)
|
||||
|
||||
enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
|
||||
And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
|
||||
|
||||
return simplify(enc_ent_prod)
|
||||
|
||||
def enc_transition_relation(self, level):
|
||||
return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
|
||||
|
||||
def enc_rs_trans(self, level):
|
||||
"""Encodes the transition relation"""
|
||||
|
||||
unused_entities = list(range(len(self.rs.background_set)))
|
||||
|
||||
enc_trans = True
|
||||
|
||||
for prod_entity in self.rs.get_reactions_by_product():
|
||||
unused_entities.remove(prod_entity)
|
||||
|
||||
enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity)))
|
||||
|
||||
for prod_entity in unused_entities:
|
||||
enc_trans = simplify(And(enc_trans, Not(self.v[level+1][prod_entity])))
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_automaton_trans(self, level):
|
||||
"""Encodes the transition relation for the context automaton"""
|
||||
|
||||
enc_trans = False
|
||||
|
||||
for src,ctx,dst in self.ca.transitions:
|
||||
src_enc = self.ca_state[level] == src
|
||||
dst_enc = self.ca_state[level+1] == dst
|
||||
|
||||
all_ent = set(range(len(self.rs.background_set)))
|
||||
incl_ctx = ctx
|
||||
excl_ctx = all_ent - incl_ctx
|
||||
|
||||
ctx_enc = True
|
||||
|
||||
for c in incl_ctx:
|
||||
ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][c]))
|
||||
for c in excl_ctx:
|
||||
ctx_enc = simplify(And(ctx_enc, Not(self.v_ctx[level][c])))
|
||||
|
||||
cur_trans = simplify(And(src_enc, ctx_enc, dst_enc))
|
||||
|
||||
enc_trans = simplify(Or(enc_trans, cur_trans))
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_state(self, level, state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
enc = True
|
||||
|
||||
state_ids = self.rs.get_state_ids(state)
|
||||
|
||||
for entity in state_ids:
|
||||
enc = And(enc, self.v[level][entity])
|
||||
|
||||
not_in_state = set(range(len(self.rs.background_set)))
|
||||
not_in_state = not_in_state.difference(set(state_ids))
|
||||
|
||||
for entity in not_in_state:
|
||||
enc = And(enc, Not(self.v[level][entity]))
|
||||
|
||||
return enc
|
||||
|
||||
def enc_non_exclusive_state(self, level, state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
enc = True
|
||||
|
||||
state_ids = self.rs.get_state_ids(state)
|
||||
|
||||
for entity in state_ids:
|
||||
enc = And(enc, self.v[level][entity])
|
||||
|
||||
return enc
|
||||
|
||||
def enc_state_with_blocking(self, level, prop):
|
||||
"""Encodes the state at the given level with blocking certain concentrations"""
|
||||
|
||||
required,blocked = prop
|
||||
|
||||
enc = True
|
||||
|
||||
required_ids = self.rs.get_state_ids(required)
|
||||
blocked_ids = self.rs.get_state_ids(blocked)
|
||||
|
||||
for e in required_ids:
|
||||
enc = And(enc, self.v[level][e])
|
||||
for e in blocked_ids:
|
||||
enc = And(enc, Not(self.v[level][e]))
|
||||
|
||||
return simplify(enc)
|
||||
|
||||
|
||||
def decode_witness(self, max_level, print_model=False):
|
||||
|
||||
m = self.solver.model()
|
||||
|
||||
if print_model:
|
||||
print(m)
|
||||
|
||||
for level in range(max_level+1):
|
||||
|
||||
print("\n[Level=" + repr(level) + "]")
|
||||
|
||||
print(" State: {", end=""),
|
||||
for var_id in range(len(self.v[level])):
|
||||
if repr(m[self.v[level][var_id]]) == "True":
|
||||
print(" " + self.rs.get_entity_name(var_id), end="")
|
||||
print(" }")
|
||||
|
||||
if level != max_level:
|
||||
print(" Context set: ", end="")
|
||||
print("{", end="")
|
||||
for var_id in range(len(self.v[level])):
|
||||
if repr(m[self.v_ctx[level][var_id]]) == "True":
|
||||
print(" " + self.rs.get_entity_name(var_id), end="")
|
||||
print(" }")
|
||||
|
||||
def check_reachability(self, state, print_witness=True, print_time=True, print_mem=True):
|
||||
"""Main testing function"""
|
||||
|
||||
if not type(state) is tuple:
|
||||
state = (state,[])
|
||||
|
||||
if print_time:
|
||||
# start = time()
|
||||
start = resource.getrusage(resource.RUSAGE_SELF).ru_utime
|
||||
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_init_state(0))
|
||||
current_level = 0
|
||||
|
||||
while True:
|
||||
print("-----[ Working at level=" + str(current_level) + " ]-----")
|
||||
stdout.flush()
|
||||
|
||||
self.prepare_all_variables()
|
||||
|
||||
# reachability test:
|
||||
print("[i] Adding the reachability test...")
