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Merge remote-tracking branch 'origin/master' into drs_examples

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This commit is contained in:
Artur Meski
2023-07-11 21:05:17 +01:00
parent 6d8ee08dd3 a1fb5836a5
commit 7505acc6a6
24 changed files with 965 additions and 727 deletions
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17
reactics-smt/colour.py
View File

@@ -1,11 +1,11 @@
C_HEADER = '\033[95m'
C_BLUE = '\033[94m'
C_GREEN = '\033[92m'
C_SOMEOTHER = '\033[93m'
C_RED = '\033[91m'
C_ENDC = '\033[0m'
C_BOLD = '\033[1m'
C_UNDERLINE = '\033[4m'
C_HEADER = "\033[95m"
C_BLUE = "\033[94m"
C_GREEN = "\033[92m"
C_SOMEOTHER = "\033[93m"
C_RED = "\033[91m"
C_ENDC = "\033[0m"
C_BOLD = "\033[1m"
C_UNDERLINE = "\033[4m"
C_MARK_INFO = C_BOLD + "[" + C_GREEN + "*" + C_ENDC + C_BOLD + "]" + C_ENDC
C_MARK_ERROR = C_BOLD + "[" + C_RED + "!" + C_ENDC + C_BOLD + "]" + C_ENDC
@@ -30,4 +30,5 @@ def print_info(s):
def print_positive(s):
print("[" + colour_str(C_BOLD, "+") + "] {:s}".format(s))
# EOF

21
reactics-smt/doc/overview.py
View File

@@ -5,26 +5,26 @@ from smt import *
from logics import *
from rsltl_shortcuts import *
def ex():
prs = ReactionSystemWithConcentrationsParam()
ent_with_conc = [("a", 3), ("b",2), ("c",1), ("h",1)]
ent_with_conc = [("a", 3), ("b", 2), ("c", 1), ("h", 1)]
for ec in ent_with_conc:
prs.add_bg_set_entity(ec)
lda = prs.get_param("lda")
prs.add_reaction([("a",1)],[("h",1)],[("b", 2)])
prs.add_reaction(lda,[("h",1)],[("c",1)])
prs.add_reaction([("a", 1)], [("h", 1)], [("b", 2)])
prs.add_reaction(lda, [("h", 1)], [("c", 1)])
##
ca = ContextAutomatonWithConcentrations(prs)
ca.add_init_state("0")
ca.add_state("1")
ca.add_transition("0", [("a", 3)], "1")
ca.add_transition("1", [], "1")
ca.add_transition("1", [("h", 1)], "1")
@@ -37,8 +37,9 @@ def ex():
checker = SmtCheckerRSCParam(crprs, optimise=True)
checker.check_rsltl(formulae_list=[f], param_constr=pc)
if __name__ == "__main__":
ex()
ex()
# EOF

24
reactics-smt/logics/bags.py
View File

@@ -1,10 +1,9 @@
from enum import Enum
BagDesc_oper = Enum(
'BagDesc_oper', 'entity true l_and l_or l_not lt le eq ge gt')
BagDesc_oper = Enum("BagDesc_oper", "entity true l_and l_or l_not lt le eq ge gt")
class BagDescription(object):
def __init__(self, f_type, L_oper=None, R_oper=None, entity=""):
self.f_type = f_type
self.left_operand = L_oper
@@ -19,9 +18,13 @@ class BagDescription(object):
if self.f_type == BagDesc_oper.true:
return "TRUE"
if self.f_type == BagDesc_oper.l_and:
return "(" + repr(self.left_operand) + " & " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " & " + repr(self.right_operand) + ")"
)
if self.f_type == BagDesc_oper.l_or:
return "(" + repr(self.left_operand) + " | " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " | " + repr(self.right_operand) + ")"
)
if self.f_type == BagDesc_oper.l_not:
return "~(" + repr(self.left_operand) + ")"
if self.f_type == BagDesc_oper.lt:
@@ -39,12 +42,14 @@ class BagDescription(object):
"""Sanity checks"""
for operand in (self.left_operand, self.right_operand):
if operand:
if not(
isinstance(operand, BagDescription)
or isinstance(operand, int)):
if not (
isinstance(operand, BagDescription) or isinstance(operand, int)
):
raise RuntimeError(
"Unexpected operand type for a bag: {:s} (type: {:s})".format(
str(operand), str(type(operand))))
str(operand), str(type(operand))
)
)
@classmethod
def f_entity(cls, entity_name):
@@ -86,4 +91,5 @@ class BagDescription(object):
def __invert__(self):
return BagDescription(BagDesc_oper.l_not, L_oper=self)
# EOF

49
reactics-smt/logics/param_constr.py
View File

@@ -1,11 +1,11 @@
from enum import Enum
ParamConstraint_oper = Enum(
'ParamConstraint_oper',
'param_entity true l_and l_or l_not lt le eq ge gt')
"ParamConstraint_oper", "param_entity true l_and l_or l_not lt le eq ge gt"
)
class ParamConstraint(object):
def __init__(self, f_type, L_oper=None, R_oper=None, param=None, entity=""):
self.f_type = f_type
self.left_operand = L_oper
@@ -21,9 +21,13 @@ class ParamConstraint(object):
if self.f_type == ParamConstraint_oper.true:
return "TRUE"
if self.f_type == ParamConstraint_oper.l_and:
return "(" + repr(self.left_operand) + " & " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " & " + repr(self.right_operand) + ")"
)
if self.f_type == ParamConstraint_oper.l_or:
return "(" + repr(self.left_operand) + " | " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " | " + repr(self.right_operand) + ")"
)
if self.f_type == ParamConstraint_oper.l_not:
return "~(" + repr(self.left_operand) + ")"
if self.f_type == ParamConstraint_oper.lt:
@@ -41,17 +45,18 @@ class ParamConstraint(object):
"""Sanity checks"""
for operand in (self.left_operand, self.right_operand):
if operand:
if not(
isinstance(operand, ParamConstraint)
or isinstance(operand, int)):
if not (
isinstance(operand, ParamConstraint) or isinstance(operand, int)
):
raise RuntimeError(
"Unexpected operand type for a bag: {:s} (type: {:s})".format(
str(operand), str(type(operand))))
str(operand), str(type(operand))
)
)
@classmethod
def f_param_ent(cls, param, entity_name):
return cls(ParamConstraint_oper.param_entity, param=param,
entity=entity_name)
return cls(ParamConstraint_oper.param_entity, param=param, entity=entity_name)
@classmethod
def f_TRUE(cls):
@@ -66,34 +71,28 @@ class ParamConstraint(object):
return cls(ParamConstraint_oper.l_not, L_oper=arg)
def __lt__(self, other):
return ParamConstraint(
ParamConstraint_oper.lt, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.lt, L_oper=self, R_oper=other)
def __le__(self, other):
return ParamConstraint(
ParamConstraint_oper.le, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.le, L_oper=self, R_oper=other)
def __eq__(self, other):
return ParamConstraint(
ParamConstraint_oper.eq, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.eq, L_oper=self, R_oper=other)
def __ge__(self, other):
return ParamConstraint(
ParamConstraint_oper.ge, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.ge, L_oper=self, R_oper=other)
def __gt__(self, other):
return ParamConstraint(
ParamConstraint_oper.gt, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.gt, L_oper=self, R_oper=other)
def __and__(self, other):
return ParamConstraint(
ParamConstraint_oper.l_and, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.l_and, L_oper=self, R_oper=other)
def __or__(self, other):
return ParamConstraint(
ParamConstraint_oper.l_or, L_oper=self, R_oper=other)
return ParamConstraint(ParamConstraint_oper.l_or, L_oper=self, R_oper=other)
def __invert__(self):
return ParamConstraint(ParamConstraint_oper.l_not, L_oper=self)
# EOF

47
reactics-smt/logics/param_constr_encoder.py
View File

@@ -14,57 +14,60 @@ class ParamConstr_Encoder(object):
# self.loop_position = None
def load_variables(self, var_rs, var_ctx, var_loop_pos):
self.v = var_rs
self.v_ctx = var_ctx
self.loop_position = var_loop_pos
def encode(self, param_constr):
if not param_constr:
raise RuntimeError("param_constr is None")
if param_constr.f_type == ParamConstraint_oper.param_entity:
return self.smt_checker.get_enc_param(
param_constr.param.name, param_constr.entity)
param_constr.param.name, param_constr.entity
)
if param_constr.f_type == ParamConstraint_oper.true:
return True
if param_constr.f_type == ParamConstraint_oper.l_and:
return And(self.encode(param_constr.left_operand),
self.encode(param_constr.right_operand))
return And(
self.encode(param_constr.left_operand),
self.encode(param_constr.right_operand),
)
if param_constr.f_type == ParamConstraint_oper.l_or:
return Or(self.encode(param_constr.left_operand),
self.encode(param_constr.right_operand))
return Or(
self.encode(param_constr.left_operand),
self.encode(param_constr.right_operand),
)
if param_constr.f_type == ParamConstraint_oper.l_not:
return Not(self.encode(param_constr.left_operand))
if param_constr.f_type == ParamConstraint_oper.lt:
return self.encode(
param_constr.left_operand) < int(
param_constr.right_operand)
return self.encode(param_constr.left_operand) < int(
param_constr.right_operand
)
if param_constr.f_type == ParamConstraint_oper.le:
return self.encode(
param_constr.left_operand) <= int(
param_constr.right_operand)
return self.encode(param_constr.left_operand) <= int(
param_constr.right_operand
)
if param_constr.f_type == ParamConstraint_oper.eq:
return self.encode(
param_constr.left_operand) == int(
param_constr.right_operand)
return self.encode(param_constr.left_operand) == int(
param_constr.right_operand
)
if param_constr.f_type == ParamConstraint_oper.ge:
return self.encode(
param_constr.left_operand) >= int(
param_constr.right_operand)
return self.encode(param_constr.left_operand) >= int(
param_constr.right_operand
)
if param_constr.f_type == ParamConstraint_oper.gt:
return self.encode(
param_constr.left_operand) > int(
param_constr.right_operand)
return self.encode(param_constr.left_operand) > int(
param_constr.right_operand
)
assert False, "Unsupported case {:s}".format(param_constr.f_type)

