Cleanup, example
This commit is contained in:
Artur Meski
@@ -161,8 +161,8 @@ class SmtCheckerRSCParam(object):
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self.path_v_improd.setdefault(path_idx, [])
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self.path_v_improd_for_entities.setdefault(path_idx, [])
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assert len(self.path_v_improd[path_idx]) == level
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assert len(self.path_v_improd_for_entities[path_idx]) == level
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# assert len(self.path_v_improd[path_idx]) == level
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# assert len(self.path_v_improd_for_entities[path_idx]) == level
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if level < 1:
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#
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@@ -172,45 +172,44 @@ class SmtCheckerRSCParam(object):
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#
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self.path_v_improd[path_idx].append(None)
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self.path_v_improd_for_entities[path_idx].append(None)
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else:
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reactions_dict = dict()
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number_of_reactions = len(self.rs.reactions)
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reactions_dict = dict()
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number_of_reactions = len(self.rs.reactions)
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all_entities_dict = dict()
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all_entities_dict = dict()
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for reaction in self.rs.reactions:
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*_, products = reaction
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for reaction in self.rs.reactions:
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*_, products = reaction
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reaction_id = self.rs.reactions.index(reaction)
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reaction_id = self.rs.reactions.index(reaction)
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entities_dict = dict()
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if is_param(products):
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for entity in self.rs.set_of_bgset_ids:
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entity_name = self.rs.get_entity_name(entity)
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new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(path_idx, level, reaction_id, entity_name))
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entities_dict[entity] = new_var
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all_entities_dict.setdefault(entity, [])
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all_entities_dict[entity].append(new_var)
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else:
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for entity, conc in products:
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entity_name = self.rs.get_entity_name(entity)
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new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(path_idx, level, reaction_id, entity_name))
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entities_dict[entity] = new_var
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all_entities_dict.setdefault(entity, [])
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all_entities_dict[entity].append(new_var)
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reactions_dict[reaction_id] = entities_dict
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entities_dict = dict()
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self.path_v_improd[path_idx].append(reactions_dict)
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self.path_v_improd_for_entities[path_idx].append(all_entities_dict)
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if is_param(products):
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for entity in self.rs.set_of_bgset_ids:
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entity_name = self.rs.get_entity_name(entity)
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new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(path_idx, level, reaction_id, entity_name))
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entities_dict[entity] = new_var
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all_entities_dict.setdefault(entity, [])
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all_entities_dict[entity].append(new_var)
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else:
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for entity, conc in products:
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entity_name = self.rs.get_entity_name(entity)
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new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(path_idx, level, reaction_id, entity_name))
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entities_dict[entity] = new_var
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all_entities_dict.setdefault(entity, [])
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all_entities_dict[entity].append(new_var)
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reactions_dict[reaction_id] = entities_dict
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self.path_v_improd[path_idx].append(reactions_dict)
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self.path_v_improd_for_entities[path_idx].append(all_entities_dict)
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def prepare_param_variables(self):
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"""
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Prepares variables for parameters
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@@ -270,8 +269,9 @@ class SmtCheckerRSCParam(object):
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for param_vars in self.v_param.values():
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for pvar in param_vars:
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self.solver.add_soft(pvar < 1)
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# self.solver.add_soft(pvar == 0)
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self.solver.minimize(pvar)
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def enc_concentration_levels_assertion(self, level, path_idx):
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"""
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Encodes assertions that (some) variables need to be >=0
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@@ -599,10 +599,48 @@ class SmtCheckerRSCParam(object):
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end="")
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print(" }")
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# Parameters
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print()
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print("\n\n Parameters:\n")
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for param_name in self.rs.parameters.keys():
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def get_enc_formulae(self, encoder, formulae_list):
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enc_form = []
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for formula in formulae_list:
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path_idx = formulae_list.index(formula)
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print_info("Generating the encoding for {:s} ({:d} of {:d})".format(
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str(formula), path_idx+1, len(formulae_list)))
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encoder.load_variables(
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var_rs=self.path_v[path_idx],
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var_ctx=self.path_v_ctx[path_idx],
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var_loop_pos=self.path_loop_position[path_idx])
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enc_form.append(encoder.get_encoding(formula, self.current_level))
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ncalls = encoder.get_ncalls()
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print_info("Cache hits: {:d}, encode calls: {:d} (approx: {:d})".format(
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encoder.get_cache_hits(), ncalls[0], ncalls[1]))
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encoder.flush_cache()
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return enc_form
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def print_witness(self, formulae_list):
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for formula in formulae_list:
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path_idx = formulae_list.index(formula)
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print("\n{:=^70}".format("[ WITNESS ]"))
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print("\n Witness for: {:s}".format(str(formula)))
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self.decode_witness(self.current_level, path_idx)
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self.print_parameter_valuations()
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def print_parameter_valuations(self):
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m = self.solver.model()
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print("\n Parameters:\n")
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for param_name in sorted(self.rs.parameters.keys()):
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print("{: >6}: ".format(param_name), end="")
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print("{", end="")
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@@ -618,9 +656,28 @@ class SmtCheckerRSCParam(object):
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" " + str(self.rs.get_entity_name(entity)) + "=" + str(var_rep),
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end="")
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print(" }")
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print()
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print("\n")
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def enc_concentration_levels_assertions_for_paths(self, level, num_of_paths):
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additional_assertions = []
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for path_idx in range(num_of_paths):
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additional_assertions.append(self.enc_concentration_levels_assertion(level, path_idx))
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additional_assertions.append(self.enc_param_concentration_levels_assertion())
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return additional_assertions
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def enc_transition_relation_for_paths(self, level, num_of_paths):
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enc_trans = []
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for path_idx in range(num_of_paths):
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enc_trans.append(self.enc_transition_relation(level, path_idx))
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return enc_trans
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def print_level(self):
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print(
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"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
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def check_rsltl(
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self, formulae_list,
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print_witness=True,
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@@ -653,10 +710,12 @@ class SmtCheckerRSCParam(object):
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for form in formulae_list:
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print_info(" "*4 + str(form))
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if print_time:
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start = resource.getrusage(resource.RUSAGE_SELF).ru_utime
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print_info("INITIALISING...")
