Clean-up
This commit is contained in:
Artur Meski
@@ -1,305 +0,0 @@
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#!/usr/bin/env python
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"""
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--- Distributed Reaction Systems Manipulation
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"""
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from sys import exit
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class DistributedReactionSystem(object):
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def __init__(self):
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self.__reactions = []
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self.__background_set = []
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self.__reactions_by_prod = []
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self.__states = []
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self.__transitions = []
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self.__init_state = None
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self.__context_sets_size = None
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@property
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def background_set(self):
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return self.__background_set
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@property
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def set_of_background_ids(self):
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return set(range(len(self.__background_set)))
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@property
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def components_count(self):
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return len(self.__reactions)
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def add_bg_set_entity(self, name):
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if not self.is_in_background_set(name):
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self.__background_set.append(name)
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else:
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print("The entity \"" + str(name) + "\" is already on the list")
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exit(1)
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def add_bg_set_entities(self, names):
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for name in names:
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self.add_bg_set_entity(name)
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def is_in_background_set(self, entity):
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"""Checks if the given name is valid wrt the background set="""
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if entity in self.__background_set:
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return True
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else:
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return False
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def get_entity_id(self, name):
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try:
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return self.__background_set.index(name)
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except ValueError:
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print("Undefined background set entity: " + repr(name))
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exit(1)
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def get_state_ids(self, state):
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ids = []
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for entity in state:
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ids.append(self.get_entity_id(entity))
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return ids
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def get_entity_name(self, entity_id):
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"""Returns the string corresponding to the entity"""
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return self.__background_set[entity_id]
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def ensure_reactions(self, k):
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while len(self.__reactions) <= k:
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self.__reactions.append([])
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def add_reaction(self, k, R, I, P):
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"""Adds a reaction"""
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if R == [] or P == []:
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print("No reactants of products defined")
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raise
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reactants = []
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for entity in R:
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reactants.append(self.get_entity_id(entity))
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inhibitors = []
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for entity in I:
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inhibitors.append(self.get_entity_id(entity))
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products = []
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for entity in P:
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products.append(self.get_entity_id(entity))
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self.ensure_reactions(k)
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self.__reactions[k].append((reactants, inhibitors, products))
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def entities_names_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += entity + ", "
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s = s[:-2]
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return s
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def entities_ids_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += self.get_entity_name(entity) + ", "
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s = s[:-2]
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return s
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def show_reactions(self):
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print("[*] Reactions:")
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for i in range(len(self.__reactions)):
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local_reactions = self.__reactions[i]
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print(" agent = " + str(i))
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for rcts,inhib,prods in local_reactions:
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print("\t - ( R={" + self.entities_ids_set_to_str(rcts) + "}, \tI={" + self.entities_ids_set_to_str(inhib) + "}, \tP={" + self.entities_ids_set_to_str(prods) + "} )")
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def show_background_set(self):
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print("[*] Background set: {" + self.entities_names_set_to_str(self.__background_set) + "}")
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def show(self):
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self.show_background_set()
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self.show_reactions()
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self.show_states()
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self.show_transitions()
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print()
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def reactions_by_product_are_cached(self, component_id):
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if len(self.__reactions_by_prod) > component_id:
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if self.__reactions_by_prod[component_id] != None:
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return True
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return False
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def get_reactions_by_product(self, component_id):
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"""Sorts reactions for the component given by component_id by their products and returns a dictionary of products"""
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if self.reactions_by_product_are_cached(component_id):
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return self.__reactions_by_prod[component_id]
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producible_entities = set()
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for reactants,inhibitors,products in self.__reactions[component_id]:
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producible_entities = producible_entities.union(set(products))
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reactions_by_prod = dict()
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for prod_entity in producible_entities:
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reactions_by_prod[prod_entity] = []
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for reactants,inhibitors,products in self.__reactions[component_id]:
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if prod_entity in products:
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reactions_by_prod[prod_entity].append([reactants,inhibitors])
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# save in cache
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while len(self.__reactions_by_prod) <= component_id: # ensure that the size of cache is right
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self.__reactions_by_prod.append(None)
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self.__reactions_by_prod[component_id] = reactions_by_prod
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return reactions_by_prod
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@property
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def states(self):
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return self.__states
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@property
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def transitions(self):
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return self.__transitions
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def add_state(self, name):
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if name not in self.__states:
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self.__states.append(name)
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else:
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print("\'%s\' already added. skipping..." % (name,))
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def add_init_state(self, name):
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self.add_state(name)
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self.__init_state = self.__states.index(name)
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def get_init_state_name(self):
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if self.__init_state == None:
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return None
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return self.__states[self.__init_state]
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def is_state(self, name):
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if name in self.__states:
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return True
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else:
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return False
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def get_state_id(self, name):
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try:
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return self.__states.index(name)
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except ValueError:
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print("Undefined context automaton state: " + repr(name))
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exit(1)
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def get_init_state_id(self):
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return self.__init_state
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def print_states(self):
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for state in self.__states:
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print(state)
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def is_valid_context_sets(self, context_sets):
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for c in context_sets:
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if not self.is_valid_context(c):
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return False
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return True
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def is_valid_context(self, context):
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if set(context).issubset(self.__background_set):
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return True
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else:
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return False
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def add_transition(self, src, label, dst):
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recipients = label[0]
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context_sets = label[1]
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if not type(context_sets) is list:
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print("Context sets must be of type list")
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exit(1)
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for s in context_sets:
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if not type(s) is set and not type(s) is list:
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print("Each context set must be of type set or list")
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exit(1)
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if self.__context_sets_size == None:
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self.__context_sets_size = len(context_sets)
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else:
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if len(context_sets) != self.__context_sets_size:
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print("Inconsistent size of the context sets: " + str(len(context_sets)) + " != " + str(self.__context_sets_size))
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exit(1)
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if not self.is_valid_context_sets(context_sets):
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raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
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if not self.is_state(src):
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raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
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if not self.is_state(dst):
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raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
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new_context_sets = []
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for c in context_sets:
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new_c_set = set()
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for e in set(c):
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new_c_set.add(self.get_entity_id(e))
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new_context_sets.append(new_c_set)
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recipients = set(recipients)
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self.__transitions.append((self.get_state_id(src),(recipients,new_context_sets),self.get_state_id(dst)))
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def context2str(self, context_sets):
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"""Converts the set of entities ids into the string with their names"""
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s = "["
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for ctx in context_sets:
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if len(ctx) == 0:
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s += " 0"
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else:
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s += " {"
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for c in ctx:
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s += " " + self.get_entity_name(c)
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s += " }"
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s += " ]"
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return s
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def show_transitions(self):
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print("[*] Context automaton transitions:")
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for transition in self.__transitions:
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str_transition = str(transition[0]) + " --( "
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str_transition += str(list(transition[1][0])) + "<=" + self.context2str(transition[1][1])
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str_transition += " )--> " + str(transition[2])
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print("\t- " + str_transition)
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def show_states(self):
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init_state_name = self.get_init_state_name()
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print("[*] Context automaton states:")
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for state in self.__states:
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print("\t- " + state, end="")
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if state == init_state_name:
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print(" [init]")
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else:
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print()
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def sanity_check(self):
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"""Performs a sanity check of the defined distributed reaction system"""
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print("[i] Performing sanity check of the DRS")
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if self.__reactions == []:
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print("No reactions defined")
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exit(1)
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if self.__background_set == []:
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print("Empty background set")
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exit(1)
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if self.__init_state == None:
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print("Initial state not specified")
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exit(1)
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if self.__context_sets_size != len(self.__reactions):
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print("Inconsistent sizes of the context sets with respect to the number of components/agents/processes: " + str(self.__context_sets_size) + " != " + str(len(self.__reactions)))
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exit(1)
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2
rssmt.py
2
rssmt.py
@@ -23,7 +23,7 @@ if profiling:
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##################################################################
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version = "2.5"
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version = "2.99"
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rsmc_banner = """
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Reaction Systems SMT-Based Model Checking
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@@ -2,5 +2,3 @@
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from smt.smt_checker_rs import SmtCheckerRS
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from smt.smt_checker_rsc import SmtCheckerRSC
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from smt.smt_checker_rsc_param import SmtCheckerRSCParam
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from smt.smt_checker_rs_na import SmtCheckerRSNA
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from smt.smt_checker_distrib_rs import SmtCheckerDistribRS
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@@ -1,530 +0,0 @@
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"""
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SMT-based Model Checking Module for RS
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"""
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from z3 import *
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from time import time
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from sys import stdout
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class SmtChecker(object):
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def __init__(self, rs):
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##############################################################
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# Encoded RS
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##############################################################
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rs.sanity_check()
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self.reaction_system = rs
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##############################################################
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# SMT variables
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##############################################################
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self.v = []
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self.v_init = []
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#self.vSucc = []
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#self.vSuccInit = []
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self.v_ctx = []
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self.next_level_to_encode = 0
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##############################################################
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# SMT solver instance
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##############################################################
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self.solver = Solver()
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#def smtVar(self, level, entityID, primed=False):
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# return "?"