|
||||
self.solver.push()
|
||||
self.solver.add(self.enc_state_with_blocking(current_level,state))
|
||||
|
||||
result = self.solver.check()
|
||||
if result == sat:
|
||||
print("\n[+] SAT at level=" + str(current_level))
|
||||
if print_witness:
|
||||
self.decode_witness(current_level)
|
||||
break
|
||||
else:
|
||||
self.solver.pop()
|
||||
|
||||
print("[i] Unrolling the transition relation")
|
||||
self.solver.add(self.enc_transition_relation(current_level))
|
||||
|
||||
print("-----[ level=" + str(current_level) + " done ]")
|
||||
current_level += 1
|
||||
|
||||
if print_time:
|
||||
# stop = time()
|
||||
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
|
||||
self.verification_time = stop-start
|
||||
print()
|
||||
print("[i] Time: " + repr(self.verification_time))
|
||||
|
||||
if print_mem:
|
||||
print("[i] Memory: " + repr(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)) + " MB")
|
||||
|
||||
def get_verification_time(self):
|
||||
return self.verification_time
|
||||
480
smt/smt_checker_rsc.py
Normal file
480
smt/smt_checker_rsc.py
Normal file
@@ -0,0 +1,480 @@
|
||||
"""
|
||||
SMT-based Model Checking Module for RS with Concentrations and Context Automaton
|
||||
"""
|
||||
|
||||
from z3 import *
|
||||
from time import time
|
||||
from sys import stdout
|
||||
from itertools import chain
|
||||
import resource
|
||||
from colour import *
|
||||
|
||||
# def simplify(x):
|
||||
# return x
|
||||
|
||||
class SmtCheckerRSC(object):
|
||||
|
||||
def __init__(self, rsca):
|
||||
|
||||
rsca.sanity_check()
|
||||
|
||||
if not rsca.is_with_concentrations():
|
||||
raise RuntimeError("RS and CA with concentrations expected")
|
||||
|
||||
self.rs = rsca.rs
|
||||
self.ca = rsca.ca
|
||||
|
||||
self.v = []
|
||||
self.v_ctx = []
|
||||
self.ca_state = []
|
||||
self.next_level_to_encode = 0
|
||||
|
||||
self.solver = Solver()
|
||||
|
||||
self.verification_time = None
|
||||
|
||||
def prepare_all_variables(self):
|
||||
"""Encodes all the variables"""
|
||||
|
||||
self.prepare_state_variables()
|
||||
self.prepare_context_variables()
|
||||
self.next_level_to_encode += 1
|
||||
|
||||
def prepare_context_variables(self):
|
||||
"""Encodes all the context variables"""
|
||||
|
||||
level = self.next_level_to_encode
|
||||
|
||||
variables = []
|
||||
for entity in self.rs.background_set:
|
||||
variables.append(Int("C"+str(level)+"_"+entity))
|
||||
|
||||
self.v_ctx.append(variables)
|
||||
|
||||
def prepare_state_variables(self):
|
||||
"""Encodes all the state variables"""
|
||||
|
||||
level = self.next_level_to_encode
|
||||
|
||||
variables = []
|
||||
for entity in self.rs.background_set:
|
||||
variables.append(Int("L"+str(level)+"_"+entity))
|
||||
self.v.append(variables)
|
||||
|
||||
self.ca_state.append(Int("CA"+str(level)+"_state"))
|
||||
|
||||
def enc_concentration_levels_assertion(self, level):
|
||||
"""Encodes assertions that (some) variables need to be >0
|
||||
|
||||
We do not need to actually control all the variables,
|
||||
only those that can possibly go below 0.
