1089 lines
38 KiB
Python
1089 lines
38 KiB
Python
from rs import *
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from smt import *
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import rs_examples
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from logics import *
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from rsltl_shortcuts import *
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from itertools import chain, combinations
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import sys
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import resource
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def powerset(iterable,N=None):
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if N is None:
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N = len(s)
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s = list(iterable)
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return chain.from_iterable(combinations(s, r) for r in range(N+1))
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def run_tests(cmd_args):
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# test_extended_automaton()
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# process()
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# heat_shock_response()
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# scalable_chain(print_system=True)
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# example44()
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# example44_param()
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# heat_shock_response_param(cmd_args)
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# simple_param(cmd_args)
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# param_gene_expression(cmd_args)
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mutex_bench_main(cmd_args)
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def mutex_bench_main(cmd_args):
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if not cmd_args.special_mode:
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print("Missing special mode parameter")
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print("* 1 - parametric")
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print("* 2 - non-parametric (with parametric implementation)")
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print("* 3 - non-parametric (with non-parametric implementation)")
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return
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smode = int(cmd_args.special_mode)
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if smode == 1:
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mutex_param_bench(cmd_args)
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elif smode == 2:
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mutex_nonparam_bench(cmd_args)
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elif smode == 3:
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mutex_nonparam_bench_oldimpl(cmd_args)
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else:
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print("Unrecognised mode")
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return
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def mutex_param_bench(cmd_args):
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"""
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Mutex Benchmark
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Parametric
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"""
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base_entities = ["out","req","in","act"]
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shared_entities = ["lock","done","s"]
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if not cmd_args.scaling_parameter:
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print("Missing scaling parameter")
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return
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n_proc = int(cmd_args.scaling_parameter)
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r = ReactionSystemWithConcentrationsParam()
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def E(a,b):
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return (a + "_" + str(b), 1)
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for i in range(n_proc):
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for ent in base_entities:
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r.add_bg_set_entity(E(ent,i))
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for ent in shared_entities:
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max_conc = 2 if ent == "lock" else 1
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r.add_bg_set_entity((ent, max_conc))
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###################################################
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Inhib = [("s",1)]
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for i in range(n_proc):
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r.add_reaction([E("out",i),E("act",i)],Inhib,[E("req",i)])
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r.add_reaction([E("out",i)],[E("act",i)],[E("out",i)])
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for j in range(n_proc):
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if i != j:
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r.add_reaction([E("req",i),E("act",i),E("act",j)],Inhib,[E("req",i)])
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r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)])
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enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)]
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r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",2)])
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r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)])
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r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)])
