correction bug dans list_dimensions sur dimension des nombres

biocham_jupyter/guinbextension/src/config/workflows/commands.py

@@ -30,6 +30,8 @@ commands = [
     "check_multistability",
     "check_oscillations",
     "cleanup_ctl",
+    "clear_dimension",
+    "clear_dimensions",
     "clear_initial_state",
     "clear_model",
     "clear_variation",

units.pl

 :- module(units,
   [
+    list_dimensions/0,
     set_dimension/3,
-    list_dimensions/0
+    clear_dimensions/0,
+    clear_dimension/1
   ]
 ).
 
@@ -12,28 +14,35 @@
 % store declared units
 :- dynamic(k_unit/3).
 
+:- biocham_silent(clear_model).
 
-set_dimension(P, U, V) :-
-  biocham_command,
-  doc('Declare dimension time^\\argument{U} and volume^\\argument{V}
-    for parameter \\argument{P}'),
-  type(P, parameter_name),
-  type(U, number),
-  type(V, number),
-  retractall(k_unit(P, _, _)),
-  assertz(k_unit(P, U, V)).
 
+%! list_dimensions.
+%
+% biocham command
+%
+% Infers dimensions (time and volume, without units) of all parameters of the model.
+%
+% Molecular concentration have dimension volume^-1
+% Reaction rates (and influence forces) have dimension time^-1
+%
+% A dimension is encoded by a couple (time exponent, volume exponent)
+% No dimension is encoded by the couple (0, 0)
+% Any dimension is encoded by a variable
+% Numbers have any dimension
 
-:- biocham_silent(clear_model).
 
 list_dimensions :-
   biocham_command,
   doc('
-    Checks the (time) dimensions of all parameters of the current model.
+    Performs a dimensional analysis of the current model. Infers the time and volume dimensions of all parameters. 
+    The dimension of a molecular concentration is volume^-1.
+    The dimension of a reaction rate or influence force is time^-1. 
+    The dimensions are considered without units.
     \\begin{example}
     \\trace{
       biocham: MM(v, k) for A => B.
-      biocham: parameter(k = 1, v = 1).
+      biocham: parameter(k = 2, v = 3).
       biocham: list_dimensions.
     }
     \\end{example}
@@ -54,6 +63,30 @@ list_dimensions :-
   print_message(error, failed_dimension(T, E)).
 
 
+set_dimension(P, U, V) :-
+  biocham_command,
+  doc('Declare dimension time^\\argument{U} . volume^\\argument{V}
+    for parameter \\argument{P}'),
+  type(P, parameter_name),
+  type(U, number),
+  type(V, number),
+  retractall(k_unit(P, _, _)),
+  assertz(k_unit(P, U, V)).
+
+
+clear_dimensions :-
+  biocham_command,
+  doc('Clear all declared dimensions'),
+  retractall(k_unit(_ , _, _)).
+
+
+clear_dimension(P) :-
+  biocham_command,
+  doc('Clear declared dimension for parameter \\argument{P}'),
+  type(P, parameter_name),
+  retractall(k_unit(P, _, _)).
+
+
 check_set_dim([]).
 
 check_set_dim([((U, V) - P) | L]) :-
@@ -110,11 +143,13 @@ find_parameter_dim(-Y, Dim, L)  :-
   !,
   find_parameter_dim(Y, Dim, L).
 
-% FIXME? force dimensionless exponentiation
+% forces exponents to be dimensionless
 find_parameter_dim(X ^ Y, (DimT, DimV), L) :-
   !,
   find_parameter_dim(X, (DT, DV), L),
-  find_parameter_dim(Y, 0, L),
+  find_parameter_dim(Y, (DYT, DYV), L),
+  DYT #= 0,
+  DYV #= 0,
   (
     (
       number(Y),
@@ -131,7 +166,7 @@ find_parameter_dim(X ^ Y, (DimT, DimV), L) :-
       DT2 = DT,
       DV2 = DV
     ;
-      Y = 1/Z,
+      Y = 1/Z, 
       DT1 = DT,
       DV1 = DV,
       DT2 = DimT,
@@ -158,7 +193,7 @@ find_parameter_dim(X ^ Y, (DimT, DimV), L) :-
     )
   ).
 
-% FIXME? correct? force Dim=0?
+% forces Dim=0 for other functions than addition and multiplication
 find_parameter_dim(log(X), (DimT, DimV), L) :-
   !,
   nb_setval(current_dim_term, log(X)),
@@ -187,11 +222,16 @@ find_parameter_dim(cos(X), (DimT, DimV), L) :-
   DimV #= 0,
   find_parameter_dim(X, (DimT, DimV), L).
 
-find_parameter_dim(N, (DimT, DimV), _) :-
+%find_parameter_dim(N, (DimT, DimV), _) :-
+%  number(N),
+%  !,
+%  DimT #= 0,
+%  DimV #= 0.
+%
+%FF Numbers may take any dimension
+find_parameter_dim(N, _Dim, _) :-
   number(N),
-  !,
-  DimT #= 0,
-  DimV #= 0.
+  !.
 
 find_parameter_dim('Time', (DimT, DimV), _) :-
   !,
@@ -200,7 +240,7 @@ find_parameter_dim('Time', (DimT, DimV), _) :-
   DimV #= 0.
 
 find_parameter_dim(X * Y, (DimT, DimV), L) :-
-  !,
+    !,
   find_parameter_dim(X, (DT1, DV1), L),
   find_parameter_dim(Y, (DT2, DV2), L),
   nb_setval(current_dim_term, X * Y),
@@ -220,13 +260,6 @@ find_parameter_dim(if(then(_C, else(A, B))), Dim, L) :-
   find_parameter_dim(A, Dim, L),
   find_parameter_dim(B, Dim, L).
 
-find_parameter_dim(P, (DimT, DimV), L) :-
-  parameter_value(P, _),
-  !,
-  member(((DT, DV) - P), L),
-  DimT #= DT,
-  DimV #= DV.
-
 find_parameter_dim([M], (DimT, DimV), _) :-
   !,
   nb_setval(current_dim_term, [M]),
@@ -240,6 +273,21 @@ find_parameter_dim(M, (DimT, DimV), _) :-
   DimT #= 0,
   DimV #= -1.
 
+find_parameter_dim(P, (DimT, DimV), L) :-
+    (
+        (
+            parameter_value(P, _), %FF should check the expression
+            member(((DT, DV) - P), L)
+        )
+    ->
+    DimT #= DT,
+    DimV #= DV
+    ;
+    true %FF the dimensions for P should be added to L (using a difference list)
+    ).
+
+
+
 
 write_dimensions([]).
 
@@ -257,10 +305,10 @@ write_dimensions([((DT, DV) - P) | L]) :-
 
 
 prolog:message(constant_species) -->
-  ['some species are constant in this model'-[]].
+  ['There are molecular species without kinetics in this model'-[]].
 
 prolog:message(no_satisfy) -->
-  ['Could not satisfy time units constraints on parameter dimensions.'-[]].
+  ['Could not satisfy all constraints on parameter dimensions.'-[]].
 
 prolog:message(failed_dimension(T, E)) -->
   ['Failed on ~w in ~w~na kinetic expression which should be time^-1'-[T, E]].