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def prepare_context_variables(self):
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"""Encodes all the context variables"""
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level = self.next_level_to_encode
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variables = []
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for entity in self.reaction_system.background_set:
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variables.append(Bool("C"+str(level)+"_"+entity))
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self.v_ctx.append(variables)
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def prepare_state_variables(self):
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"""Encodes all the state variables (including successors)"""
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level = self.next_level_to_encode
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variables = []
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#variablesSucc = []
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for entity in self.reaction_system.background_set:
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variables.append(Bool("L"+str(level)+"_"+entity))
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#variablesSucc.append(Bool("R"+str(level)+"_"+entity))
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self.v.append(variables)
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#self.vSucc.append(variablesSucc)
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self.v_init.append(Bool("L"+str(level)+"_Init"))
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#self.vSuccInit.append(Bool("R"+str(level)+"_Init"))
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def prepare_all_variables(self):
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"""Encodes all the variables"""
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self.prepare_state_variables()
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self.prepare_context_variables()
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self.next_level_to_encode += 1
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def enc_init_state(self, level):
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"""Encodes the initial state at the given level"""
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init_state_enc = self.v_init[level]
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for v in self.v[level]:
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init_state_enc = simplify(And(init_state_enc, Not(v)))
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return init_state_enc
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def enc_init_contexts(self, level):
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"""Encodes the initial contexts set at the given level"""
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init_contexts_set_enc = False # Or
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for ctx in self.reaction_system.init_contexts:
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single_ctx_enc = True # And
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not_ctx_entities = list(range(0, len(self.reaction_system.background_set)))
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for entity in ctx:
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single_ctx_enc = simplify(And(single_ctx_enc, self.v_ctx[level][entity]))
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not_ctx_entities.remove(entity)
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for entity in not_ctx_entities:
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single_ctx_enc = simplify(And(single_ctx_enc, Not(self.v_ctx[level][entity])))
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init_contexts_set_enc = simplify(Or(init_contexts_set_enc, single_ctx_enc))
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#print("initContextSetEnc: " + repr(initContextsSetEnc))
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return init_contexts_set_enc
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def enc_not_allowed_contexts(self, level):
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"""Encodes all the context entities that are not allowed in the context sets"""
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bg_set = set(range(0,len(self.reaction_system.background_set)))
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ctx_ent_set = set(self.reaction_system.context_entities)
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not_ctx_ent_set = bg_set.difference(ctx_ent_set)
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enc = True
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for entity in not_ctx_ent_set:
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enc = simplify(And(enc, Not(self.v_ctx[level][entity])))
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return enc
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def enc_enabledness(self, level, prod_entity):
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"""Encodes the enabledness condition for a given level and a given entity"""
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rcts_for_prod_entity = self.reaction_system.get_reactions_by_product()[prod_entity]
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if rcts_for_prod_entity == []:
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return False
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#encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
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# And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
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enc_rct_prod = False
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for ri_pair in rcts_for_prod_entity: # reactants-inhibitors pair
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enc_reactants = True
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enc_inhibitors = True
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for reactant in ri_pair[0]:
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][reactant], self.v_ctx[level][reactant])))
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for inhibitor in ri_pair[1]:
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enc_inhibitors = simplify(And(enc_inhibitors,
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Not(Or(self.v[level][inhibitor], self.v_ctx[level][inhibitor]))))
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enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
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#print("encEnabledness(" + repr(prodEntity) + "): " + repr(simplify(And(encInitEnab, encRctProd))))
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#return simplify(And(encInitEnab, encRctProd))
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return enc_rct_prod
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def enc_entity_production(self, level, prod_entity):
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"""Encodes the production of a given entity from a given level at level+1"""
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enc_enab_cond = self.enc_enabledness(level, prod_entity)
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enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