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r.add_reaction([("lock",1)],[("done",1)],[("lock",1)])
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lda1 = r.get_param("lda1")
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lda2 = r.get_param("lda2")
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lda3 = r.get_param("lda3")
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r.add_reaction(lda1,lda2,lda3)
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###################################################
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c = ContextAutomatonWithConcentrations(r)
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c.add_init_state("0")
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c.add_state("1")
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init_ctx = []
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for i in range(n_proc):
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init_ctx.append(E("out", i))
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# the experiments starts with adding x and y:
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c.add_transition("0", init_ctx, "1")
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all_act = powerset([E("act",i) for i in range(n_proc)], 2)
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for actions in all_act:
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actions = list(actions)
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c.add_transition("1", actions, "1")
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# for all the remaining steps we have empty context sequences
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# c.add_transition("1", [], "1")
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# c.add_transition("1", [("h", 1)], "1")
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###################################################
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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f_attack = ltl_F(True, bag_And(bag_entity("in_0") == 1, bag_entity("in_" + str(n_proc-1)) == 1))
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ent_of_Nth_proc = [ent + "_" + str(n_proc-1) for ent in base_entities] + shared_entities
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disallow = ["in_" + str(n_proc-1)]
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for ent in r.background_set:
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if ent not in ent_of_Nth_proc:
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disallow.append(ent)
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# disallow = ["in_0", "in_" + str(n_proc)] #, "req_0", "req_1"]
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lda1_disallow = [param_entity(lda1, ent) == 0 for ent in disallow]
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lda2_disallow = [param_entity(lda2, ent) == 0 for ent in disallow]
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lda3_disallow = [param_entity(lda3, ent) == 0 for ent in disallow]
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lda_disallow = lda1_disallow + lda2_disallow + lda3_disallow
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# for bent in base_entities:
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# print(param_entity(lda3, bent + "_0"))
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param_constr = param_And(*lda_disallow)
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smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
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smt_rsc.check_rsltl(formulae_list=[f_attack], param_constr=param_constr) #, max_level=4, cont_if_sat=True)
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log_suffix = ""
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if cmd_args.optimise:
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log_suffix = "_OPT"
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time=0
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mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
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filename_t="bench_mutex_param" + log_suffix + "_time.dat"
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filename_m="bench_mutex_param" + log_suffix + "_mem.dat"
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time=smt_rsc.get_verification_time()
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with open(filename_t, 'a') as f:
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log_str="{:d} {:f}\n".format(n_proc, time)
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f.write(log_str)
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with open(filename_m, 'a') as f:
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log_str="{:d} {:f}\n".format(n_proc, mem_usage)
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f.write(log_str)
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def mutex_nonparam_bench(cmd_args):
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"""
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Mutex Benchmark
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Parametric
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"""
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base_entities = ["out","req","in","act"]
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shared_entities = ["lock","done","s"]
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if not cmd_args.scaling_parameter:
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raise RuntimeError("Missing scaling parameter")
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n_proc = int(cmd_args.scaling_parameter)
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r = ReactionSystemWithConcentrationsParam()
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def E(a,b):
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return (a + "_" + str(b), 1)
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for i in range(n_proc):
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for ent in base_entities:
