194 lines
7.6 KiB
Python
Executable File
194 lines
7.6 KiB
Python
Executable File
#!/usr/bin/env python
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from rctsys import ReactionSystem,ReactionSystemWithConcentrations,ContextAutomatonWithConcentrations,ReactionSystemWithAutomaton
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from distrib_rctsys import DistributedReactionSystem
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from smtchecker import SmtChecker
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from smtcheckerpgrs import SmtCheckerPGRS
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from smtcheckerdistribrs import SmtCheckerDistribRS
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from smtcheckerrsc import SmtCheckerRSC
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import sys
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import resource
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def chain_reaction(print_system=False):
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if len(sys.argv) < 1+3:
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print("provide N M B")
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print(" B=1 - RSC")
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print(" B=0 - Translated RSC into RS")
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exit(1)
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chainLen=int(sys.argv[1]) # chain length
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maxConc=int(sys.argv[2]) # depth (max concentration)
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verify_rsc=bool(int(sys.argv[3]))
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if chainLen < 1 or maxConc < 1:
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print("be reasonable")
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exit(1)
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity(("inc",1))
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# r.add_bg_set_entity(("reset",1))
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r.add_bg_set_entity(("dec",1))
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# r.add_bg_set_entity(("x",1))
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for i in range(1,chainLen+1):
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r.add_bg_set_entity(("e_" + str(i),maxConc))
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for i in range(1,chainLen+1):
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ent = "e_" + str(i)
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# r.add_reaction_inc(ent, "inc", [(ent, 1)],[("reset",1),(ent,maxConc)])
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r.add_reaction_inc(ent, "inc", [(ent, 1)],[(ent,maxConc)])
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r.add_reaction_dec(ent, "dec", [(ent, 1)],[])
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# r.add_reaction([(ent,1),("reset",1)],[],[(ent,1)])
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if i < chainLen:
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r.add_reaction([(ent,maxConc)],[],[("e_"+str(i+1),1)])
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r.add_reaction([("e_" + str(chainLen),maxConc)],[("dec",1)],[("e_" + str(chainLen),maxConc)])
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# r.add_reaction([("e_" + str(chainLen),maxConc)],[],[("e_" + str(chainLen),maxConc)])
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c = ContextAutomatonWithConcentrations(r)
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c.add_init_state("init")
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c.add_state("working")
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c.add_transition("init", [("e_1",1),("inc",1)], "working")
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c.add_transition("working", [("inc",1)], "working")
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# c.add_transition("working", [("reset",1)], "working")
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# c.add_transition("working",[("x",1)],"working")
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rc = ReactionSystemWithAutomaton(r,c)
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if print_system:
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rc.show()
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if verify_rsc:
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smt_rsc = SmtCheckerRSC(rc)
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prop = [('e_'+str(chainLen),maxConc)]
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smt_rsc.check_reachability((prop,[]),max_level=maxConc*chainLen+10)
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# smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10)
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else:
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orc = rc.get_ordinary_reaction_system_with_automaton()
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if print_system:
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print("\nTranslated:")
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orc.show()
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smt_tr_rs = SmtCheckerPGRS(orc)
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smt_tr_rs.check_reachability(['e_'+str(chainLen)+"#"+str(maxConc)])
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# print("Reaction System with Concentrations:", smt_rsc.get_verification_time())
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# print("Reaction System from translating RSC:", smt_tr_rs.get_verification_time())
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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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if verify_rsc:
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filename_t="bench_rsc_time.log"
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filename_m="bench_rsc_mem.log"
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time=smt_rsc.get_verification_time()
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else:
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filename_t="bench_tr_rs_time.log"
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filename_m="bench_tr_rs_mem.log"
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time=smt_tr_rs.get_verification_time()
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f=open(filename_t, 'a')
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log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n"
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f.write(log_str)
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f.close()
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f=open(filename_m, 'a')
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log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n"
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f.write(log_str)
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f.close()
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def heat_shock_response(print_system=True,verify_rsc=True):