|
||||
"""
|
||||
|
||||
enc_nz = True
|
||||
|
||||
for e_i in range(len(self.rs.background_set)):
|
||||
v = self.v[level][e_i]
|
||||
v_ctx = self.v_ctx[level][e_i]
|
||||
e_max = self.rs.get_max_concentration_level(e_i)
|
||||
enc_nz = simplify(And(enc_nz, v >= 0, v_ctx >= 0, v <= e_max, v_ctx <= e_max))
|
||||
|
||||
return enc_nz
|
||||
|
||||
def enc_init_state(self, level):
|
||||
"""Encodes the initial state at the given level"""
|
||||
|
||||
rs_init_state_enc = True
|
||||
|
||||
for v in self.v[level]:
|
||||
rs_init_state_enc = simplify(And(rs_init_state_enc, v == 0)) # the initial concentration levels are zeroed
|
||||
|
||||
ca_init_state_enc = self.ca_state[level] == self.ca.get_init_state_id()
|
||||
|
||||
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
|
||||
|
||||
return init_state_enc
|
||||
|
||||
def enc_produced_concentration(self, level, prod_entity):
|
||||
"""Encodes the produced concentrations for the given level and entity"""
|
||||
|
||||
rcts_for_prod_entity = []
|
||||
if prod_entity in self.rs.get_reactions_by_product():
|
||||
rcts_for_prod_entity = self.rs.get_reactions_by_product()[prod_entity]
|
||||
|
||||
meta_reactions = []
|
||||
if prod_entity in self.rs.meta_reactions:
|
||||
meta_reactions = self.rs.meta_reactions[prod_entity]
|
||||
|
||||
permanency_inhibition = None
|
||||
if prod_entity in self.rs.permanent_entities:
|
||||
permanency_inhibition = self.rs.permanent_entities[prod_entity]
|
||||
|
||||
if rcts_for_prod_entity == [] and meta_reactions == []:
|
||||
return simplify(self.v[level+1][prod_entity] == 0) # this should never happen
|
||||
|
||||
enc_enabledness = False
|
||||
|
||||
# ----------- ordinary reactions --------------------------------------------
|
||||
|
||||
enc_rct_prod = False
|
||||
|
||||
enc_ordinary_reactions_enabledness = False
|
||||
|
||||
for reactants,inhibitors,products in rcts_for_prod_entity:
|
||||
|
||||
enc_reactants = True
|
||||
for reactant,concentration in reactants:
|
||||
enc_reactants = simplify(And(enc_reactants,
|
||||
Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
|
||||
|
||||
enc_inhibitors = True
|
||||
for inhibitor,concentration in inhibitors:
|
||||
enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
|
||||
|
||||
enc_rct_enabled = And(enc_reactants, enc_inhibitors)
|
||||
enc_products = self.v[level+1][products[0][0]] == products[0][1]
|
||||
enc_rct_prod = simplify(If(enc_rct_enabled, enc_products, enc_rct_prod))
|
||||
enc_enabledness = simplify(Or(enc_enabledness, enc_rct_enabled))
|
||||
|
||||
enc_ordinary_reactions_enabledness = simplify(Or(enc_ordinary_reactions_enabledness,enc_rct_enabled))
|
||||
|
||||
# for reactants,inhibitors,products in rcts_for_prod_entity:
|
||||
# enc_reactants = True
|
||||
# enc_inhibitors = True
|
||||
# # enc_products -- below
|
||||
#
|
||||
# for reactant,concentration in reactants:
|
||||
# enc_reactants = simplify(And(enc_reactants,
|
||||
# Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
|
||||
# for inhibitor,concentration in inhibitors:
|
||||
# enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
# And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
|
||||
#
|
||||
# enc_products = self.v[level+1][products[0][0]] == products[0][1]
|
||||
#
|
||||
# enc_enabledness = simplify(Or(enc_enabledness, And(enc_reactants, enc_inhibitors)))
|
||||
# enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors, enc_products)))
|
||||
|
||||
# -------- meta reactions ---------------------------------------------------
|
||||
|
||||
for r_type,command_entity,reactants,inhibitors in meta_reactions:
|
||||
|
||||
# command entity is e.g. 'inc' for incrementation operation
|
||||
# (inc,W) gives us the value W by which the given entity's value should be incremented
|
||||
|
||||
enc_reactants = True
|
||||
enc_inhibitors = True
|
||||
|
||||
for reactant,concentration in reactants:
|
||||
enc_reactants = simplify(And(enc_reactants,
|
||||
Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
|
||||
|
||||