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r.add_bg_set_entity(E(ent,i))
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for ent in shared_entities:
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r.add_bg_set_entity((ent, 1))
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###################################################
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Inhib = [("s",1)]
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for i in range(n_proc):
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r.add_reaction([E("out",i),E("act",i)],Inhib,[E("req",i)])
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r.add_reaction([E("out",i)],[E("act",i)],[E("out",i)])
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for j in range(n_proc):
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if i != j:
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r.add_reaction([E("req",i),E("act",i),E("act",j)],Inhib,[E("req",i)])
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r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)])
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enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)]
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r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",1)])
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r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)])
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r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)])
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r.add_reaction([("lock",1)],[("done",1)],[("lock",1)])
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r.add_reaction([E("out",n_proc-1)],[("s",1)],[("done",1),E("req",n_proc-1)])
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###################################################
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c = ContextAutomatonWithConcentrations(r)
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c.add_init_state("0")
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c.add_state("1")
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init_ctx = []
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for i in range(n_proc):
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init_ctx.append(E("out", i))
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# the experiments starts with adding x and y:
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c.add_transition("0", init_ctx, "1")
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all_act = powerset([E("act",i) for i in range(n_proc)], 2)
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for actions in all_act:
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actions = list(actions)
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c.add_transition("1", actions, "1")
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# for all the remaining steps we have empty context sequences
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# c.add_transition("1", [], "1")
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# c.add_transition("1", [("h", 1)], "1")
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###################################################
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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f_attack = ltl_F(True, bag_And(bag_entity("in_0") == 1, bag_entity("in_" + str(n_proc-1)) == 1))
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smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
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smt_rsc.check_rsltl(formulae_list=[f_attack])
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time=0
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mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
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filename_t="bench_mutex_nonparam_time.dat"
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filename_m="bench_mutex_nonparam_mem.dat"
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time=smt_rsc.get_verification_time()
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with open(filename_t, 'a') as f:
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log_str="{:d} {:f}\n".format(n_proc, time)
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f.write(log_str)
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with open(filename_m, 'a') as f:
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log_str="{:d} {:f}\n".format(n_proc, mem_usage)
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f.write(log_str)
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def mutex_nonparam_bench_oldimpl(cmd_args):
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"""
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Mutex Benchmark
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Parametric
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"""
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base_entities = ["out","req","in","act"]
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shared_entities = ["lock","done","s"]
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if not cmd_args.scaling_parameter:
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raise RuntimeError("Missing scaling parameter")
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n_proc = int(cmd_args.scaling_parameter)
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r = ReactionSystemWithConcentrations()
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def E(a,b):
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return (a + "_" + str(b), 1)
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for i in range(n_proc):
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for ent in base_entities:
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r.add_bg_set_entity(E(ent,i))
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for ent in shared_entities:
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r.add_bg_set_entity((ent, 1))
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###################################################
