AMReX-ABM · atmyers · Feb 26, 2026 · Feb 26, 2026 · Feb 26, 2026 · Feb 26, 2026
diff --git a/docs/source/usage/how_to_run.rst b/docs/source/usage/how_to_run.rst
@@ -73,6 +73,16 @@ The following are inputs for the overall simulation:
 * ``agent.air_travel_int`` (`integer`, default ``-1``)
     The number of time steps between air travel events. Set to -1 to disable all air travel events. Currently this is implemented
     only for ``ic_type = census``.
+* ``agent.weather_int`` (`integer`, default ``-1``)
+    The number of time steps between weather data updates. Set to -1 to disable the weather-dependent transmission model.
+    When enabled, ``agent.weather_filename`` and ``agent.startdate`` must also be provided.
+* ``agent.weather_filename`` (`string`)
+    Path to the CSV file containing weather data (temperature and humidity by county and week).
+    Required when ``agent.weather_int > 0``. Example data files are provided in ``ExaEpi/data/``.
+* ``agent.startdate`` (`string`)
+    Start date of the simulation in ``YYYY-MM-DD`` format (e.g. ``2020-01-01``).
+    Used to align the weather data with the simulation timeline.
+    Required when ``agent.weather_int > 0``.
 * ``agent.aggregated_diag_int`` (`integer`, default ``-1``)
     The number of time steps between writing aggregated data, for example wastewater data. Set to -1 to disable writing.
 * ``agent.aggregated_diag_prefix`` (`string`, default ``cases``)
@@ -254,6 +264,29 @@ can be specified as follows:
 where ``[disease name]`` is any of the names specified in ``agent.disease_names`` (or the
 default value), and ``[key]`` is any of the parameters listed above.
 
+The following inputs configure the weather-dependent transmission model.  These parameters are only
+used when ``agent.weather_int > 0``.  The model computes a weather-based scale factor for the
+transmission probability as a function of near-surface air temperature :math:`T` (°C) and absolute
+humidity :math:`AH` (g/m³):
+
+.. math::
+
+   p(T,\,AH) = p_{\max} \exp\!\bigl(-\beta_{AH}\,AH - \alpha_T\,\max(0,\,T - T_0)\bigr)
+
+* ``weather_transmission.p_max`` (`float`, default ``1.0``)
+    Maximum transmission scale factor (dimensionless).  At low temperature and low humidity the
+    scale factor approaches this value.  It is multiplied by the baseline transmission probability
+    ``disease.p_trans`` to give the effective transmission probability.
+* ``weather_transmission.beta_AH`` (`float`, default ``0.18``)
+    Absolute-humidity sensitivity coefficient in units of m³/g.  Larger values cause transmission
+    to decrease more rapidly as humidity increases.
+* ``weather_transmission.T0`` (`float`, default ``5.0``)
+    Temperature threshold in °C above which the temperature penalty is applied.  Below this
+    temperature the model applies no temperature-dependent reduction.
+* ``weather_transmission.alpha_T`` (`float`, default ``0.015``)
+    Temperature sensitivity coefficient in units of °C⁻¹.  Larger values cause transmission
+    to decrease more rapidly above ``T0``.
+
 In addition to the ExaEpi inputs, there are also a number of runtime options that can be configured for AMReX itself.
 Please see <https://amrex-codes.github.io/amrex/docs_html/GPU.html#inputs-parameters>`__ for more information on these options.
 

diff --git a/src/AgentContainer.H b/src/AgentContainer.H
@@ -26,6 +26,7 @@
 #include "InteractionModelLibrary.H"
 #include "Utils.H"
 #include "WeatherData.H"
+#include "WeatherTransmissionModel.H"
 
 /*! \brief Derived class from ParticleContainer that defines agents and their functions */
 class AgentContainer : public amrex::ParticleContainer<0, 0, RealIdx::nattribs, IntIdx::nattribs> {
@@ -131,6 +132,11 @@ class AgentContainer : public amrex::ParticleContainer<0, 0, RealIdx::nattribs,
     int activeWeatherWeek;
     ActiveWeather* awd;
 
+    /*! Weather-dependent transmission probability model */
+    WeatherTransmissionModel m_weather_model;
+    /*! Controls weather coupling: <= 0 disables weather scaling, > 0 enables it */
+    int m_weather_int = -1;
+
   protected:
     amrex::Real m_shelter_compliance = 0.95_rt; /*!< Shelter-in-place compliance rate */
 

diff --git a/src/AgentContainer.cpp b/src/AgentContainer.cpp
@@ -101,6 +101,13 @@ AgentContainer::AgentContainer (const amrex::Geometry& a_geom,
 
     addAttributes();
 
+    awd = nullptr;
+    {
+        amrex::ParmParse pp("agent");
+        pp.query("weather_int", m_weather_int);
+    }
+    m_weather_model.readInputs("weather_transmission");
+
     amrex::ParmParse pp("agent");
 
     pp.query("shelter_compliance", m_shelter_compliance);

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -32,7 +32,9 @@ set(_sources
     UrbanPopData.H
     UrbanPopData.cpp
     Utils.H
-    Utils.cpp)
+    Utils.cpp
+    WeatherTransmissionModel.H
+    WeatherTransmissionModel.cpp)
 