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And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
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return enc_ent_prod
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def enc_transition_relation(self, level):
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"""Encodes the transition relation"""
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unused_entities = list(range(0,len(self.reaction_system.background_set)))
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enc_trans = True
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for prod_entity in self.reaction_system.get_reactions_by_product():
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unused_entities.remove(prod_entity)
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enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity)))
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enc_trans = simplify(And(enc_trans, Not(self.v_init[level+1])))
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for prod_entity in unused_entities:
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enc_trans = simplify(And(enc_trans, Not(self.v[level+1][prod_entity])))
|
||||
|
||||
if level == 0:
|
||||
enc_init_enab = self.enc_init_contexts(level)
|
||||
else: # level > 0:
|
||||
enc_init_enab = self.enc_not_allowed_contexts(level)
|
||||
|
||||
#encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
|
||||
# And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
|
||||
|
||||
enc_trans = simplify(And(enc_trans, enc_init_enab))
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_state(self, level, state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
enc = Not(self.v_init[level])
|
||||
|
||||
state_ids = self.reaction_system.get_state_ids(state)
|
||||
|
||||
for entity in state_ids:
|
||||
enc = And(enc, self.v[level][entity])
|
||||
|
||||
not_in_state = set(range(0, len(self.reaction_system.background_set)))
|
||||
not_in_state = not_in_state.difference(set(state_ids))
|
||||
|
||||
for entity in not_in_state:
|
||||
enc = And(enc, Not(self.v[level][entity]))
|
||||
|
||||
return enc
|
||||
|
||||
def decode_witness(self, max_level):
|
||||
|
||||
m = self.solver.model()
|
||||
|
||||
for level in range(0,max_level+1):
|
||||
|
||||
print("\n[Level=" + repr(level) + "]")
|
||||
|
||||
if repr(m[self.v_init[level]]) == "True":
|
||||
print("** Initial state")
|
||||
|
||||
print("State:\n{"),
|
||||
for var_id in range(0, len(self.v[level])):
|
||||
if repr(m[self.v[level][var_id]]) == "True":
|
||||
print("\t" + self.reaction_system.get_entity_name(var_id)),
|
||||
print("}")
|
||||
|
||||
if level != max_level:
|
||||
print("Context set:"),
|
||||
print("{"),
|
||||
for var_id in range(0, len(self.v[level])):
|
||||
if repr(m[self.v_ctx[level][var_id]]) == "True":
|
||||
print("\t" + self.reaction_system.get_entity_name(var_id)),
|
||||
print("}")
|
||||
|
||||
|
||||
def check_reachability(self, state, print_witness=True, print_time=False):
|
||||
"""Main testing function"""
|
||||
|
||||
if print_time:
|
||||
start = time()
|
||||
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_init_state(0))
|
||||
current_level = 0
|
||||
|
||||
while True:
|
||||
#print("Level: " + str(current_level))
|
||||
print("\rLevel: " + str(current_level)),
|
||||
stdout.flush()
|
||||
|
||||
self.prepare_all_variables()
|
||||
|
||||
# reachability test:
|
||||
self.solver.push()
|
||||
self.solver.add(self.enc_state(current_level,state))
|
||||
|
||||
result = self.solver.check()
|
||||
print(result)
|
||||
if result == sat:
|
||||
print("\nSAT")
|
||||
if print_witness:
|
||||
self.decode_witness(current_level)
|
||||
break
|
||||
else:
|
||||
self.solver.pop()
|
||||
|
||||
self.solver.add(self.enc_transition_relation(current_level))
|
||||
|
||||
current_level += 1
|
||||
|
||||
if print_time:
|
||||
stop = time()
|
||||
print("Time: " + repr(stop-start))
|
||||
|
||||
#
|
||||
# class SmtCheckerPGRS(object):
|
||||
#
|
||||
# def __init__(self, rs):
|
||||
#
|
||||
# ##############################################################
|
||||
# # Encoded RS
|
||||
# ##############################################################
|
||||
# rs.sanity_check()
|
||||
# self.reaction_system = rs
|
||||
#
|
||||
# ##############################################################
|
||||
# # SMT variables
|
||||
# ##############################################################
|
||||
# self.v = []
|
||||
# self.v_init = []
|
||||
#
|
||||
# #self.vSucc = []
|
||||
# #self.vSuccInit = []
|
||||
#
|
||||
# self.v_ctx = []
|
||||
#
|
||||
# self.next_level_to_encode = 0
|
||||
#
|
||||
# ##############################################################
|
||||
# # SMT solver instance
|
||||
# ##############################################################
|
||||
# self.solver = Solver()
|
||||
#
|
||||
# #def smtVar(self, level, entityID, primed=False):
|
||||
# # return "?"
|
||||
#
|
||||
# def prepare_context_variables(self):
|
||||
# """Encodes all the context variables"""
|
||||
#
|
||||
# level = self.next_level_to_encode
|
||||
#
|
||||
# variables = []
|
||||
# for entity in self.reaction_system.background_set:
|
||||
# variables.append(Bool("C"+str(level)+"_"+entity))
|
||||
#
|
||||
# self.v_ctx.append(variables)
|
||||
#
|
||||
# def prepare_state_variables(self):
|
||||
# """Encodes all the state variables (including successors)"""
|
||||
#
|
||||
# level = self.next_level_to_encode
|
||||
#
|
||||
# variables = []
|
||||
# #variablesSucc = []
|
||||
# for entity in self.reaction_system.background_set:
|
||||
# variables.append(Bool("L"+str(level)+"_"+entity))
|
||||
# #variablesSucc.append(Bool("R"+str(level)+"_"+entity))
|
||||
#
|
||||
# self.v.append(variables)
|
||||
# #self.vSucc.append(variablesSucc)
|
||||
#
|
||||
# self.v_init.append(Bool("L"+str(level)+"_Init"))
|
||||
# #self.vSuccInit.append(Bool("R"+str(level)+"_Init"))
|
||||
#
|
||||
# def prepare_all_variables(self):
|
||||
# """Encodes all the variables"""
|
||||
#
|
||||
# self.prepare_state_variables()
|
||||
# self.prepare_context_variables()
|
||||
# self.next_level_to_encode += 1
|
||||
#
|
||||
# def enc_init_state(self, level):
|
||||
# """Encodes the initial state at the given level"""
|
||||
#
|
||||
# init_state_enc = self.v_init[level]
|
||||
#
|
||||
# for v in self.v[level]:
|
||||
# init_state_enc = simplify(And(init_state_enc, Not(v)))
|
||||
#
|
||||
# return init_state_enc
|
||||
#
|
||||
# def enc_init_contexts(self, level):
|
||||
# """Encodes the initial contexts set at the given level"""
|
||||
#
|
||||
# init_contexts_set_enc = False # Or
|
||||
#
|
||||
# for ctx in self.reaction_system.init_contexts:
|
||||
# single_ctx_enc = True # And
|
||||
#
|
||||
# not_ctx_entities = list(range(0, len(self.reaction_system.background_set)))
|
||||
# for entity in ctx:
|
||||
# single_ctx_enc = simplify(And(single_ctx_enc, self.v_ctx[level][entity]))
|
||||
# not_ctx_entities.remove(entity)
|
||||
#
|
||||
# for entity in not_ctx_entities:
|
||||
# single_ctx_enc = simplify(And(single_ctx_enc, Not(self.v_ctx[level][entity])))
|
||||
#
|
||||
# init_contexts_set_enc = simplify(Or(init_contexts_set_enc, single_ctx_enc))
|
||||
#
|
||||
# #print("initContextSetEnc: " + repr(initContextsSetEnc))
|
||||
# return init_contexts_set_enc
|
||||
#
|
||||
