Add the naming convention during compilation

gpac.pl

@@ -97,7 +97,9 @@ compile_from_expression(Expr, Input, Output) :-
     'Switch between a brutal or a lazy negation'
   ),
   expression_to_PIVP(Expr, PIVP),
-  main_compiler(PIVP, Input, Output).
+  PIVP = [N, _PODE, _IC],
+  abstract_names(N, Output, Name_list),
+  main_compiler(PIVP, Name_list, Input).
 
 :- doc('
   \\begin{example} Compilation of the expression 4+time^2:\n
@@ -313,8 +315,9 @@ compile_from_pivp(PIVP, Input, Output) :-
     _Reduction,
     'Determine if the binomial reduction has to be performed'
   ),
-  format_pivp(PIVP, P, Name_list),
-  main_compiler(P, Name_list, Input, Output).
+  sort_output(PIVP, Output, PIVP_sorted),
+  format_pivp(PIVP_sorted, P, Name_list),
+  main_compiler(P, Name_list, Input).
 
 :- devdoc('\\begin{todo} Compilation of the cosine function as a function of time defined as the solution of a PIVP)\n
 \\texttt{
@@ -339,7 +342,7 @@ compile_from_pivp(PIVP, Input, Output) :-
 ').
 
 
-%! main_compiler(+PIVP_list, +Name_list, +Input, +Output)
+%! main_compiler(+PIVP_list, +Name_list, +Input)
 %
 % Compile a PIVP_list, this predicate dispatch the various options of compilation
 % it first check if the PIVP should be reduce to a binomial form
@@ -347,7 +350,7 @@ compile_from_pivp(PIVP, Input, Output) :-
 % when Input is not time it then call g_to_c_PIVP/3.
 % and finally make a call to compile_to_biocham_model to make the final implementation
 
-main_compiler(PIVP_input, Name_list_raw, Input, Output):-
+main_compiler(PIVP_input, Name_list_raw, Input):-
    clear_model,
    get_option(fast_rate, Fast),
    get_option(lazy_negatives, Lazyness),
@@ -359,7 +362,7 @@ main_compiler(PIVP_input, Name_list_raw, Input, Output):-
       Name_list_non_bin = Name_list_raw
    ;
       g_to_c_PIVP(PIVP_input, PIVP_non_bin, 1.0),
-      append(Name_list_non_raw, [Input], Name_list_non_bin)
+      append(Name_list_raw, [Input], Name_list_non_bin)
    ),
    (
       Reduction = yes
@@ -369,7 +372,6 @@ main_compiler(PIVP_input, Name_list_raw, Input, Output):-
       PIVP_unsigned = PIVP_non_bin,
       Name_list_unsigned = Name_list_non_bin
    ),
-   PIVP_unsigned = [N,_PODE,_IV],
    get_option(lazy_negatives, Lazyness),
    (
       Lazyness = yes
@@ -378,7 +380,8 @@ main_compiler(PIVP_input, Name_list_raw, Input, Output):-
    ;
       lng:rewrite_PIVP_all_negated(PIVP_unsigned, PIVP, VarNeg)
    ),
-   affect_name(N,Output,Input,VarNeg,Species_names),
+   sort(VarNeg, VarNegSort),
+   negate_name(Name_list_unsigned, VarNegSort, Species_names),
    (
       \+(VarNeg = [])
    ->
@@ -783,7 +786,7 @@ compose_multivar_vector([P|PV], PL, [Q|QV]) :-
 %
 % Reduce a given PIVP to a new one which only need binomial
 
-reduce_to_binomial([N,PODE,IV],[NewN,NewPODE,NewIV]) :-
+reduce_to_binomial([N,PODE,IV], Name_list, [NewN,NewPODE,NewIV], Modified_Names) :-
    scan_order_multivarvector(PODE,Order),
    (
       Order > 2
@@ -1117,7 +1120,7 @@ generate_names(_Name_list, [], []) :- !.
 
 generate_names(Name_list, [Var|TailVar], [Name|TailName]) :-
   write_new_name(Name_list, Var, Name_as_list),
-  atomics_to_string(Name_as_list, Name),
+  atomic_list_concat(Name_as_list, Name),
   generate_names(Name_list, TailVar, TailName).
 
 
@@ -1574,42 +1577,26 @@ exponant_to_solution([Exp|Tail_exp], [Name|Tail_name], Sol, Kin) :-
    ).
 
 
-%! affect_name(+N,+Output,+Input,+Varneg,-Name_list)
+%! negate_name(+Name_list_raw, +Varneg, -Name_list)
 %
-% Create the name of the species
+% Add _p and _m to the name of variables if necessary
 
-affect_name(N,Output,Input,Varneg,Name_list) :-
-   affect_name(N,0,Output,Input,Varneg,Name_list).
+negate_name(NLR, VN, NL) :-
+  negate_name(NLR, 1, VN, NL).
 
-affect_name(N,N,_Output,_Input,_Varneg,[]) :- !.
+negate_name([], _N, [], []) :- !.
 
-affect_name(N,Nc,Output,Input,Varneg,Name_list) :-
-   get_option(lazy_negatives, Lazyness),
-   Nxt is Nc+1,
-   (
-      Nxt = 1
-   ->
-      Name = Output
-   ;
-      Lazyness = no,
-      Nxt = N
-   ->
-      Name = Input
-   ;
-      Nchar is Nxt+63,
-      char_code(Name,Nchar)
-   ),
-   (
-      member(Nxt,Varneg)
-   ->
-      name_p_m(Name,Name_p,Name_m),
-      add_reaction(fast*Name_p*Name_m for Name_p+Name_m=>_),
-      Head = [Name_p,Name_m]
-   ;
-      Head = [Name]
-   ),
-   affect_name(N,Nxt,Output,Input,Varneg,Tail),
-   append(Head,Tail,Name_list).
+negate_name([Name|TailName], N, [N|TailNeg], [Name_p,Name_m|TailNewName]) :-
+  !,
+  name_p_m(Name,Name_p,Name_m),
+  add_reaction(fast*Name_p*Name_m for Name_p+Name_m=>_),
+  NN is N+1,
+  negate_name(TailName, NN, TailNeg, TailNewName).
+
+negate_name([Name|TailName], N, VarNeg, [Name|TailNewName]) :-
+  !,
+  NN is N+1,
+  negate_name(TailName, NN, VarNeg, TailNewName).
 
 
 %! name_p_m(+Name,-Positive_name,-Negative_name)
@@ -1693,3 +1680,31 @@ expression_to_PIVP(E / F, PIVP) :-
 
 expression_to_PIVP(E, _) :-
   throw(error(illegal_expression(E), expression_to_PIVP)).
+
+
+%! abstract_names(+N, +Output, -Name_list)
+
+abstract_names(N, Output, [Output|RTail]) :-
+  Nm is N-1,
+  abstract_names(Nm, Tail),
+  reverse(Tail, RTail).
+
+abstract_names(0, []) :- !.
+
+abstract_names(N, [Head|Tail]) :-
+  Nm is N-1,
+  divmod(Nm,26,R,C),
+  Code is C+65,
+  Rep is R+1,
+  char_code(Letter, Code),
+  stutter(Rep, Letter, Head),
+  abstract_names(Nm, Tail).
+
+%! stutter(N,In,Out)
+
+stutter(1, In, In) :- !.
+
+stutter(N, In, Out) :-
+  Nm is N-1,
+  stutter(Nm, p, Tempo),
+  atom_concat(In, Tempo, Out).