Models (implementation)

This page provides an overview of Model objects oriented towards the internal structure and underlying objects. It thus documents ways of interacting directly with Model instances.

Model object structure

At its core, models in Atomica are implemented as a computational graph. The nodes in this graph are ‘compartments’, which store numbers of people, and the edges are ‘links’, which move people from one compartment to another. However, there are additional complexities associated with computing the flows between compartments, and generating other model outputs, and we thus introduce additional types of nodes into the graph representing intermediate calculations and outputs.

Model objects serve two purposes

  1. They handle integration of the model, actually performing the calculations required to run a simulation
  2. They serve as the primary storage of model outputs

The reason Model objects serve as primary storage is because the elements in the computational graph already store all of the values relevant to model output, and stores them in a manner that both facilitates their access as well as enables traversal of the relationship between quantities. The organization of the model object is as follows


where ‘Compartments’, ‘Characteristics’, and ‘Parameters’ all correspond to items in the framework, ‘Links’ correspond to transitions in the framework, and ‘Populations’ correspond to the populations listed in the databook.

We now go through each of these objects in turn.



A Compartment represents one of the compartments specified in the ‘Compartments’ sheet of the framework. A compartment stores people in a particular state (e.g., susceptible, infected). For each population, there is one Compartment for every entry in that sheet. Compartments have the following key features:

  • The vals attribute for the compartment object represents the number of people in that compartment
  • The name attribute matches the ‘Code Label’ in the framework
  • Boolean flags for birth, death, and junction compartments (tag_birth,tag_dead, and is_junction, respectively)
  • A list of Link objects, inlinks, that represents flows into the compartment
  • A list of Link objects, outlinks, that represents flows out of the compartment

A junction is a special type of compartment that is emptied at every time step, so the vals attribute should be 0 at all times.

Compartments have a number of helper methods

  • outflow which is the sum of all outgoing links at a given point in time. This can also be used as a proxy for the ‘value’ of a junction, because it corresponds to how many people had arrived in the junction at that time step.
  • expected_duration this returns the time in years that an individual would be expected to remain in the compartment if the outflow probabilities and the compartment size remained the same going into the future (i.e. in a steady state approximation)
  • expected_outflow this returns a dict showing where people in the compartment would be expected to be after 1 year, on the assumption that the outflows at each time step are probabilistic and constant

The last two methods expected_duration and expected_outflow are mainly for application diagnostic purposes.



A characteristic represents a grouping of compartments, with optional normalization. In each population, there is one Characteristic object for every entry in the ‘Characteristics’ sheet in the cascade workbook. A characteristic may be used within other characteristics and in parameter computation. A Characteristic has the following key features:

  • The vals property attribute represents either a number of people, or a fraction of people (depending on whether the denominator is set or not)
  • The includes attribute is a list whose elements are either Characteristic or Compartment objects. At each timepoint, the vals attribute of the objects in the includes list are summed together to calculate the value of the current Characteristic
  • The denominator attribute is optionally provided as a Characteristic or Compartment object. If provided, at each timepoint the sum of the includes objects will be divided by the vals attribute of the denominator. The most common usage scenario for this is to define a characteristic corresponding to a prevalance (e.g., where the includes list sums up the number of infector people, and the denominator is a characteristic including all people in the population). If a denominator is supplied, then the is_fraction flag is True for the Characteristic
  • The update(ti) method is called during integration, and computes the vals attribute at time index ti based on the includes and denominator objects
  • The dependency flag indicates whether the value of the characteristic needs to be computed during integration or not. A Characteristic is dependent if it is used in a Parameter function. If False, then the value of the characteristic will be computed at the end of integration using vectorized operations for efficiency.

To save storage space after the simulation is complete, the values for characteristics are not generally stored. Instead, the vals property attribute dynamically computes the characteristic value based on the compartment sizes, which are retained. This is useful because there are often more characteristics than compartments, and all characteristics can be computed based on compartment values. However, to avoid the computational overhead during model integration, the characteristic contains a _internal_vals member variable that actually stores the characteristic value during integration. If this is not None, then the vals method will simply return the _internal_vals array.



A parameter object provides a way to compute variables based on the value of other variables, either for use as simulation outputs, or to dynamically compute transition rates (i.e. Link values) during integration. There is one Parameter object for every entry listed in the ‘Parameters’ sheet of the cascade workbook, plus an additional Parameter for every pair of populations that has a transfer between them. Note that there is only one transfer Parameter for every pair of populations, but there is a Link between every corresponding compartment within those populations - so for example, aging from 0-4 to 5-14 will have a single Parameter representing the total number of people changing populations, and there would be links between [0-4 Sus]->[5-14 Sus] and [0-4 Vac]->[5-14 Vac].

