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1370-2 Add support for reading templated SECIR models from JSON data #1375

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1370-2 Add support for reading templated SECIR models from JSON data #1375

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8e9f700
Add support for reading templated SECIR models from JSON
julianlitz Sep 15, 2025
ccddcd1
Safer FP to int conversion
julianlitz Sep 16, 2025
5641fbd
std::round and static_cast
julianlitz Sep 16, 2025
052e31f
Fix FP metaprogramming madness.
julianlitz Sep 26, 2025
31e299a
FP fixes in Graph_Simulation.h
julianlitz Sep 26, 2025
c20d181
Resolve Issue 1382, 1383, 1384
julianlitz Sep 29, 2025
11bb56c
Implement suggestion to merge round and trunc namespace region
julianlitz Oct 1, 2025
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14 changes: 7 additions & 7 deletions cpp/memilio/mobility/metapopulation_mobility_instant.h
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Original file line number Diff line number Diff line change
Expand Up @@ -478,7 +478,7 @@ void calculate_mobility_returns(Eigen::Ref<typename TimeSeries<FP>::Vector> mobi
* detect a get_infections_relative function for the Model type.
*/
template <typename FP, class Sim>
using get_infections_relative_expr_t = decltype(get_infections_relative(
using get_infections_relative_expr_t = decltype(get_infections_relative<FP>(
std::declval<const Sim&>(), std::declval<FP>(), std::declval<const Eigen::Ref<const Eigen::VectorX<FP>>&>()));

/**
Expand Down Expand Up @@ -509,7 +509,7 @@ FP get_infections_relative(const SimulationNode<FP, Sim>& node, FP t, const Eige
* detect a get_mobility_factors function for the Model type.
*/
template <typename FP, class Sim>
using get_mobility_factors_expr_t = decltype(get_mobility_factors(
using get_mobility_factors_expr_t = decltype(get_mobility_factors<FP>(
std::declval<const Sim&>(), std::declval<FP>(), std::declval<const Eigen::Ref<const Eigen::VectorX<FP>>&>()));

/**
Expand Down Expand Up @@ -541,8 +541,8 @@ auto get_mobility_factors(const SimulationNode<FP, Sim>& node, FP t, const Eigen
* detect a get_mobility_factors function for the Model type.
*/
template <typename FP, class Sim>
using test_commuters_expr_t = decltype(test_commuters(
std::declval<Sim&>(), std::declval<Eigen::Ref<const Eigen::VectorX<FP>>&>(), std::declval<FP>()));
using test_commuters_expr_t = decltype(test_commuters<FP>(
std::declval<Sim&>(), std::declval<Eigen::Ref<Eigen::VectorX<FP>>>(), std::declval<FP>()));
Comment on lines +544 to +545
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@julianlitz julianlitz Sep 26, 2025

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Metaprogramming uses incorrect function declaration.
const& must be removed.


/**
* Test persons when moving from their source node.
Expand Down Expand Up @@ -581,7 +581,7 @@ void mio::MobilityEdge<FP>::apply_mobility(FP t, FP dt, SimulationNode<FP, Sim>&
if (dyn_npis.get_thresholds().size() > 0 &&
floating_point_greater_equal<FP>(t, m_t_last_dynamic_npi_check + dyn_npis.get_interval().get())) {
auto inf_rel =
get_infections_relative<FP, Sim>(node_from, t, node_from.get_last_state()) * dyn_npis.get_base_value();
get_infections_relative<FP>(node_from, t, node_from.get_last_state()) * dyn_npis.get_base_value();
auto exceeded_threshold = dyn_npis.get_max_exceeded_threshold(inf_rel);
if (exceeded_threshold != dyn_npis.get_thresholds().end() &&
(exceeded_threshold->first > m_dynamic_npi.first ||
Expand All @@ -602,8 +602,8 @@ void mio::MobilityEdge<FP>::apply_mobility(FP t, FP dt, SimulationNode<FP, Sim>&
if (m_return_times.get_time(i) <= t) {
auto v0 = find_value_reverse<FP>(node_to.get_result(), m_mobile_population.get_time(i), 1e-10, 1e-10);
assert(v0 != node_to.get_result().rend() && "unexpected error.");
calculate_mobility_returns<FP, Sim>(m_mobile_population[i], node_to.get_simulation(), *v0,
m_mobile_population.get_time(i), dt);
calculate_mobility_returns<FP>(m_mobile_population[i], node_to.get_simulation(), *v0,
m_mobile_population.get_time(i), dt);