# command entity needs to be present (with concentration level > 0) in order to perform the operation
|
||||
enc_reactants = simplify(And(enc_reactants,
|
||||
Or(self.v[level][command_entity] > 0, self.v_ctx[level][command_entity] > 0)))
|
||||
|
||||
for inhibitor,concentration in inhibitors:
|
||||
enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
|
||||
|
||||
if r_type == "inc":
|
||||
value_after_inc = If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) + \
|
||||
If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity])
|
||||
enc_products = self.v[level+1][prod_entity] == value_after_inc
|
||||
|
||||
elif r_type == "dec":
|
||||
value_after_dec = simplify(If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) - \
|
||||
If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity]))
|
||||
enc_products = self.v[level+1][prod_entity] == If(value_after_dec < 0, 0, value_after_dec)
|
||||
|
||||
else:
|
||||
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
|
||||
|
||||
enc_meta_reaction_enabledness = And(enc_reactants, enc_inhibitors, Not(enc_ordinary_reactions_enabledness))
|
||||
enc_enabledness = simplify(Or(enc_enabledness, enc_meta_reaction_enabledness))
|
||||
enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_meta_reaction_enabledness, enc_products)))
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
|
||||
if not permanency_inhibition == None:
|
||||
|
||||
enc_reactants = Or(self.v[level][prod_entity] >= concentration, self.v_ctx[level][prod_entity] >= concentration)
|
||||
|
||||
enc_inhibitors = True
|
||||
for inhibitor,concentration in permanency_inhibition:
|
||||
enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
|
||||
enc_products = simplify(self.v[level+1][prod_entity] == \
|
||||
If(self.v[level][prod_entity] > self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]))
|
||||
|
||||
enc_permanency_enabledness = And(enc_reactants, enc_inhibitors, Not(enc_ordinary_reactions_enabledness))
|
||||
enc_enabledness = simplify(Or(enc_enabledness, enc_permanency_enabledness))
|
||||
enc_permanency = And(enc_permanency_enabledness, enc_products)
|
||||
enc_rct_prod = simplify(Or(enc_rct_prod, enc_permanency))
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
|
||||
enc_when_to_produce_zero_conc = simplify(And(Not(enc_enabledness), self.v[level+1][prod_entity] == 0))
|
||||
|
||||
enc_rct_prod = Or(enc_rct_prod, enc_when_to_produce_zero_conc)
|
||||
return enc_rct_prod
|
||||
|
||||
# def enc_entity_production(self, level, prod_entity):
|
||||
# """Encodes the production of a given entity from a given level at level+1"""
|
||||
#
|
||||
# enc_enab_cond = self.enc_enabledness(level, prod_entity)
|
||||
#
|
||||
# enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
|
||||
# And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
|
||||
#
|
||||
# return simplify(enc_ent_prod)
|
||||
|
||||
|
||||
def enc_transition_relation(self, level):
|
||||
return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
|
||||
|
||||
def enc_rs_trans(self, level):
|
||||
"""Encodes the transition relation"""
|
||||
|
||||
unused_entities = set(range(len(self.rs.background_set)))
|
||||
|
||||
enc_trans = True
|
||||
|
||||
reactions = self.rs.get_reactions_by_product()
|
||||
meta_reactions = self.rs.meta_reactions
|
||||
|
||||
for prod_entity in chain(reactions, meta_reactions):
|
||||
unused_entities.discard(prod_entity)
|
||||
enc_trans = simplify(And(enc_trans, self.enc_produced_concentration(level, prod_entity)))
|
||||
|
||||
for prod_entity in unused_entities:
|
||||
enc_trans = simplify(And(enc_trans, self.v[level+1][prod_entity] == 0))
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_automaton_trans(self, level):
|
||||
"""Encodes the transition relation for the context automaton"""
|
||||
|
||||
enc_trans = False
|
||||
|
||||
for src,ctx,dst in self.ca.transitions:
|
||||
src_enc = self.ca_state[level] == src
|
||||
dst_enc = self.ca_state[level+1] == dst
|
||||
|
||||
all_ent = set(range(len(self.rs.background_set)))
|
||||
|
||||
incl_ctx = set([e for e,c in ctx])
|
||||
excl_ctx = all_ent - incl_ctx
