artur/reactics
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Code re-formatting

Browse Source
This commit is contained in:
Artur Meski
2019-02-23 14:41:36 +00:00
parent 59cbc00e7f
commit c3a19d81dc
21 changed files with 1333 additions and 1016 deletions
Download Patch File Download Diff File Expand all files Collapse all files

121
smt/smt_checker_rs.py
View File

@@ -7,14 +7,15 @@ from time import time
from sys import stdout
import resource
class SmtCheckerRS(object):
def __init__(self, rsca):
rsca.sanity_check()
self.rs = rsca.rs
self.ca = rsca.ca
self.ca = rsca.ca
self.v = []
self.v_ctx = []
@@ -22,7 +23,7 @@ class SmtCheckerRS(object):
self.next_level_to_encode = 0
self.solver = Solver()
self.verification_time = None
def prepare_all_variables(self):
@@ -31,7 +32,7 @@ class SmtCheckerRS(object):
self.prepare_state_variables()
self.prepare_context_variables()
self.next_level_to_encode += 1
def prepare_context_variables(self):
"""Encodes all the context variables"""
@@ -45,44 +46,46 @@ class SmtCheckerRS(object):
def prepare_rs_state_variables(self):
"""Encodes all the state variables of the reaction system"""
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)
def prepare_context_controller_variables(self):
"""Encodes all the variables required for controlling context sequences"""
level = self.next_level_to_encode
self.ca_state.append(Int("CA"+str(level)+"_state"))
def prepare_state_variables(self):
"""Encodes all the state variables"""
self.prepare_rs_state_variables()
self.prepare_context_controller_variables()
self.prepare_context_controller_variables()
def enc_rs_init_state(self, level):
"""Encodes the initial state for the reaction system"""
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
# the initial state is empty
rs_init_state_enc = simplify(And(rs_init_state_enc, Not(v)))
return rs_init_state_enc
def enc_context_controller_init_state(self, level):
"""Encodes the initial state for controlling context sequences"""
return self.ca_state[level] == self.ca.get_init_state_id()
def enc_init_state(self, level):
"""Encodes the initial state at the given level"""
init_state_enc = simplify(And(self.enc_rs_init_state(level), self.enc_context_controller_init_state(level)))
init_state_enc = simplify(And(self.enc_rs_init_state(
level), self.enc_context_controller_init_state(level)))
return init_state_enc
@@ -95,17 +98,18 @@ class SmtCheckerRS(object):
return 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_inhibitors = True
for reactant in reactants:
enc_reactants = simplify(And(enc_reactants,
Or(self.v[level][reactant], self.v_ctx[level][reactant])))
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_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)))
enc_rct_prod = simplify(
Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
return enc_rct_prod
@@ -114,15 +118,19 @@ class SmtCheckerRS(object):
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])))
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):
"""Encodes the combined transition relation"""
return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
return simplify(
And(self.enc_rs_trans(level),
self.enc_automaton_trans(level)))
def enc_rs_trans(self, level):
"""Encodes the transition relation"""
@@ -133,43 +141,46 @@ class SmtCheckerRS(object):
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)))
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])))
enc_trans = simplify(
And(enc_trans, Not(self.v[level+1][prod_entity])))
return enc_trans
def enc_automaton_single_trans(self, level, transition):
src,ctx,dst = transition
src, ctx, dst = transition
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])))
enc_single_trans = simplify(And(src_enc, ctx_enc, dst_enc))
return enc_single_trans
def enc_automaton_trans(self, level):
"""Encodes the transition relation for the context automaton"""
enc_trans = False
for transition in self.ca.transitions:
enc_trans = simplify(Or(enc_trans, self.enc_automaton_single_trans(level, transition)))
for transition in self.ca.transitions:
enc_trans = simplify(
Or(enc_trans, self.enc_automaton_single_trans(level, transition)))
return enc_trans
def enc_state(self, level, state):
@@ -201,14 +212,14 @@ class SmtCheckerRS(object):
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
required, blocked = prop
enc = True
required_ids = self.rs.get_state_ids(required)
blocked_ids = self.rs.get_state_ids(blocked)
@@ -219,7 +230,6 @@ class SmtCheckerRS(object):
return simplify(enc)
def decode_witness(self, max_level, print_model=False):
m = self.solver.model()
@@ -245,11 +255,12 @@ class SmtCheckerRS(object):
print(" " + self.rs.get_entity_name(var_id), end="")
print(" }")
def check_reachability(self, state, print_witness=True, print_time=True, print_mem=True):
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,[])
state = (state, [])
if print_time:
# start = time()
@@ -266,9 +277,9 @@ class SmtCheckerRS(object):
self.prepare_all_variables()
# reachability test:
print("[i] Adding the reachability test...")
print("[i] Adding the reachability test...")
self.solver.push()
self.solver.add(self.enc_state_with_blocking(current_level,state))
self.solver.add(self.enc_state_with_blocking(current_level, state))
result = self.solver.check()
if result == sat:
@@ -278,7 +289,7 @@ class SmtCheckerRS(object):
break
else:
self.solver.pop()
print("[i] Unrolling the transition relation")
self.solver.add(self.enc_transition_relation(current_level))
@@ -291,9 +302,13 @@ class SmtCheckerRS(object):
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")
print(
"[i] Memory: " +
repr(
resource.getrusage(resource.RUSAGE_SELF).ru_maxrss /
(1024 * 1024)) + " MB")
def get_verification_time(self):
return self.verification_time