Commit 43dd146b authored by SOLIMAN Sylvain's avatar SOLIMAN Sylvain
Browse files

initial.bc finally gone

parent 9efcba80
......@@ -99,7 +99,8 @@ initialize :-
set_draw_graph_driver(graph_pdf),
nb_setval(graph_pdf, 0),
nb_setval(current_models, []),
load_biocham('library:initial'),
new_model,
set_model_name('initial'),
\+ (
initial_command(Command),
\+ (
......
......@@ -75,6 +75,8 @@ check_conservations :-
check_conservation(C, Conserv)
).
:- initial(option(conservation_size: 4)).
search_conservations :-
biocham_command,
......
option(
fast_rate: 1000,
time: 20,
show: {},
method: bsimp, % msbdf,
error_epsilon_absolute: 1e-6,
error_epsilon_relative: 1e-6,
initial_step_size: 1e-6,
maximum_step_size: 1e-2,
minimum_step_size: 1e-5,
precision: 6, %5
nusmv_initial_states: all,
nusmv_counter_example: no,
boolean_semantics: negative,
logscale: '',
against: 'Time',
conservation_size: 4,
query: current_spec,
output_to_library: no,
simplify_variable_init: no, % used in odefunction.pl
zero_ultra_mm: no % used in odefunction.pl
).
......@@ -114,6 +114,14 @@ filter(no_filter).
filter(only_extrema).
:- grammar_doc('\\emphright{Only keeps the points that are an extremum for some variable.}').
:- initial(option(method: bsimp)).
:- initial(option(error_epsilon_absolute: 1e-6)).
:- initial(option(error_epsilon_relative: 1e-6)).
:- initial(option(initial_step_size: 1e-6)).
:- initial(option(maximum_step_size: 1e-2)).
:- initial(option(minimum_step_size: 1e-5)).
:- initial(option(precision: 6)).
:- initial(option(time: 20)).
:- initial(option(stochastic_conversion: 100)).
:- initial(option(stochastic_thresholding: 1000)).
......
......@@ -30,13 +30,13 @@
boolean_semantics(positive).
% Default. Set in library/initial.bc
boolean_semantics(negative).
:- doc('\\emphright{The default value is \\texttt{negative}}').
:- initial(option(boolean_semantics: negative)).
:- grammar(nusmv_initial_states).
% Default. Set in library/initial.bc
nusmv_initial_states(all).
nusmv_initial_states(some).
......@@ -47,6 +47,10 @@ nusmv_initial_states(all_or_some).
\\texttt{all_or_some} tries for all initial states, and if that fails, for
some}').
:- initial(option(nusmv_initial_states: all)).
:- initial(option(nusmv_counter_example: no)).
:- initial(option(query: current_spec)).
check_ctl :-
biocham_command,
......
......@@ -408,6 +408,9 @@ add_function(FunctionList) :-
delete_item(OdeSystem).
:- initial(option(simplify_variable_init: no)).
:- initial(option(zero_ultra_mm: no)).
%% compile_program(+InputFile:atom) is det
%
% Compiles a high-level imperative program from a string.
......
......@@ -31,6 +31,10 @@ axes(xy).
% store plot options for a future export_plot
:- dynamic(logscale/1, show/1, against/1).
:- initial(option(show: {})).
:- initial(option(logscale: '')).
:- initial(option(against: 'Time')).
plot :-
biocham_command,
......
......@@ -379,6 +379,8 @@ filter_out_boundaries([_ * H | T], TT) :-
filter_out_boundaries(T, TTT)
).
:- initial(option(output_to_library: no)).
download_curated_biomodel(Id) :-
biocham_command,
......
......@@ -89,6 +89,8 @@ wgpac_well_formed(Y :: B) :-
object(Y),
wgpac_box_free(B, Y).
:- initial(option(fast_rate: 1000)).
compile_wgpac(WgpacSet) :-
biocham_command,
......
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