59
reactics-smt/logics/rsltl.py
View File

@@ -4,14 +4,13 @@ from enum import Enum
from logics.bags import *
rsLTL_form_type = Enum(
'rsLTL_form_type',
'bag l_and l_or l_not l_implies t_globally t_finally t_next t_until t_release')
"rsLTL_form_type",
"bag l_and l_or l_not l_implies t_globally t_finally t_next t_until t_release",
)
class Formula_rsLTL(object):
def __init__(
self, f_type, L_oper=None, R_oper=None, sub_oper=None, bag=None):
def __init__(self, f_type, L_oper=None, R_oper=None, sub_oper=None, bag=None):
self.f_type = f_type
self.left_operand = L_oper
self.right_operand = R_oper
@@ -21,7 +20,10 @@ class Formula_rsLTL(object):
# it's silly, but it's a frequent mistake
if callable(sub_oper):
raise RuntimeError(
"sub_oper should not be a function. Missing () for {0}?".format(sub_oper))
"sub_oper should not be a function. Missing () for {0}?".format(
sub_oper
)
)
if isinstance(self.left_operand, BagDescription):
self.left_operand = Formula_rsLTL.f_bag(self.left_operand)
@@ -43,21 +45,37 @@ class Formula_rsLTL(object):
if self.f_type == rsLTL_form_type.t_next:
return "X[" + repr(self.sub_operand) + "](" + repr(self.left_operand) + ")"
if self.f_type == rsLTL_form_type.l_and:
return "(" + repr(self.left_operand) + " & " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " & " + repr(self.right_operand) + ")"
)
if self.f_type == rsLTL_form_type.l_or:
return "(" + repr(self.left_operand) + " | " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " | " + repr(self.right_operand) + ")"
)
if self.f_type == rsLTL_form_type.l_implies:
return "(" + repr(self.left_operand) + " => " + repr(self.right_operand) + ")"
return (
"(" + repr(self.left_operand) + " => " + repr(self.right_operand) + ")"
)
if self.f_type == rsLTL_form_type.t_until:
return "(" + repr(
self.left_operand) + " U[" + repr(
self.sub_operand) + "] " + repr(
self.right_operand) + ")"
return (
"("
+ repr(self.left_operand)
+ " U["
+ repr(self.sub_operand)
+ "] "
+ repr(self.right_operand)
+ ")"
)
if self.f_type == rsLTL_form_type.t_release:
return "(" + repr(
self.left_operand) + " R[" + repr(
self.sub_operand) + "] " + repr(
self.right_operand) + ")"
return (
"("
+ repr(self.left_operand)
+ " R["
+ repr(self.sub_operand)
+ "] "
+ repr(self.right_operand)
+ ")"
)
@property
def is_bag(self):
@@ -93,8 +111,7 @@ class Formula_rsLTL(object):
@classmethod
def f_U(cls, sub, arg_L, arg_R):
return cls(
rsLTL_form_type.t_until, L_oper=arg_L, R_oper=arg_R, sub_oper=sub)
return cls(rsLTL_form_type.t_until, L_oper=arg_L, R_oper=arg_R, sub_oper=sub)
@classmethod
def f_F(cls, sub, arg_L):
@@ -102,9 +119,7 @@ class Formula_rsLTL(object):
@classmethod
def f_R(cls, sub, arg_L, arg_R):
return cls(
rsLTL_form_type.t_release, L_oper=arg_L, R_oper=arg_R,
sub_oper=sub)
return cls(rsLTL_form_type.t_release, L_oper=arg_L, R_oper=arg_R, sub_oper=sub)
def __and__(self, other):
return Formula_rsLTL(rsLTL_form_type.l_and, L_oper=self, R_oper=other)

188
reactics-smt/logics/rsltl_encoder.py
View File

@@ -24,13 +24,11 @@ class rsLTL_Encoder(object):
self.init_ncalls()
def load_variables(self, var_rs, var_ctx, var_loop_pos):
self.v = var_rs
self.v_ctx = var_ctx
self.loop_position = var_loop_pos
def get_encoding(self, formula, bound):
assert self.v is not None
assert self.v_ctx is not None
assert self.loop_position is not None
@@ -49,8 +47,8 @@ class rsLTL_Encoder(object):
Cache for formulae encodings
"""
self.cache_hits = 0
self.enc_fcache = [{} for level in range(0, bound+1)]
self.enc_fcache_approx = [{} for level in range(0, bound+1)]
self.enc_fcache = [{} for level in range(0, bound + 1)]
self.enc_fcache_approx = [{} for level in range(0, bound + 1)]
def cache_save(self, formula, level, formula_encoding):
self.enc_fcache[level][formula] = formula_encoding
@@ -83,7 +81,6 @@ class rsLTL_Encoder(object):
return (self.ncalls_encode, self.ncalls_encode_approx)
def encode_bag(self, bag_formula, level, context=False):
if not bag_formula:
raise RuntimeError("bag_formula is None")
@@ -100,41 +97,42 @@ class rsLTL_Encoder(object):
if bag_formula.f_type == BagDesc_oper.l_and:
return And(
self.encode_bag(bag_formula.left_operand, level, context),
self.encode_bag(bag_formula.right_operand, level, context))
self.encode_bag(bag_formula.right_operand, level, context),
)
if bag_formula.f_type == BagDesc_oper.l_or:
return Or(
self.encode_bag(bag_formula.left_operand, level, context),
self.encode_bag(bag_formula.right_operand, level, context))
self.encode_bag(bag_formula.right_operand, level, context),
)
if bag_formula.f_type == BagDesc_oper.l_not:
return Not(self.encode_bag(
bag_formula.left_operand, level, context))
return Not(self.encode_bag(bag_formula.left_operand, level, context))
if bag_formula.f_type == BagDesc_oper.lt:
return self.encode_bag(
bag_formula.left_operand, level, context) < int(
bag_formula.right_operand)
return self.encode_bag(bag_formula.left_operand, level, context) < int(
bag_formula.right_operand
)
if bag_formula.f_type == BagDesc_oper.le:
return self.encode_bag(
bag_formula.left_operand, level, context) <= int(
bag_formula.right_operand)
return self.encode_bag(bag_formula.left_operand, level, context) <= int(
bag_formula.right_operand
)
if bag_formula.f_type == BagDesc_oper.eq:
return self.encode_bag(
bag_formula.left_operand, level, context) == int(
bag_formula.right_operand)
return self.encode_bag(bag_formula.left_operand, level, context) == int(
bag_formula.right_operand
)
if bag_formula.f_type == BagDesc_oper.ge:
return self.encode_bag(
bag_formula.left_operand, level, context) >= int(
bag_formula.right_operand)
return self.encode_bag(bag_formula.left_operand, level, context) >= int(
bag_formula.right_operand
)
if bag_formula.f_type == BagDesc_oper.gt:
return self.encode_bag(
bag_formula.left_operand, level, context) > int(
bag_formula.right_operand)
return self.encode_bag(bag_formula.left_operand, level, context) > int(
bag_formula.right_operand
)
assert False, "Unsupported case {:s}".format(bag_formula.f_type)
@@ -149,7 +147,6 @@ class rsLTL_Encoder(object):
return res
def encode(self, formula, level, bound):
self.ncalls_encode += 1
from_cache = self.cache_query(formula, level)
@@ -159,12 +156,12 @@ class rsLTL_Encoder(object):
enc = None
if not isinstance(formula, Formula_rsLTL):
raise NotImplementedError(
"Unsupported formula type: " + str(type(formula)))
raise NotImplementedError("Unsupported formula type: " + str(type(formula)))
if level > bound:
raise RuntimeError(
"level > bound. Unexpected behaviour. The encoding does not support levels higher than a bound.")
"level > bound. Unexpected behaviour. The encoding does not support levels higher than a bound."
)
if formula.f_type == rsLTL_form_type.bag:
enc = self.encode_bag_state(formula.bag_descr, level)
@@ -179,33 +176,40 @@ class rsLTL_Encoder(object):
elif formula.f_type == rsLTL_form_type.l_and:
enc = And(
self.encode(formula.left_operand, level, bound),
self.encode(formula.right_operand, level, bound)
self.encode(formula.right_operand, level, bound),
)
elif formula.f_type == rsLTL_form_type.l_or:
enc = Or(
self.encode(formula.left_operand, level, bound),
self.encode(formula.right_operand, level, bound)
self.encode(formula.right_operand, level, bound),
)
elif formula.f_type == rsLTL_form_type.l_implies:
enc = Implies(
self.encode(formula.left_operand, level, bound),
self.encode(formula.right_operand, level, bound)
self.encode(formula.right_operand, level, bound),
)
elif formula.f_type == rsLTL_form_type.t_next:
if level < bound:
enc = And(
self.encode(formula.left_operand, level + 1, bound),
self.encode_bag_ctx(formula.sub_operand, level)
self.encode_bag_ctx(formula.sub_operand, level),
)
else:
# level == bound
enc = False
for loop_level in range(1, bound+1):
enc = simplify(Or(enc, And(self.loop_position == loop_level, self.encode(
formula.left_operand, loop_level, bound))))
for loop_level in range(1, bound + 1):
enc = simplify(
Or(
enc,
And(
self.loop_position == loop_level,
self.encode(formula.left_operand, loop_level, bound),
),
)
)
enc = And(enc, self.encode_bag_ctx(formula.sub_operand, level))
enc = simplify(enc)
@@ -214,22 +218,25 @@ class rsLTL_Encoder(object):
enc = And(
self.encode(formula.left_operand, level, bound),
self.encode_bag_ctx(formula.sub_operand, level),
self.encode(formula, level + 1, bound)
self.encode(formula, level + 1, bound),
)
else:
# level == bound
enc_loops = False
for loop_level in range(1, bound+1):
enc_loops = simplify(Or(enc_loops,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound),
)
))
for loop_level in range(1, bound + 1):
enc_loops = simplify(
Or(
enc_loops,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound),
),
)
)
enc = And(
self.encode(formula.left_operand, bound, bound),
enc_loops,
self.encode_bag_ctx(formula.sub_operand, level)
self.encode_bag_ctx(formula.sub_operand, level),
)
enc = simplify(enc)
@@ -239,25 +246,26 @@ class rsLTL_Encoder(object):
self.encode(formula.left_operand, level, bound),
And(
self.encode_bag_ctx(formula.sub_operand, level),
self.encode(formula, level + 1, bound)
)
self.encode(formula, level + 1, bound),
),
)
else:
# level == bound
enc_loops = False
for loop_level in range(1, bound+1):
enc_loops = simplify(Or(enc_loops,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound),
)
))
for loop_level in range(1, bound + 1):
enc_loops = simplify(
Or(
enc_loops,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound),
),
)
)
# print(enc)
enc = Or(self.encode(formula.left_operand, bound, bound),
And(
enc_loops,
self.encode_bag_ctx(formula.sub_operand, level)
)
enc = Or(
self.encode(formula.left_operand, bound, bound),
And(enc_loops, self.encode_bag_ctx(formula.sub_operand, level)),
)
enc = simplify(enc)
@@ -268,21 +276,24 @@ class rsLTL_Encoder(object):
else:
# level == bound
inner_enc = False
for loop_level in range(1, bound+1):
inner_enc = simplify(Or(inner_enc,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound)
)
))
for loop_level in range(1, bound + 1):
inner_enc = simplify(
Or(
inner_enc,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound),
),
)
)
enc = Or(
self.encode(formula.right_operand, level, bound),
And(
self.encode(formula.left_operand, level, bound),
inner_enc,
self.encode_bag_ctx(formula.sub_operand, level)
)
self.encode_bag_ctx(formula.sub_operand, level),
),
)
elif formula.f_type == rsLTL_form_type.t_release:
@@ -291,23 +302,23 @@ class rsLTL_Encoder(object):
else:
# level == bound
inner_enc = False
for loop_level in range(1, bound+1):
inner_enc = simplify(Or(inner_enc,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound)
)
))
for loop_level in range(1, bound + 1):
inner_enc = simplify(
Or(
inner_enc,
And(
self.loop_position == loop_level,
self.encode_approx(formula, loop_level, bound),
),
)
)
enc = And(
self.encode(formula.right_operand, level, bound),
Or(
self.encode(formula.left_operand, level, bound),
And(
inner_enc,
self.encode_bag_ctx(formula.sub_operand, level)
)
)
And(inner_enc, self.encode_bag_ctx(formula.sub_operand, level)),
),
)
else:
@@ -341,8 +352,8 @@ class rsLTL_Encoder(object):
And(
self.encode(formula.left_operand, level, bound),
self.encode_approx(formula, level + 1, bound),
self.encode_bag_ctx(formula.sub_operand, level)
)
self.encode_bag_ctx(formula.sub_operand, level),
),
)
else:
# level == bound
@@ -356,9 +367,9 @@ class rsLTL_Encoder(object):
self.encode(formula.left_operand, level, bound),
And(
self.encode_approx(formula, level + 1, bound),
self.encode_bag_ctx(formula.sub_operand, level)
)
)
self.encode_bag_ctx(formula.sub_operand, level),
),
),
)
else:
# level == bound
@@ -369,7 +380,7 @@ class rsLTL_Encoder(object):
enc = And(
self.encode(formula.left_operand, level, bound),
self.encode_bag_ctx(formula.sub_operand, level),
self.encode_approx(formula, level + 1, bound)
self.encode_approx(formula, level + 1, bound),
)
else:
# level == bound
@@ -381,16 +392,15 @@ class rsLTL_Encoder(object):
self.encode(formula.left_operand, level, bound),
And(
self.encode_bag_ctx(formula.sub_operand, level),
self.encode_approx(formula, level + 1, bound)
)
self.encode_approx(formula, level + 1, bound),
),
)
else:
# level == bound
enc = self.encode(formula.left_operand, bound, bound)
else:
raise NotImplementedError(
"Unsupported operator in approximation encoding")
raise NotImplementedError("Unsupported operator in approximation encoding")
if enc is None:
raise RuntimeError("Encoding is NONE. Should never happen")

