removed useless rescaled system, now working

tropical.pl

@@ -101,18 +101,12 @@ conserve(L, D) :-
 % P-invariants already computed to enforce constraints on the exponents Ai
 set_conservations(Ai, Places) :-
   nb_getval(base, B),
-  (
-    B \= 0
-  ->
-    invariants:vars(Vars),
-    length(Ai, N),
-    length(Bi, N),
-    reorder_place_vars(Ai, Bi, Places, Vars),
-    get_initial_values(Vars, Di),
-    set_conservations_rec(B, Bi, Di)
-  ;
-    true
-  ),
+  invariants:vars(Vars),
+  length(Ai, N),
+  length(Bi, N),
+  reorder_place_vars(Ai, Bi, Places, Vars),
+  get_initial_values(Vars, Di),
+  set_conservations_rec(B, Bi, Di),
   set_constant_vars.
 
 
@@ -303,6 +297,7 @@ get_equilibrations(Vars, Ai, E, DE) :-
     ),
     L
   ),
+  debug(tropical, "ODEs: ~w", [L]),
   get_equilibrations_rec(L, Vars, Ai, E, DE).
 
 
@@ -323,7 +318,7 @@ get_equilibrations_rec([(S, O) | L], Vars, Ai, [E | EE], [DE | DEE]) :-
 
 
 substract_rec(L, A, LA) :-
-  maplist(L, reverse_minus(A), LA).
+  maplist(tropical:reverse_minus(A), L, LA).
 
 
 reverse_minus(A, B, B - A).
@@ -334,7 +329,7 @@ show_rescaling([], []) :-
 
 show_rescaling([A | AA], [V | VV]) :-
   epsilon_degree(A, D),
-  format("~p_ = ~p~p~n", [V, D, V]),
+  format("~w' = ~w~w~n", [V, D, V]),
   show_rescaling(AA, VV).
 
 
@@ -363,152 +358,6 @@ epsilon_degree(D, A) :-
   ).
 
