# Models¶

MOSFiT has been designed to be modular and easily modifiable by users to alter, combine, and create physical models to approximate the behavior of observed transients. On this page we walk through some basics on how a user might alter an existing model shipped with the code, and how they could go about creating their own model.

## List of built-in models¶

Model name Description Reference(s)
default Nickel-cobalt decay 1994ApJS…92..527N
csm Interacting CSM-SNe 2013ApJ…773…76C
csmni CSM + NiCo decay See default & csm
exppow Analytical engine
ia NiCo decay + I-band
ic NiCo decay + radio
magnetar Magnetar engine w/ simple SED 2017ApJ…850…55N
magni Above + NiCo decay
rprocess Kilonova 2017ApJ…851L..21V
kilonova Kilonova 2017ApJ…851L..21V
slsn Magnetar + modified SED + constraints 2017ApJ…850…55N
tde Tidal disruption events 2018arXiv180108221M
 [*] In development.

## Altering an existing model¶

For many simple alterations to a model, such as adjusting input priors, setting variables remain free and which should be fixed, and adding/removing modules to the call stack, the user only needs to modify copies of the model JSON files. For these sorts of minor changes, no Python code should need to be modified by the user!

For this example, we’ll presume that the user will be modifying the slsn model. First, the user should create a new run directory and run MOSFiT there once to copy the model JSON files to that run directory:

mkdir slsn_run
cd slsn_run
python -m mosfit -m slsn


After running, the user will notice four directories will have been created in the run directory: models, modules, jupyter, and products. models will contain a clone of the models directory structure, with the parameters.json files for each model copied into each model folder, modules contains a clone of the modules directory structure, etc.

### Changing parameter priors¶

From your run directory, navigate into the models/slsn directory and edit the parameters.json file in your favorite text editor:

cd models/slsn
vim parameters.json


You’ll notice that parameters.json file is fairly bare-bones, containing only a list of model parameters and their allowed value ranges:

{
"nhhost":{
"min_value":1.0e16,
"max_value":1.0e23,
"log":true
},
"Pspin":{
"min_value":1.0,
"max_value":10.0
},
"Bfield":{
"min_value":0.1,
"max_value":10.0
},
"Mns":{
"min_value":1.0,
"max_value":2.0
},
}


Now, change the range of allowed neutron star masses to something else:

{
"Mns":{
"min_value":1.5,
"max_value":2.5
},
}


Congratulations! You have just modified your first MOSFiT model. It should be noted that even this very minor change, which affects the range of a single parameter, would generate a completely different model hash than the default model, distinguishing it from any other models that might have been uploaded by other users using the default settings.

You can also use more complex priors within the same file. For example:

{
"Mns":{
"class":"gaussian",
"mu":1.4,
"sigma":0.4,
"min_value":0.1,
"max_value":3.0,
"log":false
}
}


A list of available priors is below; for all prior types, min_value and max_value specify the minimum and maximum allowed parameter values, and log will apply the prior to the log transform of the parameter.

parameter $$\Pi\sim {\rm constant}$$
gaussian $$\Pi\sim \exp\left(\frac{-(x-\mu)^2}{2\sigma^2}\right)$$ $$\mu$$ (mu), $$\sigma$$ (sigma)
powerlaw $$\Pi\sim x^{-\alpha}$$ $$\alpha$$ (alpha)

### Swapping modules¶

Let’s say you want to modify the SLSN model such that transform applied to the input engine luminosity is not diffusion, but instead viscosity (if the light of a SLSN was say filtered through an accretion disk rather than a dense envelope). To make this change, the user would want to swap out the diffusion module used by slsn for the viscous module. This can be accomplished by editing the slsn.json model file. The model files are not copied into the model directories by default (as they may change from version to version of MOSFiT), but a README file with the full path to the model is copied to all model folders to make it easy for the user to copy the relevant JSON files:

cd models/slsn
vim slsn.json


To swap diffusion for viscous, the user would remove the blocks of JSON that refer to the diffusion module:

{
"kappagamma":{
"kind":"parameter",
"value":10.0,
"class":"parameter",
"latex":"\\kappa_\\gamma\\,({\\rm cm}^{2}\\,{\\rm g}^{-1})"
},
"diffusion":{
"kind":"transform",
"inputs":[
"magnetar",
"kappa",
"kappagamma",
"mejecta",
"texplosion",
"vejecta"
]
},
"temperature_floor":{
"kind":"photosphere",
"inputs":[
"texplosion",
"diffusion",
"temperature"
]
},
"slsn_constraints":{
"kind":"constraint",
"inputs":[
"mejecta",
"vejecta",
"kappa",
"tnebular_min",
"Pspin",
"Mns",
"diffusion",
"texplosion",
"redshift",
"alltimes",
"neutrino_energy"
]
},
}


and replace them with blocks appropriate for viscous:

{
"Tviscous":{
"kind":"parameter",
"value":1.0,
"class":"parameter",
"latex":"T_{\\rm viscous}"
},
"viscous":{
"kind":"transform",
"inputs":[
"magnetar",
"texplosion",
"Tviscous"
]
},
"temperature_floor":{
"kind":"photosphere",
"inputs":[
"texplosion",
"viscous",
"temperature"
]
},
"slsn_constraints":{
"kind":"constraint",
"inputs":[
"mejecta",
"vejecta",
"kappa",
"tnebular_min",
"Pspin",
"Mns",
"viscous",
"texplosion",
"redshift",
"alltimes",
"neutrino_energy"
]
},
}


As can be seen above, this involved removal of definitions of free parameters that only applied to diffusion (kappagamma), the addition of a new free parameter for viscous (Tviscous), and replacement of various inputs that depended on diffusion with viscous.

The user should also modify the parameters.json file to remove free parameters that are no longer in use:

{
"kappagamma":{
"min_value":0.1,
"max_value":1.0e4,
"log":true
},
}


and to the define the priors of their new free parameters:

{
"Tviscous":{
"min_value":1.0e-3,
"max_value":1.0e5,
"log":true
},
}


## Creating a new model¶

If users would like to create a brand new model for the MOSFiT platform, it is easiest to duplicate one of the existing models that most closely resembles the model they wish to create.

If you go this route, we highly recommend that you fork MOSFiT on GitHub and clone your fork, with development being done in the cloned mosfit directory:

git clone https://github.com/your_github_username/MOSFiT.git
cd mosfit


Copy one of the existing models as a starting point:

cp -R models/slsn models/my_model_that_explains_everything


Inside this directory are two files: a model_name.json file and a parameters.json file. We must edit both files to run our new model.

First, the model_name.json file should be edited to include your model’s:

• Parameters
• Engine(s)
• Diffusion prescription
• Photosphere prescription
• SED prescription
• The photometry module

Optionally, your model file can also include an extinction prescription.

Then, you need to edit the parameters.json to include the priors on all ofyour model parameters. If no prior is specified, the variable will be set to a constant.

You can invoke the model using:

python -m my_model_that_explains_everything


If your model requires a new engine, you can create this engine by again copying an existing engine:

cp modules/engines/nickelcobalt.py my_new_engine.py


Then plug this engine into your model’s json file.