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RS with context automaton (we embed CA with RS)

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This commit is contained in:
Artur Meski
2018-03-03 21:19:13 +00:00
parent f121ce12fd
commit c853e40ad7
10 changed files with 93 additions and 149 deletions
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2
Makefile
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@@ -10,7 +10,7 @@ CXXFLAGS = -std=c++14 $(CXXFLAGS_SILENT)
#CXXFLAGS = -std=c++14 -O3 -DPUBLIC_RELEASE -DNDEBUG #-g
LDLIBS = $(CUDD_INCLUDE)
OBJ = rs.o symrs.o mc.o rsin_driver.o rsin_parser.o rsin_parser.lex.o formrsctl.o
OBJ = rs.o ctx_aut.o symrs.o mc.o rsin_driver.o rsin_parser.o rsin_parser.lex.o formrsctl.o
all: main

2
mc.cc
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@@ -117,7 +117,7 @@ void ModelChecker::printReachWithSucc(void)
cleanup();
}
bool ModelChecker::checkReach(const RctSys::Entities testState)
bool ModelChecker::checkReach(const Entities testState)
{
if (opts->measure)
opts->ver_time = cpuTime();

2
mc.hh
View File

@@ -67,7 +67,7 @@ public:
void printReach(void);
void printReachWithSucc(void);
bool checkReach(const RctSys::Entities testState);
bool checkReach(const Entities testState);
bool checkRSCTL(FormRSCTL *form);
bool checkRSCTLfull(FormRSCTL *form);
bool checkRSCTLbmc(FormRSCTL *form);

68
rs.cc
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@@ -8,6 +8,11 @@
#include "rs.hh"
RctSys::RctSys(void)
{
ctx_aut = nullptr;
}
bool RctSys::hasEntity(std::string name)
{
if (entities_names.find(name) == entities_names.end())
@@ -40,7 +45,7 @@ std::string RctSys::getEntityName(Entity entityID)
}
}
RctSys::Entity RctSys::getEntityID(std::string name)
Entity RctSys::getEntityID(std::string name)
{
if (!hasEntity(name))
{
@@ -166,52 +171,21 @@ void RctSys::printSystem(void)
showInitialStates();
showActionEntities();
showReactions();
}
bool CtxAut::hasState(std::string name)
{
if (states_names.find(name) == states_names.end())
return false;
else
return true;
}
CtxAut::State CtxAut::getStateID(std::string name)
{
if (!hasState(name))
{
FERROR("No such state: " << name);
}
return states_names[name];
}
void CtxAut::addState(std::string name)
{
if (!hasState(name))
{
State new_state_id = states_ids.size();
VERB_L2("Adding state: " << name << " index=" << new_state_id);
states_ids.push_back(name);
states_names[name] = new_state_id;
}
}
void CtxAut::pushContextEntity(RctSys::Entity entity_id)
{
tmpEntities.insert(entity_id);
}
void CtxAut::addTransition(std::string srcStateName, std::string dstStateName)
{
VERB_L3("Saving transition");
Transition new_transition;
new_transition.src_state = getStateID(srcStateName);
new_transition.ctx = tmpEntities;
tmpEntities.clear();
new_transition.dst_state = getStateID(dstStateName);
if (ctx_aut != nullptr)
{
ctx_aut->printAutomaton();
}
}
void RctSys::ctxAutEnable(void)
{
assert(ctx_aut == nullptr);
ctx_aut = new CtxAut;
}
void RctSys::ctxAutAddState(std::string stateName)
{
assert(ctx_aut != nullptr);
}

84
rs.hh
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@@ -15,6 +15,8 @@
#include <vector>
#include <string>
#include <cstdlib>
#include "types.hh"
#include "ctx_aut.hh"
#include "macro.hh"
#include "options.hh"
#include "memtime.hh"
@@ -26,38 +28,9 @@ class RctSys
{
friend class SymRS;
friend class SymRSstate;
public:
typedef unsigned int Entity;
typedef std::set<Entity> Entities;
struct Reaction {
Entities rctt;
Entities inhib;
Entities prod;
};
typedef std::vector<Reaction> Reactions;
typedef std::vector<std::string> EntitiesByIds;
typedef std::map<std::string, Entity> EntitiesByName;
typedef std::set<Entities> EntitiesSets;
private:
Reactions reactions;
EntitiesSets initStates;
Entities actionEntities;
EntitiesByIds entities_ids;
EntitiesByName entities_names;
Entities tmpReactants;
Entities tmpInhibitors;
Entities tmpProducts;
Entities tmpState;
Entity getEntityID(std::string entityName);
Options *opts;
public:
RctSys(void);
void setOptions(Options *opts)
{
this->opts = opts;
@@ -93,40 +66,31 @@ class RctSys
void showInitialStates(void);
void showActionEntities(void);
void printSystem(void);
};
// Context Automaton
class CtxAut
{
public:
typedef unsigned int State;
typedef std::vector<std::string> StatesById;
typedef std::map<std::string, State> StatesByName;
struct Transition {
State src_state;
RctSys::Entities ctx;
State dst_state;
};
bool hasState(std::string name);
void addState(std::string stateName);
State getStateID(std::string name);
void addTransition(std::string srcStateName, std::string dstStateName);
void pushContextEntity(RctSys::Entity entity_id);
void setOptions(Options *opts) { this->opts = opts; }
void ctxAutEnable(void);
void ctxAutAddState(std::string stateName);
private:
Options *opts;
StatesById states_ids;
StatesByName states_names;
RctSys::Entities tmpEntities;
};
Reactions reactions;
EntitiesSets initStates;
Entities actionEntities;
CtxAut *ctx_aut;
EntitiesByIds entities_ids;
EntitiesByName entities_names;
Entities tmpReactants;
Entities tmpInhibitors;
Entities tmpProducts;
Entities tmpState;
Options *opts;
Entity getEntityID(std::string entityName);
class RctSysWithCtxAut : public RctSys
{
// friend class CtxAut;
CtxAut ctx_aut;
};
#endif

