from rs import * from smt import * import rs_examples from logics import * from rsltl_shortcuts import * from itertools import chain, combinations import sys import resource def powerset(iterable,N=None): if N is None: N = len(s) s = list(iterable) return chain.from_iterable(combinations(s, r) for r in range(N+1)) def run_tests(cmd_args): # test_extended_automaton() # process() # heat_shock_response() # scalable_chain(print_system=True) # example44() # example44_param() # heat_shock_response_param(cmd_args) # simple_param(cmd_args) # param_gene_expression(cmd_args) mutex_bench_main(cmd_args) def mutex_bench_main(cmd_args): if not cmd_args.special_mode: print("Missing special mode parameter") print("* 1 - parametric") print("* 2 - non-parametric (with parametric implementation)") print("* 3 - non-parametric (with non-parametric implementation)") return smode = int(cmd_args.special_mode) if smode == 1: mutex_param_bench(cmd_args) elif smode == 2: mutex_nonparam_bench(cmd_args) elif smode == 3: mutex_nonparam_bench_oldimpl(cmd_args) else: print("Unrecognised mode") return def mutex_param_bench(cmd_args): """ Mutex Benchmark Parametric """ base_entities = ["out","req","in","act"] shared_entities = ["lock","done","s"] if not cmd_args.scaling_parameter: print("Missing scaling parameter") return n_proc = int(cmd_args.scaling_parameter) r = ReactionSystemWithConcentrationsParam() def E(a,b,c=1): return (a + "_" + str(b), c) for i in range(n_proc): for ent in base_entities: max_conc = 1 if ent == "in": max_conc = 3 elif ent == "req": max_conc = 2 r.add_bg_set_entity(E(ent,i,max_conc)) for ent in shared_entities: max_conc = 1 r.add_bg_set_entity((ent, max_conc)) ################################################### Inhib = [("s",1)] for i in range(n_proc): r.add_reaction([E("out",i),E("act",i)],Inhib,[E("req",i)]) r.add_reaction([E("out",i)],[E("act",i)],[E("out",i)]) for j in range(n_proc): if i != j: r.add_reaction([E("req",i),E("act",i),E("act",j)],Inhib,[E("req",i)]) r.add_reaction([E("req",i)],[E("act",i)],[E("req",i,2)]) enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)] r.add_reaction([E("req",i,2),E("act",i)],enter_inhib,[E("in",i,3), ("lock",1)]) r.add_reaction([E("in",i,3),E("act",i)],Inhib,[E("in",i,2)]) r.add_reaction([E("in",i,2),E("act",i)],Inhib,[E("in",i,1)]) r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)]) r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)]) r.add_reaction([("lock",1)],[("done",1)],[("lock",1)]) lda1 = r.get_param("lda1") lda2 = r.get_param("lda2") lda3 = r.get_param("lda3") r.add_reaction(lda1,lda2,lda3) ################################################### c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") init_ctx = [] for i in range(n_proc): init_ctx.append(E("out", i)) # the experiments starts with adding x and y: c.add_transition("0", init_ctx, "1") all_act = powerset([E("act",i) for i in range(n_proc)], 2) for actions in all_act: actions = list(actions) c.add_transition("1", actions, "1") # for all the remaining steps we have empty context sequences # c.add_transition("1", [], "1") # c.add_transition("1", [("h", 1)], "1") ################################################### rc = ReactionSystemWithAutomaton(r, c) rc.show() f_attack = ltl_F(True, bag_And(bag_entity("in_0") == 1, bag_entity("in_" + str(n_proc-1)) == 1)) ent_of_Nth_proc = [ent + "_" + str(n_proc-1) for ent in base_entities] + shared_entities disallow = ["in_" + str(n_proc-1)] for ent in r.background_set: if ent not in ent_of_Nth_proc: disallow.append(ent) disallow.append("act_" + str(n_proc-1)) # disallow = ["in_0", "in_" + str(n_proc)] #, "req_0", "req_1"] lda1_disallow = [param_entity(lda1, ent) == 0 for ent in disallow] lda2_disallow = [param_entity(lda2, ent) == 0 for ent in disallow] lda3_disallow = [param_entity(lda3, ent) == 0 for ent in disallow] lda_disallow = lda1_disallow + lda2_disallow + lda3_disallow # for bent in base_entities: # print(param_entity(lda3, bent + "_0")) param_constr = param_And(*lda_disallow) smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise) smt_rsc.check_rsltl(formulae_list=[f_attack], param_constr=param_constr) #, max_level=4, cont_if_sat=True) log_suffix = "" if cmd_args.optimise: log_suffix = "_OPT" time=0 mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024) filename_t="bench_mutex_param" + log_suffix + "_time.dat" filename_m="bench_mutex_param" + log_suffix + "_mem.dat" time=smt_rsc.get_verification_time() with open(filename_t, 'a') as f: log_str="{:d} {:f}\n".format(n_proc, time) f.write(log_str) with open(filename_m, 'a') as f: log_str="{:d} {:f}\n".format(n_proc, mem_usage) f.write(log_str) def mutex_nonparam_bench(cmd_args): """ Mutex Benchmark Parametric """ base_entities = ["out","req","in","act"] shared_entities = ["lock","done","s"] if not cmd_args.scaling_parameter: raise RuntimeError("Missing scaling parameter") n_proc = int(cmd_args.scaling_parameter) r = ReactionSystemWithConcentrationsParam() def E(a,b): return (a + "_" + str(b), 1) for i in range(n_proc): for ent in base_entities: r.add_bg_set_entity(E(ent,i)) for ent in shared_entities: r.add_bg_set_entity((ent, 1)) ################################################### Inhib = [("s",1)] for i in range(n_proc): r.add_reaction([E("out",i),E("act",i)],Inhib,[E("req",i)]) r.add_reaction([E("out",i)],[E("act",i)],[E("out",i)]) for j in range(n_proc): if i != j: r.add_reaction([E("req",i),E("act",i),E("act",j)],Inhib,[E("req",i)]) r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)]) enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)] r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",1)]) r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)]) r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)]) r.add_reaction([("lock",1)],[("done",1)],[("lock",1)]) r.add_reaction([E("out",n_proc-1)],[("s",1)],[("done",1),E("req",n_proc-1)]) ################################################### c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") init_ctx = [] for i in range(n_proc): init_ctx.append(E("out", i)) # the experiments starts with adding x and y: c.add_transition("0", init_ctx, "1") all_act = powerset([E("act",i) for i in range(n_proc)], 2) for actions in all_act: actions = list(actions) c.add_transition("1", actions, "1") # for all the remaining steps we have empty context sequences # c.add_transition("1", [], "1") # c.add_transition("1", [("h", 1)], "1") ################################################### rc = ReactionSystemWithAutomaton(r, c) rc.show() f_attack = ltl_F(True, bag_And(bag_entity("in_0") == 1, bag_entity("in_" + str(n_proc-1)) == 1)) smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise) smt_rsc.check_rsltl(formulae_list=[f_attack]) time=0 mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024) filename_t="bench_mutex_nonparam_time.dat" filename_m="bench_mutex_nonparam_mem.dat" time=smt_rsc.get_verification_time() with open(filename_t, 'a') as f: log_str="{:d} {:f}\n".format(n_proc, time) f.write(log_str) with open(filename_m, 'a') as f: log_str="{:d} {:f}\n".format(n_proc, mem_usage) f.write(log_str) def mutex_nonparam_bench_oldimpl(cmd_args): """ Mutex Benchmark Parametric """ base_entities = ["out","req","in","act"] shared_entities = ["lock","done","s"] if not cmd_args.scaling_parameter: raise RuntimeError("Missing scaling parameter") n_proc = int(cmd_args.scaling_parameter) r = ReactionSystemWithConcentrations() def E(a,b): return (a + "_" + str(b), 1) for i in range(n_proc): for ent in base_entities: r.add_bg_set_entity(E(ent,i)) for ent in shared_entities: r.add_bg_set_entity((ent, 1)) ################################################### Inhib = [("s",1)] for i in