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Inhib = [("s",1)]
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for i in range(n_proc):
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r.add_reaction([E("out",i),E("act",i)],Inhib,[E("req",i)])
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r.add_reaction([E("out",i)],[E("act",i)],[E("out",i)])
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for j in range(n_proc):
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if i != j:
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r.add_reaction([E("req",i),E("act",i),E("act",j)],Inhib,[E("req",i)])
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r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)])
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enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)]
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r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",1)])
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r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)])
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r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)])
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r.add_reaction([("lock",1)],[("done",1)],[("lock",1)])
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r.add_reaction([E("out",n_proc-1)],[("s",1)],[("done",1),E("req",n_proc-1)])
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###################################################
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c = ContextAutomatonWithConcentrations(r)
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c.add_init_state("0")
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c.add_state("1")
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init_ctx = []
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for i in range(n_proc):
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init_ctx.append(E("out", i))
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# the experiments starts with adding x and y:
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c.add_transition("0", init_ctx, "1")
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all_act = powerset([E("act",i) for i in range(n_proc)], 2)
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for actions in all_act:
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actions = list(actions)
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c.add_transition("1", actions, "1")
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# for all the remaining steps we have empty context sequences
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# c.add_transition("1", [], "1")
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# c.add_transition("1", [("h", 1)], "1")
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###################################################
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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f_attack = ltl_F(True, bag_And(bag_entity("in_0") == 1, bag_entity("in_" + str(n_proc-1)) == 1))
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smt_rsc = SmtCheckerRSC(rc)
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smt_rsc.check_rsltl(formula=f_attack)
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time=0
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mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
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filename_t="bench_mutex_nonparam_oldimpl_time.dat"
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filename_m="bench_mutex_nonparam_oldimpl_mem.dat"
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time=smt_rsc.get_verification_time()
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with open(filename_t, 'a') as f:
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log_str="{:d} {:f}\n".format(n_proc, time)
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f.write(log_str)
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with open(filename_m, 'a') as f:
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log_str="{:d} {:f}\n".format(n_proc, mem_usage)
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f.write(log_str)
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def param_gene_expression(cmd_args):
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"""
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Simple gene expression example with parameters
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"""
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r = ReactionSystemWithConcentrationsParam()
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r.add_bg_set_entity(("x", 1))
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r.add_bg_set_entity(("xp", 1))
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r.add_bg_set_entity(("X", 1))
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r.add_bg_set_entity(("y", 1))
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r.add_bg_set_entity(("yp", 1))
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r.add_bg_set_entity(("Y", 1))
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r.add_bg_set_entity(("h", 1))
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r.add_bg_set_entity(("Q", 1))
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all_entities = set(r.background_set)
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lda0 = r.get_param("lda0")
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lda1 = r.get_param("lda1")
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lda2 = r.get_param("lda2")
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lda3 = r.get_param("lda3")
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r.add_reaction([("x",1)],[("h",1)],[("x",1)])
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# r.add_reaction([("x",1)],[("h",1)],[("xp",1)])
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r.add_reaction(lda0, [("h",1)],[("xp",1)])