# def enc_not_allowed_contexts(self, level):
|
||||
# """Encodes all the context entities that are not allowed in the context sets"""
|
||||
#
|
||||
# bg_set = set(range(0,len(self.reaction_system.background_set)))
|
||||
# ctx_ent_set = set(self.reaction_system.context_entities)
|
||||
#
|
||||
# not_ctx_ent_set = bg_set.difference(ctx_ent_set)
|
||||
#
|
||||
# enc = True
|
||||
# for entity in not_ctx_ent_set:
|
||||
# enc = simplify(And(enc, Not(self.v_ctx[level][entity])))
|
||||
#
|
||||
# return enc
|
||||
#
|
||||
# def enc_enabledness(self, level, prod_entity):
|
||||
# """Encodes the enabledness condition for a given level and a given entity"""
|
||||
#
|
||||
# rcts_for_prod_entity = self.reaction_system.get_reactions_by_product()[prod_entity]
|
||||
#
|
||||
# if rcts_for_prod_entity == []:
|
||||
# return False
|
||||
#
|
||||
# #encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
|
||||
# # And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
|
||||
#
|
||||
# enc_rct_prod = False
|
||||
# for ri_pair in rcts_for_prod_entity: # reactants-inhibitors pair
|
||||
# enc_reactants = True
|
||||
# enc_inhibitors = True
|
||||
# for reactant in ri_pair[0]:
|
||||
# enc_reactants = simplify(And(enc_reactants,
|
||||
# Or(self.v[level][reactant], self.v_ctx[level][reactant])))
|
||||
# for inhibitor in ri_pair[1]:
|
||||
# enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
# Not(Or(self.v[level][inhibitor], self.v_ctx[level][inhibitor]))))
|
||||
#
|
||||
# enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors)))
|
||||
#
|
||||
# #print("encEnabledness(" + repr(prodEntity) + "): " + repr(simplify(And(encInitEnab, encRctProd))))
|
||||
# #return simplify(And(encInitEnab, encRctProd))
|
||||
# return enc_rct_prod
|
||||
#
|
||||
# def enc_entity_production(self, level, prod_entity):
|
||||
# """Encodes the production of a given entity from a given level at level+1"""
|
||||
#
|
||||
# enc_enab_cond = self.enc_enabledness(level, prod_entity)
|
||||
#
|
||||
# enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
|
||||
# And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
|
||||
#
|
||||
# return enc_ent_prod
|
||||
#
|
||||
# def enc_transition_relation(self, level):
|
||||
# """Encodes the transition relation"""
|
||||
#
|
||||
# unused_entities = list(range(0,len(self.reaction_system.background_set)))
|
||||
#
|
||||
# enc_trans = True
|
||||
#
|
||||
# for prod_entity in self.reaction_system.get_reactions_by_product():
|
||||
# unused_entities.remove(prod_entity)
|
||||
#
|
||||
# enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity)))
|
||||
#
|
||||
# enc_trans = simplify(And(enc_trans, Not(self.v_init[level+1])))
|
||||
#
|
||||
# for prod_entity in unused_entities:
|
||||
# enc_trans = simplify(And(enc_trans, Not(self.v[level+1][prod_entity])))
|
||||
#
|
||||
# if level == 0:
|
||||
# enc_init_enab = self.enc_init_contexts(level)
|
||||
# else: # level > 0:
|
||||
# enc_init_enab = self.enc_not_allowed_contexts(level)
|
||||
#
|
||||
# #encInitEnab = simplify(Or(And(self.vInit[level], self.encInitContexts(level)),
|
||||
# # And(Not(self.vInit[level]), self.encNotAllowedContexts(level))))
|
||||
#
|
||||
# enc_trans = simplify(And(enc_trans, enc_init_enab))
|
||||
#
|
||||
# return enc_trans
|
||||
#
|
||||
# def enc_state(self, level, state):
|
||||
# """Encodes the state at the given level"""
|
||||
#
|
||||
# enc = Not(self.v_init[level])
|
||||
#
|
||||
# state_ids = self.reaction_system.get_state_ids(state)
|
||||
#
|
||||
# for entity in state_ids:
|
||||
# enc = And(enc, self.v[level][entity])
|
||||
#
|
||||
# not_in_state = set(range(0, len(self.reaction_system.background_set)))
|
||||
# not_in_state = not_in_state.difference(set(state_ids))
|
||||
#
|
||||
# for entity in not_in_state:
|
||||
# enc = And(enc, Not(self.v[level][entity]))
|
||||
#
|
||||
# return enc
|
||||
#
|
||||
# def decode_witness(self, max_level):
|
||||
#
|
||||
# m = self.solver.model()
|
||||
#
|
||||
# for level in range(0,max_level+1):
|
||||
#
|
||||
# print("\n[Level=" + repr(level) + "]")
|
||||
#
|
||||
# if repr(m[self.v_init[level]]) == "True":
|
||||
# print("** Initial state")
|
||||
#
|
||||
# print("State:\n{"),
|
||||
# for var_id in range(0, len(self.v[level])):
|
||||
# if repr(m[self.v[level][var_id]]) == "True":
|
||||
# print("\t" + self.reaction_system.get_entity_name(var_id)),
|
||||
# print("}")
|
||||
#
|
||||
# if level != max_level:
|
||||
# print("Context set:"),
|
||||
# print("{"),
|
||||
# for var_id in range(0, len(self.v[level])):
|
||||
# if repr(m[self.v_ctx[level][var_id]]) == "True":
|
||||
# print("\t" + self.reaction_system.get_entity_name(var_id)),
|
||||
# print("}")
|
||||
#
|
||||
#
|
||||
# def check_reachability(self, state, print_witness=True, print_time=False):
|
||||
# """Main testing function"""
|
||||
#
|
||||
# if print_time:
|
||||
# start = time()
|
||||
#
|
||||
# self.prepare_all_variables()
|
||||
# self.solver.add(self.enc_init_state(0))
|
||||
# current_level = 0
|
||||
#
|
||||
# while True:
|
||||
# #print("Level: " + str(current_level))
|
||||
# print("\rLevel: " + str(current_level)),
|
||||
# stdout.flush()
|
||||
#
|
||||
# self.prepare_all_variables()
|
||||
#
|
||||
# # reachability test:
|
||||
# self.solver.push()
|
||||
# self.solver.add(self.enc_state(current_level,state))
|
||||
#
|
||||
# result = self.solver.check()
|
||||
# print(result)
|
||||
# if result == sat:
|
||||
# print("\nSAT")
|
||||
# if print_witness:
|
||||
# self.decode_witness(current_level)
|
||||
# break
|
||||
# else:
|
||||
# self.solver.pop()
|
||||
#
|
||||
# self.solver.add(self.enc_transition_relation(current_level))
|
||||
#
|
||||
# current_level += 1
|
||||
#
|
||||
# if print_time:
|
||||
# stop = time()
|
||||
# print("Time: " + repr(stop-start))
|
||||
@@ -1,432 +0,0 @@
|
||||
"""
|
||||
SMT-based Model Checking Module for RS with Context Automaton
|
||||
"""
|
||||
|
||||
from z3 import *
|
||||
from time import time,sleep
|
||||
from sys import stdout
|
||||
import resource
|
||||
|
||||
# def simplify(x):
|
||||
# return x
|
||||
|
||||
class SmtCheckerDistribRS(object):
|
||||
|
||||
def __init__(self, drs, debug_level=1):
|
||||
|
||||
print("[i] Initialising the SMT module")
|
||||
|
||||
drs.sanity_check()
|
||||
|
||||
self.solver = Solver()
|
||||
|
||||
self.debug_level = debug_level
|
||||
self.drs = drs
|
||||
self.n_components = self.drs.components_count
|
||||
|
||||
# encoding variables
|
||||
self.v = [] # level -> component -> variables
|
||||
self.v_ctx = []
|
||||
self.v_act = [] # indicators of which component is active
|
||||
self.ca_state = []
|
||||
|
||||
self.level_to_encode = 0
|
||||
|
||||
def prepare_all_variables(self):
|
||||
"""Encodes the required variables"""
|
||||
|
||||
self.prepare_state_variables()
|
||||
self.prepare_context_variables()
|
||||
self.prepare_activity_variables()
|
||||
|
||||
self.level_to_encode += 1 # prepare for the next invocation
|
||||
|
||||
def prepare_context_variables(self):
|
||||
"""Encodes the context variables"""
|
||||
|
||||
level = self.level_to_encode
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Preparing context variables for level=" + str(level))
|
||||
|
||||
level_variables = []
|
||||
|
||||
for i in range(self.n_components):
|
||||
|
||||
comp_variables = []
|
||||
|
||||
for entity in self.drs.background_set:
|
||||