6
reactics-smt/rs/__init__.py
View File

@@ -2,7 +2,11 @@ from rs.reaction_system import ReactionSystem
from rs.context_automaton import ContextAutomaton
from rs.reaction_system_with_concentrations import ReactionSystemWithConcentrations
from rs.reaction_system_with_concentrations_param import ReactionSystemWithConcentrationsParam, ParameterObj, is_param
from rs.reaction_system_with_concentrations_param import (
ReactionSystemWithConcentrationsParam,
ParameterObj,
is_param,
)
from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
from rs.extended_context_automaton import ExtendedContextAutomaton

17
reactics-smt/rs/context_automaton.py
View File

@@ -3,7 +3,6 @@ from colour import *
class ContextAutomaton(object):
def __init__(self, reaction_system):
self._states = []
self._transitions = []
@@ -40,7 +39,7 @@ class ContextAutomaton(object):
if name not in self._states:
self._states.append(name)
else:
print("\'%s\' already added. skipping..." % (name,))
print("'%s' already added. skipping..." % (name,))
def add_states(self, states_set):
for st in states_set:
@@ -101,15 +100,14 @@ class ContextAutomaton(object):
if not self.is_valid_context(context_set):
raise RuntimeError(
"one of the entities in the context set is unknown (undefined)!")
"one of the entities in the context set is unknown (undefined)!"
)
if not self.is_state(src):
raise RuntimeError(
"\"" + src + "\" is an unknown (undefined) state")
raise RuntimeError('"' + src + '" is an unknown (undefined) state')
if not self.is_state(dst):
raise RuntimeError(
"\"" + dst + "\" is an unknown (undefined) state")
raise RuntimeError('"' + dst + '" is an unknown (undefined) state')
new_context_set = set()
for e in set(context_set):
@@ -118,8 +116,8 @@ class ContextAutomaton(object):
self._prod_entities |= new_context_set
self._transitions.append(
(self.get_state_id(src),
new_context_set, self.get_state_id(dst)))
(self.get_state_id(src), new_context_set, self.get_state_id(dst))
)
def rsset2str(self, elements):
"""Converts the set of entities ids into the string with their names"""
@@ -168,4 +166,5 @@ class ContextAutomaton(object):
self.show_transitions()
self.show_prod_entities()
# EOF

38
reactics-smt/rs/context_automaton_with_concentrations.py
View File

@@ -5,15 +5,13 @@ from rs.context_automaton import ContextAutomaton
class ContextAutomatonWithConcentrations(ContextAutomaton):
def __init__(self, reaction_system):
super(ContextAutomatonWithConcentrations,
self).__init__(reaction_system)
super(ContextAutomatonWithConcentrations, self).__init__(reaction_system)
def is_valid_context(self, context):
if set(
[e for e, lvl in context]).issubset(
self._reaction_system.background_set):
if set([e for e, lvl in context]).issubset(
self._reaction_system.background_set
):
return True
else:
return False
@@ -33,45 +31,38 @@ class ContextAutomatonWithConcentrations(ContextAutomaton):
if not self.is_valid_context(context_set):
raise RuntimeError(
"one of the entities in the context set is unknown (undefined)!")
"one of the entities in the context set is unknown (undefined)!"
)
if not self.is_state(src):
raise RuntimeError(
"\"" + src + "\" is an unknown (undefined) state")
raise RuntimeError('"' + src + '" is an unknown (undefined) state')
if not self.is_state(dst):
raise RuntimeError(
"\"" + dst + "\" is an unknown (undefined) state")
raise RuntimeError('"' + dst + '" is an unknown (undefined) state')
new_context_set = set()
for ent, lvl in set(context_set):
new_context_set.add(
(self._reaction_system.get_entity_id(ent), lvl))
new_context_set.add((self._reaction_system.get_entity_id(ent), lvl))
self._transitions.append(
(self.get_state_id(src),
new_context_set, self.get_state_id(dst)))
(self.get_state_id(src), new_context_set, self.get_state_id(dst))
)
def get_automaton_with_flat_contexts(self, ordinary_reaction_system):
ca = ContextAutomaton(ordinary_reaction_system)
ca._states = self._states
ca._init_state = self._init_state
for src, ctx, dst in self._transitions:
new_ctx = set()
for ent, conc in ctx:
for i in range(1, conc+1):
n = self._reaction_system.get_entity_name(
ent) + "#" + str(i)
for i in range(1, conc + 1):
n = self._reaction_system.get_entity_name(ent) + "#" + str(i)
ca._reaction_system.ensure_bg_set_entity(n)
new_ctx.add(n)
ca.add_transition(
ca.get_state_name(src),
new_ctx, ca.get_state_name(dst))
ca.add_transition(ca.get_state_name(src), new_ctx, ca.get_state_name(dst))
return ca
@@ -80,4 +71,5 @@ class ContextAutomatonWithConcentrations(ContextAutomaton):
self.show_states()
self.show_transitions()
# EOF

32
reactics-smt/rs/extended_context_automaton.py
View File

@@ -75,23 +75,24 @@ class ExtendedContextAutomaton(ContextAutomaton):
if not self.is_valid_rs_set(ctx_reactants):
raise RuntimeError(
"one of the entities in the reactants set is unknown (undefined)!")
"one of the entities in the reactants set is unknown (undefined)!"
)
if not self.is_valid_rs_set(ctx_inhibitors):
raise RuntimeError(
"one of the entities in the inhibitors set is unknown (undefined)!")
"one of the entities in the inhibitors set is unknown (undefined)!"
)
if not self.is_valid_rs_set(ctx_products):
raise RuntimeError(
"one of the entities in the context set is unknown (undefined)!")
"one of the entities in the context set is unknown (undefined)!"
)
if not self.is_state(src):
raise RuntimeError(
"\"" + src + "\" is an unknown (undefined) state")
raise RuntimeError('"' + src + '" is an unknown (undefined) state')
if not self.is_state(dst):
raise RuntimeError(
"\"" + dst + "\" is an unknown (undefined) state")
raise RuntimeError('"' + dst + '" is an unknown (undefined) state')
src_id = self.get_state_id(src)
dst_id = self.get_state_id(dst)
@@ -119,8 +120,15 @@ class ExtendedContextAutomaton(ContextAutomaton):
for src_id, act_id, reaction, dst_id in self._transitions:
str_transition = self.get_state_name(src_id) + " --( "
str_transition += "<" + self.get_actions_str(act_id) + "> | "
str_transition += "( " + self.rsset2str(reaction[0]) + "," + self.rsset2str(
reaction[1]) + "," + self.rsset2str(reaction[2]) + " )"
str_transition += (
"( "
+ self.rsset2str(reaction[0])
+ ","
+ self.rsset2str(reaction[1])
+ ","
+ self.rsset2str(reaction[2])
+ " )"
)
str_transition += " )--> " + self.get_state_name(dst_id)
print(" - " + str_transition)
@@ -130,7 +138,7 @@ class ExtendedContextAutomaton(ContextAutomaton):
if action_name not in self._actions:
self._actions.append(action_name)
else:
print("\'%s\' already added. skipping..." % (action_name,))
print("'%s' already added. skipping..." % (action_name,))
def get_action_id(self, action_name):
"""For an action name returns its id"""
@@ -138,8 +146,7 @@ class ExtendedContextAutomaton(ContextAutomaton):
try:
return self._actions.index(action_name)
except ValueError:
print_error("Undefined context automaton action: " +
repr(action_name))
print_error("Undefined context automaton action: " + repr(action_name))
exit(1)
def get_action_name(self, action_id):
@@ -173,4 +180,5 @@ class ExtendedContextAutomaton(ContextAutomaton):
super(ExtendedContextAutomaton, self).show()
self.show_actions()
# EOF

15
reactics-smt/rs/network_of_context_automata.py
View File

@@ -3,7 +3,6 @@ from colour import *
class NetworkOfContextAutomata(object):
def __init__(self, reaction_system, context_automata):
self.automata = []
self._reaction_system = reaction_system
@@ -44,14 +43,14 @@ class NetworkOfContextAutomata(object):
for automaton in self.automata:
if automaton.reaction_system != self._reaction_system:
print_error(
"Mismatching reaction system used in \"" +
str(automaton.name) + "\"!!!")
'Mismatching reaction system used in "'
+ str(automaton.name)
+ '"!!!'
)
exit(1)
def show_prod_entities(self):
print(
C_MARK_INFO +
" Possible context-products for the network of automata:")
print(C_MARK_INFO + " Possible context-products for the network of automata:")
for entity in self.prod_entities:
print(" - " + self._reaction_system.get_entity_name(entity))
@@ -96,7 +95,8 @@ class NetworkOfContextAutomata(object):
for entity in aut.prod_entities:
self._actions_for_products.setdefault(entity, set())
self._actions_for_products[entity] |= aut.get_actions_producing_entity(
entity)
entity
)
def show(self):
print()
@@ -108,4 +108,5 @@ class NetworkOfContextAutomata(object):
self.show_prod_entities()
self.show_actions()
# EOF

46
reactics-smt/rs/reaction_system.py
View File

@@ -3,9 +3,7 @@ from colour import *
class ReactionSystem(object):
def __init__(self):
self.reactions = []
self.background_set = []
@@ -30,8 +28,7 @@ class ReactionSystem(object):
def assume_not_in_bgset(self, name):
if self.is_in_background_set(name):
raise RuntimeError(
"The entity " + name + " is already on the list")
raise RuntimeError("The entity " + name + " is already on the list")
def add_bg_set_entity(self, name):
self.assume_not_in_bgset(name)
@@ -106,7 +103,6 @@ class ReactionSystem(object):
self.init_contexts.append(integers)
def set_context_entities(self, entities):
for entity in entities:
entity_id = self.get_entity_id(entity)
self.context_entities.append(entity_id)
@@ -131,20 +127,36 @@ class ReactionSystem(object):
def show_reactions(self, soft=False):
print(C_MARK_INFO + " Reactions:")
if soft and len(self.reactions) > 50:
print(" -> there are more than 50 reactions (" +
str(len(self.reactions)) + ")")
print(
" -> there are more than 50 reactions ("
+ str(len(self.reactions))
+ ")"
)
else:
print(
" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants", " inhibitors", " products"))
" " * 4
+ "{0: ^35}{1: ^25}{2: ^15}".format(
"reactants", " inhibitors", " products"
)
)
for reaction in self.reactions:
# print("\t( R={" + self.state_to_str(reaction[0]) + "}, I={" + self.state_to_str(reaction[1]) + "}, P={" + self.state_to_str(reaction[2]) + "} )")
print(" " + "- {0: ^35}{1: ^25}{2: ^15}".format("{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }"))
print(
" "
+ "- {0: ^35}{1: ^25}{2: ^15}".format(
"{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }",
)
)
def show_background_set(self):
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
C_MARK_INFO
+ " Background set: {"
+ self.entities_names_set_to_str(self.background_set)
+ "}"
)
def show_initial_contexts(self):
if len(self.init_contexts) > 0:
@@ -155,10 +167,12 @@ class ReactionSystem(object):
def show_context_entities(self):
if len(self.context_entities) > 0:
print(
C_MARK_INFO + " Context entities: " + self.entities_ids_set_to_str(self.context_entities))
C_MARK_INFO
+ " Context entities: "
+ self.entities_ids_set_to_str(self.context_entities)
)
def show(self, soft=False):
self.show_background_set()
self.show_initial_contexts()
self.show_reactions(soft)
@@ -181,8 +195,7 @@ class ReactionSystem(object):
reactions_by_prod[prod_entity] = []
for reaction in self.reactions:
if prod_entity in reaction[2]:
reactions_by_prod[prod_entity].append(
[reaction[0], reaction[1]])
reactions_by_prod[prod_entity].append([reaction[0], reaction[1]])
# save in cache
self.reactions_by_prod = reactions_by_prod
@@ -200,4 +213,5 @@ class ReactionSystem(object):
print("Empty background set")
exit(1)
# EOF

