440 lines
13 KiB
Python
Executable File
440 lines
13 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 toy_ex1():
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rs = ReactionSystem()
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#rs.add_bg_set_entities(["a","b","x","c"])
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#rs.add_reaction(["a","b"],["x"],["c"])
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#rs.add_reaction(["c"],["a"],["a"])
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#rs.add_reaction(["a"],["x"],["c"])
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#rs.set_context_entities(["b"])
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#rs.add_initial_context_set(["a","b"])
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#rs.add_bg_set_entities(["a", "b", "c", "d", "e", "f", "x", "y","1","2","3","4","5","6"])
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rs.add_bg_set_entities(list("qwertyuiopasdfghjklzxcvbnm"))
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rs.add_reaction(["a"], ["x"], ["b"])
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rs.add_reaction(["b"], ["x"], ["c"])
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rs.add_reaction(["c","f"], ["x"], ["d"])
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rs.add_reaction(["d"], ["x"], ["e"])
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rs.set_context_entities(["f","g","h"])
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rs.add_initial_context_set(["a"])
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return rs
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def toy_ex2():
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rs = ReactionSystem()
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rs.add_bg_set_entities(["a","b","c","d","d_comp","e","f","x"])
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rs.add_reaction(["a"],["x"],["b"])
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rs.add_reaction(["b"],["a"],["c"])
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rs.add_reaction(["c"],["x"],["d"])
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rs.add_reaction(["d","d_comp"],["e"],["f"])
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rs.add_reaction(["f"],["a"],["e"])
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rs.set_context_entities(["d_comp", "e", "x"])
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rs.add_initial_context_set(["a"])
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return rs
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def toy_ex3():
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rs = ReactionSystem()
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rs.add_bg_set_entities(["1","2","3","4"])
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rs.add_reaction(["1","4"],["2"],["1","2"])
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rs.add_reaction(["2"],["3"],["1","3","4"])
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rs.add_reaction(["1","3"],["2"],["1","2"])
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rs.add_reaction(["3"],["2"],["1"])
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rs.add_initial_context_set(["1","4"])
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rs.set_context_entities(["4"])
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return rs
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def bitctr(bits):
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rs = ReactionSystem()
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n = bits
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for i in range(0,bits):
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rs.addBgSetEntity("p" + str(i))
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rs.addBgSetEntity("dec")
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rs.addBgSetEntity("inc")
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# (1) no dec, no inc
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for j in range(0,bits):
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rs.add_reaction(["p"+str(j)], ["dec","inc"], ["p"+str(j)])
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# (2) increment
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rs.add_reaction(["inc"],["dec","p0"],["p0"])
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for j in range(1,bits):
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R = ["inc"]
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for k in range(0,j):
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R.append("p"+str(k))
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I = ["dec","p"+str(j)]
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P = ["p"+str(j)]
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rs.add_reaction(R, I, P)
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for j in range(0,bits):
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for k in range(j+1,bits):
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rs.add_reaction(["inc","p"+str(k)], ["dec","p"+str(j)], ["p"+str(k)])
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# (3) decrement
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for j in range(0,bits):
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R=["dec"]
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I=["inc"]
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for k in range(0,j+1):
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I.append("p"+str(k))
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P=["p"+str(j)]
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rs.add_reaction(R, I, P)
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for j in range(0,bits):
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for k in range(j+1,bits):
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rs.add_reaction(["dec","p"+str(j),"p"+str(k)], ["inc"], ["p"+str(k)])
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rs.set_context_entities(["dec","inc"])
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rs.add_initial_context_set(["inc"])
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return rs
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def ca_toy_ex1():
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rs = ReactionSystem()
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rs.add_bg_set_entities(list("axbcdfegh"))
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rs.add_reaction(["a"], ["x"], ["b"])
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rs.add_reaction(["b"], ["x"], ["c"])
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rs.add_reaction(["c","f"], ["x"], ["d"])
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rs.add_reaction(["d"], ["x"], ["e"])
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#rs.set_context_entities(["f","g","h"])
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#rs.add_initial_context_set(["a"])
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ca = ContextAutomaton(rs)
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ca.add_init_state("1")
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ca.add_state("2")
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ca.add_transition("1", ["a"], "2")
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ca.add_transition("2", [], "2")
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ca.add_transition("2", ["f"], "2")
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ca.add_transition("2", ["x"], "2")
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rsca = ReactionSystemWithAutomaton(rs,ca)
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return rsca
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def ca_toy_ex1_property1():
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return ["e"]
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def ca_bitctr(bits):
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rs = ReactionSystem()
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n = bits
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for i in range(0,bits):
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rs.add_bg_set_entities(["p" + str(i)])
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rs.add_bg_set_entities(["dec"])
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rs.add_bg_set_entities(["inc"])
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# (1) no dec, no inc
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for j in range(0,bits):
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rs.add_reaction(["p"+str(j)], ["dec","inc"], ["p"+str(j)])
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# (2) increment
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rs.add_reaction(["inc"],["dec","p0"],["p0"])
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for j in range(1,bits):
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R = ["inc"]
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for k in range(0,j):
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R.append("p"+str(k))
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I = ["dec","p"+str(j)]
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P = ["p"+str(j)]
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rs.add_reaction(R, I, P)
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for j in range(0,bits):
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for k in range(j+1,bits):
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rs.add_reaction(["inc","p"+str(k)], ["dec","p"+str(j)], ["p"+str(k)])
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# (3) decrement
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for j in range(0,bits):
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R=["dec"]
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I=["inc"]
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for k in range(0,j+1):
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I.append("p"+str(k))
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P=["p"+str(j)]
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rs.add_reaction(R, I, P)
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for j in range(0,bits):
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for k in range(j+1,bits):
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rs.add_reaction(["dec","p"+str(j),"p"+str(k)], ["inc"], ["p"+str(k)])
