Formulae for Scalable Chain; some fixes and improvements

logics/rsltl.py

@@ -3,8 +3,7 @@ from enum import Enum
 
 from logics.bags import *
 
-rsLTL_form_type = Enum('rsLTL_form_type', 'bag l_and l_or l_not t_globally t_finally t_next t_until t_release')
+rsLTL_form_type = Enum('rsLTL_form_type', 'bag l_and l_or l_not l_implies t_globally t_finally t_next t_until t_release')
-
 
 class Formula_rsLTL(object):
     
@@ -35,6 +34,8 @@ class Formula_rsLTL(object):
             return "( " + repr(self.left_operand) + " & " + repr(self.right_operand) + " )"
         if self.f_type == rsLTL_form_type.l_or:
             return "( " + repr(self.left_operand) + " | " + repr(self.right_operand) + " )"
+        if self.f_type == rsLTL_form_type.l_implies:
+            return "( " + repr(self.left_operand) + " => " + repr(self.right_operand) + " )"
         if self.f_type == rsLTL_form_type.t_until:
             return "( " + repr(self.left_operand) + " U[" + repr(self.sub_operand) + "]" + repr(self.right_operand) + " )"
         if self.f_type == rsLTL_form_type.t_release:
@@ -68,6 +69,10 @@ class Formula_rsLTL(object):
     def f_R(cls, sub, arg_L, arg_R):
         return cls(rsLTL_form_type.t_release, L_oper = arg_L, R_oper = arg_R, sub_oper = sub)
         
+    @classmethod
+    def f_Implies(cls, arg_L, arg_R):
+        return cls(rsLTL_form_type.l_implies, L_oper = arg_L, R_oper = arg_R)
+        
     def __and__(self, other):
         return Formula_rsLTL(rsLTL_form_type.l_and, L_oper = self, R_oper = other)
     

logics/rsltl_encoder.py

@@ -1,5 +1,8 @@
 from logics.rsltl import *
 
+def simplify(x):
+    return x
+
 class rsLTL_Encoder(object):
     """Class for encoding rsLTL formulae for a given smt_checker instance"""
         
@@ -10,8 +13,20 @@ class rsLTL_Encoder(object):
         self.rs = smt_checker.rs
         self.loop_position = smt_checker.loop_position
         
+        self.init_ncalls()
+        
+    def init_ncalls(self):
+        self.ncalls_encode = 0
+        self.ncalls_encode_approx = 0
+        
+    def get_ncalls(self):
+        return (self.ncalls_encode, self.ncalls_encode_approx)
+        
     def encode_bag(self, bag_formula, level, context=False):
-                
+
+        if not bag_formula:
+            raise RuntimeError("bag_formula is None")
+
         if bag_formula.f_type == BagDesc_oper.entity:
             entity_id = self.rs.get_entity_id(bag_formula.entity)
             if context:
@@ -56,6 +71,8 @@ class rsLTL_Encoder(object):
       
     def encode(self, formula, level, bound):
         
+        self.ncalls_encode += 1
+        
         if not isinstance(formula, Formula_rsLTL):
             raise NotImplementedError("Unsupported formula type: " + str(type(formula)))
         
@@ -76,20 +93,26 @@ class rsLTL_Encoder(object):
             return And(
                     self.encode(formula.left_operand, level, bound), 
                     self.encode(formula.right_operand, level, bound)
-                )
+            )
 
         elif formula.f_type == rsLTL_form_type.l_or:
             return Or(
                     self.encode(formula.left_operand, level, bound), 
                     self.encode(formula.right_operand, level, bound)
-                )
+            )
 