|
||||
|
||||
ctx_enc = True
|
||||
|
||||
for e,c in ctx:
|
||||
ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][e] == c))
|
||||
|
||||
for e in excl_ctx:
|
||||
ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][e] == 0))
|
||||
|
||||
cur_trans = simplify(And(src_enc, ctx_enc, dst_enc))
|
||||
enc_trans = simplify(Or(enc_trans, cur_trans))
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_exact_state(self, level, state):
|
||||
"""Encodes the state at the given level with the exact concentration values"""
|
||||
|
||||
raise RuntimeError("Should not be used with RSC")
|
||||
|
||||
# enc = True
|
||||
# used_entities_ids = self.rs.get_state_ids(state)
|
||||
#
|
||||
# for ent,conc in state:
|
||||
# e_id = self.rs.get_entity_id(ent)
|
||||
# enc = And(enc, self.v[level][e_id] == conc)
|
||||
#
|
||||
# not_in_state = set(range(len(self.rs.background_set)))
|
||||
# not_in_state = not_in_state.difference(set(used_entities_ids))
|
||||
#
|
||||
# for entity in not_in_state:
|
||||
# enc = And(enc, self.v[level][entity] == 0)
|
||||
#
|
||||
# return simplify(enc)
|
||||
|
||||
def enc_min_state(self, level, state):
|
||||
"""Encodes the state at the given level with the minimal required concentration levels"""
|
||||
|
||||
enc = True
|
||||
for ent,conc in state:
|
||||
e_id = self.rs.get_entity_id(ent)
|
||||
enc = And(enc, self.v[level][e_id] >= conc)
|
||||
|
||||
# state_ids = self.rs.get_state_ids(state)
|
||||
#
|
||||
# for entity in state_ids:
|
||||
# enc = And(enc, self.v[level][entity])
|
||||
|
||||
return simplify(enc)
|
||||
|
||||
def enc_state_with_blocking(self, level, prop):
|
||||
"""Encodes the state at the given level with blocking certain concentrations"""
|
||||
|
||||
required,blocked = prop
|
||||
|
||||
enc = True
|
||||
for ent,conc in required:
|
||||
e_id = self.rs.get_entity_id(ent)
|
||||
enc = And(enc, self.v[level][e_id] >= conc)
|
||||
|
||||
for ent,conc in blocked:
|
||||
e_id = self.rs.get_entity_id(ent)
|
||||
enc = And(enc, self.v[level][e_id] < conc)
|
||||
|
||||
return simplify(enc)
|
||||
|
||||
def decode_witness(self, max_level, print_model=False):
|
||||
|
||||
m = self.solver.model()
|
||||
|
||||
if print_model:
|
||||
print(m)
|
||||
|
||||
for level in range(max_level+1):
|
||||
|
||||
print("\n{: >70}".format("[ level=" + repr(level) + " ]"))
|
||||
|
||||
print(" State: {", end=""),
|
||||
for var_id in range(len(self.v[level])):
|
||||
var_rep = repr(m[self.v[level][var_id]])
|
||||
if not var_rep.isdigit():
|
||||
raise RuntimeError("unexpected: representation is not a positive integer")
|
||||
if int(var_rep) > 0:
|
||||
print(" " + self.rs.get_entity_name(var_id) + "=" + var_rep, end="")
|
||||
# print(" " + repr(m[self.v[level][var_id]]), end="")
|
||||
print(" }")
|
||||
|
||||
if level != max_level:
|
||||
print(" Context set: ", end="")
|
||||
print("{", end="")
|
||||
for var_id in range(len(self.v[level])):
|
||||
var_rep = repr(m[self.v_ctx[level][var_id]])
|
||||
if not var_rep.isdigit():
|
||||
raise RuntimeError("unexpected: representation is not a positive integer")
|
||||
if int(var_rep) > 0:
|
||||
print(" " + self.rs.get_entity_name(var_id) + "=" + var_rep, end="")
|
||||
print(" }")
|
||||
|
||||
def check_reachability(self, state, print_witness=True,
|
||||
print_time=True, print_mem=True, max_level=100):
|
||||
"""Main testing function"""
|
||||
|
||||
if print_time:
|
||||
# start = time()
|
||||
start = resource.getrusage(resource.RUSAGE_SELF).ru_utime
|
||||
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_init_state(0))
|
||||
current_level = 0
|
||||
|
||||
self.prepare_all_variables()
|
||||
|
||||
self.solver.add(self.enc_concentration_levels_assertion(0))
|
||||
|
||||
while True:
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_concentration_levels_assertion(current_level+1))
|
||||
|
||||
print("\n{:-^70}".format("[ Working at level=" + str(current_level) + " ]"))
|
||||
stdout.flush()
|
||||
|
||||
# reachability test:
|
||||
print("[" + colour_str(C_BOLD, "i") + "] Adding the reachability test...")