comp_variables.append(Bool("Ctx"+str(level)+"V"+str(i)+"_"+entity))
|
||||
|
||||
level_variables.append(comp_variables)
|
||||
|
||||
self.v_ctx.append(level_variables)
|
||||
|
||||
def prepare_activity_variables(self):
|
||||
"""Encodes the activity variables"""
|
||||
|
||||
level = self.level_to_encode
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Preparing activity variables for level=" + str(level))
|
||||
|
||||
level_variables = []
|
||||
|
||||
for i in range(self.n_components):
|
||||
# L - level, A - activity indicator
|
||||
level_variables.append(Bool("L"+str(level)+"A"+str(i)))
|
||||
|
||||
self.v_act.append(level_variables)
|
||||
|
||||
def prepare_state_variables(self):
|
||||
"""Encodes all the state variables"""
|
||||
|
||||
level = self.level_to_encode
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Preparing state variables for level=" + str(level))
|
||||
|
||||
level_variables = [] # level vars
|
||||
|
||||
for i in range(self.n_components):
|
||||
|
||||
comp_variables = []
|
||||
|
||||
for entity in self.drs.background_set:
|
||||
# L - level, V - component
|
||||
comp_variables.append(Bool("L"+str(level)+"V"+str(i)+"_"+entity))
|
||||
|
||||
level_variables.append(comp_variables)
|
||||
|
||||
self.v.append(level_variables)
|
||||
|
||||
# single state variable for CA
|
||||
self.ca_state.append(Int("CA"+str(level)+"_state"))
|
||||
|
||||
def enc_init_state(self, level):
|
||||
"""Encodes the initial state at the given level"""
|
||||
|
||||
if self.debug_level > 1:
|
||||
print("[ii] Encoding the initial state for level=" + str(level))
|
||||
|
||||
rs_init_state_enc = True
|
||||
|
||||
for i in range(self.n_components):
|
||||
for v in self.v[level][i]:
|
||||
rs_init_state_enc = simplify(And(rs_init_state_enc, Not(v))) # the initial state is empty
|
||||
|
||||
ca_init_state_enc = self.ca_state[level] == self.drs.get_init_state_id()
|
||||
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
|
||||
|
||||
# print ("init_state_enc:\n", init_state_enc)
|
||||
|
||||
return init_state_enc
|
||||
|
||||
def enc_enabledness(self, level, prod_entity, component_id):
|
||||
"""Encodes the enabledness condition for a given level and a given entity"""
|
||||
|
||||
rcts_for_prod_entity = self.drs.get_reactions_by_product(component_id)[prod_entity]
|
||||
|
||||
if rcts_for_prod_entity == []:
|
||||
return False
|
||||
|
||||
enc_rct_prod = False
|
||||
for reactants,inhibitors in rcts_for_prod_entity:
|
||||
|
||||
|
||||
enc_reactants = True
|
||||
for reactant in reactants:
|
||||
|
||||
enc_active_reactants = False
|
||||
for i in range(self.n_components):
|
||||
enc_active_reactants = simplify(Or(enc_active_reactants,
|
||||
And( Or(self.v[level][i][reactant], self.v_ctx[level][i][reactant]), self.v_act[level][i] )))
|
||||
|
||||
enc_reactants = And(enc_reactants, enc_active_reactants)
|
||||
|
||||
|
||||
enc_inhibitors = True
|
||||
for inhibitor in inhibitors:
|
||||
|
||||
enc_active_inhibitors = True
|
||||
for i in range(self.n_components):
|
||||
enc_active_inhibitors = simplify(And(enc_active_inhibitors,
|
||||
And(
|
||||
Or( And(Not(self.v[level][i][inhibitor]), Not(self.v_ctx[level][i][inhibitor])), Not(self.v_act[level][i]) )
|
||||
)))
|
||||
|
||||
enc_inhibitors = simplify(And(enc_inhibitors, enc_active_inhibitors))
|
||||
|
||||
# print("--> enc_inhibitors\n", enc_inhibitors)
|
||||
enc_rct_prod = Or(enc_rct_prod, And(enc_reactants, enc_inhibitors))
|
||||
|
||||
# print("enc_rct_prod:\n", enc_rct_prod)
|
||||
|
||||
enc_rct_prod = simplify(enc_rct_prod)
|
||||
|
||||
return enc_rct_prod
|
||||
|
||||
def enc_entity_production(self, level, prod_entity, component_id):
|
||||
"""Encodes the production of a given entity at level+1 from a given level"""
|
||||
|
||||
enc_enab_cond = self.enc_enabledness(level, prod_entity, component_id)
|
||||
|
||||
enc_base_ent_prod = simplify(Or(And(enc_enab_cond, self.v[level+1][component_id][prod_entity]),
|
||||
And(Not(enc_enab_cond), Not(self.v[level+1][component_id][prod_entity]))))
|
||||
|
||||
enc_active_ent_prod = simplify(And(self.v_act[level][component_id], enc_base_ent_prod))
|
||||
enc_inactive_ent_prod = simplify(And(
|
||||
Not(self.v_act[level][component_id]),
|
||||
self.v[level][component_id][prod_entity] == self.v[level+1][component_id][prod_entity]))
|
||||
|
||||
enc_ent_prod = Or(enc_active_ent_prod, enc_inactive_ent_prod)
|
||||
|
||||
# print("enc_ent_prod:\n", enc_ent_prod)
|
||||
|
||||
return simplify(enc_ent_prod)
|
||||
|
||||
def enc_rs_trans(self, level):
|
||||
"""Encodes the transition relation"""
|
||||
|
||||
enc_trans = True
|
||||
|
||||
for component_id in range(self.n_components):
|
||||
|
||||
print("\rEncoding for reactions: %d/%d" % (component_id,self.n_components-1), flush=True, end="")
|
||||
|
||||
unused_entities = list(range(len(self.drs.background_set)))
|
||||
|
||||
for prod_entity in self.drs.get_reactions_by_product(component_id):
|
||||
unused_entities.remove(prod_entity)
|
||||
|
||||
enc_trans = simplify(And(enc_trans, self.enc_entity_production(level, prod_entity, component_id)))
|
||||
|
||||
for prod_entity in unused_entities:
|
||||
enc_trans = simplify(And(enc_trans, Not(self.v[level+1][component_id][prod_entity])))
|
||||
|
||||
print()
|
||||
# print("enc_rs_trans:\n", enc_trans)
|
||||
|
||||
enc_trans = simplify(enc_trans)
|
||||
|
||||
return enc_trans
|
||||
|
||||
def enc_automaton_trans(self, level):
|
||||
"""Encodes the transition relation for the context automaton"""
|
||||
|
||||
enc_trans = False
|
||||
|
||||
i = 0
|
||||
for src,(components,ctx_set),dst in self.drs.transitions:
|
||||
src_enc = self.ca_state[level] == src
|
||||
dst_enc = self.ca_state[level+1] == dst
|
||||
|
||||
print("\rEncoding for context automaton: %d/%d" % (i,len(self.drs.transitions)-1), flush=True, end="")
|
||||
|
||||
i = i + 1
|
||||
|
||||
# contexts {
|
||||
ctx_set_enc = True
|
||||
for comp_id in range(self.n_components):
|
||||
|
||||
all_ent = set(range(len(self.drs.background_set)))
|
||||
incl_ctx = ctx_set[comp_id]
|
||||
excl_ctx = all_ent - incl_ctx
|
||||
|
||||
ctx_enc = True
|
||||
|
||||
for c in incl_ctx:
|
||||
ctx_enc = And(ctx_enc, self.v_ctx[level][comp_id][c])
|
||||
for c in excl_ctx:
|
||||
ctx_enc = And(ctx_enc, Not(self.v_ctx[level][comp_id][c]))
|
||||
|
||||
ctx_set_enc = And(ctx_set_enc, ctx_enc)
|
||||
# } contexts
|
||||
|
||||
# active components {
|
||||
all_active = set(range(self.n_components))
|
||||
incl_comp = components
|
||||
excl_comp = all_active - incl_comp
|
||||
|
||||
active_components_enc = True
|
||||
for comp_id in incl_comp:
|
||||
active_components_enc = And(active_components_enc, self.v_act[level][comp_id])
|
||||
for comp_id in excl_comp:
|
||||
active_components_enc = And(active_components_enc, Not(self.v_act[level][comp_id]))
|
||||
# } active components
|
||||
|
||||
cur_trans = And(src_enc, ctx_set_enc, active_components_enc, dst_enc)
|
||||
|
||||
enc_trans = Or(enc_trans, cur_trans)
|
||||
|
||||
print()
|
||||
|
||||
enc_trans = simplify(enc_trans)
|
||||
|
||||
# print("enc_automaton_trans:\n", enc_trans)
|
||||
return enc_trans
|
||||
|
||||
def enc_transition_relation(self, level):
|
||||
|
||||
rs_enc = self.enc_rs_trans(level)
|
||||
aut_enc = self.enc_automaton_trans(level)
|
||||
|
||||
print("Conjunction...", flush=True, end="")
|
||||
|
||||
c = simplify(And(rs_enc, aut_enc))
|
||||
|
||||
print("done.")