3
reactics-smt/rs/reaction_system_with_autnet.py
View File

@@ -1,6 +1,4 @@
class ReactionSystemWithNetworkOfAutomata(object):
def __init__(self, reaction_system, context_automata):
self.rs = reaction_system
self.cas = context_automata
@@ -9,4 +7,5 @@ class ReactionSystemWithNetworkOfAutomata(object):
self.rs.show(soft)
self.cas.show()
# EOF

8
reactics-smt/rs/reaction_system_with_automaton.py
View File

@@ -1,10 +1,11 @@
from rs.reaction_system_with_concentrations import ReactionSystemWithConcentrations
from rs.reaction_system_with_concentrations_param import ReactionSystemWithConcentrationsParam
from rs.reaction_system_with_concentrations_param import (
ReactionSystemWithConcentrationsParam,
)
from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
class ReactionSystemWithAutomaton(object):
def __init__(self, reaction_system, context_automaton):
self.rs = reaction_system
self.ca = context_automaton
@@ -15,7 +16,7 @@ class ReactionSystemWithAutomaton(object):
def is_concentr_and_param_compatible(self):
"""
Checks if the underlying RS/CA are compatible
Checks if the underlying RS/CA are compatible
with parameters and concentrations
"""
if not isinstance(self.rs, ReactionSystemWithConcentrationsParam):
@@ -35,7 +36,6 @@ class ReactionSystemWithAutomaton(object):
pass
def get_ordinary_reaction_system_with_automaton(self):
if not self.is_with_concentrations():
raise RuntimeError("Not RS/CA with concentrations")

114
reactics-smt/rs/reaction_system_with_concentrations.py
View File

@@ -5,9 +5,7 @@ from rs.reaction_system import ReactionSystem
class ReactionSystemWithConcentrations(ReactionSystem):
def __init__(self):
self.reactions = []
self.meta_reactions = dict()
self.permanent_entities = dict()
@@ -26,8 +24,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
name = e
print("\nWARNING: no maximal concentration level specified for:", e, "\n")
else:
raise RuntimeError(
"Bad entity type when adding background set element")
raise RuntimeError("Bad entity type when adding background set element")
self.assume_not_in_bgset(name)
self.background_set.append(name)
@@ -41,7 +38,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
self.max_concentration = def_max_conc
def get_max_concentration_level(self, e):
if e in self.max_conc_per_ent:
return self.max_conc_per_ent[e]
else:
@@ -69,8 +65,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def has_non_zero_concentration(self, elem):
if elem[1] < 1:
raise RuntimeError(
"Unexpected concentration level in state: " + str(elem))
raise RuntimeError("Unexpected concentration level in state: " + str(elem))
def process_rip(self, R, I, P, ignore_empty_R=False):
"""Chcecks concentration levels and converts entities names into their ids"""
@@ -123,21 +118,25 @@ class ReactionSystemWithConcentrations(ReactionSystem):
"""Adds a macro/meta reaction for increasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id, [])
self.meta_reactions[incr_entity_id].append(
("inc", self.get_entity_id(incrementer), reactants, inhibitors))
("inc", self.get_entity_id(incrementer), reactants, inhibitors)
)
def add_reaction_dec(self, decr_entity, decrementer, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id, [])
self.meta_reactions[decr_entity_id].append(
("dec", self.get_entity_id(decrementer), reactants, inhibitors))
("dec", self.get_entity_id(decrementer), reactants, inhibitors)
)
def add_permanency(self, ent, I):
"""Sets entity to be permanent unless it is inhibited"""
@@ -145,8 +144,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
ent_id = self.get_entity_id(ent)
if ent_id in self.permanent_entities:
raise RuntimeError(
"Permanency for {0} already defined.".format(ent))
raise RuntimeError("Permanency for {0} already defined.".format(ent))
inhibitors = self.process_rip([], I, [], ignore_empty_R=True)[1]
self.permanent_entities[ent_id] = inhibitors
@@ -177,31 +175,50 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def show_background_set(self):
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
C_MARK_INFO
+ " Background set: {"
+ self.entities_names_set_to_str(self.background_set)
+ "}"
)
def show_meta_reactions(self):
print(C_MARK_INFO + " Meta reactions:")
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
if r_type == "inc" or r_type == "dec":
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + " ) Command=( " + self.get_entity_name(
command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
print(
" - [ Type="
+ repr(r_type)
+ " Operand=( "
+ self.get_entity_name(param_ent)
+ " ) Command=( "
+ self.get_entity_name(command)
+ " ) ] -- ( R={"
+ self.state_to_str(reactants)
+ "}, I={"
+ self.state_to_str(inhibitors)
+ "} )"
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show_max_concentrations(self):
print(
C_MARK_INFO +
" Maximal allowed concentration levels (for optimized translation to RS):")
C_MARK_INFO
+ " Maximal allowed concentration levels (for optimized translation to RS):"
)
for e, max_conc in self.max_conc_per_ent.items():
print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e), max_conc))
def show_permanent_entities(self):
print(C_MARK_INFO + " Permanent entities:")
for e, inhibitors in self.permanent_entities.items():
print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}"))
print(
" - {0:^20}{1:<6}".format(
self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}",
)
)
def show(self, soft=False):
self.show_background_set()
@@ -220,8 +237,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
for reaction in self.reactions:
product_entities = [e for e, c in reaction[2]]
producible_entities = producible_entities.union(
set(product_entities))
producible_entities = producible_entities.union(set(product_entities))
reactions_by_prod = {}
@@ -242,18 +258,20 @@ class ReactionSystemWithConcentrations(ReactionSystem):
# we need to order the reactions w.r.t. the concentration levels produced (increasing order)
for i in range(0, len(rcts_for_p_e)):
checked_conc = rcts_for_p_e[i][2][0][1]
if prod_conc <= checked_conc:
insert_place = i
break
if insert_place == None: # empty or the is only one element which is smaller than the element being added
if (
insert_place == None
): # empty or the is only one element which is smaller than the element being added
# we append (to the end)
rcts_for_p_e.append((reactants, inhibitors, products))
else:
rcts_for_p_e.insert(
insert_place, (reactants, inhibitors, products))
insert_place, (reactants, inhibitors, products)
)
# save in cache
self.reactions_by_prod = reactions_by_prod
@@ -261,11 +279,9 @@ class ReactionSystemWithConcentrations(ReactionSystem):
return reactions_by_prod
def get_reaction_system(self):
rs = ReactionSystem()
for reactants, inhibitors, products in self.reactions:
new_reactants = []
new_inhibitors = []
new_products = []
@@ -281,7 +297,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
new_inhibitors.append(n)
for ent, conc in products:
for i in range(1, conc+1):
for i in range(1, conc + 1):
n = self.get_entity_name(ent) + "#" + str(i)
rs.ensure_bg_set_entity(n)
new_products.append(n)
@@ -290,7 +306,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
param_ent_name = self.get_entity_name(param_ent)
new_reactants = []
@@ -312,16 +327,15 @@ class ReactionSystemWithConcentrations(ReactionSystem):
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(command))
+ self.get_entity_name(command)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
for l in range(1, max_cmd_c+1):
for l in range(1, max_cmd_c + 1):
cmd_ent = self.get_entity_name(command) + "#" + str(l)
rs.ensure_bg_set_entity(cmd_ent)
if r_type == "inc":
# pre_conc -- predecessor concentration
# succ_conc -- successor concentration concentration
@@ -329,8 +343,8 @@ class ReactionSystemWithConcentrations(ReactionSystem):
pre_conc = param_ent_name + "#" + str(i)
rs.ensure_bg_set_entity(pre_conc)
new_products = []
succ_value = i+l
for j in range(1, succ_value+1):
succ_value = i + l
for j in range(1, succ_value + 1):
if j > self.max_concentration:
break
new_p = param_ent_name + "#" + str(j)
@@ -340,15 +354,16 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
elif r_type == "dec":
for i in range(1, self.max_concentration+1):
for i in range(1, self.max_concentration + 1):
pre_conc = param_ent_name + "#" + str(i)
rs.ensure_bg_set_entity(pre_conc)
new_products = []
succ_value = i-l
for j in range(1, succ_value+1):
succ_value = i - l
for j in range(1, succ_value + 1):
if j > self.max_concentration:
break
new_p = param_ent_name + "#" + str(j)
@@ -358,28 +373,29 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
"Unknown meta-reaction type: " + repr(r_type)
)
for ent, inhibitors in self.permanent_entities.items():
max_c = self.max_concentration
if ent in self.max_conc_per_ent:
max_c = self.max_conc_per_ent[ent]
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(ent))
+ self.get_entity_name(ent)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
def e_value(i):
return self.get_entity_name(ent) + "#" + str(i)
for value in range(1, max_c+1):
for value in range(1, max_c + 1):
new_reactants = []
new_inhibitors = []
new_products = []
@@ -391,7 +407,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.ensure_bg_set_entity(n)
new_inhibitors.append(n)
for i in range(1, value+1):
for i in range(1, value + 1):
new_products.append(e_value(i))
rs.add_reaction(new_reactants, new_inhibitors, new_products)
@@ -400,7 +416,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
class ReactionSystemWithAutomaton(object):
def __init__(self, reaction_system, context_automaton):
self.rs = reaction_system
self.ca = context_automaton
@@ -420,7 +435,6 @@ class ReactionSystemWithAutomaton(object):
pass
def get_ordinary_reaction_system_with_automaton(self):
if not self.is_with_concentrations():
raise RuntimeError("Not RS/CA with concentrations")