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r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)])
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r.add_reaction([("X",1),("Y",1)],[("h",1)],[("Q",1)])
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## y
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# r.add_reaction([("y",1)],[("h",1)],[("y",1)])
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# r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
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# r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
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r.add_reaction([("y",1)],[("h",1)],lda1)
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r.add_reaction(lda2,[("h",1)],[("yp",1)])
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r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3)
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c = ContextAutomatonWithConcentrations(r)
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c.add_init_state("0")
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c.add_state("1")
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# the experiments starts with adding x and y:
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c.add_transition("0", [("y", 1),("x",1)], "1")
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# for all the remaining steps we have empty context sequences
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c.add_transition("1", [], "1")
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c.add_transition("1", [("h", 1)], "1")
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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# f_x1 = ltl_G(True, ltl_Implies(
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# exact_state(["x"], all_entities),
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# ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
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# f_x2 = ltl_G(True, ltl_Implies(
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# exact_state(["x", "xp"], all_entities),
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# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
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# reachability
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reach_y = ltl_F(bag_entity("h") == 0, "y")
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reach_yp = ltl_F(bag_entity("h") == 0, "yp")
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reach_Y = ltl_F(bag_entity("h") == 0, "Y")
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#
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phi_r = ltl_And(reach_y, reach_yp, reach_Y)
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# rules
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phi_c1 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_entity("y") > 0,
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ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0))))
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phi_c2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_And(bag_entity("y") > 0, bag_entity("yp") > 0),
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ltl_F(True, bag_entity("Y") > 0)))
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# delayed_Y = ltl_X(True, ltl_And(bag_entity("Y") == 0, ltl_X(True, bag_entity("Y") == 0)))
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# delayed_Y = ltl_X(True, bag_entity("Y") == 0)
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delayed_Q = ltl_And(bag_entity("Q") == 0, ltl_X(True, ltl_And(bag_entity("Q") == 0, ltl_X(True, ltl_And(bag_entity("Q") == 0, ltl_F(True, bag_entity("Q") > 0))))))
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obs_1 = ltl_And(phi_r, phi_c1, phi_c2, delayed_Q)
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# Observation related to A_x:
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obs_2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_entity("x") > 0,
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ltl_X(True, bag_And(bag_entity("x") > 0, bag_entity("xp") > 0))))
|
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|
|
|
|
# obs_2 = ltl_And(f_y2, reach_y, reach_Y, delayed_Y, delayed_Q)
|
|
|
|
# f_x2 = ltl_G(True, ltl_Implies(
|
|
# exact_state(["x", "xp"], all_entities),
|
|
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
|
|
#
|
|
|
|
related_to_x = ["x", "xp", "X"]
|
|
related_to_y = ["y", "yp", "Y"]
|
|
params_for_x = [lda0]
|
|
params_for_y = [lda1, lda2, lda3]
|
|
|
|
|
|
|
|
no_x_in_y = param_True()
|
|
for par in params_for_y:
|
|
for ent in related_to_x:
|
|
no_x_in_y = param_And(no_x_in_y, param_entity(par, ent) == 0)
|
|
|
|
no_y_in_x = param_True()
|
|
for par in params_for_x:
|
|
for ent in related_to_y:
|
|
no_y_in_x = param_And(no_y_in_x, param_entity(par, ent) == 0)
|
|
|
|
# param_constr = param_And(param_entity(lda3, "Y") > 0, param_entity(lda3, "X") == 0, param_entity(lda2, "Q") == 0, param_entity(lda1, "yp") == 0, param_entity(lda1, "Y") == 0)
|
|
param_constr = param_And(no_y_in_x, no_x_in_y)
|
|
|
|
smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
|
|
#
|
|
smt_rsc.check_rsltl(
|
|
formulae_list=[obs_1,obs_2],
|
|
param_constr=param_constr,
|
|
) #, max_level=4, cont_if_sat=True)
|
|
|
|
|
|
def gene_expression_full(cmd_args):
|
|
"""
|
|
Simple gene expression example
|
|
"""
|
|
r = ReactionSystemWithConcentrationsParam()
|
|
|
|
r.add_bg_set_entity(("x", 1))
|
|
r.add_bg_set_entity(("xp", 1))
|
|
r.add_bg_set_entity(("X", 1))
|
|
|
|
r.add_bg_set_entity(("y", 1))
|
|
r.add_bg_set_entity(("yp", 1))
|
|
r.add_bg_set_entity(("Y", 1))
|
|
|
|
r.add_bg_set_entity(("z", 1))
|
|
r.add_bg_set_entity(("zp", 1))
|
|
r.add_bg_set_entity(("Z", 1))
|
|
|
|
r.add_bg_set_entity(("h", 1))
|
|
r.add_bg_set_entity(("Q", 1))
|
|
r.add_bg_set_entity(("U", 1))
|
|
|
|
all_entities = set(r.background_set)
|
|
|
|
r.add_reaction([("x",1)],[("h",1)],[("x",1)])
|
|
r.add_reaction([("x",1)],[("h",1)],[("xp",1)])
|
|
r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)])
|
|
|
|
## y
|
|