 
-rescale_system(E, S) :-
-  eval_rec(E, EE),
-  get_rescaled_odes(EE, O),
-  sort_by_scale_rec(O, OO),
-  predsort(compare_first_degree, OO, S).
-
-
-print_system([]) :-
-  nl.
-
-print_system([(Species, ODE) | L]) :-
-  format("d~p/dt = ", [Species]),
-  print_ode(ODE),
-  print_system(L).
-
-
-print_ode([]) :-
-  write('0\n').
-
-print_ode([(D, T) | O]) :-
-  epsilon_degree(D, A),
-  print(A),
-  (
-    A \= '',
-    T = _ + _
-  ->
-    format("(~p)", [T])
-  ;
-    print(T)
-  ),
-  (
-    O == []
-  ->
-    nl
-  ;
-    print(' + '),
-    print_ode(O)
-  ).
-
-
-compare_first_degree(Result, (S1, [(D1, _) | _]), (S2, [(D2, _) | _])) :-
-  compare(Result, (D1, S1), (D2, S2)).
-
-
-get_rescaled_odes([], []).
-
-get_rescaled_odes([(LPos, LNeg) | E], [(Species, O) | OO]) :-
-  retract(ode(Species, T)),
-  rescale_to(T, LPos, LNeg, O),
-  get_rescaled_odes(E, OO).
-
-
-rescale_to(E + N * T, Pos, Neg, EEE) :-
-  !,
-  rescale_to(N * T, Pos1, Neg1, RT),
-  append(RT, EE, EEE),
-  append(Pos1, LPos, Pos),
-  append(Neg1, LNeg, Neg),
-  rescale_to(E, LPos, LNeg, EE).
-
-rescale_to(N * (A + B), Pos, Neg, EE) :-
-  !,
-  rescale_to(N * A + N * B, Pos, Neg, EE).
-
-rescale_to(N * (A - B), Pos, Neg, EE) :-
-  !,
-  M is -N,
-  rescale_to(N * A + M * B, Pos, Neg, EE).
-
-rescale_to(_ * T, [], [], []) :-
-  is_zero(T),
-  !.
-
-rescale_to(N * T, LPos, LNeg, [RT]) :-
-  !,
-  (
-    N > 0
-  ->
-    LPos = [Exp],
-    LNeg = []
-  ;
-    LNeg = [Exp],
-    LPos = []
-  ),
-  RT = (Exp, N * T).
-
-sort_by_scale_rec([], []).
-
-sort_by_scale_rec([(Species, Ode) | L], [(Species, SOde) | LL]) :-
-  sort_by_scale(Ode, SOde),
-  sort_by_scale_rec(L, LL).
-
-
-sort_by_scale(L, SL) :-
-  sort_by_scale_aux(L, SL, []).
-
-
-sort_by_scale_aux([], L, L).
-
-sort_by_scale_aux([H | T], SL, L) :-
-  merge_by_scale(L, H, LL),
-  sort_by_scale_aux(T, SL, LL).
-
-
-merge_by_scale([(N, T1) | L], (N, T2), [(N, T1 + T2) | L]) :-
-  !.
-
-merge_by_scale([(N, T1) | L], (M, T2), [(N, T1) | LL]) :-
-  N < M,
-  !,
-  merge_by_scale(L, (M, T2), LL).
-
-merge_by_scale(L, (M, T2), [(M, T2) | L]).
-
-
-eval_rec([], []) :-
-  !.
-
-eval_rec([H | T], [HH | TT]) :-
-  !,
-  eval_rec(H, HH),
-  eval_rec(T, TT).
-
-eval_rec((A, B), (AA, BB)) :-
-  !,
-  eval_rec(A, AA),
-  eval_rec(B, BB).
-
-eval_rec(A, B) :-
-  B is A.
-
-
-% FIXME add rescaled conservation to S1
-reduce_system([], [], []).
-
-reduce_system([(Species, [(D, T) | _]) | ODEs], [T = 0 | S1], S2) :-
-  D < 0,
-  format("~p is a fast variable with invariant manifold ~p = 0~n", [Species, T]),
-  reduce_system(ODEs, S1, S2).
-
-reduce_system([(Species, [(D, T) | L]) | ODEs], S1, [(Species, [(D, T) | L]) | S2]) :-
-  D >= 0,
-  format("~p is a slow variable~n", [Species]),
-  reduce_system(ODEs, S1, S2).
-
-
 % look for an atom as a leaf of a term, not trying to unify FD vars
 atom_is_subterm(_, Y) :-
   var(Y),
@@ -621,9 +470,7 @@ tropicalize :-
   ;
     find_pinvar(4)
   ),
-  % FIXME why is this needed?
-  !,
-  debug(tropical, "invar done~n", []),
+  debug(tropical, "invar done", []),
   statistics(cputime, Time0),
   molecules_vars(Vars),
   length(Vars, VL),
@@ -637,10 +484,11 @@ tropicalize :-
       between(2, Max, Power),
       MaxD is 2^Power
     ),
-    debug(tropical, "about to set conservations…~n", []),
+    debug(tropical, "about to set conservations… (Max = ~w)", [MaxD]),
     set_conservations(Ai, Vars),
-    debug(tropical, "conservations done~n", []),
-    get_equilibrations(Vars, Ai, E, DE),
+    debug(tropical, "conservations done", []),
+    get_equilibrations(Vars, Ai, E, _DE),
+    debug(tropical, "equilibrations: ~w", [E]),
     (
       Partial == 0
     ->
@@ -662,20 +510,14 @@ tropicalize :-
     labeling([bisect], Ai),    % ffc makes biomodel 407 slow...
     % bisect slightly better
     (
-      Ovidiu \= 0
+      nb_current(ovidiu_file, _)
     ->
       show_rescaling_ovidiu(Ai)
     ;
       write('\nfound a complete equilibration leading to the rescaling:\n'),
-      show_rescaling(Ai, Vars),
-      rescale_system(DE, S),
-      write('using old variable names, here is the rescaled system:\n'),
-      print_system(S),
-      reduce_system(S, _S1, S2),
-      % FIXME should use S1 to simplify S2
-      write('\nreduced system:\n'),
-      print_system(S2)
-    )
+      show_rescaling(Ai, Vars)
+    ),
+    fail
   ;
     write('\nNo (more) complete equilibration\n'),
     (