A Parameter has the following key features:

  • The links attribute stores a list of Links that derive their value from the Parameter object. If this list is empty, then the Parameter is either a dependency for another Parameter, or an Output object.
  • The vals attribute represents either a transition rate (in units of fraction/probability or number of people) or otherwise a quantity with unknown units. If a parameter represents a transition rate, its units are assumed to be annualized, and will be converted to timestep-based values during integration (the method for conversion depends on units attribute of the Parameter). At construction, the Parameter is loaded in with values supplied from the parset if values are available
  • The fcn_str optionally specifies a formula that is used to compute the value of the Parameter dynamically
  • If an fcn_str is provided, the deps list contains a list of objects whose values are used in the fcn_str formula. Allowed objects are Compartments, Characteristics, Parameters, and Links. A Characteristic or Parameter that appears in a deps list is considered a dependency and the value of that object needs to be computed during integration. If a Parameter is used to supply values for a transition, then it is considered a dependency, and it, together with all of the variables in the deps list, needs to be computed during integration. Otherwise, ths parameter is only used for output, and it is computed using vector operations at the end of the simulation. Because parameters are used to compute values for links, the inclusion of Links in parameter functions is only permitted if the parameter is not a dependency (i.e., if it is an output).
  • The dependency flag indicates whether the value of the parameter needs to be computed during integration or not. A Parameter is dependent if it appears in the deps list of another Parameter, or if the links list is not empty (which indicates the parameter value is required during integration to supply the flow rates for the links).
  • The scale_factor rescales the parameter value - this is the calibration y-factor
  • The limits property optionally specifies lower and upper bounds for the parameter value. These are hard limits that are applied right before the Link values are computed, so they are implemented after any programs or special operations (i.e. interactions) are computed
  • The pop_aggregation flag specifies whether the parameter value will be computed in Model.update_pars or in Parameter.update(). Parameter aggregation across populations (e.g. for cross-population disease transmission) is governed by the special functions SRC_POP_AVG and TGT_POP_AVG and these calculations are implemented in Model.update_pars because they require multiple Parameter objects.
  • The update(ti) method is called during integration, and computes the vals attribute at time index ti based on the fcn_str if it is not None
  • The source_popsize(ti) method is used to compute the number of people reached by this Parameter at time index ti, which is required when computing Program disaggregations if the Parameter is in number units. The source_popsize is defined as the sum of the source compartment sizes for every Link whose parameter is supplied by this Parameter i.e., it is sum([Link.source.vals[ti] for Link in Parameter.links]). As this value may be accessed multiple times when computing programs, it is internally cached for efficiency.
  • The Note that transfer parameters currently do not support having a function - instead, they only draw their values directly from interpolated data. This is because transfer parameters link populations, and as such they are specified in the databook rather than in the framework.



A Population stores lists the base objects listed above, all associated with a single population. It has the following key features:

  • comps is a list of Compartment objects
  • characs is a list of Characteristic objects
  • links is a list of Link objects
  • pars is a list of Parameter objects
  • The get_comp(name), get_links(name), get_charac(name), and get_par(name) methods return their respective objects based on the name attribute, which allows objects to be located within a population based on their name. This is implemented as a dictionary lookup to improve performance
  • The get_variable(name) will return a list of variables with that name, regardless of their type. It also supports looking up links based on source_name:dest_name:par_name syntax where each of those quantities is optional. For example, sus:vac returns all links between compartments sus and vac.
  • The popsize(ti) method returns the number of people in all compartments (except birth and death) at timepoint ti. However, typically this value is accessed via a Characteristic which improves efficiency (such a Characteristic is typically defined anyway, so that it can be used as an output or in a Parameter function).
  • The gen_cascade function takes in a settings object, and constructs and wires together all of the compartments, characteristics, links, and parameters required. It is called automatically by the Population constructor.
  • The initialize_compartments method assigns the initial compartment values based on the characteristics provided in the parset.


The Model object is a class that contains all of the Populations for a simulation, and has methods to perform integration. Its key attributes are:

  • pops a list of population groups that this model subdivides into.
  • interactions stores the data associated with inter-population interactions
  • par_list is a list of all parameters code names in the model for use during integration
  • programs_active is True or False depending on whether programs will be used or not
  • progset is a copy of the progset (containing the program-related parameters) used for this run
  • program_instructions is a copy of the program instructions used for this simulation run
  • t is the simulation time vector, shared by all variables within this model
  • dt is the simulation time step
  • framework is a copy of the framework which stores metadata associated with all of the integration objects (these may be user-customized if the user has added extra columns to the framework file) as well as stores the cascades and plot information used by the Result object for plotting and exporting
  • _vars_by_pop a cache to look up lists of variables by name across populations
  • _t_index keeps track of array index for current timepoint data within all compartments.
  • _program_cache caches some program values for use during integration

The key methods are

  • build which constructs required populations. As noted above, the Population constructor instantiates objects representing the cascade within a population. However, if transfers are present, then there are also Parameters and Links representing cross-population interactions. These are stored in the source Population so that they can be treated the same as all other Parameters and Links during integration, but they are instantiated by because they are intrinsically properties that intrinsically span populations.
  • process which actually integrates the simulation
  • The run_model which wraps building, processing, and computing results. The input consists of settings, a parset, and optionally a progset and ProgramInstructions, and the output is a Result

Note that the Model forms the primary storage of the Result object, and thus it is possible to retrieve detailed output from the model run by querying the Result object. This also means that there is minimal post-processing time to reorganize the model outputs, because they are generally accessed in-place.