# r.add_reaction([("y",1)],[("h",1)],[("y",1)])
|
|
# r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
|
|
# r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
|
|
lda1 = r.get_param("lda1")
|
|
lda2 = r.get_param("lda2")
|
|
lda3 = r.get_param("lda3")
|
|
r.add_reaction([("y",1)],[("h",1)],lda1)
|
|
r.add_reaction(lda2,[("Q",1)],[("yp",1)])
|
|
r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3)
|
|
|
|
r.add_reaction([("z",1)],[("h",1)],[("z",1)])
|
|
r.add_reaction([("z",1)], [("X",1)], [("zp",1)])
|
|
r.add_reaction([("z",1),("zp",1)],[("h",1)],[("Z",1)])
|
|
|
|
r.add_reaction([("U",1),("X",1)],[("h",1)],[("Q",1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
|
|
# the experiments starts with adding x and y:
|
|
c.add_transition("0", [("x", 1),("y", 1)], "1")
|
|
|
|
# for all the remaining steps we have empty context sequences
|
|
c.add_transition("1", [], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r, c)
|
|
rc.show()
|
|
|
|
# f_x1 = ltl_G(True, ltl_Implies(
|
|
# exact_state(["x"], all_entities),
|
|
# ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
|
|
# f_x2 = ltl_G(True, ltl_Implies(
|
|
# exact_state(["x", "xp"], all_entities),
|
|
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
|
|
|
|
reach_yp = ltl_F(True, "yp")
|
|
reach_Y = ltl_F(True, "Y")
|
|
reach_y = ltl_F(True, "y")
|
|
|
|
f_y1 = ltl_G(bag_entity("h") == 0, ltl_Implies(
|
|
bag_And(bag_entity("Q") == 0, bag_entity("y") > 0),
|
|
ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0))))
|
|
|
|
f_y2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
|
|
bag_And(bag_entity("y") > 0, bag_entity("yp") > 0),
|
|
ltl_F(True, bag_entity("Y") > 0)))
|
|
|
|
obs_1 = ltl_And(f_y1, reach_y)
|
|
obs_2 = ltl_And(f_y2, reach_y, reach_Y)
|
|
|
|
# f_x2 = ltl_G(True, ltl_Implies(
|
|
# exact_state(["x", "xp"], all_entities),
|
|
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
|
|
#
|
|
|
|
smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
|
|
#
|
|
smt_rsc.check_rsltl(formulae_list=[obs_1, obs_2], max_level=3, cont_if_sat=True)
|
|
|
|
# smt_rsc.check_rsltl(formula=f_x1, print_witness=True)
|
|
|
|
|
|
def trivial_param():
|
|
|
|
r = ReactionSystemWithConcentrationsParam()
|
|
r.add_bg_set_entity(("x", 3))
|
|
r.add_bg_set_entity(("c", 3))
|
|
r.add_bg_set_entity(("final", 1))
|
|
|
|
param_p1 = r.get_param("P1")
|
|
|
|
r.add_reaction(param_p1, [("c", 1)], [("final", 1)])
|
|
# r.add_reaction([("x", 1)], [("c", 1)], [("final", 1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("x", 1)], "1")
|
|
c.add_transition("1", [], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r, c)
|
|
rc.show()
|
|
smt_rsc = SmtCheckerRSCParam(rc)
|
|
|
|
f1 = ltl_F(True, bag_entity("final") >= 1)
|
|
|
|
# f1 = Formula_rsLTL.f_F(
|
|
# BagDescription.f_TRUE(),
|
|
# BagDescription.f_entity("final") >= 1)
|
|
|
|
#
|
|
# WARNING: depth limit is set
|
|
#
|
|
smt_rsc.check_rsltl(formula=f1, max_level=10, print_witness=True)
|
|
|
|
|
|
def simple_param(cmd_args):
|
|
|
|
r = ReactionSystemWithConcentrationsParam()
|
|
r.add_bg_set_entity(("x", 3))
|
|
r.add_bg_set_entity(("y", 3))
|
|
r.add_bg_set_entity(("c", 3))
|
|
r.add_bg_set_entity(("z", 3))
|
|
r.add_bg_set_entity(("final", 1))
|
|
|
|
param_p1 = r.get_param("P1")
|
|
|
|
r.add_reaction([("x", 1)], [("c", 1)], [("y", 2)])
|
|
# r.add_reaction([("y", 1)], [("c", 1)], [("z", 1)])
|
|
r.add_reaction([("y", 1)], [("c", 1)], r.get_param("P2"))
|
|
r.add_reaction(param_p1, [("x", 1)], [("final", 1)])
|
|
# r.add_reaction([("z", 1)], [("x", 1)], [("final", 1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("x", 1)], "1")
|
|
c.add_transition("1", [], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r, c)
|
|
rc.show()
|
|
|
|
smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
|
|
|
|
f1 = Formula_rsLTL.f_F(
|
|
BagDescription.f_TRUE(),
|
|
BagDescription.f_entity("final") >= 1)
|
|
|
|
#
|
|
# WARNING: depth limit is set
|
|
#
|
|
smt_rsc.check_rsltl(formula=f1, max_level=10, print_witness=True, cont_if_sat=False)
|
|
|
|
|
|
def heat_shock_response_param(cmd_args, print_system=True):
|
|
|
|
stress_temp = 42
|
|
max_temp = 50
|
|
|
|
r = ReactionSystemWithConcentrationsParam()
|
|
r.add_bg_set_entity(("hsp",1))
|
|
r.add_bg_set_entity(("hsf",1))
|
|
r.add_bg_set_entity(("hsf2",1))
|
|
r.add_bg_set_entity(("hsf3",1))
|
|
r.add_bg_set_entity(("hse",1))
|
|
r.add_bg_set_entity(("mfp",1))
|
|
r.add_bg_set_entity(("prot",1))
|
|
r.add_bg_set_entity(("hsf3:hse",1))
|
|
r.add_bg_set_entity(("hsp:mfp",1))
|
|
r.add_bg_set_entity(("hsp:hsf",1))
|
|
r.add_bg_set_entity(("stress",1))
|
|
r.add_bg_set_entity(("no_stress",1))
|
|
|
|
param_p1 = r.get_param("P1")
|
|
|
|
r.add_reaction([("hsf",1)], [("hsp",1)], [("hsf3",1)])
|
|
r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)])
|
|
r.add_reaction([("hsf3",1)], [("hse",1),("hsp",1)],[("hsf",1)])
|
|
r.add_reaction([("hsf3",1),("hsp",1),("mfp",1)], [("hse",1)], [("hsf",1)])
|
|
r.add_reaction([("hsf3",1),("hse",1)], [("hsp",1)], [("hsf3:hse",1)])
|
|
r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[], [("hsf3:hse",1)])
|
|
r.add_reaction([("hse",1)], [("hsf3",1)], [("hse",1)])
|
|
r.add_reaction([("hsp",1),("hsf3",1),("hse",1)], [("mfp",1)], [("hse",1)])
|
|
r.add_reaction([("hsf3:hse",1)], [("hsp",1)], [("hsp",1),("hsf3:hse",1)])
|
|
r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[], [("hsp",1),("hsf3:hse",1)])
|
|
r.add_reaction([("hsf",1),("hsp",1)], [("mfp",1)], [("hsp:hsf",1)])
|
|
r.add_reaction([("hsp:hsf",1),("stress",1)],[], [("hsf",1),("hsp",1)])
|
|
r.add_reaction([("hsp:hsf",1)], [("stress",1)],[("hsp:hsf",1)])
|
|
r.add_reaction([("hsp",1),("hsf3:hse",1)], [("mfp",1)], [("hse",1),("hsp:hsf",1)])
|
|
r.add_reaction([("stress",1),("prot",1)], [], [("mfp",1),("prot",1)])
|
|
r.add_reaction([("prot",1)], [("stress",1)], [("prot",1)])
|
|
r.add_reaction([("hsp",1),("mfp",1)], [], [("hsp:mfp",1)])
|
|
r.add_reaction([("mfp",1)], [("hsp",1)], [("mfp",1)])
|
|
r.add_reaction([("hsp:mfp",1)], [], [("hsp",1),("prot",1)])
|
|
|
|
# r.add_reaction_inc("temp", "heat", [("temp",1)],[("temp",max_temp)])
|
|