18
rsin_driver.cc
View File

@@ -16,8 +16,8 @@ rsin_driver::rsin_driver(RctSys *rs)
void rsin_driver::initialise(void)
{
this->rs = nullptr;
this->rsctlform = nullptr;
rs = nullptr;
rsctlform = nullptr;
opts = nullptr;
use_ctx_aut = false;
use_concentrations = false;
@@ -79,14 +79,11 @@ void rsin_driver::ensureReactionSystemReady(void)
void rsin_driver::setupReactionSystem(void)
{
assert(rs == nullptr);
if (use_ctx_aut)
{
rs = new RctSysWithCtxAut;
}
else
{
rs = new RctSys;
}
rs = new RctSys;
if (use_ctx_aut) VERB("Using RS with CA")
else VERB("Using ordinary RS")
rs->setOptions(opts);
}
@@ -96,3 +93,4 @@ RctSys *rsin_driver::getReactionSystem(void)
assert(rs != nullptr);
return rs;
}

10
rsin_driver.hh
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@@ -25,13 +25,10 @@ public:
virtual ~rsin_driver();
//std::map<std::string, int> variables;
RctSys *rs;
FormRSCTL *rsctlform;
Options *opts;
//
// options in configuration file
//
// options in configuration file:
bool use_ctx_aut;
bool use_concentrations;
@@ -49,19 +46,22 @@ public:
FormRSCTL *getFormRSCTL(void);
void ensureOptionsAllowed(void);
void useContextAutomaton(void) { ensureOptionsAllowed(); use_ctx_aut = true; };
void useContextAutomaton(void) { ensureOptionsAllowed(); use_ctx_aut = true; getReactionSystem()->ctxAutEnable(); };
void useConcentrations(void) { ensureOptionsAllowed(); use_concentrations = true; };
void ensureReactionSystemReady(void);
void setupReactionSystem(void);
RctSys *getReactionSystem(void);
CtxAut *getCtxAut(void);
// Error handling.
void error(const yy::location &l, const std::string &m);
void error(const std::string &m);
private:
RctSys *rs;
void initialise(void);
};

9
rsin_parser.yy
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@@ -91,7 +91,12 @@ options:
;
option:
| USE_CTX_AUT { }
| USE_CTX_AUT {
driver.useContextAutomaton();
}
| USE_CONCENTRATIONS {
driver.useConcentrations();
}
;
/*
@@ -190,6 +195,8 @@ ctxaut:
;
autstate: IDENTIFIER {
driver.getReactionSystem()->ctxAutAddState(*$1);
free($1);
}
;

