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This commit is contained in:
Artur Meski
2019-09-22 18:23:59 +01:00
parent c6b0d874da
commit acc4998613
2 changed files with 64 additions and 50 deletions
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78
examples/smt/chain_reaction.py
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@@ -26,54 +26,63 @@ from smt import *
import sys import sys
import resource import resource
def chain_reaction(print_system=False): def chain_reaction(print_system=False):
if len(sys.argv) < 1+3: if len(sys.argv) < 1 + 3:
print("provide N M B") print("{source} <N> <M> <type>".format(source=sys.argv[0]))
print(" B=1 - RSC") print()
print(" B=0 - RSC translated into RS") print("* N,M -- integers (scaling parameters)")
print("* type:")
print(" - 1 - RSC")
print(" - 0 - RSC translated into RS")
print()
exit(1) exit(1)
chainLen=int(sys.argv[1]) # chain length chainLen = int(sys.argv[1])
maxConc=int(sys.argv[2]) # depth (max concentration) maxConc = int(sys.argv[2]) # depth (max concentration)
verify_rsc=bool(int(sys.argv[3])) verify_rsc = bool(int(sys.argv[3]))
if chainLen < 1 or maxConc < 1: if chainLen < 1 or maxConc < 1:
print("be reasonable") print("be reasonable")
exit(1) exit(1)
r = ReactionSystemWithConcentrations() r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("inc",1)) r.add_bg_set_entity(("inc", 1))
r.add_bg_set_entity(("dec",1)) r.add_bg_set_entity(("dec", 1))
for i in range(1,chainLen+1): for i in range(1, chainLen + 1):
r.add_bg_set_entity(("e_" + str(i),maxConc)) r.add_bg_set_entity(("e_" + str(i), maxConc))
for i in range(1,chainLen+1): for i in range(1, chainLen + 1):
ent = "e_" + str(i) ent = "e_" + str(i)
r.add_reaction_inc(ent, "inc", [(ent, 1)],[(ent,maxConc)]) r.add_reaction_inc(ent, "inc", [(ent, 1)], [(ent, maxConc)])
r.add_reaction_dec(ent, "dec", [(ent, 1)],[]) r.add_reaction_dec(ent, "dec", [(ent, 1)], [])
if i < chainLen: if i < chainLen:
r.add_reaction([(ent,maxConc)],[],[("e_"+str(i+1),1)]) r.add_reaction([(ent, maxConc)], [], [("e_" + str(i + 1), 1)])
r.add_reaction([("e_" + str(chainLen),maxConc)],[("dec",1)],[("e_" + str(chainLen),maxConc)]) r.add_reaction(
[("e_" + str(chainLen), maxConc)],
[("dec", 1)],
[("e_" + str(chainLen), maxConc)],
)
c = ContextAutomatonWithConcentrations(r) c = ContextAutomatonWithConcentrations(r)
c.add_init_state("init") c.add_init_state("init")
c.add_state("working") c.add_state("working")
c.add_transition("init", [("e_1",1),("inc",1)], "working") c.add_transition("init", [("e_1", 1), ("inc", 1)], "working")
c.add_transition("working", [("inc",1)], "working") c.add_transition("working", [("inc", 1)], "working")
rc = ReactionSystemWithAutomaton(r,c) rc = ReactionSystemWithAutomaton(r, c)
if print_system: if print_system:
rc.show() rc.show()
if verify_rsc: if verify_rsc:
smt_rsc = SmtCheckerRSC(rc) smt_rsc = SmtCheckerRSC(rc)
prop = [('e_'+str(chainLen),maxConc)] prop = [("e_" + str(chainLen), maxConc)]
smt_rsc.check_reachability((prop,[]),max_level=maxConc*chainLen+10) smt_rsc.check_reachability((prop, []), max_level=maxConc * chainLen + 10)
else: else:
orc = rc.get_ordinary_reaction_system_with_automaton() orc = rc.get_ordinary_reaction_system_with_automaton()
@@ -81,26 +90,26 @@ def chain_reaction(print_system=False):
print("\nTranslated:") print("\nTranslated:")
orc.show() orc.show()
smt_tr_rs = SmtCheckerRS(orc) smt_tr_rs = SmtCheckerRS(orc)
smt_tr_rs.check_reachability(['e_'+str(chainLen)+"#"+str(maxConc)]) smt_tr_rs.check_reachability(["e_" + str(chainLen) + "#" + str(maxConc)])
time=0 time = 0
mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024) mem_usage = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / (1024 * 1024)
if verify_rsc: if verify_rsc:
filename_t="bench_rsc_time.log" filename_t = "bench_rsc_time.log"
filename_m="bench_rsc_mem.log" filename_m = "bench_rsc_mem.log"
time=smt_rsc.get_verification_time() time = smt_rsc.get_verification_time()
else: else:
filename_t="bench_tr_rs_time.log" filename_t = "bench_tr_rs_time.log"
filename_m="bench_tr_rs_mem.log" filename_m = "bench_tr_rs_mem.log"
time=smt_tr_rs.get_verification_time() time = smt_tr_rs.get_verification_time()
f=open(filename_t, 'a') f = open(filename_t, "a")
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n" log_str = "(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n"
f.write(log_str) f.write(log_str)
f.close() f.close()
f=open(filename_m, 'a') f = open(filename_m, "a")
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n" log_str = "(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n"
f.write(log_str) f.write(log_str)
f.close() f.close()
@@ -109,6 +118,7 @@ def main():
chain_reaction() chain_reaction()
if __name__ == "__main__": if __name__ == "__main__":
main() main()

4
examples/smt/heat_shock_response.py
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@@ -112,6 +112,10 @@ def heat_shock_response(print_system=True, verify_rsc=True):
smt_tr_rs.check_reachability(rs_prop) smt_tr_rs.check_reachability(rs_prop)
def state_translate_rsc2rs(p):
return [e[0] + "#" + str(e[1]) for e in p]
def main(): def main():
heat_shock_response() heat_shock_response()