# r.add_reaction_dec("temp", "cool", [("temp",1)],[])
|
|
|
|
# r.add_permanency("temp",[("heat",1),("cool",1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("no_stress",1)], "1")
|
|
c.add_transition("1", [("stress",1)], "1")
|
|
c.add_transition("1", [("no_stress",1)], "1")
|
|
c.add_transition("1", [], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r,c)
|
|
|
|
if print_system:
|
|
rc.show()
|
|
|
|
# prop_req = [("hsp:hsf",1),("hse",1),("prot",1)]
|
|
# prop_block = [("temp",stress_temp)]
|
|
# prop_req = [ ("mfp",1) ]
|
|
# prop_block = [ ]
|
|
# prop = (prop_req,prop_block)
|
|
# rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
|
|
#
|
|
|
|
# f_reach_mfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("mfp") > 0) )
|
|
f_reach_mfp = ltl_F(True, bag_entity("mfp") > 0)
|
|
|
|
f_reach_hspmfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("hsp:mfp") > 0) )
|
|
|
|
smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
|
|
|
|
smt_rsc.check_rsltl(formulae_list=[f_reach_mfp, f_reach_hspmfp])
|
|
|
|
|
|
# (1) if we keep increasing the temperature the protein will eventually misfold
|
|
# f_mfp_when_heating = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("mfp") > 0) )
|
|
# )
|
|
# smt_rsc.check_rsltl(formula=f_mfp_when_heating)
|
|
|
|
# (2) when heating, we finally exceed the stress_temp
|
|
# f_2 = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("temp") > stress_temp))
|
|
# )
|
|
# smt_rsc.check_rsltl(formula=f_2)
|
|
|
|
# smt_rsc.check_reachability(prop,max_level=40)
|
|
|
|
def example44_param():
|
|
|
|
r = ReactionSystemWithConcentrationsParam()
|
|
r.add_bg_set_entity(("x", 2))
|
|
r.add_bg_set_entity(("y", 4))
|
|
r.add_bg_set_entity(("h", 2))
|
|
r.add_bg_set_entity(("m", 1))
|
|
|
|
r.add_reaction([("y", 1), ("x", 1)], [("y", 2), ("h", 1)], [("y", 2)])
|
|
r.add_reaction([("y", 2), ("x", 2)], [("y", 3), ("h", 1)], [("y", 3)])
|
|
r.add_reaction([("y", 3), ("h", 1)], [("y", 4), ("h", 2)], [("y", 4)])
|
|
r.add_reaction([("y", 4), ("h", 1)], [("h", 2)], [("y", 3)])
|
|
r.add_reaction([("y", 4), ("x", 2)], [("h", 1)], [("y", 2)])
|
|
r.add_reaction([("m", 1)], [("y", 3)], [("m", 1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("y", 1), ("m", 1), ("x", 1)], "1")
|
|
c.add_transition("1", [("x", 1)], "1")
|
|
c.add_transition("1", [("x", 1), ("h", 1)], "1")
|
|
c.add_transition("1", [("x", 2)], "1")
|
|
c.add_transition("1", [("x", 2), ("h", 1)], "1")
|
|
c.add_transition("1", [("h", 1)], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r, c)
|
|
rc.show()
|
|
smt_rsc = SmtCheckerRSCParam(rc)
|
|
|
|
# Universal property which seems to be true: (holds also existentially)
|
|
f1 = Formula_rsLTL.f_G(BagDescription.f_entity("x") > 0,
|
|
Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") >= 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# lets see if we can find a counterexample to this property:
|
|
neg_f1 = Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
Formula_rsLTL.f_And(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") < 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# we fix the property f1
|
|
# this one holds:
|
|
f2 = Formula_rsLTL.f_G(
|
|
BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1) &
|
|
(BagDescription.f_entity("h") < 1),
|
|
BagDescription.f_entity("y") >= 3)))
|
|
|
|
# neg_f1 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_And(
|
|
# (BagDescription.f_entity('y') > 0),
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 1,
|
|
# BagDescription.f_entity("y") < 3
|
|
# )
|
|
# )
|
|
# )
|
|
# ))
|
|
smt_rsc.check_rsltl(formula=neg_f1)
|
|
|
|
|
|
def example44():
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("x", 2))
|
|
r.add_bg_set_entity(("y", 4))
|
|
r.add_bg_set_entity(("h", 2))
|
|
r.add_bg_set_entity(("m", 1))
|
|
|
|
r.add_reaction([("y", 1), ("x", 1)], [("y", 2), ("h", 1)], [("y", 2)])
|
|
r.add_reaction([("y", 2), ("x", 2)], [("y", 3), ("h", 1)], [("y", 3)])
|
|
r.add_reaction([("y", 3), ("h", 1)], [("y", 4), ("h", 2)], [("y", 4)])
|
|
r.add_reaction([("y", 4), ("h", 1)], [("h", 2)], [("y", 3)])
|
|
r.add_reaction([("y", 4), ("x", 2)], [("h", 1)], [("y", 2)])
|
|
r.add_reaction([("m", 1)], [("y", 3)], [("m", 1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("y", 1), ("m", 1), ("x", 1)], "1")
|
|
c.add_transition("1", [("x", 1)], "1")
|
|
c.add_transition("1", [("x", 1), ("h", 1)], "1")
|
|
c.add_transition("1", [("x", 2)], "1")
|
|
c.add_transition("1", [("x", 2), ("h", 1)], "1")
|
|
c.add_transition("1", [("h", 1)], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r, c)
|
|
rc.show()
|
|
smt_rsc = SmtCheckerRSC(rc)
|
|
|
|
# Universal property which seems to be true: (holds also existentially)
|
|
f1 = Formula_rsLTL.f_G(BagDescription.f_entity("x") > 0,
|
|
Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") >= 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# lets see if we can find a counterexample to this property:
|
|
neg_f1 = Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
Formula_rsLTL.f_And(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") < 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# we fix the property f1
|
|
# this one holds:
|
|
f2 = Formula_rsLTL.f_G(
|
|
BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1) &
|
|
(BagDescription.f_entity("h") < 1),
|
|
BagDescription.f_entity("y") >= 3)))
|
|
|
|
# neg_f1 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_And(
|
|
# (BagDescription.f_entity('y') > 0),
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 1,
|
|
# BagDescription.f_entity("y") < 3
|
|
# )
|
|
# )
|
|
# )
|
|
# ))
|
|
smt_rsc.check_rsltl(formula=neg_f1)
|
|
|
|
|
|
def heat_shock_response(print_system=True):
|
|
|
|
stress_temp = 42
|
|
max_temp = 50
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("hsp",1))
|
|
r.add_bg_set_entity(("hsf",1))
|
|
r.add_bg_set_entity(("hsf2",1))
|
|
r.add_bg_set_entity(("hsf3",1))
|
|
r.add_bg_set_entity(("hse",1))
|
|
r.add_bg_set_entity(("mfp",1))
|
|
r.add_bg_set_entity(("prot",1))
|
|
r.add_bg_set_entity(("hsf3:hse",1))
|
|
r.add_bg_set_entity(("hsp:mfp",1))
|
|
r.add_bg_set_entity(("hsp:hsf",1))
|
|
r.add_bg_set_entity(("temp",max_temp))