|
||||
|
||||
return c
|
||||
|
||||
def enc_state(self, level, global_state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
if len(global_state) != self.n_components:
|
||||
print("EEE: Wrong size of the global state! " + "(is " + str(len(global_state)) + ", should be " + str(self.n_components) + ")")
|
||||
exit(1)
|
||||
|
||||
enc = True
|
||||
|
||||
if self.debug_level > 2:
|
||||
print("[iii] Encoding exclusive/exact global state " + str(global_state) + " for level=" + str(level))
|
||||
|
||||
for i in range(self.n_components):
|
||||
local_state = global_state[i]
|
||||
|
||||
local_state_ids = self.drs.get_state_ids(local_state)
|
||||
|
||||
for entity in local_state_ids:
|
||||
enc = And(enc, self.v[level][i][entity])
|
||||
|
||||
not_in_state = self.drs.set_of_background_ids - set(local_state_ids)
|
||||
|
||||
for e_id in not_in_state:
|
||||
enc = simplify(And(enc, Not(self.v[level][i][e_id])))
|
||||
|
||||
simplify(enc)
|
||||
# print("state:\n", enc)
|
||||
return enc
|
||||
|
||||
def enc_inclusive_state(self, level, global_state):
|
||||
"""Encodes the state at the given level"""
|
||||
|
||||
if len(global_state) != self.n_components:
|
||||
print("EEE: Wrong size of the global state! " + "(is " + str(len(global_state)) + ", should be " + str(self.n_components) + ")")
|
||||
exit(1)
|
||||
|
||||
enc = True
|
||||
|
||||
if self.debug_level > 2:
|
||||
print("[iii] Encoding inclusive/general global state " + str(global_state) + " for level=" + str(level))
|
||||
|
||||
for i in range(self.n_components):
|
||||
local_state = global_state[i]
|
||||
|
||||
local_state_ids = self.drs.get_state_ids(local_state)
|
||||
|
||||
for entity in local_state_ids:
|
||||
enc = And(enc, self.v[level][i][entity])
|
||||
|
||||
simplify(enc)
|
||||
return enc
|
||||
|
||||
def decode_witness(self, max_level, print_model=False):
|
||||
|
||||
m = self.solver.model()
|
||||
|
||||
print("\nWitness:")
|
||||
|
||||
if print_model:
|
||||
print(m)
|
||||
|
||||
for level in range(max_level+1):
|
||||
|
||||
print("\n[Level=" + repr(level) + "]")
|
||||
|
||||
#print(m)
|
||||
#print(self.v[level][0][2])
|
||||
#print(m[self.v[level][0][2]])
|
||||
|
||||
print(" State: {", end=""),
|
||||
for c in range(self.n_components):
|
||||
print(" <", end="")
|
||||
for var_id in range(len(self.v[level][c])):
|
||||
if repr(m[self.v[level][c][var_id]]) == "True":
|
||||
print(" " + self.drs.get_entity_name(var_id), end="")
|
||||
print(" >", end="")
|
||||
print(" }")
|
||||
|
||||
if level != max_level:
|
||||
print(" Context set: ", end="")
|
||||
print("{", end="")
|
||||
for c in range(self.n_components):
|
||||
print(" <", end="")
|
||||
for var_id in range(len(self.v[level][c])):
|
||||
if repr(m[self.v_ctx[level][c][var_id]]) == "True":
|
||||
print(" " + self.drs.get_entity_name(var_id), end="")
|
||||
print(" >", end="")
|
||||
print(" }")
|
||||
|
||||
print(" Active components:", end="")
|
||||
for c in range(self.n_components):
|
||||
if repr(m[self.v_act[level][c]]) == "True":
|
||||
print(" " + str(c), end="")
|
||||
print()
|
||||
|
||||
|
||||
|
||||
def check_reachability(self, state, exclusive_state=False, print_witness=True, print_time=False, print_mem=False, max_level=100):
|
||||
"""Reachability checking"""
|
||||
|
||||
print("[i] Checking reachability...")
|
||||
|
||||
if print_time:
|
||||
start = time()
|
||||
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_init_state(0))
|
||||
current_level = 0
|
||||
|
||||
while True:
|
||||
|
||||
self.prepare_all_variables()
|
||||
|
||||
print("-----[ Working at level=" + str(current_level) + " ]-----")
|
||||
stdout.flush()
|
||||
|
||||
# reachability test:
|
||||
self.solver.push()
|
||||
print("[i] Adding the reachability test...")
|
||||
if exclusive_state == False:
|
||||
self.solver.add(self.enc_inclusive_state(current_level,state))
|
||||
else:
|
||||
self.solver.add(self.enc_state(current_level,state))
|
||||
|
||||
result = self.solver.check()
|
||||
if result == sat:
|
||||
print("\n[+] SAT at level=" + str(current_level))
|
||||
if print_witness:
|
||||
self.decode_witness(current_level)
|
||||
break
|
||||
else:
|
||||
self.solver.pop()
|
||||
|
||||
print("[i] Unrolling the transition relation")
|
||||
self.solver.add(self.enc_transition_relation(current_level))
|
||||
|
||||
print("-----[ level=" + str(current_level) + " done ]")
|
||||
current_level += 1
|
||||
|
||||
if current_level > max_level:
|
||||
print("Stopping at level=" + str(max_level))
|
||||
break
|
||||
|
||||
if print_time:
|
||||
stop = time()
|
||||
print()
|
||||
print("==== Time: " + repr(stop-start))
|
||||
|
||||
if print_mem:
|
||||
usage=resource.getrusage(resource.RUSAGE_SELF)
|
||||
print("MEM: usertime=%s systime=%s mem=%sMB" % (usage[0],usage[1], (resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024**2)))
|
||||
@@ -1,174 +0,0 @@
|
||||
"""
|
||||
SMT-based Model Checking Module for RS with Context Automaton
|
||||
"""
|
||||
|
||||
from z3 import *
|
||||
from time import time
|
||||
from sys import stdout
|
||||
import resource
|
||||
|
||||
from smt.smt_checker_rs import SmtCheckerRS
|
||||
|
||||
class SmtCheckerRSNA(SmtCheckerRS):
|
||||
"""SMT-based Model Checking for Reaction Systems with Network of Automata"""
|
||||
|
||||
def __init__(self, reaction_system_with_netaut):
|
||||
|
||||
self.rs = reaction_system_with_netaut.rs
|
||||
self.canet = reaction_system_with_netaut.cas
|
||||
|
||||
self.number_of_automata = self.canet.number_of_automata
|
||||
|
||||
self.v = []
|
||||
self.v_ctx = []
|
||||
self.v_canet_states = []
|
||||
self.v_canet_actions = []
|
||||
self.next_level_to_encode = 0
|
||||
|
||||
self.solver = Solver()
|
||||
|
||||
self.verification_time = None
|
||||
|
||||
def prepare_context_controller_variables(self):
|
||||
"""Encodes all the state variables"""
|
||||
|
||||
level = self.next_level_to_encode
|
||||
|
||||
ca_states = []
|
||||
for ca_id in range(self.number_of_automata):
|
||||
ca_states.append(Int("CA"+str(level)+"_a"+str(ca_id)+"_state"))
|
||||
self.v_canet_states.append(ca_states)
