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Examples, invocation script

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Artur Meski
2019-09-22 18:18:35 +01:00
parent f1122cafa2
commit 2166bc38f0
3 changed files with 71 additions and 12 deletions
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115
examples/smt/chain_reaction.py Normal file
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#!/usr/bin/env python
#
# Copyright (c) 2015-2019 Artur Meski
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
from rs import *
from smt import *
import sys
import resource
def chain_reaction(print_system=False):
if len(sys.argv) < 1+3:
print("provide N M B")
print(" B=1 - RSC")
print(" B=0 - RSC translated into RS")
exit(1)
chainLen=int(sys.argv[1]) # chain length
maxConc=int(sys.argv[2]) # depth (max concentration)
verify_rsc=bool(int(sys.argv[3]))
if chainLen < 1 or maxConc < 1:
print("be reasonable")
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()
if verify_rsc:
smt_rsc = SmtCheckerRSC(rc)
prop = [('e_'+str(chainLen),maxConc)]
smt_rsc.check_reachability((prop,[]),max_level=maxConc*chainLen+10)
else:
orc = rc.get_ordinary_reaction_system_with_automaton()
if print_system:
print("\nTranslated:")
orc.show()
smt_tr_rs = SmtCheckerRS(orc)
smt_tr_rs.check_reachability(['e_'+str(chainLen)+"#"+str(maxConc)])
time=0
mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
if verify_rsc:
filename_t="bench_rsc_time.log"
filename_m="bench_rsc_mem.log"
time=smt_rsc.get_verification_time()
else:
filename_t="bench_tr_rs_time.log"
filename_m="bench_tr_rs_mem.log"
time=smt_tr_rs.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()
def main():
chain_reaction()
if __name__ == "__main__":
main()
# EOF

122
examples/smt/heat_shock_response.py Executable file
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#!/usr/bin/env python
#
# Copyright (c) 2015-2019 Artur Meski
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
from rs import *
from smt import *
import sys
import resource
def heat_shock_response(print_system=True, verify_rsc=True):
if len(sys.argv) < 1+1:
print("{source} <type>".format(source=sys.argv[0]))
print("type:")
print(" - 1 -- RSC")
print(" - 0 -- RSC translated into RS")
print()
exit(1)
verify_rsc=bool(int(sys.argv[1]))
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 = [ ("mfp",1) ]
prop_block = [ ]
prop = (prop_req,prop_block)
rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
if verify_rsc:
smt_rsc = SmtCheckerRSC(rc)
smt_rsc.check_reachability(prop,max_level=40)
else:
orc = rc.get_ordinary_reaction_system_with_automaton()
if print_system:
print("\nTranslated:")
orc.show()
smt_tr_rs = SmtCheckerRS(orc)
smt_tr_rs.check_reachability(rs_prop)
def main():
heat_shock_response()
if __name__ == "__main__":
main()
# EOF