|
|
r.add_bg_set_entity(("heat",1))
|
|
r.add_bg_set_entity(("cool",1))
|
|
|
|
r.add_reaction([("hsf",1)], [("hsp",1)], [("hsf3",1)])
|
|
r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)])
|
|
r.add_reaction([("hsf3",1)], [("hse",1),("hsp",1)],[("hsf",1)])
|
|
r.add_reaction([("hsf3",1),("hsp",1),("mfp",1)], [("hse",1)], [("hsf",1)])
|
|
r.add_reaction([("hsf3",1),("hse",1)], [("hsp",1)], [("hsf3:hse",1)])
|
|
r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[], [("hsf3:hse",1)])
|
|
r.add_reaction([("hse",1)], [("hsf3",1)], [("hse",1)])
|
|
r.add_reaction([("hsp",1),("hsf3",1),("hse",1)], [("mfp",1)], [("hse",1)])
|
|
r.add_reaction([("hsf3:hse",1)], [("hsp",1)], [("hsp",1),("hsf3:hse",1)])
|
|
r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[], [("hsp",1),("hsf3:hse",1)])
|
|
r.add_reaction([("hsf",1),("hsp",1)], [("mfp",1)], [("hsp:hsf",1)])
|
|
r.add_reaction([("hsp:hsf",1),("temp",stress_temp)],[], [("hsf",1),("hsp",1)])
|
|
r.add_reaction([("hsp:hsf",1)], [("temp",stress_temp)],[("hsp:hsf",1)])
|
|
r.add_reaction([("hsp",1),("hsf3:hse",1)], [("mfp",1)], [("hse",1),("hsp:hsf",1)])
|
|
r.add_reaction([("temp",stress_temp),("prot",1)], [], [("mfp",1),("prot",1)])
|
|
r.add_reaction([("prot",1)], [("temp",stress_temp)], [("prot",1)])
|
|
r.add_reaction([("hsp",1),("mfp",1)], [], [("hsp:mfp",1)])
|
|
r.add_reaction([("mfp",1)], [("hsp",1)], [("mfp",1)])
|
|
r.add_reaction([("hsp:mfp",1)], [], [("hsp",1),("prot",1)])
|
|
|
|
r.add_reaction_inc("temp", "heat", [("temp",1)],[("temp",max_temp)])
|
|
r.add_reaction_dec("temp", "cool", [("temp",1)],[])
|
|
|
|
r.add_permanency("temp",[("heat",1),("cool",1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1")
|
|
c.add_transition("1", [("cool",1)], "1")
|
|
c.add_transition("1", [("heat",1)], "1")
|
|
c.add_transition("1", [], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r,c)
|
|
|
|
if print_system:
|
|
rc.show()
|
|
|
|
# prop_req = [("hsp:hsf",1),("hse",1),("prot",1)]
|
|
# prop_block = [("temp",stress_temp)]
|
|
# prop_req = [ ("mfp",1) ]
|
|
# prop_block = [ ]
|
|
# prop = (prop_req,prop_block)
|
|
# rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
|
|
#
|
|
# f_reach_mfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("mfp") > 0) )
|
|
|
|
smt_rsc = SmtCheckerRSC(rc)
|
|
|
|
# (1) if we keep increasing the temperature the protein will eventually misfold
|
|
# f_mfp_when_heating = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("mfp") > 0) )
|
|
# )
|
|
# smt_rsc.check_rsltl(formula=f_mfp_when_heating)
|
|
|
|
# (2) when heating, we finally exceed the stress_temp
|
|
f_2 = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("temp") > stress_temp))
|
|
)
|
|
smt_rsc.check_rsltl(formula=f_2)
|
|
|
|
# smt_rsc.check_reachability(prop,max_level=40)
|
|
|
|
def state_translate_rsc2rs(p):
|
|
return [e[0] + "#" + str(e[1]) for e in p]
|
|
|
|
|
|
def scalable_chain(print_system=False):
|
|
|
|
if len(sys.argv) < 1+3:
|
|
print("arguments: <chainLen> <maxConc> <formulaNumber>")
|
|
exit(1)
|
|
|
|
chainLen=int(sys.argv[1]) # chain length
|
|
maxConc=int(sys.argv[2]) # depth (max concentration)
|
|
formula_number=int(sys.argv[3])
|
|
|
|
if chainLen < 1 or maxConc < 1:
|
|
print("be reasonable")
|
|
exit(1)
|
|
if not formula_number in range(1,5+1):
|
|
print("formulaNumber must be in 1..5")
|
|
exit(1)
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("inc",1))
|
|
r.add_bg_set_entity(("dec",1))
|
|
|
|
for i in range(1,chainLen+1):
|
|
r.add_bg_set_entity(("e_" + str(i),maxConc))
|
|
|
|
for i in range(1,chainLen+1):
|
|
ent = "e_" + str(i)
|
|
r.add_reaction_inc(ent, "inc", [(ent, 1)],[(ent,maxConc)])
|
|
r.add_reaction_dec(ent, "dec", [(ent, 1)],[])
|
|
if i < chainLen:
|
|
r.add_reaction([(ent,maxConc)],[],[("e_"+str(i+1),1)])
|
|
|
|
r.add_reaction([("e_" + str(chainLen),maxConc)],[("dec",1)],[("e_" + str(chainLen),maxConc)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("init")
|
|
c.add_state("working")
|
|
c.add_transition("init", [("e_1",1),("inc",1)], "working")
|
|
c.add_transition("working", [("inc",1)], "working")
|
|
|
|
rc = ReactionSystemWithAutomaton(r,c)
|
|
|
|
if print_system:
|
|
rc.show()
|
|
|
|
smt_rsc = SmtCheckerRSC(rc)
|
|
|
|
if formula_number == 1:
|
|
f_1 = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, (BagDescription.f_entity('e_'+str(chainLen)) >= maxConc) )
|
|
smt_rsc.check_rsltl(formula=f_1)
|
|
elif formula_number == 2:
|
|
f_tmp = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, (BagDescription.f_entity('e_'+str(chainLen)) == maxConc) )
|
|
for i in range(chainLen-1,0,-1):
|
|
f_tmp = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, f_tmp & (BagDescription.f_entity('e_'+str(i)) == maxConc) )
|
|
f_2 = f_tmp
|
|
smt_rsc.check_rsltl(formula=f_2)
|
|
elif formula_number == 3:
|
|
f_3 = Formula_rsLTL.f_G( BagDescription.f_TRUE(),
|
|
Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('e_1') == 1),
|
|
Formula_rsLTL.f_F(
|
|
BagDescription.f_entity("inc") > 0,
|
|
(BagDescription.f_entity('e_'+str(chainLen)) == maxConc)
|
|
)
|
|
)
|
|
)
|
|
print(i)
|
|
smt_rsc.check_rsltl(formula=f_3)
|
|
elif formula_number == 4:
|
|
f_4 = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0 , BagDescription.f_entity('e_1') == maxConc )
|
|
smt_rsc.check_rsltl(formula=f_4)
|
|
|
|
elif formula_number == 5:
|
|
f_5 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_U( BagDescription.f_entity("inc") > 0 , BagDescription.f_entity('e_1') > 0, BagDescription.f_entity('e_2') > 0 ) )
|
|
smt_rsc.check_rsltl(formula=f_5)
|
|
|
|
###########################################################################
|
|
|
|
time=0
|
|
mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
|
|
filename_t="bench_rsc_F" + str(formula_number) + "_time.log"
|
|
filename_m="bench_rsc_F" + str(formula_number) + "_mem.log"
|
|
time=smt_rsc.get_verification_time()
|
|
|
|
f=open(filename_t, 'a')
|
|
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n"
|
|
f.write(log_str)
|
|
f.close()
|
|
|
|
f=open(filename_m, 'a')
|
|
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n"
|
|
f.write(log_str)
|
|
f.close()
|
|
|