Fixed species flag is violated in SSA simulations

[GoogleCodeExporter]

What steps will reproduce the problem?
1.Add fixed species to model, e.g.  $0()
2.Add synthesis rule:  0 -> A()  k
3.Simulate with SSA option

What is the expected output? What do you see instead?
The synthesis rule should create an A molecule and leave 0 unchanged since it 
has the fixed flag. Run_network (v3.0) reports that 0() is a fixed (boundary 
condition) species. However, the fixed flag is not respected and the population 
of 0() decrements when the rule fires.

Original issue reported on code.google.com by justinshogg on 2 May 2012 at 2:54

[GoogleCodeExporter]

# This model will reproduce the fixed species bug in SSA
begin model
begin parameters
    ksynth 1.0
    kdeg   0.1
end parameters
begin molecule types
    A()
    0()
end molecule types
begin seed species
    A()   0
    $0()  1
end seed species
begin observables
    Molecules  A_tot  A()
    Molecules  Null   0()
end observables
begin reaction rules
    0   -> A()   ksynth
    A() -> 0     kdeg
end reaction rules
end model

generate_network({overwrite=>1})
simulate_ssa({t_start=>0,t_end=>50,n_steps=>50})

Original comment by justinshogg on 2 May 2012 at 2:56

[GoogleCodeExporter]

Original comment by justinshogg on 2 May 2012 at 3:00

• Changed title: Fixed species flag is violated in SSA simulations

[GoogleCodeExporter]

Fixed bug in network::update_concentrations()

Original comment by lh64@cornell.edu on 2 May 2012 at 6:02

• Changed state: Fixed