|
||||
self.solver.push()
|
||||
|
||||
self.solver.add(self.enc_state_with_blocking(current_level,state))
|
||||
|
||||
result = self.solver.check()
|
||||
if result == sat:
|
||||
print("[" + colour_str(C_BOLD, "+") + "] " + colour_str(C_GREEN, "SAT at level=" + str(current_level)))
|
||||
if print_witness:
|
||||
print("\n{:=^70}".format("[ WITNESS ]"))
|
||||
self.decode_witness(current_level)
|
||||
break
|
||||
else:
|
||||
self.solver.pop()
|
||||
|
||||
print("[" + colour_str(C_BOLD, "i") + "] Unrolling the transition relation")
|
||||
self.solver.add(self.enc_transition_relation(current_level))
|
||||
|
||||
print("{:->70}".format("[ level=" + str(current_level) + " done ]"))
|
||||
current_level += 1
|
||||
|
||||
if current_level > max_level:
|
||||
print("Stopping at level=" + str(max_level))
|
||||
break
|
||||
|
||||
if print_time:
|
||||
# stop = time()
|
||||
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
|
||||
self.verification_time = stop-start
|
||||
print()
|
||||
print("\n[i] {: >60}".format(" Time: " + repr(self.verification_time) + " s"))
|
||||
|
||||
if print_mem:
|
||||
print("[i] {: >60}".format(" Memory: " + repr(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)) + " MB"))
|
||||
|
||||
def get_verification_time(self):
|
||||
return self.verification_time
|
||||
|
||||
def show_encoding(self, state, print_witness=True,
|
||||
print_time=False, print_mem=False, max_level=100):
|
||||
"""Encoding debug function"""
|
||||
|
||||
self.prepare_all_variables()
|
||||
init_s = self.enc_init_state(0)
|
||||
print(init_s)
|
||||
self.solver.add(init_s)
|
||||
current_level = 0
|
||||
|
||||
self.prepare_all_variables()
|
||||
|
||||
while True:
|
||||
self.prepare_all_variables()
|
||||
|
||||
print("-----[ Working at level=" + str(current_level) + " ]-----")
|
||||
stdout.flush()
|
||||
|
||||
# reachability test:
|
||||
print("[i] Adding the reachability test...")
|
||||
self.solver.push()
|
||||
|
||||
s = self.enc_min_state(current_level,state)
|
||||
print("Test: ", s)
|
||||
|
||||
self.solver.add(s)
|
||||
|
||||
result = self.solver.check()
|
||||
if result == sat:
|
||||
print("\n[+] " + colour_str(C_RED, "SAT at level=" + str(current_level)))
|
||||
if print_witness:
|
||||
self.decode_witness(current_level)
|
||||
break
|
||||
else:
|
||||
self.solver.pop()
|
||||
|
||||
print("[i] Unrolling the transition relation")
|
||||
t = self.enc_transition_relation(current_level)
|
||||
print(t)
|
||||
self.solver.add(t)
|
||||
|
||||
print("-----[ level=" + str(current_level) + " done ]")
|
||||
current_level += 1
|
||||
|
||||
if current_level > max_level:
|
||||
print("Stopping at level=" + str(max_level))
|
||||
break
|
||||
else:
|
||||
x=input("Next level? ")
|
||||
x=x.lower()
|
||||
if not (x == "y" or x == "yes"):
|
||||
break
|
||||
|
||||
Reference in New Issue
Block a user