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Refactor: initial split of person into multiple files
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| Original file line number | Diff line number | Diff line change |
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| #include "exateppabm/household.h" | ||
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| #include "flamegpu/flamegpu.h" | ||
| #include "exateppabm/demographics.h" | ||
| #include "exateppabm/disease.h" | ||
| #include "exateppabm/person.h" | ||
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| namespace exateppabm { | ||
| namespace household { | ||
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| /** | ||
| * Agent function for person agents to emit their public information, i.e. infection status to their household | ||
| */ | ||
| FLAMEGPU_AGENT_FUNCTION(emitHouseholdStatus, flamegpu::MessageNone, flamegpu::MessageBucket) { | ||
| // Households of 1 don't need to do any messaging, there is no one to infect | ||
| std::uint8_t householdSize = FLAMEGPU->getVariable<std::uint8_t>(person::v::HOUSEHOLD_SIZE); | ||
| if (householdSize > 1) { | ||
| // output public properties to bucket message, keyed by household | ||
| // Agent ID to avoid self messaging | ||
| FLAMEGPU->message_out.setVariable<flamegpu::id_t>(person::message::household_status::ID, FLAMEGPU->getVariable<flamegpu::id_t>(person::v::ID)); | ||
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| // Household index | ||
| // @todo - typedef or using statement for the household index type? | ||
| std::uint32_t householdIdx = FLAMEGPU->getVariable<std::uint32_t>(person::v::HOUSEHOLD_IDX); | ||
| FLAMEGPU->message_out.setVariable<std::uint32_t>(person::v::HOUSEHOLD_IDX, householdIdx); | ||
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| FLAMEGPU->message_out.setVariable<disease::SEIR::InfectionStateUnderlyingType>(person::v:: | ||
| INFECTION_STATE, FLAMEGPU->getVariable<disease::SEIR::InfectionStateUnderlyingType>(person::v::INFECTION_STATE)); | ||
| FLAMEGPU->message_out.setVariable<demographics::AgeUnderlyingType>(person::v::AGE_DEMOGRAPHIC, FLAMEGPU->getVariable<demographics::AgeUnderlyingType>(person::v::AGE_DEMOGRAPHIC)); | ||
| // Set the message key, the house hold idx for bucket messaging @Todo | ||
| FLAMEGPU->message_out.setKey(householdIdx); | ||
| } | ||
| return flamegpu::ALIVE; | ||
| } | ||
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| /** | ||
| * Very naive agent interaction for infection spread via house hold contact | ||
| * | ||
| * Agents iterate messages from their household members, potentially becoming infected | ||
| * | ||
| * @todo - refactor this somewhere else? | ||
| * @todo - add per network behaviours? | ||
| */ | ||
| FLAMEGPU_AGENT_FUNCTION(interactHousehold, flamegpu::MessageBucket, flamegpu::MessageNone) { | ||
| // Get my ID to avoid self messages | ||
| const flamegpu::id_t id = FLAMEGPU->getVariable<flamegpu::id_t>(person::v::ID); // FLAMEGPU->getID(); | ||
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| // Get the probability of infection | ||
| float p_s2e = FLAMEGPU->environment.getProperty<float>("p_interaction_susceptible_to_exposed"); | ||
| // Scale it for household interactions | ||
| p_s2e *= FLAMEGPU->environment.getProperty<float>("relative_transmission_household"); | ||
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| // Get my household index | ||
| auto householdIdx = FLAMEGPU->getVariable<std::uint32_t>(person::v::HOUSEHOLD_IDX); | ||
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| // Get my age demographic | ||
| auto demographic = FLAMEGPU->getVariable<demographics::AgeUnderlyingType>(person::v::AGE_DEMOGRAPHIC); | ||
| // Get my susceptibility modifier and modify it. | ||
| float relativeSusceptibility = FLAMEGPU->environment.getProperty<float, demographics::AGE_COUNT>("relative_susceptibility_per_demographic", demographic); | ||
| // Scale the probability of transmission | ||
| p_s2e *= relativeSusceptibility; | ||
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| // Check if the current individual is susceptible to being infected | ||
| auto infectionState = FLAMEGPU->getVariable<disease::SEIR::InfectionStateUnderlyingType>(person::v::INFECTION_STATE); | ||
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| // @todo - this will need to change for contact tracing, the message interaction will need to occur regardless. | ||
| if (infectionState == disease::SEIR::Susceptible) { | ||
| // Variable to store the duration of the exposed phase (if exposed) | ||
| float stateDuration = 0.f; | ||
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| // Iterate messages from anyone within the household | ||
| for (const auto &message : FLAMEGPU->message_in(householdIdx)) { | ||
| // Ignore self messages (can't infect oneself) | ||
| if (message.getVariable<flamegpu::id_t>(person::message::household_status::ID) != id) { | ||
| // Ignore messages from other households | ||
| if (message.getVariable<std::uint32_t>(person::v::HOUSEHOLD_IDX) == householdIdx) { | ||
| // Check if the other agent is infected | ||
| if (message.getVariable<disease::SEIR::InfectionStateUnderlyingType>(person::v::INFECTION_STATE) == disease::SEIR::InfectionState::Infected) { | ||
| // Roll a dice | ||
| float r = FLAMEGPU->random.uniform<float>(); | ||
| if (r < p_s2e) { | ||
| // I have been exposed | ||
| infectionState = disease::SEIR::InfectionState::Exposed; | ||
| // Generate how long until I am infected | ||
| float mean = FLAMEGPU->environment.getProperty<float>("mean_time_to_infected"); | ||
| float sd = FLAMEGPU->environment.getProperty<float>("sd_time_to_infected"); | ||
| stateDuration = (FLAMEGPU->random.normal<float>() * sd) + mean; | ||
| // @todo - for now only any exposure matters. This may want to change when quantity of exposure is important? | ||
