directive duration 20000000.0 points 1000
directive plot <I> 
(* This example takes 16 irreversible steps to copy "00111".  Probabilistic irreversibility implementation from LNCS Qian et al.  *)
(* Use "infinite" semantics, just-in-time (JIT) simulation with the "polymer" option checked. *)
(* Simulates a closed system with initial fuel that gets used up. *)
(* Look at the "final state" to see the molecules at the end. *)

def Fuel = 20

def stack(N,Qp,Qm,P,Bp,Bm) = 
  ( N * <T^>[Qp* T^*]<P>{Qm}
  | N * <Bp T^>
  | N * <P T^>
  )
  
def stacksym(N,Qp,Qm,P,Xp,Xm) =
  ( N * {T^}[P T^]:[Xp T^]{Qp}
  | N * <Xp T^>
  )
  
def unirev(N,Xp,Xm,Ap,Am) = 
  ( N * {T^*}[Xp T^]:[Am T^]<Ap>
  | N * <Xp T^>
  | N * <T^ Am>
  | N * <Xm>[T^ Xp]:[T^ Am]{T^*}
  )
  
def biirrev(N,Xp,Xm,Yp,Ym,Ap,Am,Bp,Bm) =
  ( N * {T^*}[Xp T^]:[Yp T^]:[Am T^]<Ap>:[Bm T^]<Bp>:[I]
  | N * <Xp T^>
  | N * <Yp T^>
  | N * <T^ Am>
  | N * <T^ Bm>
  | N * <T^ I>
  )

( stack(Fuel,Q1p,Q1m,P1,B1p,B1m)
| stacksym(Fuel,Q1p,Q1m,P1,p01,m01)
| stacksym(Fuel,Q1p,Q1m,P1,p11,m11)
| stack(Fuel,Q2p,Q2m,P2,B2p,B2m)
| stacksym(Fuel,Q2p,Q2m,P2,p02,m02)
| stacksym(Fuel,Q2p,Q2m,P2,p12,m12)
| stack(Fuel,Q3p,Q3m,P3,B3p,B3m)
| stacksym(Fuel,Q3p,Q3m,P3,p03,m03)
| stacksym(Fuel,Q3p,Q3m,P3,p13,m13)
| unirev(Fuel,Q1p,Q1m,Qp,Qm)
| unirev(Fuel,Q2p,Q2m,Qp,Qm)
| unirev(Fuel,Q3p,Q3m,Qp,Qm)
| biirrev(Fuel,S1p,S1m,p01,m01,S2p,S2m,Qp,Qm)
| biirrev(Fuel,S1p,S1m,p11,m11,S4p,S4m,Qp,Qm)
| biirrev(Fuel,S1p,S1m,B1p,B1m,S6p,S6m,B1p,B1m)
| biirrev(Fuel,S2p,S2m,Qp,Qm,S3p,S3m,p02,m02)
| biirrev(Fuel,S3p,S3m,Qp,Qm,S1p,S1m,p03,m03)
| biirrev(Fuel,S4p,S4m,Qp,Qm,S5p,S5m,p12,m12)
| biirrev(Fuel,S5p,S5m,Qp,Qm,S1p,S1m,p13,m13)
| <S1m T^ S1p>
| <Qm T^ Qp>
| <B1m>[T^ B1p]:[T^ Q1p*]::[T^* P1]:<m01>[T^ p01]:[T^ Q1p*]::[T^* P1]:<m01>[T^ p01]:[T^ Q1p*]::[T^* P1]:<m11>[T^ p11]:[T^ Q1p*]::[T^* P1]:<m11>[T^ p11]:[T^ Q1p*]::[T^* P1]:<m11>[T^ p11]:[T^ Q1p*]<T^* P1>
| <B2m>[T^ B2p]:[T^ Q2p*]<T^* P2>
| <B3m>[T^ B3p]:[T^ Q3p*]<T^* P3>
)