+        elif formula.f_type == rsLTL_form_type.l_implies:
+            return Implies(
+                    self.encode(formula.left_operand, level, bound), 
+                    self.encode(formula.right_operand, level, bound)
+            )
+            
         elif formula.f_type == rsLTL_form_type.t_next:
             if level < bound:
                 enc = And(
                         self.encode(formula.left_operand, level + 1, bound), 
                         self.encode_bag_ctx(formula.sub_operand, level)
-                    )
+                )
             else: 
                 # level == bound
                 enc = False
@@ -107,22 +130,22 @@ class rsLTL_Encoder(object):
                         self.encode(formula.left_operand, level, bound),
                         self.encode_bag_ctx(formula.sub_operand, level),
                         self.encode(formula, level + 1, bound)
-                    )
+                )
             else:
                 # level == bound
                 enc_loops = False
                 for loop_level in range(1, bound+1):
                     enc_loops = Or(enc_loops, 
-                            And(
+                        And(
-                                self.loop_position == loop_level,
+                            self.loop_position == loop_level,
-                                self.encode_approx(formula, loop_level, bound),
+                            self.encode_approx(formula, loop_level, bound),
-                            )
                         )
-                enc = And(
-                        self.encode(formula.left_operand, bound, bound),
-                        enc_loops, 
-                        self.encode_bag_ctx(formula.sub_operand, level)
                     )
+                enc = And(
+                    self.encode(formula.left_operand, bound, bound),
+                    enc_loops, 
+                    self.encode_bag_ctx(formula.sub_operand, level)
+                )
                 enc = simplify(enc)  
 
             return enc
@@ -218,6 +241,9 @@ class rsLTL_Encoder(object):
         
         Used by encode()
         """
+        
+        self.ncalls_encode_approx += 1
+        
         if formula.f_type == rsLTL_form_type.t_until:
             if level < bound:
                 enc = Or(

rs_testing.py

@@ -9,7 +9,8 @@ def run_tests():
     
     # test_extended_automaton()
     # process()
-    heat_shock_response()
+    # heat_shock_response()
+    scalable_chain(print_system=True)
     
 def heat_shock_response(print_system=True):
 
@@ -96,7 +97,97 @@ def heat_shock_response(print_system=True):
 
 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+2:
+        print("provide <chainLen> <maxConc>")
+        exit(1)
+
+    chainLen=int(sys.argv[1]) # chain length
+    maxConc=int(sys.argv[2]) # depth (max concentration)
+        
+    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()
+    
+    smt_rsc = SmtCheckerRSC(rc)
+
+    prop = [('e_'+str(chainLen),maxConc)]
+    # smt_rsc.check_reachability((prop,[]),max_level=maxConc*chainLen+10)
+
+    # smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10)
+
+    # (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)
+
+    # (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)
+    
+    # (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(i)) == maxConc)
+    #         )
+    #     )
+    # )
+    # smt_rsc.check_rsltl(formula=f_3)
+    
+    ###########################################################################
+
+    time=0
+    mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
+    filename_t="bench_rsc_time.log"
+    filename_m="bench_rsc_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()
+
+
 def test_rsLTL():
 
     r = ReactionSystemWithConcentrations()

smt/smt_checker_rsc.py

@@ -383,6 +383,7 @@ class SmtCheckerRSC(object):
         self.reset()
         
         print("[" + colour_str(C_BOLD, "i") + "] Running rsLTL bounded model checking")
+        print("[" + colour_str(C_BOLD, "i") + "] Formula: " + str(formula))
         
         if print_time:
             # start = time()
@@ -407,8 +408,11 @@ class SmtCheckerRSC(object):
 
             # reachability test:
             self.solver.push()
-            print("[" + colour_str(C_BOLD, "i") + "] Adding the formula encoding...")
+            print("[" + colour_str(C_BOLD, "i") + "] Generating the formula encoding...")
+            encoder.init_ncalls()
             f = encoder.encode(formula, 0, self.current_level)
+            print("[" + colour_str(C_BOLD, "i") + "] Encode calls: " + str(encoder.get_ncalls()))
+            print("[" + colour_str(C_BOLD, "i") + "] Adding the formula to the solver...")
             self.solver.add(f)
             
             print("[" + colour_str(C_BOLD, "i") + "] Adding the loops encoding...")