90
reactics-smt/rs/reaction_system_with_concentrations_param.py
View File

@@ -5,7 +5,6 @@ from rs.reaction_system import ReactionSystem
class ParameterObj(object):
def __init__(self, name):
self.name = name
@@ -21,9 +20,7 @@ def is_param(some_object):
class ReactionSystemWithConcentrationsParam(ReactionSystem):
def __init__(self):
self.reactions = []
self.parameters = dict()
self.meta_reactions = dict()
@@ -43,8 +40,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
name = e
print("\nWARNING: no maximal concentration level specified for:", e, "\n")
else:
raise RuntimeError(
"Bad entity type when adding background set element")
raise RuntimeError("Bad entity type when adding background set element")
self.assume_not_in_bgset(name)
self.background_set.append(name)
@@ -76,7 +72,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.parameters[param_key].idx = len(self.parameters)
def get_max_concentration_level(self, e):
if e in self.max_conc_per_ent:
return self.max_conc_per_ent[e]
else:
@@ -113,17 +108,18 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def terminate_on_invalid_concentration(self, entity, level):
if not self.is_valid_concentration_for_entity(entity, level):
print("FATAL. Invalid entity concentration: {:s}={:d}".format(entity, level))
print(
"FATAL. Invalid entity concentration: {:s}={:d}".format(entity, level)
)
exit(1)
def get_state_ids(self, state):
"""Returns entities of the given state without levels"""
return [self.get_entity_id(e) for e in state]
def has_non_zero_concentration(self, elem):
if elem[1] < 1:
raise RuntimeError(
"Unexpected concentration level in state: " + str(elem))
raise RuntimeError("Unexpected concentration level in state: " + str(elem))
def process_rip(self, R, I, P, ignore_empty_R=False):
"""Chcecks concentration levels and converts entities names into their ids"""
@@ -207,21 +203,25 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
"""Adds a macro/meta reaction for increasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id, [])
self.meta_reactions[incr_entity_id].append(
("inc", self.get_entity_id(incrementer), reactants, inhibitors))
("inc", self.get_entity_id(incrementer), reactants, inhibitors)
)
def add_reaction_dec(self, decr_entity, decrementer, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id, [])
self.meta_reactions[decr_entity_id].append(
("dec", self.get_entity_id(decrementer), reactants, inhibitors))
("dec", self.get_entity_id(decrementer), reactants, inhibitors)
)
def add_permanency(self, ent, I):
"""Sets entity to be permanent unless it is inhibited"""
@@ -229,8 +229,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
ent_id = self.get_entity_id(ent)
if ent_id in self.permanent_entities:
raise RuntimeError(
"Permanency for {0} already defined.".format(ent))
raise RuntimeError("Permanency for {0} already defined.".format(ent))
inhibitors = self.process_rip([], I, [], ignore_empty_R=True)[1]
self.permanent_entities[ent_id] = inhibitors
@@ -269,18 +268,32 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def show_background_set(self):
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
C_MARK_INFO
+ " Background set: {"
+ self.entities_names_set_to_str(self.background_set)
+ "}"
)
def show_meta_reactions(self):
print(C_MARK_INFO + " Meta reactions:")
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
if r_type == "inc" or r_type == "dec":
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + " ) Command=( " + self.get_entity_name(
command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
print(
" - [ Type="
+ repr(r_type)
+ " Operand=( "
+ self.get_entity_name(param_ent)
+ " ) Command=( "
+ self.get_entity_name(command)
+ " ) ] -- ( R={"
+ self.state_to_str(reactants)
+ "}, I={"
+ self.state_to_str(inhibitors)
+ "} )"
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show_max_concentrations(self):
print(C_MARK_INFO + " Maximal allowed concentration levels:")
@@ -290,8 +303,12 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def show_permanent_entities(self):
print(C_MARK_INFO + " Permanent entities:")
for e, inhibitors in self.permanent_entities.items():
print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}"))
print(
" - {0:^20}{1:<6}".format(
self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}",
)
)
def show(self, soft=False):
self.show_background_set()
@@ -303,7 +320,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def get_producible_entities(self):
"""
Returns the set of entities that appear as products of
Returns the set of entities that appear as products of
reactions.
"""
@@ -311,8 +328,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
for reaction in self.reactions:
product_entities = [e for e, c in reaction[2] if c > 0]
producible_entities = producible_entities.union(
set(product_entities))
producible_entities = producible_entities.union(set(product_entities))
return producible_entities
@@ -324,7 +340,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs = ReactionSystem()
for reactants, inhibitors, products in self.reactions:
new_reactants = []
new_inhibitors = []
new_products = []
@@ -349,7 +364,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
param_ent_name = self.get_entity_name(param_ent)
new_reactants = []
@@ -371,16 +385,15 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(command))
+ self.get_entity_name(command)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
for l in range(1, max_cmd_c + 1):
cmd_ent = self.get_entity_name(command) + "#" + str(l)
rs.ensure_bg_set_entity(cmd_ent)
if r_type == "inc":
# pre_conc -- predecessor concentration
# succ_conc -- successor concentration concentration
@@ -399,7 +412,8 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
elif r_type == "dec":
for i in range(1, self.max_concentration + 1):
@@ -417,28 +431,29 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
"Unknown meta-reaction type: " + repr(r_type)
)
for ent, inhibitors in self.permanent_entities.items():
max_c = self.max_concentration
if ent in self.max_conc_per_ent:
max_c = self.max_conc_per_ent[ent]
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(ent))
+ self.get_entity_name(ent)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
def e_value(i):
return self.get_entity_name(ent) + "#" + str(i)
for value in range(1, max_c + 1):
new_reactants = []
new_inhibitors = []
new_products = []
@@ -457,4 +472,5 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
return rs
# EOF

5
reactics-smt/rsltl_shortcuts.py
View File

@@ -27,8 +27,7 @@ def bag_And(*args):
assert len(args) > 1
last = get_bag_if_str(args[0])
for arg in args[1:]:
last = BagDescription.f_And(
last, get_bag_if_str(arg))
last = BagDescription.f_And(last, get_bag_if_str(arg))
return last
@@ -46,7 +45,6 @@ def exact_state(contained_entities, all_entities):
expr.append(ent == 0)
if len(expr) > 0:
last = expr[0]
for e in expr[1:]:
last = BagDescription.f_And(last, e)
@@ -107,5 +105,6 @@ def param_And(*args):
last = ParamConstraint.f_And(last, arg)
return last
def param_True():
return ParamConstraint.f_TRUE()

38
reactics-smt/rssmt.py
View File

@@ -24,12 +24,16 @@ if profiling:
##################################################################
version = "2.99"
rsmc_banner = """
rsmc_banner = (
"""
Reaction Systems SMT-Based Model Checking
Version: """ + version + """
Version: """
+ version
+ """
Author: Artur Meski <artur.meski@gmail.com>
"""
)
##################################################################
@@ -40,6 +44,7 @@ def print_banner():
print(colour_str(C_GREEN, " " + 3 * "-" + " "), line)
print()
##################################################################
@@ -48,22 +53,30 @@ def main():
parser = argparse.ArgumentParser()
parser.add_argument("-v", "--verbose",
help="turn verbosity on", action="store_true")
parser.add_argument("-o", "--optimise",
help="minimise the parametric computation result",
action="store_true")
parser.add_argument(
"-n", "--scaling-parameter",
help="scaling parameter value (used in some benchmarks)")
parser.add_argument("-s", "--special_mode",
help="special mode (used in some benchmarks)")
"-v", "--verbose", help="turn verbosity on", action="store_true"
)
parser.add_argument(
"-o",
"--optimise",
help="minimise the parametric computation result",
action="store_true",
)
parser.add_argument(
"-n",
"--scaling-parameter",
help="scaling parameter value (used in some benchmarks)",
)
parser.add_argument(
"-s", "--special_mode", help="special mode (used in some benchmarks)"
)
args = parser.parse_args()
print_banner()
rs_testing.run_tests(args)
##################################################################
@@ -71,7 +84,8 @@ if __name__ == "__main__":
try:
if profiling:
import profile
profile.run('main()')
profile.run("main()")
else:
main()
except KeyboardInterrupt:

8
reactics-smt/scripts/avg.py
View File

@@ -5,7 +5,6 @@ from os import listdir
def proc_files(files):
fs = []
for f in files:
try:
@@ -17,7 +16,6 @@ def proc_files(files):
done = False
result = []
while not done:
index = "NONE"
val_sum = 0
@@ -30,7 +28,7 @@ def proc_files(files):
sline = line.split()
assert(len(sline) == 2)
assert len(sline) == 2
index, value = sline
value = float(value)
@@ -40,7 +38,7 @@ def proc_files(files):
# print(sline)
else:
val_avg = val_sum/len(fs)
val_avg = val_sum / len(fs)
result.append("{:s}\t{:f}".format(index, val_avg))
result.append("")
@@ -48,7 +46,6 @@ def proc_files(files):
def proc_dirs(dirs):
first_dir = dirs[0]
for f in listdir(first_dir):
@@ -59,7 +56,6 @@ def proc_dirs(dirs):
def main():
proc_dirs(sys.argv[1:])
# proc_files(sys.argv[1:])

2
reactics-smt/smt/__init__.py
View File

@@ -1,4 +1,4 @@
#from smt.smt_checker import SmtChecker
# from smt.smt_checker import SmtChecker
from smt.smt_checker_rs import SmtCheckerRS
from smt.smt_checker_rsc import SmtCheckerRSC
from smt.smt_checker_rsc_param import SmtCheckerRSCParam

74
reactics-smt/smt/smt_checker_rs.py
View File

@@ -9,9 +9,7 @@ import resource
class SmtCheckerRS(object):
def __init__(self, rsca):
rsca.sanity_check()
self.rs = rsca.rs
@@ -40,7 +38,7 @@ class SmtCheckerRS(object):
variables = []
for entity in self.rs.background_set:
variables.append(Bool("C"+str(level)+"_"+entity))
variables.append(Bool("C" + str(level) + "_" + entity))
self.v_ctx.append(variables)
@@ -51,7 +49,7 @@ class SmtCheckerRS(object):
variables = []
for entity in self.rs.background_set:
variables.append(Bool("L"+str(level)+"_"+entity))
variables.append(Bool("L" + str(level) + "_" + entity))
self.v.append(variables)
def prepare_context_controller_variables(self):
@@ -59,7 +57,7 @@ class SmtCheckerRS(object):
level = self.next_level_to_encode
self.ca_state.append(Int("CA"+str(level)+"_state"))
self.ca_state.append(Int("CA" + str(level) + "_state"))
def prepare_state_variables(self):
"""Encodes all the state variables"""
@@ -84,8 +82,12 @@ class SmtCheckerRS(object):
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
@@ -102,14 +104,23 @@ class SmtCheckerRS(object):
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)))
Or(enc_rct_prod, And(enc_reactants, enc_inhibitors))
)
return enc_rct_prod
@@ -120,17 +131,15 @@ class SmtCheckerRS(object):
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])))
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"""
@@ -143,20 +152,19 @@ class SmtCheckerRS(object):
unused_entities.remove(prod_entity)
enc_trans = simplify(
And(enc_trans, self.enc_entity_production(level, prod_entity)))
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_enc = self.ca_state[level] == src
dst_enc = self.ca_state[level+1] == dst
dst_enc = self.ca_state[level + 1] == dst
all_ent = set(range(len(self.rs.background_set)))
incl_ctx = ctx
@@ -179,7 +187,8 @@ class SmtCheckerRS(object):
enc_trans = False
for transition in self.ca.transitions:
enc_trans = simplify(
Or(enc_trans, self.enc_automaton_single_trans(level, transition)))
Or(enc_trans, self.enc_automaton_single_trans(level, transition))
)
return enc_trans
@@ -231,14 +240,12 @@ class SmtCheckerRS(object):
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):
for level in range(max_level + 1):
print("\n[Level=" + repr(level) + "]")
print(" State: {", end=""),
@@ -256,7 +263,8 @@ class SmtCheckerRS(object):
print(" }")
def check_reachability(
self, state, print_witness=True, print_time=True, print_mem=True):
self, state, print_witness=True, print_time=True, print_mem=True
):
"""Main testing function"""
if not type(state) is tuple:
@@ -299,16 +307,18 @@ class SmtCheckerRS(object):
if print_time:
# stop = time()
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.verification_time = stop-start
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")
"[i] Memory: "
+ repr(
resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / (1024 * 1024)
)
+ " MB"
)
def get_verification_time(self):
return self.verification_time