| // Increment the infection counter for this individual | ||
| FLAMEGPU->setVariable<std::uint32_t>(person::v::INFECTION_COUNT, FLAMEGPU->getVariable<std::uint32_t>(person::v::INFECTION_COUNT) + 1); | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| // If newly exposed, store the value in global device memory. | ||
| if (infectionState == disease::SEIR::InfectionState::Exposed) { | ||
| FLAMEGPU->setVariable<disease::SEIR::InfectionStateUnderlyingType>(person::v::INFECTION_STATE, infectionState); | ||
| FLAMEGPU->setVariable<float>(person::v::INFECTION_STATE_DURATION, stateDuration); | ||
| } | ||
| } | ||
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| return flamegpu::ALIVE; | ||
| } | ||
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| void define(flamegpu::ModelDescription& model, const exateppabm::input::config& params) { | ||
| // Define related model environment properties | ||
| flamegpu::EnvironmentDescription env = model.Environment(); | ||
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| // define the per interaction type scale factor within households | ||
| env.newProperty<float>("relative_transmission_household", params.relative_transmission_household); | ||
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| // Get a handle to the existing person agent type, which should have already been defined. | ||
| flamegpu::AgentDescription agent = model.Agent(person::NAME); | ||
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| // Household network variables. @todo - refactor to a separate network location? | ||
| agent.newVariable<std::uint32_t>(person::v::HOUSEHOLD_IDX); | ||
| agent.newVariable<std::uint8_t>(person::v::HOUSEHOLD_SIZE); | ||
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| // Message list containing a persons current status for households (id, location, infection status) | ||
| flamegpu::MessageBucket::Description householdStatusMessage = model.newMessage<flamegpu::MessageBucket>(person::message::household_status::_NAME); | ||
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| // Set the maximum bucket index to the population size. Ideally this would be household count, but that is not known at model definition time. | ||
| // In the future this would be possible once https://github.com/FLAMEGPU/FLAMEGPU2/issues/710 is implemented | ||
| householdStatusMessage.setUpperBound(params.n_total); | ||
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| // Add the agent id to the message. | ||
| householdStatusMessage.newVariable<flamegpu::id_t>(person::message::household_status::ID); | ||
| // Add the household index | ||
| householdStatusMessage.newVariable<std::uint32_t>(person::v::HOUSEHOLD_IDX); | ||
| // Add a variable for the agent's infections status | ||
| householdStatusMessage.newVariable<disease::SEIR::InfectionStateUnderlyingType>(person::v::INFECTION_STATE); | ||
| // Demographic? | ||
| householdStatusMessage.newVariable<demographics::AgeUnderlyingType>(person::v::AGE_DEMOGRAPHIC); | ||
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| // emit current status to the household | ||
| flamegpu::AgentFunctionDescription emitHouseholdStatusDesc = agent.newFunction("emitHouseholdStatus", emitHouseholdStatus); | ||
| emitHouseholdStatusDesc.setMessageOutput(person::message::household_status::_NAME); | ||
| emitHouseholdStatusDesc.setMessageOutputOptional(true); | ||
| emitHouseholdStatusDesc.setInitialState(person::states::DEFAULT); | ||
| emitHouseholdStatusDesc.setEndState(person::states::DEFAULT); | ||
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| // Interact with other agents in the household via their messages | ||
| flamegpu::AgentFunctionDescription interactHouseholdDesc = agent.newFunction("interactHousehold", interactHousehold); | ||
| interactHouseholdDesc.setMessageInput(person::message::household_status::_NAME); | ||
| interactHouseholdDesc.setInitialState(person::states::DEFAULT); | ||
| interactHouseholdDesc.setEndState(person::states::DEFAULT); | ||
| } | ||
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| void appendLayers(flamegpu::ModelDescription& model) { | ||
| { | ||
| auto layer = model.newLayer(); | ||
| layer.addAgentFunction(person::NAME, "emitHouseholdStatus"); | ||
| } | ||
| { | ||
| auto layer = model.newLayer(); | ||
| layer.addAgentFunction(person::NAME, "interactHousehold"); | ||
| } | ||
| } | ||
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| } // namespace household | ||
| } // namespace exateppabm |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| #pragma once | ||
| #include "flamegpu/flamegpu.h" | ||
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| #include "exateppabm/input.h" | ||
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| namespace exateppabm { | ||
| namespace household { | ||
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| /** | ||
| * Define flame gpu 2 model properties and functions related to households | ||
| * | ||
| * @param model flamegpu2 model description object to mutate | ||
| * @param params model parameters from parameters file | ||
| */ | ||
| void define(flamegpu::ModelDescription& model, const exateppabm::input::config& params); | ||
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| /** | ||
| * Append household related agent functions to the flame gpu control flow using layers. This is intended to be called within person::appendLayers | ||
| * | ||
| * Does not use the DAG abstraction due to previously encountered bugs with split compilation units which have not yet been pinned down / resolved. | ||
| * | ||
| * @param model flamegpu2 model description object to mutate | ||
| */ | ||
| void appendLayers(flamegpu::ModelDescription& model); | ||
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| } // namespace household | ||
| } // namespace exateppabm |
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