Building the model proceeds in the following stages

  1. Population objects are instantiated
  2. Initial characteristic values used to compute the initial compartment sizes, which are loaded into the Compartment objects
  3. Populate the Parameter objects with interpolated data values, for all data that is present
  4. Instantiate the Parameter and Link objects associated with transfers, and populate these Parameter objects with the transfer data values



The integration workflow is an interative process, alternating between updating the compartment sizes, and updating the link values. The main integration loop is in Model.process(). The stages are as follows

self.update_comps() # This writes values to comp.vals[ti+1] so this will be out of bounds if self._t_index == self.t.size-1
self._t_index += 1  # Step the simulation forward
  • In the first stage, Model.update_comps() updates the compartment values using the values contained in the Links. The link values will have been set at the end of the previous time step. Junction compartment sizes are skipped because they are always zero and dealt with separately.

  • In the second stage, Model.update_pars() updates the parameter values. The parameter update proceeds as follows:

    1. First, if a program has a function, that function is evaluated
    2. If programs are active, the parameter value is overwritten using the program set
    3. If averaging over populations is required, this is performed now and the parameter values are again updated
    4. If the program has limits, the value is clipped to the allowed range
  • In the third stage, Model.update_links(), the parameter values are propagated into the link objects. This proceeds as follows:

    1. The proposed link values are computed as a number of people. This involves rescaling the parameter value onto the simulation time step, and converting it to a number of people. This conversion depends on the units that the parameter is in, and is performed here. Note that if a parameter is in units of number of people, the outflow is disaggregated proportionately over all of the links at this step, depending on what fraction of the total number of people reached by the parameter are attributable to each link.
    2. If a compartment would become negative because the proposed link values flowing out of a compartment exceed the number of people in that compartment, all of the outgoing links for that compartment are rescaled such that the total number of people leaving matches the compartment’s size. Note that only people currently in the compartment are eligible to leave the compartment, so it is not possible for new inflows to contribute to outflows.

    This update is only performed for links that flow out of non-junction compartments. This is because outflows from junctions are resolved in the next step.

  • In the final stage, Model.update_junctions() computes the junction outflows. This is performed at this point in order to ensure that junction outflow links have a non-NaN value at the last timestep. To resolve the junction outflows:

    1. The number of people in the junction is determined by adding up the value of all of the incoming links
    2. The outflow links are calculated based on the parameters governing transitions out of junctions - these must be in ‘proportion’ units so no timestep rescaling is necessary
    3. If the outflow is into a non-junction compartment, then nothing further needs to be done, because the downstream compartment will be updated by Model.update_comps() at the next timestep. However, if the outflow is into another junction, that junction’s value is updated, and the junction calculation is re-run to flush those people as well.
    4. The calculation proceeds until all people have left the junctions. An infinite loop can occur if there is a cycle between junctions, without any normal compartments between them. In that case, the loop will be aborted with an error.

    Note that the initialization might result in junctions having a nonzero number of people at the first time step. Therefore, the junctions need to be flushed prior to the simulation starting. This is performed by updating the parameters and junctions, and then updating the parameters, links, and junctions again. For the initial flush, a special flag is passed to update_junctions which tells it to use the junction’s current nonzero initial value, instead of summing over incoming links

At the end of integration, the values for non-dependent parameters need to be computed - this is also performed in model.process().

Linking and unlinking

The network of integration objects makes it easy to traverse the graph to trace back quantities. For example, link.source.outlinks would be a list of all of the outgoing links for the source compartment given an initial link. Because cyclical references are common (e.g, a link has a source which has that link in source.outlinks) an additional step is needed in order to be able to pickle and unpickle Model objects. This step recursively replaces all of the references with IDs. It proceeds as follows

  • Model.unlink replaces references with IDs in all of it’s properties. Then it calls Population.unlink() on every population. Population.unlink() replaces all of its references, and then calls Variable.unlink() on all of its variables. This allows variables to control how they unlink themselves, which is important because some variables have references that others do not (e.g., Characteristics have includes while Parameters have deps). At the end of this process, the variables are only stored once in the Population lists e.g. Population.comps()
  • Model.relink reverses this. First it assembles a dict mapping ID to objects. Then it calls relink on all populations, passing in this dict of objects. In turn, Variables can relink themselves using this dict. The dict needs to be constructed at the Model level so that Population objects can relink transfers that span populations

The whole process is transparent to the user, because it is controlled by the __getstate__, __setstate__ and __deepcopy__ methods, so users generally will never see a Model object in an unlinked state.