372
reactics-smt/smt/smt_checker_rsc.py
View File

@@ -16,9 +16,7 @@ from logics import rsLTL_Encoder
class SmtCheckerRSC(object):
def __init__(self, rsca):
rsca.sanity_check()
if not rsca.is_with_concentrations():
@@ -62,7 +60,7 @@ class SmtCheckerRSC(object):
variables = []
for entity in self.rs.background_set:
variables.append(Int("C"+str(level)+"_"+entity))
variables.append(Int("C" + str(level) + "_" + entity))
self.v_ctx.append(variables)
@@ -73,10 +71,10 @@ class SmtCheckerRSC(object):
variables = []
for entity in self.rs.background_set:
variables.append(Int("L"+str(level)+"_"+entity))
variables.append(Int("L" + str(level) + "_" + entity))
self.v.append(variables)
self.ca_state.append(Int("CA"+str(level)+"_state"))
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
@@ -92,7 +90,8 @@ class SmtCheckerRSC(object):
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))
And(enc_nz, v >= 0, v_ctx >= 0, v <= e_max, v_ctx <= e_max)
)
return enc_nz
@@ -116,8 +115,7 @@ class SmtCheckerRSC(object):
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]
rcts_for_prod_entity = self.rs.get_reactions_by_product()[prod_entity]
meta_reactions = []
if prod_entity in self.rs.meta_reactions:
@@ -129,7 +127,7 @@ class SmtCheckerRSC(object):
if rcts_for_prod_entity == [] and meta_reactions == []:
# this should never happen
return simplify(self.v[level+1][prod_entity] == 0)
return simplify(self.v[level + 1][prod_entity] == 0)
enc_enabledness = False
@@ -140,30 +138,42 @@ class SmtCheckerRSC(object):
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_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_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_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))
Or(enc_ordinary_reactions_enabledness, enc_rct_enabled)
)
# -------- 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
@@ -171,100 +181,127 @@ class SmtCheckerRSC(object):
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)))
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)))
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)))
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],
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_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
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],
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)
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))
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
enc_meta_reaction_enabledness = And(
enc_reactants, enc_inhibitors,
Not(enc_ordinary_reactions_enabledness))
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)))
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_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_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 + 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]))
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_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))
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_transition_relation(self, level):
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"""
@@ -279,11 +316,11 @@ class SmtCheckerRSC(object):
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)))
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))
enc_trans = simplify(And(enc_trans, self.v[level + 1][prod_entity] == 0))
return enc_trans
@@ -294,7 +331,7 @@ class SmtCheckerRSC(object):
for src, ctx, dst in self.ca.transitions:
src_enc = self.ca_state[level] == src
dst_enc = self.ca_state[level+1] == dst
dst_enc = self.ca_state[level + 1] == dst
all_ent = set(range(len(self.rs.background_set)))
@@ -346,14 +383,12 @@ class SmtCheckerRSC(object):
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):
for level in range(max_level + 1):
print("\n{: >70}".format("[ level=" + repr(level) + " ]"))
print(" State: {", end=""),
@@ -361,11 +396,10 @@ class SmtCheckerRSC(object):
var_rep = repr(m[self.v[level][var_id]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
"unexpected: representation is not a positive integer"
)
if int(var_rep) > 0:
print(
" " + self.rs.get_entity_name(var_id) + "=" + var_rep,
end="")
print(" " + self.rs.get_entity_name(var_id) + "=" + var_rep, end="")
# print(" " + repr(m[self.v[level][var_id]]), end="")
print(" }")
@@ -376,22 +410,28 @@ class SmtCheckerRSC(object):
var_rep = repr(m[self.v_ctx[level][var_id]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
"unexpected: representation is not a positive integer"
)
if int(var_rep) > 0:
print(
" " + self.rs.get_entity_name(var_id) + "=" + var_rep,
end="")
end="",
)
print(" }")
def check_rsltl(
self, formula, print_witness=True, print_time=True, print_mem=True,
max_level=None):
self,
formula,
print_witness=True,
print_time=True,
print_mem=True,
max_level=None,
):
"""Bounded Model Checking for rsLTL properties"""
self.reset()
print("[" + colour_str(C_BOLD, "i") +
"] Running rsLTL bounded model checking")
print("[" + colour_str(C_BOLD, "i") + "] Running rsLTL bounded model checking")
print("[" + colour_str(C_BOLD, "i") + "] Formula: " + str(formula))
if print_time:
@@ -408,48 +448,61 @@ class SmtCheckerRSC(object):
encoder = rsLTL_Encoder(self)
encoder.load_variables(
var_rs=self.v,
var_ctx=self.v_ctx,
var_loop_pos=self.loop_position)
var_rs=self.v, var_ctx=self.v_ctx, var_loop_pos=self.loop_position
)
while True:
self.prepare_all_variables()
self.solver.add(
self.enc_concentration_levels_assertion(
self.current_level + 1))
self.enc_concentration_levels_assertion(self.current_level + 1)
)
print(
"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
"\n{:-^70}".format(
"[ Working at level=" + str(self.current_level) + " ]"
)
)
stdout.flush()
# reachability test:
self.solver.push()
print("[" + colour_str(C_BOLD, "i") +
"] Generating the formula encoding...")
print(
"[" + colour_str(C_BOLD, "i") + "] Generating the formula encoding..."
)
f = encoder.get_encoding(formula, self.current_level)
ncalls = encoder.get_ncalls()
print("[" + colour_str(C_BOLD, "i") + "] Cache hits: " +
str(encoder.get_cache_hits()) + ", encode calls: " +
str(ncalls[0]) + " (approx: " + str(ncalls[1]) + ")")
print("[" + colour_str(C_BOLD, "i") +
"] Adding the formula to the solver...")
print(
"["
+ colour_str(C_BOLD, "i")
+ "] Cache hits: "
+ str(encoder.get_cache_hits())
+ ", encode calls: "
+ str(ncalls[0])
+ " (approx: "
+ str(ncalls[1])
+ ")"
)
print(
"[" + colour_str(C_BOLD, "i") + "] Adding the formula to the solver..."
)
encoder.flush_cache()
self.solver.add(f)
print("[" + colour_str(C_BOLD, "i") +
"] Adding the loops encoding...")
print("[" + colour_str(C_BOLD, "i") + "] Adding the loops encoding...")
self.solver.add(self.get_loop_encodings())
result = self.solver.check()
if result == sat:
print(
"[" + colour_str(C_BOLD, "+") + "] " +
colour_str(
C_GREEN, "SAT at level=" + str(self.current_level)))
"["
+ colour_str(C_BOLD, "+")
+ "] "
+ colour_str(C_GREEN, "SAT at level=" + str(self.current_level))
)
if print_witness:
print("\n{:=^70}".format("[ WITNESS ]"))
self.decode_witness(self.current_level)
@@ -457,12 +510,10 @@ class SmtCheckerRSC(object):
else:
self.solver.pop()
print("[" + colour_str(C_BOLD, "i") +
"] Unrolling the transition relation")
print("[" + colour_str(C_BOLD, "i") + "] Unrolling the transition relation")
self.solver.add(self.enc_transition_relation(self.current_level))
print(
"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
print("{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
self.current_level += 1
if not max_level is None and self.current_level > max_level:
@@ -472,25 +523,29 @@ class SmtCheckerRSC(object):
if print_time:
# stop = time()
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.verification_time = stop-start
self.verification_time = stop - start
print()
print(
"\n[i] {: >60}".format(
" Time: " + repr(self.verification_time) + " s"))
"\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"))
" Memory: "
+ repr(
resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
/ (1024 * 1024)
)
+ " MB"
)
)
def dummy_unroll(self, levels):
"""Unrolls the variables for testing purposes"""
self.current_level = -1
for i in range(levels+1):
for i in range(levels + 1):
self.prepare_all_variables()
self.current_level += 1
@@ -511,7 +566,6 @@ class SmtCheckerRSC(object):
return eq_enc
def get_loop_encodings(self):
k = self.current_level
loop_var = self.loop_position
@@ -523,14 +577,16 @@ class SmtCheckerRSC(object):
Therefore, the encoding starts at 1, not at 0.
"""
for i in range(1, k+1):
loop_enc = simplify(And(loop_enc, Implies(
loop_var == i, self.state_equality(i-1, k))))
for i in range(1, k + 1):
loop_enc = simplify(
And(loop_enc, Implies(loop_var == i, self.state_equality(i - 1, k)))
)
return loop_enc
def check_reachability(self, state, print_witness=True,
print_time=True, print_mem=True, max_level=1000):
def check_reachability(
self, state, print_witness=True, print_time=True, print_mem=True, max_level=1000
):
"""Main testing function"""
self.reset()
@@ -550,27 +606,30 @@ class SmtCheckerRSC(object):
while True:
self.prepare_all_variables()
self.solver.add(
self.enc_concentration_levels_assertion(
self.current_level + 1))
self.enc_concentration_levels_assertion(self.current_level + 1)
)
print(
"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
"\n{:-^70}".format(
"[ Working at level=" + str(self.current_level) + " ]"
)
)
stdout.flush()
# reachability test:
print("[" + colour_str(C_BOLD, "i") +
"] Adding the reachability test...")
print("[" + colour_str(C_BOLD, "i") + "] Adding the reachability test...")
self.solver.push()
self.solver.add(self.enc_state_with_blocking(
self.current_level, state))
self.solver.add(self.enc_state_with_blocking(self.current_level, state))
result = self.solver.check()
if result == sat:
print(
"[" + colour_str(C_BOLD, "+") + "] " +
colour_str(
C_GREEN, "SAT at level=" + str(self.current_level)))
"["
+ colour_str(C_BOLD, "+")
+ "] "
+ colour_str(C_GREEN, "SAT at level=" + str(self.current_level))
)
if print_witness:
print("\n{:=^70}".format("[ WITNESS ]"))
self.decode_witness(self.current_level)
@@ -578,12 +637,10 @@ class SmtCheckerRSC(object):
else:
self.solver.pop()
print("[" + colour_str(C_BOLD, "i") +
"] Unrolling the transition relation")
print("[" + colour_str(C_BOLD, "i") + "] Unrolling the transition relation")
self.solver.add(self.enc_transition_relation(self.current_level))
print(
"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
print("{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
self.current_level += 1
if self.current_level > max_level:
@@ -593,25 +650,35 @@ class SmtCheckerRSC(object):
if print_time:
# stop = time()
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.verification_time = stop-start
self.verification_time = stop - start
print()
print(
"\n[i] {: >60}".format(
" Time: " + repr(self.verification_time) + " s"))
"\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"))
" 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):
def show_encoding(
self,
state,
print_witness=True,
print_time=False,
print_mem=False,
max_level=100,
):
"""Encoding debug function"""
self.reset()
@@ -627,8 +694,7 @@ class SmtCheckerRSC(object):
while True:
self.prepare_all_variables()
print(
"-----[ Working at level=" + str(self.current_level) + " ]-----")
print("-----[ Working at level=" + str(self.current_level) + " ]-----")
stdout.flush()
# reachability test:
@@ -643,9 +709,9 @@ class SmtCheckerRSC(object):
result = self.solver.check()
if result == sat:
print(
"\n[+] " +
colour_str(
C_RED, "SAT at level=" + str(self.current_level)))
"\n[+] "
+ colour_str(C_RED, "SAT at level=" + str(self.current_level))
)
if print_witness:
self.decode_witness(self.current_level)
break