//the lower-order return calculation may in rare cases produce negative compartments,
//especially at the beginning of the simulation.
Expand Down
4 changes: 2 additions & 2 deletions cpp/models/ode_secir/model.h
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Expand Up @@ -659,7 +659,7 @@ IOResult<FP> get_reproduction_number(FP t_value, const Simulation<FP, Base>& sim
* @tparam FP floating point type, e.g., double.
* @tparam Base simulation type that uses a secir compartment model; see Simulation.
*/
template <typename FP, class Base = mio::Simulation<Model<FP>, FP>>
template <typename FP, class Base = mio::Simulation<FP, Model<FP>>>
auto get_mobility_factors(const Simulation<FP, Base>& sim, FP /*t*/, const Eigen::Ref<const Eigen::VectorX<FP>>& y)
{
auto& params = sim.get_model().parameters;
Expand Down Expand Up @@ -689,7 +689,7 @@ auto get_mobility_factors(const Simulation<FP, Base>& sim, FP /*t*/, const Eigen
return factors;
}

template <typename FP, class Base = mio::Simulation<Model<FP>, FP>>
template <typename FP, class Base = mio::Simulation<FP, Model<FP>>>
auto test_commuters(Simulation<FP, Base>& sim, Eigen::Ref<Eigen::VectorX<FP>> mobile_population, FP time)
{
auto& model = sim.get_model();
Expand Down
4 changes: 2 additions & 2 deletions cpp/models/ode_secirts/model.h
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Original file line number Diff line number Diff line change
Expand Up @@ -896,7 +896,7 @@ FP get_infections_relative(const Simulation<FP, Base>& sim, FP /*t*/, const Eige
* @return vector expression, same size as y, with migration factors per compartment.
* @tparam Base simulation type that uses a SECIRS-type compartment model. see Simulation.
*/
template <typename FP, class Base = mio::Simulation<Model<FP>, FP>>
template <typename FP, class Base = mio::Simulation<FP, Model<FP>>>
auto get_migration_factors(const Simulation<Base>& sim, FP /*t*/, const Eigen::Ref<const Eigen::VectorX<FP>>& y)
{
auto& params = sim.get_model().parameters;
Expand Down Expand Up @@ -943,7 +943,7 @@ auto get_migration_factors(const Simulation<Base>& sim, FP /*t*/, const Eigen::R
* @param[in,out] migrated Vector representing the number of commuters in each state.
* @param[in] time Current simulation time, used to determine the commuter detection period.
*/
template <typename FP, class Base = mio::Simulation<Model<FP>, FP>>
template <typename FP, class Base = mio::Simulation<FP, Model<FP>>>
auto test_commuters(Simulation<FP, Base>& sim, Eigen::Ref<Eigen::VectorX<FP>> migrated, FP time)
{
auto& model = sim.get_model();
Expand Down
4 changes: 2 additions & 2 deletions cpp/models/ode_secirvvs/model.h
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Original file line number Diff line number Diff line change
Expand Up @@ -825,7 +825,7 @@ FP get_infections_relative(const Simulation<FP, Base>& sim, FP /*t*/, const Eige
* @return vector expression, same size as y, with mobility factors per compartment.
* @tparam Base simulation type that uses a secir compartment model. see Simulation.
*/
template <typename FP, class Base = mio::Simulation<Model<FP>, FP>>
template <typename FP, class Base = mio::Simulation<FP, Model<FP>>>
auto get_mobility_factors(const Simulation<Base>& sim, FP /*t*/, const Eigen::Ref<const Eigen::VectorX<FP>>& y)

{
Expand Down Expand Up @@ -866,7 +866,7 @@ auto get_mobility_factors(const Simulation<Base>& sim, FP /*t*/, const Eigen::Re
return factors;
}

template <typename FP, class Base = mio::Simulation<Model<FP>, FP>>
template <typename FP, class Base = mio::Simulation<FP, Model<FP>>>
auto test_commuters(Simulation<FP, Base>& sim, Eigen::Ref<Eigen::VectorX<FP>> mobile_population, FP time)
{
auto& model = sim.get_model();
Expand Down
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