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Transitioning boolean variables to integer variables in the SMT encoding.

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Artur Meski
2016-02-16 21:57:55 +01:00
parent 6018df00d8
commit 8853589ff8
1 changed files with 66 additions and 50 deletions
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116
smtcheckerrsc.py
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@@ -11,9 +11,12 @@ class SmtCheckerRSC(object):
def __init__(self, rsca): def __init__(self, rsca):
rsca.sanity_check() rsca.sanity_check()
if not rsca.is_with_concentrations():
raise RuntimeError("RS and CA with concentrations expected")
self.rs = rsca.rs self.rs = rsca.rs
self.ca = rsca.ca self.ca = rsca.ca
self.v = [] self.v = []
self.v_ctx = [] self.v_ctx = []
@@ -36,7 +39,7 @@ class SmtCheckerRSC(object):
variables = [] variables = []
for entity in self.rs.background_set: for entity in self.rs.background_set:
variables.append(Bool("C"+str(level)+"_"+entity)) variables.append(Int("C"+str(level)+"_"+entity))
self.v_ctx.append(variables) self.v_ctx.append(variables)
@@ -47,7 +50,7 @@ class SmtCheckerRSC(object):
variables = [] variables = []
for entity in self.rs.background_set: for entity in self.rs.background_set:
variables.append(Bool("L"+str(level)+"_"+entity)) variables.append(Int("L"+str(level)+"_"+entity))
self.v.append(variables) self.v.append(variables)
self.ca_state.append(Int("CA"+str(level)+"_state")) self.ca_state.append(Int("CA"+str(level)+"_state"))
@@ -58,7 +61,7 @@ class SmtCheckerRSC(object):
rs_init_state_enc = True rs_init_state_enc = True
for v in self.v[level]: for v in self.v[level]:
rs_init_state_enc = simplify(And(rs_init_state_enc, Not(v))) # the initial state is empty 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() ca_init_state_enc = self.ca_state[level] == self.ca.get_init_state_id()
@@ -74,6 +77,15 @@ class SmtCheckerRSC(object):
if rcts_for_prod_entity == []: if rcts_for_prod_entity == []:
return False return False
#
# TODO:
#
# czy potrzebujemy get_reactions_by_product?
# czy może wystarczy jak zakodujemy reakcje jako trójki?
#
# ... na pewno musi być informacja o produkowanym stężeniu
#
enc_rct_prod = False enc_rct_prod = False
for reactants,inhibitors in rcts_for_prod_entity: for reactants,inhibitors in rcts_for_prod_entity:
enc_reactants = True enc_reactants = True
@@ -83,7 +95,7 @@ class SmtCheckerRSC(object):
Or(self.v[level][reactant], self.v_ctx[level][reactant]))) Or(self.v[level][reactant], self.v_ctx[level][reactant])))
for inhibitor in inhibitors: for inhibitor in inhibitors:
enc_inhibitors = simplify(And(enc_inhibitors, enc_inhibitors = simplify(And(enc_inhibitors,
Not(Or(self.v[level][inhibitor], self.v_ctx[level][inhibitor])))) And(self.v[level][inhibitor], self.v_ctx[level][inhibitor])))
enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors))) enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
@@ -140,40 +152,42 @@ class SmtCheckerRSC(object):
ctx_enc = simplify(And(ctx_enc, Not(self.v_ctx[level][c]))) ctx_enc = simplify(And(ctx_enc, Not(self.v_ctx[level][c])))
cur_trans = simplify(And(src_enc, ctx_enc, dst_enc)) cur_trans = simplify(And(src_enc, ctx_enc, dst_enc))
enc_trans = simplify(Or(enc_trans, cur_trans)) enc_trans = simplify(Or(enc_trans, cur_trans))
return enc_trans return enc_trans
def enc_state(self, level, state): def enc_exact_state(self, level, state):
"""Encodes the state at the given level""" """Encodes the state at the given level with the exact concentration values"""
enc = True enc = True
used_entities_ids = self.rs.get_state_ids(state)
state_ids = self.rs.get_state_ids(state)
for ent,conc in state:
for entity in state_ids: e_id = self.rs.get_entity_id(ent)
enc = And(enc, self.v[level][entity]) enc = And(enc, self.v[level][e_id] == conc)
not_in_state = set(range(len(self.rs.background_set))) not_in_state = set(range(len(self.rs.background_set)))
not_in_state = not_in_state.difference(set(state_ids)) not_in_state = not_in_state.difference(set(used_entities_ids))
for entity in not_in_state: for entity in not_in_state:
enc = And(enc, Not(self.v[level][entity])) enc = And(enc, self.v[level][entity] == 0)
return enc return simplify(enc)
def enc_non_exclusive_state(self, level, state): def enc_min_state(self, level, state):
"""Encodes the state at the given level""" """Encodes the state at the given level with the minimal required concentration levels"""
enc = True 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) # state_ids = self.rs.get_state_ids(state)
#
# for entity in state_ids:
# enc = And(enc, self.v[level][entity])
for entity in state_ids: return simplify(enc)
enc = And(enc, self.v[level][entity])
return enc
def decode_witness(self, max_level, print_model=False): def decode_witness(self, max_level, print_model=False):
@@ -209,32 +223,34 @@ class SmtCheckerRSC(object):
self.prepare_all_variables() self.prepare_all_variables()
self.solver.add(self.enc_init_state(0)) self.solver.add(self.enc_init_state(0))
current_level = 0 current_level = 0
print(self.enc_exact_state(current_level,state))
while True: # while True:
print("\r[i] Level: " + str(current_level), end="") # print("\r[i] Level: " + str(current_level), end="")
stdout.flush() # stdout.flush()
#
self.prepare_all_variables() # self.prepare_all_variables()
#
# reachability test: # # reachability test:
self.solver.push() # self.solver.push()
self.solver.add(self.enc_state(current_level,state)) # self.solver.add(self.enc_state(current_level,state))
#
result = self.solver.check() # result = self.solver.check()
if result == sat: # if result == sat:
print("\n[+] SAT at level=" + str(current_level)) # print("\n[+] SAT at level=" + str(current_level))
if print_witness: # if print_witness:
self.decode_witness(current_level) # self.decode_witness(current_level)
break # break
else: # else:
self.solver.pop() # self.solver.pop()
#
self.solver.add(self.enc_transition_relation(current_level)) # self.solver.add(self.enc_transition_relation(current_level))
#
current_level += 1 # current_level += 1
#
if print_time: # if print_time:
stop = time() # stop = time()
print() # print()
print("[i] Time: " + repr(stop-start)) # print("[i] Time: " + repr(stop-start))