419
reactics-smt/smt/smt_checker_rsc_param.py
View File

@@ -23,14 +23,13 @@ def z3_max(a, b):
class SmtCheckerRSCParam(object):
def __init__(self, rsca, optimise=False):
rsca.sanity_check()
if not rsca.is_concentr_and_param_compatible():
raise RuntimeError(
"RS and CA with concentrations (and parameters) expected")
"RS and CA with concentrations (and parameters) expected"
)
self.rs = rsca.rs
self.ca = rsca.ca
@@ -92,7 +91,6 @@ class SmtCheckerRSCParam(object):
self.initialise()
def prepare_all_variables(self, num_of_paths):
for path_idx in range(num_of_paths):
self.prepare_all_path_variables(path_idx)
self.next_level_to_encode += 1
@@ -100,8 +98,11 @@ class SmtCheckerRSCParam(object):
def prepare_all_path_variables(self, path_idx):
"""Prepares the variables for a given path index"""
print_info("Preparing variables for path={:d} (level={:d})".format(
path_idx, self.next_level_to_encode))
print_info(
"Preparing variables for path={:d} (level={:d})".format(
path_idx, self.next_level_to_encode
)
)
self.prepare_state_variables(path_idx)
self.prepare_context_variables(path_idx)
@@ -111,8 +112,7 @@ class SmtCheckerRSCParam(object):
def prepare_loop_position_variables(self, path_idx):
"""Prepares the variables for loop positions"""
self.path_loop_position[path_idx] = Int(
"p{:d}_loop_pos".format(path_idx))
self.path_loop_position[path_idx] = Int("p{:d}_loop_pos".format(path_idx))
def prepare_context_variables(self, path_idx):
"""Prepares all the context variables"""
@@ -188,22 +188,26 @@ class SmtCheckerRSCParam(object):
entities_dict = dict()
if is_param(products):
for entity in self.rs.set_of_bgset_ids:
entity_name = self.rs.get_entity_name(entity)
new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(
path_idx, level, reaction_id, entity_name))
new_var = Int(
"p{:d}L{:d}_ImProd_r{:d}_{:s}".format(
path_idx, level, reaction_id, entity_name
)
)
entities_dict[entity] = new_var
all_entities_dict.setdefault(entity, [])
all_entities_dict[entity].append(new_var)
else:
for entity, conc in products:
entity_name = self.rs.get_entity_name(entity)
new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(
path_idx, level, reaction_id, entity_name))
new_var = Int(
"p{:d}L{:d}_ImProd_r{:d}_{:s}".format(
path_idx, level, reaction_id, entity_name
)
)
entities_dict[entity] = new_var
all_entities_dict.setdefault(entity, [])
@@ -224,14 +228,13 @@ class SmtCheckerRSCParam(object):
"""
for param_name in self.rs.parameters.keys():
# we start collecting bg-related vars for the given param
vars_for_param = []
for entity in self.rs.ordered_list_of_bgset_ids:
new_var = Int(
"Pm{:s}_{:s}".format(
param_name, self.rs.get_entity_name(entity)))
"Pm{:s}_{:s}".format(param_name, self.rs.get_entity_name(entity))
)
vars_for_param.append(new_var)
self.v_param[param_name] = vars_for_param
@@ -266,23 +269,17 @@ class SmtCheckerRSCParam(object):
enc_non_empty = True
for param_vars in self.v_param.values():
enc_param_at_least_one = False
for pvar in param_vars:
# TODO: fixed upper limit: 100 (have a per-param setting for that)
enc_param_gz = simplify(
And(enc_param_gz, pvar >= 0, pvar < 100))
enc_param_at_least_one = simplify(
Or(enc_param_at_least_one, pvar > 0))
enc_param_gz = simplify(And(enc_param_gz, pvar >= 0, pvar < 100))
enc_param_at_least_one = simplify(Or(enc_param_at_least_one, pvar > 0))
enc_non_empty = simplify(
And(enc_non_empty, enc_param_at_least_one))
enc_non_empty = simplify(And(enc_non_empty, enc_param_at_least_one))
return simplify(And(enc_param_gz, enc_non_empty))
def assert_param_optimisation(self):
for param_vars in self.v_param.values():
for pvar in param_vars:
# self.solver.add_soft(pvar == 0)
@@ -296,8 +293,11 @@ class SmtCheckerRSCParam(object):
only those that can possibly go below 0.
"""
print_info("Concentration level assertions for path={:d} (level={:d})".format(
path_idx, level))
print_info(
"Concentration level assertions for path={:d} (level={:d})".format(
path_idx, level
)
)
enc_gz = True
@@ -305,15 +305,14 @@ class SmtCheckerRSCParam(object):
var = self.path_v[path_idx][level][e_i]
var_ctx = self.path_v_ctx[path_idx][level][e_i]
e_max = self.rs.get_max_concentration_level(e_i)
enc_gz = simplify(And(enc_gz, var >= 0, var_ctx >=
0, var <= e_max, var_ctx <= e_max))
enc_gz = simplify(
And(enc_gz, var >= 0, var_ctx >= 0, var <= e_max, var_ctx <= e_max)
)
vars_per_reaction = self.path_v_improd_for_entities[path_idx][
level + 1]
vars_per_reaction = self.path_v_improd_for_entities[path_idx][level + 1]
if e_i in vars_per_reaction:
for var_improd in vars_per_reaction[e_i]:
enc_gz = simplify(
And(enc_gz, var_improd >= 0, var_improd <= e_max))
enc_gz = simplify(And(enc_gz, var_improd >= 0, var_improd <= e_max))
return enc_gz
@@ -326,7 +325,8 @@ class SmtCheckerRSCParam(object):
# the initial concentration levels are zeroed
rs_init_state_enc = simplify(And(rs_init_state_enc, v == 0))
ca_init_state_enc = self.path_ca_state[path_idx][level] == self.ca.get_init_state_id(
ca_init_state_enc = (
self.path_ca_state[path_idx][level] == self.ca.get_init_state_id()
)
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
@@ -335,8 +335,11 @@ class SmtCheckerRSCParam(object):
def enc_transition_relation(self, level, path_idx):
return simplify(
And(self.enc_rs_trans(level, path_idx),
self.enc_automaton_trans(level, path_idx)))
And(
self.enc_rs_trans(level, path_idx),
self.enc_automaton_trans(level, path_idx),
)
)
def enc_param_sanity_for_reactions(self):
"""R < I constraint (R n I = 0)"""
@@ -344,23 +347,21 @@ class SmtCheckerRSCParam(object):
rct_inh_constr = True
for reactants, inhibitors, products in self.rs.reactions:
if is_param(reactants) or is_param(inhibitors):
# 1. R and I
if is_param(reactants) and is_param(inhibitors):
rct_param_name = reactants.name
inh_param_name = inhibitors.name
for entity in self.rs.set_of_bgset_ids:
rct_inh_constr = And(rct_inh_constr,
Implies(
self.v_param
[inh_param_name][entity] > 0,
self.v_param
[rct_param_name][entity] <
self.v_param
[inh_param_name][entity]))
rct_inh_constr = And(
rct_inh_constr,
Implies(
self.v_param[inh_param_name][entity] > 0,
self.v_param[rct_param_name][entity]
< self.v_param[inh_param_name][entity],
),
)
elif (not is_param(reactants)) and is_param(inhibitors):
inh_param_name = inhibitors.name
@@ -370,8 +371,10 @@ class SmtCheckerRSCParam(object):
rct_inh_constr = And(
rct_inh_constr,
Implies(
self.v_param[inh_param_name][entity] > 0, conc <
self.v_param[inh_param_name][entity]))
self.v_param[inh_param_name][entity] > 0,
conc < self.v_param[inh_param_name][entity],
),
)
elif is_param(reactants) and (not is_param(inhibitors)):
rct_param_name = reactants.name
@@ -379,7 +382,8 @@ class SmtCheckerRSCParam(object):
for entity, conc in inhibitors:
assert conc > 0, "Unexpected concentration level!"
rct_inh_constr = And(
rct_inh_constr, self.v_param[rct_param_name][entity] < conc)
rct_inh_constr, self.v_param[rct_param_name][entity] < conc
)
return rct_inh_constr
@@ -405,31 +409,52 @@ class SmtCheckerRSCParam(object):
if is_param(reactants):
param_name = reactants.name
for entity in self.rs.set_of_bgset_ids:
enc_reactants = And(enc_reactants, Or(
self.v_param[param_name][entity] == 0,
self.path_v[path_idx][level][entity] >= self.v_param[param_name][entity],
self.path_v_ctx[path_idx][level][entity] >= self.v_param[param_name][entity]))
enc_reactants = And(
enc_reactants,
Or(
self.v_param[param_name][entity] == 0,
self.path_v[path_idx][level][entity]
>= self.v_param[param_name][entity],
self.path_v_ctx[path_idx][level][entity]
>= self.v_param[param_name][entity],
),
)
else:
for entity, conc in reactants:
enc_reactants = And(enc_reactants, Or(
self.path_v[path_idx][level][entity] >= conc,
self.path_v_ctx[path_idx][level][entity] >= conc))
enc_reactants = And(
enc_reactants,
Or(
self.path_v[path_idx][level][entity] >= conc,
self.path_v_ctx[path_idx][level][entity] >= conc,
),
)
# ** INHIBITORS ******************************************
enc_inhibitors = True
if is_param(inhibitors):
param_name = inhibitors.name
for entity in self.rs.set_of_bgset_ids:
enc_inhibitors = And(enc_inhibitors, Or(
self.v_param[param_name][entity] == 0,
And(
self.path_v[path_idx][level][entity] < self.v_param[param_name][entity],
self.path_v_ctx[path_idx][level][entity] < self.v_param[param_name][entity])))
enc_inhibitors = And(
enc_inhibitors,
Or(
self.v_param[param_name][entity] == 0,
And(
self.path_v[path_idx][level][entity]
< self.v_param[param_name][entity],
self.path_v_ctx[path_idx][level][entity]
< self.v_param[param_name][entity],
),
),
)
else:
for entity, conc in inhibitors:
enc_inhibitors = And(enc_inhibitors, And(
self.path_v[path_idx][level][entity] < conc,
self.path_v_ctx[path_idx][level][entity] < conc))
enc_inhibitors = And(
enc_inhibitors,
And(
self.path_v[path_idx][level][entity] < conc,
self.path_v_ctx[path_idx][level][entity] < conc,
),
)
# ** PRODUCTS *******************************************
enc_products = True
@@ -438,26 +463,38 @@ class SmtCheckerRSCParam(object):
for entity in self.rs.set_of_bgset_ids:
enc_products = simplify(
And(
enc_products, self.
path_v_improd[path_idx]
[level + 1][reaction_id]
[entity] == self.v_param
[param_name][entity]))
enc_products,
self.path_v_improd[path_idx][level + 1][reaction_id][entity]
== self.v_param[param_name][entity],
)
)
else:
for entity, conc in products:
enc_products = simplify(And(
enc_products, self.path_v_improd[path_idx][level + 1][reaction_id][entity] == conc))
enc_products = simplify(
And(
enc_products,
self.path_v_improd[path_idx][level + 1][reaction_id][entity]
== conc,
)
)
# Nothing is produced (when the reaction is disabled)
enc_no_prod = True
if is_param(products):
for entity in self.rs.set_of_bgset_ids:
enc_no_prod = And(
enc_no_prod, self.path_v_improd[path_idx][level + 1][reaction_id][entity] == 0)
enc_no_prod,
self.path_v_improd[path_idx][level + 1][reaction_id][entity] == 0,
)
else:
for entity, _ in products:
enc_no_prod = simplify(And(
enc_no_prod, self.path_v_improd[path_idx][level + 1][reaction_id][entity] == 0))
enc_no_prod = simplify(
And(
enc_no_prod,
self.path_v_improd[path_idx][level + 1][reaction_id][entity]
== 0,
)
)
#
# (R and I) iff P
@@ -467,8 +504,7 @@ class SmtCheckerRSCParam(object):
#
# ~(R and I) iff P_zero
#
enc_not_enabled = Not(
And(enc_reactants, enc_inhibitors)) == enc_no_prod
enc_not_enabled = Not(And(enc_reactants, enc_inhibitors)) == enc_no_prod
enc_reaction = And(enc_enabled, enc_not_enabled)
@@ -491,7 +527,12 @@ class SmtCheckerRSCParam(object):
enc_cond = False
for entity in self.rs.set_of_bgset_ids:
enc_cond = simplify(
Or(enc_cond, self.path_v[path_idx][level][entity] > 0, self.path_v_ctx[path_idx][level][entity] > 0))
Or(
enc_cond,
self.path_v[path_idx][level][entity] > 0,
self.path_v_ctx[path_idx][level][entity] > 0,
)
)
return enc_cond
@@ -533,25 +574,29 @@ class SmtCheckerRSCParam(object):
# =>
# {products}[level+1]
#
current_v_improd_for_entities = self.path_v_improd_for_entities[path_idx][level + 1]
current_v_improd_for_entities = self.path_v_improd_for_entities[path_idx][
level + 1
]
for entity in self.rs.set_of_bgset_ids:
per_reaction_vars = current_v_improd_for_entities.get(entity, [])
enc_max_prod = simplify(And(
enc_max_prod, self.path_v[path_idx][level + 1][entity] == self.enc_max(per_reaction_vars)))
enc_max_prod = simplify(
And(
enc_max_prod,
self.path_v[path_idx][level + 1][entity]
== self.enc_max(per_reaction_vars),
)
)
# make sure at least one entity is >0
enc_general_cond = self.enc_general_reaction_enabledness(
level, path_idx)