|
||||
|
||||
# We do not encode actions when there are no transitions needed.
|
||||
if level > 0:
|
||||
ca_actions = []
|
||||
for ca in self.canet.automata:
|
||||
for act_id in range(ca.number_of_actions):
|
||||
ca_actions.append(Bool("CA"+str(level-1)+"_a"+str(self.canet.automata.index(ca))+"_act"+str(act_id)))
|
||||
self.v_canet_actions.append(ca_actions)
|
||||
|
||||
def enc_context_controller_init_state(self, level):
|
||||
"""Encodes the initial state for the network of automata"""
|
||||
|
||||
canet_init_state_enc = True
|
||||
for ca_idx in range(self.number_of_automata):
|
||||
ca_init_state_enc = self.v_canet_states[level][ca_idx] == self.canet.automata[ca_idx].get_init_state_id()
|
||||
canet_init_state_enc = simplify(And(canet_init_state_enc, ca_init_state_enc))
|
||||
|
||||
return canet_init_state_enc
|
||||
|
||||
def enc_transition_relation(self, level):
|
||||
return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
|
||||
|
||||
def enc_reactants_ids(self, level, set_of_ids):
|
||||
"""Encodes reactants given by their ids in RS"""
|
||||
|
||||
enc_ents = True
|
||||
for r_id in set_of_ids:
|
||||
enc_ents = simplify(And(enc_ents, self.v[level][r_id]))
|
||||
return enc_ents
|
||||
|
||||
def enc_inhibitors_ids(self, level, set_of_ids):
|
||||
"""Encodes inhibitors given by their ids in RS"""
|
||||
|
||||
enc_ents = True
|
||||
for i_id in set_of_ids:
|
||||
enc_ents = simplify(And(enc_ents, Not(self.v[level][i_id])))
|
||||
return enc_ents
|
||||
|
||||
def enc_context_single_transition(self, level, automaton, transition):
|
||||
""""""
|
||||
|
||||
src_id, act_ids, (r_ids, i_ids, p_ids), dst_id = transition
|
||||
|
||||
enc_transition = self.v_canet_states[level][automaton] == src_id
|
||||
enc_transition = simplify(And(enc_transition, self.enc_reactants_ids(level, r_ids), self.enc_inhibitors_ids(level, i_ids)))
|
||||
enc_transition = simplify(And(enc_transition, self.v_canet_states[level+1][automaton] == dst_id))
|
||||
# ACTIONS NOT ENCODED!
|
||||
|
||||
print(enc_transition)
|
||||
return enc_transition
|
||||
|
||||
def enc_context_entity_production(self, level, entity):
|
||||
"""Encodes the automata transitions and the production for a given entity"""
|
||||
|
||||
enc_production = False
|
||||
|
||||
actions_producing_ent = self.canet.get_actions_producing_entity(entity)
|
||||
enc_prod_action = False
|
||||
|
||||
for act in actions_producing_ent:
|
||||
|
||||
# automata_with_act = self.canet.get_automata_with_action(act)
|
||||
enc_aut_with_act = True
|
||||
|
||||
for aut_id in self.canet.automata_ids:
|
||||
|
||||
aut = self.canet.automata[aut_id]
|
||||
|
||||
t_producing_entity = aut.get_transitions_producing_entity(entity)
|
||||
|
||||
enc_t_producing_entity = False
|
||||
|
||||
if t_producing_entity:
|
||||
# for the automata that produce the entity we take
|
||||
# all the transitions that produce it:
|
||||
|
||||
|
||||
for t in t_producing_entity:
|
||||
enc_t_producing_entity = simplify(Or(enc_t_producing_entity, self.enc_context_single_transition(level, aut_id, t)))
|
||||
|
||||
else:
|
||||
# for all the automata that do not produce the entity
|
||||
# we encode the transitions that synchronise with the action:
|
||||
|
||||
pass
|
||||
|
||||
enc_aut_with_act = simplify(And(enc_aut_with_act, enc_t_producing_entity))
|
||||
|
||||
enc_prod_action = simplify(Or(enc_prod_action, enc_aut_with_act))
|
||||
|
||||
# TODO
|
||||
# for aut in remaining_automata_which_do_not_contain_act:
|
||||
# encode no change
|
||||
|
||||
enc_production = enc_prod_action
|
||||
|
||||
return enc_production
|
||||
|
||||
def enc_automaton_trans(self, level):
|
||||
"""Encodes the transition relation for the context automaton"""
|
||||
|
||||
enc_trans = True
|
||||
|
||||
prod_context = self.canet.prod_entities
|
||||
never_produced_context = self.rs.set_of_bgset_ids - prod_context
|
||||
|
||||
# (1) producible entities:
|
||||
for ent in prod_context:
|
||||
enc_trans = simplify(And(enc_trans, self.enc_context_entity_production(level, ent)))
|
||||
|
||||
|
||||
# (2) entities that are never produced:
|
||||
|
||||
# (3) TODO: no entity, empty set of entities: transitions with no entities
|
||||
# simplify((enc_trans, self.enc_context_no_entity_production(level)))
|
||||
# TRANSITIONS PRODUCING EMPTY SETS
|
||||
|
||||
print(enc_trans)
|
||||
|
||||
return enc_trans
|
||||
|
||||
def check_reachability(self, state, print_witness=True, print_time=True, print_mem=True):
|
||||
"""The main method for checking reachability"""
|
||||
|
||||
self.prepare_all_variables()
|
||||
self.solver.add(self.enc_init_state(0))
|
||||
current_level = 0
|
||||
self.prepare_all_variables()
|
||||
self.prepare_all_variables()
|
||||
self.prepare_all_variables()
|
||||
self.prepare_all_variables()
|
||||
|
||||
print(self.enc_automaton_trans(0))
|
||||
|
||||
@@ -153,23 +153,6 @@ class SmtCheckerRSC(object):
|
||||
|
||||
enc_ordinary_reactions_enabledness = simplify(Or(enc_ordinary_reactions_enabledness,enc_rct_enabled))
|
||||
|
||||
# for reactants,inhibitors,products in rcts_for_prod_entity:
|
||||
# enc_reactants = True
|
||||
# enc_inhibitors = True
|
||||
# # enc_products -- below
|
||||
#
|
||||
# for reactant,concentration in reactants:
|
||||
# enc_reactants = simplify(And(enc_reactants,
|
||||
# Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
|
||||
# for inhibitor,concentration in inhibitors:
|
||||
# enc_inhibitors = simplify(And(enc_inhibitors,
|
||||
# And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
|
||||
#
|
||||
# enc_products = self.v[level+1][products[0][0]] == products[0][1]
|
||||
#
|
||||
# enc_enabledness = simplify(Or(enc_enabledness, And(enc_reactants, enc_inhibitors)))
|