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self.prepare_all_variables(num_of_paths)
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if print_time:
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start_time = resource.getrusage(resource.RUSAGE_SELF).ru_utime
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self.prepare_all_variables(num_of_paths)
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self.load_varset_for_path(0)
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@@ -668,26 +727,21 @@ class SmtCheckerRSCParam(object):
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self.current_level = 0
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self.prepare_all_variables(num_of_paths)
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# self.prepare_all_variables(num_of_paths)
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# assertions for all the paths and parameters
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additional_assertions = []
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for path_idx in range(num_of_paths):
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additional_assertions.append(self.enc_concentration_levels_assertion(0, path_idx))
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additional_assertions.append(self.enc_param_concentration_levels_assertion())
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self.solver_add(additional_assertions)
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self.solver_add(self.enc_concentration_levels_assertions_for_paths(0, num_of_paths))
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self.solver_add(self.enc_param_concentration_levels_assertion())
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encoder = rsLTL_Encoder(self)
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if self.optimise:
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self.assert_param_optimisation()
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encoder = rsLTL_Encoder(self)
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print_info("Iterating...")
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print_info("STARTING TO ITERATE...")
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while True:
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print(
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"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
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# stdout.flush()
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@@ -695,36 +749,18 @@ class SmtCheckerRSCParam(object):
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# reachability test:
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self.solver.push()
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enc_form = []
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for formula in formulae_list:
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path_idx = formulae_list.index(formula)
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print_info("Generating the encoding for {:s} ({:d} of {:d})".format(
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str(formula), path_idx+1, len(formulae_list)))
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encoder.load_variables(
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var_rs=self.path_v[path_idx],
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var_ctx=self.path_v_ctx[path_idx],
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var_loop_pos=self.path_loop_position[path_idx])
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enc_form.append(encoder.get_encoding(formula, self.current_level))
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ncalls = encoder.get_ncalls()
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print_info("Cache hits: {:d}, encode calls: {:d} (approx: {:d})".format(
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encoder.get_cache_hits(), ncalls[0], ncalls[1]))
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encoder.flush_cache()
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# Encoding all the formulae
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enc_form = self.get_enc_formulae(encoder, formulae_list)
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print_info("Adding the formulae to the solver...")
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# print (enc_form)
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self.solver_add(enc_form)
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print_info("Adding the loops encoding...")
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# Loops encoding
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print_info("Adding the encoding for the loops...")
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self.solver_add(self.get_loop_encodings())
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# if self.optimise:
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# self.assert_param_optimisation()
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print_info("Testing satisfiability...")
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result = self.solver.check()
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if result == sat:
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@@ -732,55 +768,49 @@ class SmtCheckerRSCParam(object):
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"SAT at level={:d}".format(self.current_level)))
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# print(self.solver.model())
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if print_witness:
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for formula in formulae_list:
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path_idx = formulae_list.index(formula)
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print("\n{:=^70}".format("[ WITNESS ]"))
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print("\n Witness for: {:s}".format(str(formula)))
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self.decode_witness(self.current_level, path_idx)
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self.print_witness(formulae_list)
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if not cont_if_sat:
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break
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else:
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print_info("Unsat")
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print_info("UNSAT")
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self.solver.pop()
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self.prepare_all_variables(num_of_paths)
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# assertions for all the paths
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additional_assertions = []
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for path_idx in range(num_of_paths):
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additional_assertions.append(
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self.enc_concentration_levels_assertion(self.current_level + 1, path_idx))
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self.solver_add(additional_assertions)
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self.solver_add(self.enc_concentration_levels_assertions_for_paths(self.current_level + 1, num_of_paths))
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print_info("Unrolling the transition relation")
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for path_idx in range(num_of_paths):
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self.solver_add(self.enc_transition_relation(self.current_level, path_idx))
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self.solver_add(self.enc_transition_relation_for_paths(self.current_level, num_of_paths))
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self.print_level()
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print(
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"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))
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self.current_level += 1
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if not max_level is None and self.current_level > max_level:
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print("Stopping at level=" + str(max_level))
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print_info("Stopping at level=" + str(max_level))
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break
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if print_time:
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# stop = time()
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stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
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self.verification_time = stop - start
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print()
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print(
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"\n[i] {: >60}".format(
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" Time: " + repr(self.verification_time) + " s"))
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self.print_time(start_time)
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if print_mem:
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print(
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"[i] {: >60}".format(
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" Memory: " +
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repr(
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resource.getrusage(resource.RUSAGE_SELF).ru_maxrss /
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(1024 * 1024)) + " MB"))
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self.print_mem()
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def print_time(self, start):
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stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
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self.verification_time = stop - start
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print()
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print_info("{: >60}".format(
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" Time: " + repr(self.verification_time) + " s"))
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def print_mem(self):
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print_info(
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"{: >60}".format(
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" Memory: " +
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repr(
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resource.getrusage(resource.RUSAGE_SELF).ru_maxrss /
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(1024 * 1024)) + " MB"))
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def dummy_unroll(self, levels):
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"""Unrolls the variables for testing purposes"""
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