BasicSSASolver not structuring output data correctly

[technodivergent]

Model:

class DayModel(gillespy2.Model):
    def __init__(self, parameter_values=None, init_v=0):
        # initialize
        gillespy2.Model.__init__(self, name="Macrophage")
        
        # species
        S_ = gillespy2.Species(name='S_', initial_value=4e3) # low = 4e3; mid = 2e4; high = 1e7
        
        A_ = gillespy2.Species(name='A_', initial_value=6e9) # A = Sa/(k2*S+MuA)
        
        H1 = gillespy2.Species(name='H1', initial_value=0)
        H2 = gillespy2.Species(name='H2', initial_value=0)
        H3 = gillespy2.Species(name='H3', initial_value=0)
        H4 = gillespy2.Species(name='H4', initial_value=0)
        H5 = gillespy2.Species(name='H5', initial_value=0)
        H6 = gillespy2.Species(name='H6', initial_value=0)
        
        HLN1 = gillespy2.Species(name='HLN1', initial_value=0)
        HLN2 = gillespy2.Species(name='HLN2', initial_value=0)
        HLN3 = gillespy2.Species(name='HLN3', initial_value=0)
        HLN4 = gillespy2.Species(name='HLN4', initial_value=0)
        HLN5 = gillespy2.Species(name='HLN5', initial_value=0)
        HLN6 = gillespy2.Species(name='HLN6', initial_value=0)
        
        self.add_species([S_,A_,H1,H2,H3,H4,H5,H6,HLN1,HLN2,HLN3,HLN4,HLN5,HLN6])
        
        # parameters
        # num(spores) per macrophage
        ns = gillespy2.Parameter(name='ns', expression=3) # avg = 3.38
        
        # rate of phagocytosis
        k2 = gillespy2.Parameter(name='k2', expression=1e-5)
        
        # migration to TMLN
        k3 = gillespy2.Parameter(name='k3', expression=1e3)

        # source of macrophages per hour
        Sa = gillespy2.Parameter(name='Sa', expression=3e8)
        
        # decay rate of macrophages
        MuA = gillespy2.Parameter(name='MuA', expression=0.05)
        
        self.add_parameter([ns,k2,k3,Sa,MuA])
        
        # reactions
        R1 = gillespy2.Reaction(
            name='R1',
            reactants={S_:1, A_:1},
            products={H1:1},
            rate=k2
        )
        
        R2 = gillespy2.Reaction(
            name='R2',
            reactants={S_:1, H1:1},
            products={H2:1},
            rate=k2
        )
        
        R3 = gillespy2.Reaction(
            name='R3',
            reactants={S_:1, H2:1},
            products={H3:1},
            rate=k2
        )
        
        R4 = gillespy2.Reaction(
            name='R4',
            reactants={S_:1, H3:1},
            products={H4:1},
            rate=k2
        )
        
        R5 = gillespy2.Reaction(
            name='R5',
            reactants={S_:1, H4:1},
            products={H5:1},
            rate=k2
        )
        
        R6 = gillespy2.Reaction(
            name='R6',
            reactants={S_:1, H5:1},
            products={H6:1},
            rate=k2
        )
        
        # To the lung
        R7 = gillespy2.Reaction(
            name='R7',
            reactants={H1:1},
            products={HLN1:1},
            rate=k3
        )
        
        R8 = gillespy2.Reaction(
            name='R8',
            reactants={H2:1},
            products={HLN2:1},
            rate=k3
        )
        
        R9 = gillespy2.Reaction(
            name='R9',
            reactants={H3:1},
            products={HLN3:1},
            rate=k3
        )
        
        R10 = gillespy2.Reaction(
            name='R10',
            reactants={H4:1},
            products={HLN4:1},
            rate=k3
        )
        
        R11 = gillespy2.Reaction(
            name='R11',
            reactants={H5:1},
            products={HLN5:1},
            rate=k3
        )
        
        R12 = gillespy2.Reaction(
            name='R12',
            reactants={H6:1},
            products={HLN6:1},
            rate=k3
        )
                
        self.add_reaction([R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12])
        t = numpy.linspace(0,40,801)
        self.timespan(t)
        #print(t)

When running this model through the BasicSSASolver, the results array is not always structured in a manner consistent with the other solvers while at other times it is.

For instance:
When using the value k3 <= 0.25, I can print/plot results[0]['time']
When using the value k3 >= 0.26, I must use results['time'] instead

[technodivergent]

Lung Submodel.zip
@seanebum

And on a different machine, the values aren't delineated between .25 and .26, but using 1e3 and 1e-3 seem to break it.

[seanebum]

I have been looking into this issue today and trying to replicate it. I have tried multiple values for k3 (1e-3, 1e-2, .1, .2, .25, .26, .3, .4, .5) And have not been able to reproduce the error. I'm attaching the notebook I used for testing.

…

On Wed, Jan 30, 2019 at 9:06 AM Brian Drawert ***@***.***> wrote: Assigned #50 <#50> to @seanebum <https://github.com/seanebum>. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#50 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AVyQXiBI_68y3BgZXeGxLHeYIRpi1bfaks5vIacCgaJpZM4aVM9F> .

[seanebum]

What is interesting is that there is no code in python.basic_ssa_solver.py to allow it to return information in any other structure. It only contains the code for show_labels=True, and always returns results[trajectory(list)][species_key(dict)][save_time(list)]

…

On Thu, Jan 31, 2019 at 4:10 PM Sean Matthew ***@***.***> wrote: I have been looking into this issue today and trying to replicate it. I have tried multiple values for k3 (1e-3, 1e-2, .1, .2, .25, .26, .3, .4, .5) And have not been able to reproduce the error. I'm attaching the notebook I used for testing. On Wed, Jan 30, 2019 at 9:06 AM Brian Drawert ***@***.***> wrote: > Assigned #50 <#50> to > @seanebum <https://github.com/seanebum>. > > — > You are receiving this because you were assigned. > Reply to this email directly, view it on GitHub > <#50 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AVyQXiBI_68y3BgZXeGxLHeYIRpi1bfaks5vIacCgaJpZM4aVM9F> > . >

[briandrawert]

This is now: Fix show_labels in BasicSSASolver

[briandrawert]

Made vestigial by #57