range(n_proc): r.add_reaction([E("out",i),E("act",i)],Inhib,[E("req",i)]) r.add_reaction([E("out",i)],[E("act",i)],[E("out",i)]) for j in range(n_proc): if i != j: r.add_reaction([E("req",i),E("act",i),E("act",j)],Inhib,[E("req",i)]) r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)]) enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)] r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",1)]) r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)]) r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)]) r.add_reaction([("lock",1)],[("done",1)],[("lock",1)]) r.add_reaction([E("out",n_proc-1)],[("s",1)],[("done",1),E("req",n_proc-1)]) ################################################### c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") init_ctx = [] for i in range(n_proc): init_ctx.append(E("out", i)) # the experiments starts with adding x and y: c.add_transition("0", init_ctx, "1") all_act = powerset([E("act",i) for i in range(n_proc)], 2) for actions in all_act: actions = list(actions) c.add_transition("1", actions, "1") # for all the remaining steps we have empty context sequences # c.add_transition("1", [], "1") # c.add_transition("1", [("h", 1)], "1") ################################################### rc = ReactionSystemWithAutomaton(r, c) rc.show() f_attack = ltl_F(True, bag_And(bag_entity("in_0") == 1, bag_entity("in_" + str(n_proc-1)) == 1)) smt_rsc = SmtCheckerRSC(rc) smt_rsc.check_rsltl(formula=f_attack) time=0 mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024) filename_t="bench_mutex_nonparam_oldimpl_time.dat" filename_m="bench_mutex_nonparam_oldimpl_mem.dat" time=smt_rsc.get_verification_time() with open(filename_t, 'a') as f: log_str="{:d} {:f}\n".format(n_proc, time) f.write(log_str) with open(filename_m, 'a') as f: log_str="{:d} {:f}\n".format(n_proc, mem_usage) f.write(log_str) def param_gene_expression(cmd_args): """ Simple gene expression example with parameters """ 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(("h", 1)) r.add_bg_set_entity(("Q", 1)) all_entities = set(r.background_set) lda0 = r.get_param("lda0") lda1 = r.get_param("lda1") lda2 = r.get_param("lda2") lda3 = r.get_param("lda3") r.add_reaction([("x",1)],[("h",1)],[("x",1)]) # r.add_reaction([("x",1)],[("h",1)],[("xp",1)]) r.add_reaction(lda0, [("h",1)],[("xp",1)]) r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)]) r.add_reaction([("X",1),("Y",1)],[("h",1)],[("Q",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)]) r.add_reaction([("y",1)],[("h",1)],lda1) r.add_reaction(lda2,[("h",1)],[("yp",1)]) r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3) c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") # the experiments starts with adding x and y: c.add_transition("0", [("y", 1),("x",1)], "1") # for all the remaining steps we have empty context sequences c.add_transition("1", [], "1") c.add_transition("1", [("h", 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)))) # reachability reach_y = ltl_F(bag_entity("h") == 0, "y") reach_yp = ltl_F(bag_entity("h") == 0, "yp") reach_Y = ltl_F(bag_entity("h") == 0, "Y") # phi_r = ltl_And(reach_y, reach_yp, reach_Y) # rules phi_c1 = ltl_G(bag_entity("h") == 0, ltl_Implies( bag_entity("y") > 0, ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0)))) phi_c2 = 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))) # delayed_Y = ltl_X(True, ltl_And(bag_entity("Y") == 0, ltl_X(True, bag_entity("Y") == 0))) # delayed_Y = ltl_X(True, bag_entity("Y") == 0) 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)))))) obs_1 = ltl_And(phi_r, phi_c1, phi_c2, delayed_Q) # Observation related to A_x: obs_2 = ltl_G(bag_entity("h") == 0, ltl_Implies( bag_entity("x") > 0, ltl_X(True, bag_And(bag_entity("x") > 0, bag_entity("xp") > 0)))) # 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: ") 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()