||||
# enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors, enc_products)))
|
||||
|
||||
# -------- meta reactions ---------------------------------------------------
|
||||
|
||||
for r_type,command_entity,reactants,inhibitors in meta_reactions:
|
||||
@@ -234,17 +217,6 @@ class SmtCheckerRSC(object):
|
||||
enc_rct_prod = Or(enc_rct_prod, enc_when_to_produce_zero_conc)
|
||||
return enc_rct_prod
|
||||
|
||||
# def enc_entity_production(self, level, prod_entity):
|
||||
# """Encodes the production of a given entity from a given level at level+1"""
|
||||
#
|
||||
# enc_enab_cond = self.enc_enabledness(level, prod_entity)
|
||||
#
|
||||
# enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
|
||||
# And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
|
||||
#
|
||||
# return simplify(enc_ent_prod)
|
||||
|
||||
|
||||
def enc_transition_relation(self, level):
|
||||
return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
|
||||
|
||||
@@ -299,21 +271,6 @@ class SmtCheckerRSC(object):
|
||||
|
||||
raise RuntimeError("Should not be used with RSC")
|
||||
|
||||
# enc = True
|
||||
# used_entities_ids = self.rs.get_state_ids(state)
|
||||
#
|
||||
# for ent,conc in state:
|
||||
# e_id = self.rs.get_entity_id(ent)
|
||||
# enc = And(enc, self.v[level][e_id] == conc)
|
||||
#
|
||||
# not_in_state = set(range(len(self.rs.background_set)))
|
||||
# not_in_state = not_in_state.difference(set(used_entities_ids))
|
||||
#
|
||||
# for entity in not_in_state:
|
||||
# enc = And(enc, self.v[level][entity] == 0)
|
||||
#
|
||||
# return simplify(enc)
|
||||
|
||||
def enc_min_state(self, level, state):
|
||||
"""Encodes the state at the given level with the minimal required concentration levels"""
|
||||
|
||||
@@ -322,11 +279,6 @@ class SmtCheckerRSC(object):
|
||||
e_id = self.rs.get_entity_id(ent)
|
||||
enc = And(enc, self.v[level][e_id] >= conc)
|
||||
|
||||
# state_ids = self.rs.get_state_ids(state)
|
||||
#
|
||||
# for entity in state_ids:
|
||||
# enc = And(enc, self.v[level][entity])
|
||||
|
||||
return simplify(enc)
|
||||
|
||||
def enc_state_with_blocking(self, level, prop):
|
||||
|
||||
@@ -62,14 +62,13 @@ class SmtCheckerRSCParam(object):
|
||||
|
||||
self.next_level_to_encode = 0
|
||||
|
||||
# this is probably not needed anymore:
|
||||
# self.producible_entities = self.rs.get_producible_entities()
|
||||
# self.improducible_entities = set(self.rs.get_state_ids(self.rs.background_set)) - self.producible_entities
|
||||
|
||||
#
|
||||
# WARNING: improd vs. improducible
|
||||
# there is some confusion related to the variables naming:
|
||||
# improd - intermediate products
|
||||
# improducible - entities that are never produces (there is no reaction that produces that entity)
|
||||
# there is some confusion related to the variable naming:
|
||||
#
|
||||
# * improd - intermediate products
|
||||
# * improducible - entities that are never produces (there is no reaction that produces that entity)
|
||||
#
|
||||
|
||||
# TODO: number of loops == number of paths
|
||||
self.loop_position = None
|
||||
@@ -162,9 +161,6 @@ class SmtCheckerRSCParam(object):
|
||||
self.path_v_improd.setdefault(path_idx, [])
|
||||
self.path_v_improd_for_entities.setdefault(path_idx, [])
|
||||
|
||||
# assert len(self.path_v_improd[path_idx]) == level
|
||||
# assert len(self.path_v_improd_for_entities[path_idx]) == level
|
||||
|
||||
if level < 1:
|
||||
#
|
||||
# If we are at level==0, we add a dummy "level"
|
||||
@@ -580,11 +576,6 @@ class SmtCheckerRSCParam(object):
|
||||
e_id = self.rs.get_entity_id(ent)
|
||||
enc = And(enc, self.v[level][e_id] >= conc)
|
||||
|
||||
# state_ids = self.rs.get_state_ids(state)
|
||||
#
|
||||
# for entity in state_ids:
|
||||
# enc = And(enc, self.v[level][entity])
|
||||
|
||||
return simplify(enc)
|
||||
|
||||
def enc_state_with_blocking(self, level, prop):
|
||||
@@ -629,7 +620,6 @@ class SmtCheckerRSCParam(object):
|
||||
print(
|
||||
" " + self.rs.get_entity_name(var_id) + "=" + var_rep,
|
||||
end="")
|
||||
# print(" " + repr(m[self.v[level][var_id]]), end="")
|
||||
print(" }")
|
||||
|
||||
if level != max_level:
|
||||
@@ -748,16 +738,10 @@ class SmtCheckerRSCParam(object):
|
||||
if not isinstance(formulae_list, (list, tuple)):
|
||||
print_error("Expected a list of formulae")
|
||||
|
||||
#print_info("Parameter constraint: {:s}".format(str(param_constr)))
|
||||
#print_info("Parameter constraint defined")
|
||||
|
||||
|
||||
self.reset()
|
||||
|
||||
num_of_paths = len(formulae_list)
|
||||
|
||||
# formula = formulae[0]
|
||||
|
||||
print_info("Running rsLTL bounded model checking")
|
||||
print_info("Tested formulae:")
|
||||
for form in formulae_list:
|
||||
@@ -780,8 +764,6 @@ class SmtCheckerRSCParam(object):
|
||||
|
||||
self.current_level = 0
|
||||
|
||||
# self.prepare_all_variables(num_of_paths)
|
||||
|
||||
# assertions for all the paths and parameters
|
||||
self.solver_add(self.enc_concentration_levels_assertions_for_paths(0, num_of_paths))
|
||||
self.solver_add(self.enc_param_concentration_levels_assertion())
|
||||
@@ -803,7 +785,6 @@ class SmtCheckerRSCParam(object):
|
||||
|
||||
print(
|
||||
"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
|
||||
# stdout.flush()
|
||||
|
||||
# reachability test:
|
||||
self.solver.push()
|
||||
@@ -817,9 +798,6 @@ class SmtCheckerRSCParam(object):
|
||||
print_info("Adding the encoding for the loops...")
|
||||
self.solver_add(self.get_loop_encodings())
|
||||
|
||||
# if self.optimise:
|
||||
# self.assert_param_optimisation()
|
||||
|
||||
print_info("Testing satisfiability...")
|
||||
result = self.solver.check()
|
||||
if result == sat:
|
||||
|
||||
Reference in New Issue
Block a user