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ca = ContextAutomaton(rs)
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ca.add_init_state("1")
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ca.add_transition("1", ["inc"], "1")
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ca.add_transition("1", ["inc","dec"], "1")
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ca.add_transition("1", ["dec"], "1")
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rsca = ReactionSystemWithAutomaton(rs,ca)
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return rsca
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def ca_bitctr_property(bits):
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state = []
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for i in range(0,bits):
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state.append("p"+str(i))
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return state
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def drs_toy_ex1():
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drs = DistributedReactionSystem()
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drs.add_bg_set_entities(list("axbcd"))
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drs.add_reaction(0, ["a"], ["x"], ["b"])
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drs.add_reaction(0, ["b"], ["c"], ["d"])
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drs.add_reaction(1, ["a"], [], ["b"])
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drs.add_init_state("init")
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drs.add_state("working")
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drs.add_transition("init", ([0],[ ["a"], ["a"] ]), "working")
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drs.add_transition("working", ([1],[ ["b"], ["a"] ]), "working")
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return drs
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def drs_toy_ex1_property1():
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return [["b"],["b"]]
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def drs_mutex(k):
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drs = DistributedReactionSystem()
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ctrl = k
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# agents = 0 ... (k-1)
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drs.add_bg_set_entities(["lock", "busy", "release", "req", "out", "in"])
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drs.add_reaction(ctrl, ["lock"], ["release"], ["lock"])
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drs.add_reaction(ctrl, ["req"], [], ["lock"])
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for i in range(k):
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#drs.add_reaction(i, ["out"], [], ["req"])
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drs.add_reaction(i, ["out","busy"], [], ["out"])
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drs.add_reaction(i, ["out"], [], ["req"])
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drs.add_reaction(i, ["req"], ["lock"], ["in"])
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drs.add_reaction(i, ["in"], ["busy"], ["out","release"])
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drs.add_reaction(i, ["in","busy"], [], ["in"])
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drs.add_reaction(i, ["req", "lock"], [], ["req"])
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drs.add_init_state("0")
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drs.add_state("1")
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all_out = [["out"] for i in range(k)]
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all_out.append([]) # empty context for the controller
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all_empty = [[] for i in range(k+1)]
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drs.add_transition("0", ([i for i in range(k+1)], all_out), "1")
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for i in range(k):
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drs.add_transition("1", ([i,ctrl], all_empty), "1")
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one_busy = [[] for x in range(k+1)]
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one_busy[i] = ["busy"]
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drs.add_transition("1", ([i,ctrl], one_busy), "1")
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return drs
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def drs_mutex_property1(k):
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state = [["in"]]
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state.extend([[] for i in range(k)])
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return state
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def run_counter_exp():
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if len(sys.argv) < 1+1:
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print("provide N")
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exit(1)
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N=int(sys.argv[1])
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity("e")
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r.add_bg_set_entity("inc")
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r.add_reaction_inc("e",[("e",1),("inc",1)],[("e",N)])
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# for i in range(1,N):
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# r.add_reaction([("e",i),("inc",1)],[("e",N)],[("e",i+1)])
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# r.show()
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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),("inc",1)], "working")
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c.add_transition("working", [("inc",1)], "working")
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# c.show()
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rc = ReactionSystemWithAutomaton(r,c)
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rc.show()
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smt_rsc = SmtCheckerRSC(rc)
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smt_rsc.check_reachability([('e',N)],print_time=True,max_level=N)
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orc = rc.get_ordinary_reaction_system_with_automaton()
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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(N)],print_time=True)
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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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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(("dec",1))
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for i in range(1,chainLen+1):
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r.add_bg_set_entity("e_" + str(i))
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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)],[(ent,maxConc)])
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r.add_reaction_dec(ent, "dec", [(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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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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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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filename=""
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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 blood_glucose_regulation(print_system=True):
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity(("inc_insulin",1))
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r.add_bg_set_entity(("dec_insulin",1))
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r.add_bg_set_entity(("inc_glycemia",1))
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r.add_bg_set_entity(("dec_glycemia",1))
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r.add_bg_set_entity(("inc_glucagon",1))
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r.add_bg_set_entities([("sugar",1),("aspartame",1),("glycemia",3),("glucagon",1),("insulin",2)])
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# r.add_reaction([],[],[])
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r.add_reaction([("sugar",1)],[],[("inc_insulin",1),("inc_glycemia",1)])
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r.add_reaction([("aspartame",1)],[],[("insulin",1)])
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r.add_reaction_without_reactants([],[("glycemia",1)],[("insulin",1)])
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r.add_reaction([("glycemia",3)],[],[("insulin",1)])
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r.add_reaction([("insulin",2)],[],[("dec_glycemia",1)])
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r.add_reaction([("insulin",1),("glycemia",3)],[],[("dec_glycemia",1)])
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r.add_reaction([("insulin",1)],[("glycemia",2)],[("dec_glycemia",1)])
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r.add_reaction([("glucagon",1)],[],[("glycemia",1)])
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# inc/dec:
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r.add_reaction_inc("glycemia", "inc_glycemia", [],[("glycemia",3),("dec_glycemia",1)])
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r.add_reaction_inc("glycemia", "dec_glycemia", [],[("glycemia",1),("inc_glycemia",1)])
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# potrzebne sa reakcje, ktore utrzymaja okresolna molekule na tym samym poziomie
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# -> przed podtrzymaniem trzeba sie upewnic, ze jednak jakas reakcja nie chce zmienic tego poziomu
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r.add_permanency("sugar",[])
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# moje:
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r.add_reaction([("sugar",1)],[],[("sugar",1)])
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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", [("sugar",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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# 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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