14
symrs.cc
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@@ -8,7 +8,7 @@
#include "symrs.hh"
BDD SymRS::encEntity_raw(RctSys::Entity entity, bool succ) const
BDD SymRS::encEntity_raw(Entity entity, bool succ) const
{
BDD r;
@@ -20,7 +20,7 @@ BDD SymRS::encEntity_raw(RctSys::Entity entity, bool succ) const
return r;
}
BDD SymRS::encEntitiesConj_raw(const RctSys::Entities &entities, bool succ)
BDD SymRS::encEntitiesConj_raw(const Entities &entities, bool succ)
{
BDD r = BDD_TRUE;
@@ -33,7 +33,7 @@ BDD SymRS::encEntitiesConj_raw(const RctSys::Entities &entities, bool succ)
return r;
}
BDD SymRS::encEntitiesDisj_raw(const RctSys::Entities &entities, bool succ)
BDD SymRS::encEntitiesDisj_raw(const Entities &entities, bool succ)
{
BDD r = BDD_FALSE;
@@ -46,7 +46,7 @@ BDD SymRS::encEntitiesDisj_raw(const RctSys::Entities &entities, bool succ)
return r;
}
BDD SymRS::encStateActEntitiesConj(const RctSys::Entities &entities)
BDD SymRS::encStateActEntitiesConj(const Entities &entities)
{
BDD r = BDD_TRUE;
@@ -62,7 +62,7 @@ BDD SymRS::encStateActEntitiesConj(const RctSys::Entities &entities)
return r;
}
BDD SymRS::encStateActEntitiesDisj(const RctSys::Entities &entities)
BDD SymRS::encStateActEntitiesDisj(const Entities &entities)
{
BDD r = BDD_FALSE;
@@ -182,7 +182,7 @@ void SymRS::encodeTransitions(void)
cond.rctt = rs->reactions[i].rctt;
cond.inhib = rs->reactions[i].inhib;
for (RctSys::Entities::iterator p = rs->reactions[i].prod.begin();
for (Entities::iterator p = rs->reactions[i].prod.begin();
p != rs->reactions[i].prod.end(); ++p)
{
dr[*p].push_back(cond);
@@ -289,7 +289,7 @@ void SymRS::encodeTransitions(void)
VERB("Reactions ready");
}
BDD SymRS::getEncState(const RctSys::Entities &entities)
BDD SymRS::getEncState(const Entities &entities)
{
assert(0);
//BDD state = compState(encEntitiesConj(rs->initState));

33
symrs.hh
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@@ -14,6 +14,7 @@
#include <map>
#include <cassert>
#include "cudd.hh"
#include "types.hh"
#include "macro.hh"
#include "bdd_macro.hh"
#include "rs.hh"
@@ -36,11 +37,11 @@ class SymRS
Options *opts;
struct ReactionCond {
RctSys::Entities rctt;
RctSys::Entities inhib;
Entities rctt;
Entities inhib;
};
typedef vector<ReactionCond> ReactionConds;
typedef map<RctSys::Entity,ReactionConds> DecompReactions;
typedef map<Entity,ReactionConds> DecompReactions;
typedef std::vector<int> StateEntityToAction;
StateEntityToAction stateToAct;
@@ -62,33 +63,33 @@ class SymRS
unsigned int totalStateVars;
unsigned int totalActions;
BDD encEntity_raw(RctSys::Entity entity, bool succ) const;
BDD encEntity(RctSys::Entity entity) const {
BDD encEntity_raw(Entity entity, bool succ) const;
BDD encEntity(Entity entity) const {
return encEntity_raw(entity, false);
}
BDD encActEntity(RctSys::Entity entity) const {
BDD encActEntity(Entity entity) const {
assert(entity < pv_act->size());
return (*pv_act)[entity];
}
BDD encEntitySucc(RctSys::Entity entity) const {
BDD encEntitySucc(Entity entity) const {
return encEntity_raw(entity, true);
}
BDD encEntitiesConj_raw(const RctSys::Entities &entities, bool succ);
BDD encEntitiesConj(const RctSys::Entities &entities) {
BDD encEntitiesConj_raw(const Entities &entities, bool succ);
BDD encEntitiesConj(const Entities &entities) {
return encEntitiesConj_raw(entities, false);
}
BDD encEntitiesConjSucc(const RctSys::Entities &entities) {
BDD encEntitiesConjSucc(const Entities &entities) {
return encEntitiesConj_raw(entities, true);
}
BDD encEntitiesDisj_raw(const RctSys::Entities &entities, bool succ);
BDD encEntitiesDisj(const RctSys::Entities &entities) {
BDD encEntitiesDisj_raw(const Entities &entities, bool succ);
BDD encEntitiesDisj(const Entities &entities) {
return encEntitiesDisj_raw(entities, false);
}
BDD encEntitiesDisjSucc(const RctSys::Entities &entities) {
BDD encEntitiesDisjSucc(const Entities &entities) {
return encEntitiesDisj_raw(entities, true);
}
BDD encStateActEntitiesConj(const RctSys::Entities &entities);
BDD encStateActEntitiesDisj(const RctSys::Entities &entities);
BDD encStateActEntitiesConj(const Entities &entities);
BDD encStateActEntitiesDisj(const Entities &entities);
/**
* @brief Complements an encoding of a given state by negating all the variables that are not set to true
@@ -134,7 +135,7 @@ public:
BDD *getEncPVact_E(void) { return pv_act_E; }
vector<BDD> *getEncPartTrans(void) { return partTrans; }
BDD *getEncMonoTrans(void) { return monoTrans; }
BDD getEncState(const RctSys::Entities &entities);
BDD getEncState(const Entities &entities);
BDD *getEncInitStates(void) { return initStates; }
Cudd *getCuddMgr(void) { return cuddMgr; }
unsigned int getTotalStateVars(void) { return totalStateVars; }