enc_general_cond = self.enc_general_reaction_enabledness(level, path_idx)
enc_trans_with_max = simplify(
And(enc_general_cond, enc_max_prod, enc_trans))
enc_trans_with_max = simplify(And(enc_general_cond, enc_max_prod, enc_trans))
# print(enc_trans_with_max)
return enc_trans_with_max
def enc_max(self, elements):
enc = None
if elements == []:
@@ -561,7 +606,6 @@ class SmtCheckerRSCParam(object):
enc = z3_max(0, elements[0])
elif len(elements) > 1:
enc = 0
for i in range(len(elements) - 1):
enc = z3_max(enc, z3_max(elements[i], elements[i + 1]))
@@ -575,7 +619,7 @@ class SmtCheckerRSCParam(object):
for src, ctx, dst in self.ca.transitions:
src_enc = self.path_ca_state[path_idx][level] == src
dst_enc = self.path_ca_state[path_idx][level+1] == dst
dst_enc = self.path_ca_state[path_idx][level + 1] == dst
all_ent = set(range(len(self.rs.background_set)))
@@ -586,11 +630,13 @@ class SmtCheckerRSCParam(object):
for e, c in ctx:
ctx_enc = simplify(
And(ctx_enc, self.path_v_ctx[path_idx][level][e] == c))
And(ctx_enc, self.path_v_ctx[path_idx][level][e] == c)
)
for e in excl_ctx:
ctx_enc = simplify(
And(ctx_enc, self.path_v_ctx[path_idx][level][e] == 0))
And(ctx_enc, self.path_v_ctx[path_idx][level][e] == 0)
)
cur_trans = simplify(And(src_enc, ctx_enc, dst_enc))
enc_trans = simplify(Or(enc_trans, cur_trans))
@@ -641,7 +687,6 @@ class SmtCheckerRSCParam(object):
print(m)
for level in range(max_level + 1):
print("\n{: >70}".format("[ level=" + repr(level) + " ]"))
print(" State: {", end=""),
@@ -649,11 +694,10 @@ class SmtCheckerRSCParam(object):
var_rep = repr(m[self.path_v[path_idx][level][var_id]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
"unexpected: representation is not a positive integer"
)
if int(var_rep) > 0:
print(
" " + self.rs.get_entity_name(var_id) + "=" + var_rep,
end="")
print(" " + self.rs.get_entity_name(var_id) + "=" + var_rep, end="")
print(" }")
if level != max_level:
@@ -663,11 +707,13 @@ class SmtCheckerRSCParam(object):
var_rep = repr(m[self.path_v_ctx[path_idx][level][var_id]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
"unexpected: representation is not a positive integer"
)
if int(var_rep) > 0:
print(
" " + self.rs.get_entity_name(var_id) + "=" + var_rep,
end="")
end="",
)
print(" }")
print()
@@ -675,29 +721,34 @@ class SmtCheckerRSCParam(object):
def get_enc_formulae(self, encoder, formulae_list):
enc_form = []
for formula in formulae_list:
path_idx = formulae_list.index(formula)
print_info("Generating the encoding for {:s} ({:d} of {:d})".format(
str(formula), path_idx+1, len(formulae_list)))
print_info(
"Generating the encoding for {:s} ({:d} of {:d})".format(
str(formula), path_idx + 1, len(formulae_list)
)
)
encoder.load_variables(
var_rs=self.path_v[path_idx],
var_ctx=self.path_v_ctx[path_idx],
var_loop_pos=self.path_loop_position[path_idx])
var_loop_pos=self.path_loop_position[path_idx],
)
enc_form.append(encoder.get_encoding(formula, self.current_level))
ncalls = encoder.get_ncalls()
print_info("Cache hits: {:d}, encode calls: {:d} (approx: {:d})".format(
encoder.get_cache_hits(), ncalls[0], ncalls[1]))
print_info(
"Cache hits: {:d}, encode calls: {:d} (approx: {:d})".format(
encoder.get_cache_hits(), ncalls[0], ncalls[1]
)
)
encoder.flush_cache()
return enc_form
def print_witness(self, formulae_list):
for formula in formulae_list:
path_idx = formulae_list.index(formula)
print("\n{:=^70}".format("[ WITNESS ]"))
@@ -707,7 +758,6 @@ class SmtCheckerRSCParam(object):
self.print_parameter_valuations()
def print_parameter_valuations(self):
m = self.solver.model()
print("\n Parameters:\n")
@@ -721,25 +771,24 @@ class SmtCheckerRSCParam(object):
var_rep = repr(m[params[entity]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
"unexpected: representation is not a positive integer"
)
if int(var_rep) > 0:
print(
" " + str(self.rs.get_entity_name(entity)) + "=" +
str(var_rep),
end="")
" " + str(self.rs.get_entity_name(entity)) + "=" + str(var_rep),
end="",
)
print(" }")
print()
def enc_concentration_levels_assertions_for_paths(
self, level, num_of_paths):
def enc_concentration_levels_assertions_for_paths(self, level, num_of_paths):
additional_assertions = []
for path_idx in range(num_of_paths):
additional_assertions.append(
self.enc_concentration_levels_assertion(level, path_idx))
additional_assertions.append(
self.enc_param_concentration_levels_assertion())
self.enc_concentration_levels_assertion(level, path_idx)
)
additional_assertions.append(self.enc_param_concentration_levels_assertion())
return additional_assertions
@@ -750,22 +799,25 @@ class SmtCheckerRSCParam(object):
return enc_trans
def print_level(self):
print(
"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
print("{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
def check_rsltl(
self, formulae_list,
print_witness=True,
print_time=True, print_mem=True,
max_level=None, cont_if_sat=False,
param_constr=None):
self,
formulae_list,
print_witness=True,
print_time=True,
print_mem=True,
max_level=None,
cont_if_sat=False,
param_constr=None,
):
"""
Bounded Model Checking for rsLTL properties
* print_witness -- prints the decoded witness
* print_time -- prints the time consumed
* print_mem -- prints the memory consumed
* max_level -- if not None, the methods
* max_level -- if not None, the methods
stops at the specified level
* cont_if_sat -- if True, then the method
continues up until max_level is
@@ -783,7 +835,7 @@ class SmtCheckerRSCParam(object):
print_info("Running rsLTL bounded model checking")
print_info("Tested formulae:")
for form in formulae_list:
print_info(" "*4 + str(form))
print_info(" " * 4 + str(form))
print_info("INITIALISING...")
@@ -804,8 +856,8 @@ class SmtCheckerRSCParam(object):
# assertions for all the paths and parameters
self.solver_add(
self.enc_concentration_levels_assertions_for_paths(
0, num_of_paths))
self.enc_concentration_levels_assertions_for_paths(0, num_of_paths)
)
self.solver_add(self.enc_param_concentration_levels_assertion())
self.solver_add(self.enc_param_sanity_for_reactions())
@@ -822,9 +874,11 @@ class SmtCheckerRSCParam(object):
print_info("STARTING TO ITERATE...")
while True:
print(
"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
"\n{:-^70}".format(
"[ Working at level=" + str(self.current_level) + " ]"
)
)
# reachability test:
self.solver.push()
@@ -841,8 +895,9 @@ class SmtCheckerRSCParam(object):
print_info("Testing satisfiability...")
result = self.solver.check()
if result == sat:
print_positive(green_str(
"SAT at level={:d}".format(self.current_level)))
print_positive(
green_str("SAT at level={:d}".format(self.current_level))
)
# print(self.solver.model())
if print_witness:
self.print_witness(formulae_list)
@@ -861,11 +916,14 @@ class SmtCheckerRSCParam(object):
# assertions for all the paths
self.solver_add(
self.enc_concentration_levels_assertions_for_paths(
self.current_level + 1, num_of_paths))
self.current_level + 1, num_of_paths
)
)
print_info("Unrolling the transition relation")
self.solver_add(self.enc_transition_relation_for_paths(
self.current_level, num_of_paths))
self.solver_add(
self.enc_transition_relation_for_paths(self.current_level, num_of_paths)
)
self.print_level()
@@ -880,22 +938,24 @@ class SmtCheckerRSCParam(object):
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.verification_time = stop - start
print()
print_info("{: >60}".format(
" Time: " + repr(self.verification_time) + " s"))
print_info("{: >60}".format(" Time: " + repr(self.verification_time) + " s"))
def print_mem(self):
print_info(
"{: >60}".format(
" Memory: " +
repr(
resource.getrusage(resource.RUSAGE_SELF).ru_maxrss /
(1024 * 1024)) + " MB"))
" Memory: "
+ repr(
resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / (1024 * 1024)
)
+ " MB"
)
)
def dummy_unroll(self, levels):
"""Unrolls the variables for testing purposes"""
self.current_level = -1
for i in range(levels+1):
for i in range(levels + 1):
self.prepare_all_variables()
self.current_level += 1
@@ -916,7 +976,6 @@ class SmtCheckerRSCParam(object):
return eq_enc
def get_loop_encodings(self):
k = self.current_level
loop_var = self.loop_position
@@ -928,9 +987,10 @@ class SmtCheckerRSCParam(object):
Therefore, the encoding starts at 1, not at 0.
"""
for i in range(1, k+1):
loop_enc = simplify(And(loop_enc, Implies(
loop_var == i, self.state_equality(i-1, k))))
for i in range(1, k + 1):
loop_enc = simplify(
And(loop_enc, Implies(loop_var == i, self.state_equality(i - 1, k)))
)
return loop_enc
@@ -947,8 +1007,9 @@ class SmtCheckerRSCParam(object):
self.solver.add(expression)
def check_reachability(self, state, print_witness=True,
print_time=True, print_mem=True, max_level=1000):
def check_reachability(
self, state, print_witness=True, print_time=True, print_mem=True, max_level=1000
):
"""Main testing function"""
self.reset()
@@ -968,27 +1029,30 @@ class SmtCheckerRSCParam(object):
while True:
self.prepare_all_variables()
self.solver_add(
self.enc_concentration_levels_assertion(
self.current_level + 1))
self.enc_concentration_levels_assertion(self.current_level + 1)
)
print(
"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
"\n{:-^70}".format(
"[ Working at level=" + str(self.current_level) + " ]"
)
)
stdout.flush()
# reachability test:
print("[" + colour_str(C_BOLD, "i") +
"] Adding the reachability test...")
print("[" + colour_str(C_BOLD, "i") + "] Adding the reachability test...")
self.solver.push()
self.solver_add(self.enc_state_with_blocking(
self.current_level, state))
self.solver_add(self.enc_state_with_blocking(self.current_level, state))
result = self.solver.check()
if result == sat:
print(
"[" + colour_str(C_BOLD, "+") + "] " +
colour_str(
C_GREEN, "SAT at level=" + str(self.current_level)))
"["
+ colour_str(C_BOLD, "+")
+ "] "
+ colour_str(C_GREEN, "SAT at level=" + str(self.current_level))
)
if print_witness:
print("\n{:=^70}".format("[ WITNESS ]"))
self.decode_witness(self.current_level)
@@ -996,12 +1060,10 @@ class SmtCheckerRSCParam(object):
else:
self.solver.pop()
print("[" + colour_str(C_BOLD, "i") +
"] Unrolling the transition relation")
print("[" + colour_str(C_BOLD, "i") + "] Unrolling the transition relation")
self.solver_add(self.enc_transition_relation(self.current_level))
print(
"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
print("{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
self.current_level += 1
if self.current_level > max_level:
@@ -1011,25 +1073,35 @@ class SmtCheckerRSCParam(object):
if print_time:
# stop = time()
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.verification_time = stop-start
self.verification_time = stop - start
print()
print(
"\n[i] {: >60}".format(
" Time: " + repr(self.verification_time) + " s"))
"\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"))
" 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):
def show_encoding(
self,
state,
print_witness=True,
print_time=False,
print_mem=False,
max_level=100,
):
"""Encoding debug function"""
self.reset()
@@ -1045,8 +1117,7 @@ class SmtCheckerRSCParam(object):
while True:
self.prepare_all_variables()
print(
"-----[ Working at level=" + str(self.current_level) + " ]-----")
print("-----[ Working at level=" + str(self.current_level) + " ]-----")
stdout.flush()
# reachability test:
@@ -1061,9 +1132,9 @@ class SmtCheckerRSCParam(object):
result = self.solver.check()
if result == sat:
print(
"\n[+] " +
colour_str(
C_RED, "SAT at level=" + str(self.current_level)))
"\n[+] "
+ colour_str(C_RED, "SAT at level=" + str(self.current_level))
)
if print_witness:
self.decode_witness(self.current_level)
break