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if len(sys.argv) < 1+1:
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print("provide B")
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print(" B=1 - RSC")
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print(" B=0 - Translated RSC into RS")
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exit(1)
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verify_rsc=bool(int(sys.argv[1]))
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stress_temp = 42
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max_temp = 50
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity(("hsp",1))
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r.add_bg_set_entity(("hsf",1))
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r.add_bg_set_entity(("hsf2",1))
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r.add_bg_set_entity(("hsf3",1))
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r.add_bg_set_entity(("hse",1))
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r.add_bg_set_entity(("mfp",1))
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r.add_bg_set_entity(("prot",1))
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r.add_bg_set_entity(("hsf3:hse",1))
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r.add_bg_set_entity(("hsp:mfp",1))
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r.add_bg_set_entity(("hsp:hsf",1))
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r.add_bg_set_entity(("temp",max_temp))
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r.add_bg_set_entity(("heat",1))
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r.add_bg_set_entity(("cool",1))
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r.add_reaction([("hsf",1)], [("hsp",1)], [("hsf3",1)])
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r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)])
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r.add_reaction([("hsf3",1)], [("hse",1),("hsp",1)],[("hsf",1)])
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r.add_reaction([("hsf3",1),("hsp",1),("mfp",1)], [("hse",1)], [("hsf",1)])
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r.add_reaction([("hsf3",1),("hse",1)], [("hsp",1)], [("hsf3:hse",1)])
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r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[], [("hsf3:hse",1)])
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r.add_reaction([("hse",1)], [("hsf3",1)], [("hse",1)])
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r.add_reaction([("hsp",1),("hsf3",1),("hse",1)], [("mfp",1)], [("hse",1)])
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r.add_reaction([("hsf3:hse",1)], [("hsp",1)], [("hsp",1),("hsf3:hse",1)])
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r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[], [("hsp",1),("hsf3:hse",1)])
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r.add_reaction([("hsf",1),("hsp",1)], [("mfp",1)], [("hsp:hsf",1)])
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r.add_reaction([("hsp:hsf",1),("temp",stress_temp)],[], [("hsf",1),("hsp",1)])
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r.add_reaction([("hsp:hsf",1)], [("temp",stress_temp)],[("hsp:hsf",1)])
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r.add_reaction([("hsp",1),("hsf3:hse",1)], [("mfp",1)], [("hse",1),("hsp:hsf",1)])
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r.add_reaction([("temp",stress_temp),("prot",1)], [], [("mfp",1),("prot",1)])
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r.add_reaction([("prot",1)], [("temp",stress_temp)], [("prot",1)])
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r.add_reaction([("hsp",1),("mfp",1)], [], [("hsp:mfp",1)])
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r.add_reaction([("mfp",1)], [("hsp",1)], [("mfp",1)])
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r.add_reaction([("hsp:mfp",1)], [], [("hsp",1),("prot",1)])
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r.add_reaction_inc("temp", "heat", [("temp",1)],[("temp",max_temp)])
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r.add_reaction_dec("temp", "cool", [("temp",1)],[])
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r.add_permanency("temp",[("heat",1),("cool",1)])
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#r.add_permanency("temp",[])
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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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# c.add_transition("0", [("prot",1), ("temp",35)], "1")
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c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1")
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#-> c.add_transition("0", [("hse",1),("prot",1),("hsp:hsf",1),("temp",stress_temp)], "1")
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# c.add_transition("0", [("hsp",1),("prot",1),("hsf3:hse",1),("mfp",1),("hsp:mfp",1),("temp",30)], "1")
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c.add_transition("1", [("cool",1)], "1")
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c.add_transition("1", [("heat",1)], "1")
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c.add_transition("1", [], "1")
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# c.add_transition("1", [("sugar",1)], "1")
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rc = ReactionSystemWithAutomaton(r,c)
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if print_system:
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rc.show()
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# prop_req = [("hsp:hsf",1),("hse",1),("prot",1)]
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# prop_block = [("temp",stress_temp)]
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prop_req = [ ("mfp",1) ]
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prop_block = [ ]
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prop = (prop_req,prop_block)
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rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
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if verify_rsc:
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smt_rsc = SmtCheckerRSC(rc)
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smt_rsc.check_reachability(prop,max_level=40)
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else:
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orc = rc.get_ordinary_reaction_system_with_automaton()
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if print_system:
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print("\nTranslated:")
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orc.show()
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smt_tr_rs = SmtCheckerPGRS(orc)
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smt_tr_rs.check_reachability(rs_prop)
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def state_translate_rsc2rs(p):
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return [e[0] + "#" + str(e[1]) for e in p]
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