 # List of input files
 set(_input_files)

diff --git a/src/InteractionModHome.H b/src/InteractionModHome.H
@@ -177,7 +177,10 @@ void InteractionModHome<PCType, PTDType, PType>::fastInteractHome (PCType& agent
                     auto prob_ptr = soa.GetRealData(RealIdx::nattribs + r0(d) + RealIdxDisease::prob).data();
                     auto lparm = agents.getDiseaseParameters_d(d);
                     auto lparm_h = agents.getDiseaseParameters_h(d);
-                    Real scale = 1.0_rt; // TODO this should vary based on cell
+                    auto weatherIdxPtr = soa.GetIntData(IntIdx::weatherLookup).data();
+                    auto varVec = agents.awd != nullptr ? agents.awd->varVec.data() : nullptr;
+                    auto weather_model = agents.m_weather_model;
+                    int a_weather_int = agents.m_weather_int;
                     Real infect = (1.0_rt - lparm_h->vac_eff);
                     // loop to count infectious agents in each group
                     auto d_ptr = getCommunityIndex.comm_to_local_index_d.data();
@@ -235,8 +238,14 @@ void InteractionModHome<PCType, PTDType, PType>::fastInteractHome (PCType& agent
                             int family_i = community * max_family + family_ptr[i];
                             int num_infected_family = infected_family_d_ptr[family_i];
                             int num_infected_family_asymp = infected_family_asymp_d_ptr[family_i];
-                            Real family_prob = 1.0_rt - infect * xmit_family_prob * scale;
-                            Real family_prob_asymp = 1.0_rt - lparm->asymp_relative_inf * infect * xmit_family_prob * scale;
+                            Real weather_scale = 1.0_rt;
+                            if (a_weather_int > 0 && varVec != nullptr && weatherIdxPtr[i] >= 0) {
+                                weatherVars wvar = varVec[weatherIdxPtr[i]];
+                                weather_scale = weather_model(wvar);
+                            }
+                            Real family_prob = 1.0_rt - infect * xmit_family_prob * weather_scale;
+                            Real family_prob_asymp =
+                                    1.0_rt - lparm->asymp_relative_inf * infect * xmit_family_prob * weather_scale;
                             prob_ptr[i] *= static_cast<ParticleReal>(std::pow(family_prob, num_infected_family));
                             prob_ptr[i] *= static_cast<ParticleReal>(std::pow(family_prob_asymp, num_infected_family_asymp));
                             if (!ptd.m_idata[IntIdx::withdrawn][i]) {
@@ -245,15 +254,15 @@ void InteractionModHome<PCType, PTDType, PType>::fastInteractHome (PCType& agent
                                 int cluster_i = community * max_hcs + hh_cluster_ptr[i];
                                 int num_infected_nc = infected_nc_d_ptr[cluster_i] - num_infected_family_not_withdrawn;
                                 AMREX_ALWAYS_ASSERT(num_infected_nc >= 0);
-                                Real nc_prob = 1.0_rt - infect * xmit_nc_prob * scale;
+                                Real nc_prob = 1.0_rt - infect * xmit_nc_prob * weather_scale;
                                 prob_ptr[i] *= static_cast<ParticleReal>(std::pow(nc_prob, num_infected_nc));
                                 // same for asymptomatic
                                 int num_infected_family_not_withdrawn_asymp = infected_family_not_withdrawn_asymp_d_ptr[family_i];
                                 AMREX_ALWAYS_ASSERT(num_infected_family_asymp >= num_infected_family_not_withdrawn_asymp);
                                 int num_infected_nc_asymp =
                                         infected_nc_asymp_d_ptr[cluster_i] - num_infected_family_not_withdrawn_asymp;
                                 AMREX_ALWAYS_ASSERT(num_infected_nc_asymp >= 0);
-                                Real nc_prob_asymp = 1.0_rt - lparm->asymp_relative_inf * infect * xmit_nc_prob * scale;
+                                Real nc_prob_asymp = 1.0_rt - lparm->asymp_relative_inf * infect * xmit_nc_prob * weather_scale;
                                 prob_ptr[i] *= static_cast<ParticleReal>(std::pow(nc_prob_asymp, num_infected_nc_asymp));
                             }
                         }

diff --git a/src/InteractionModHomeNborhood.H b/src/InteractionModHomeNborhood.H
@@ -138,7 +138,10 @@ void InteractionModHomeNborhood<PCType, PTDType, PType>::fastInteractHomeNborhoo
                 auto prob_ptr = soa.GetRealData(RealIdx::nattribs + r0(d) + RealIdxDisease::prob).data();
                 auto lparm = agents.getDiseaseParameters_d(d);
                 auto lparm_h = agents.getDiseaseParameters_h(d);
-                Real scale = 1.0_rt; // TODO this should vary based on cell
+                auto weatherIdxPtr = soa.GetIntData(IntIdx::weatherLookup).data();
+                auto varVec = agents.awd != nullptr ? agents.awd->varVec.data() : nullptr;
+                auto weather_model = agents.m_weather_model;
+                int a_weather_int = agents.m_weather_int;
                 Real infect = 1.0_rt - lparm_h->vac_eff;
                 auto d_ptr = getCommunityIndex.comm_to_local_index_d.data();
 
@@ -176,15 +179,23 @@ void InteractionModHomeNborhood<PCType, PTDType, PType>::fastInteractHomeNborhoo
                                 infected_community_asymp_d_ptr[community] - num_infected_nborhood_asymp;
 
                         AMREX_ALWAYS_ASSERT(num_infected_community >= 0);
-                        Real comm_prob = 1.0_prt - infect * lparm->xmit_comm[ptd.m_idata[IntIdx::age_group][i]] * scale;
+                        Real weather_scale = 1.0_rt;
+                        if (a_weather_int > 0 && varVec != nullptr && weatherIdxPtr[i] >= 0) {
+                            weatherVars wvar = varVec[weatherIdxPtr[i]];
+                            weather_scale = weather_model(wvar);
+                        }
+                        Real comm_prob = 1.0_prt - infect * lparm->xmit_comm[ptd.m_idata[IntIdx::age_group][i]] * weather_scale;
                         Real comm_prob_asymp = 1.0_prt - lparm->asymp_relative_inf * infect *
-                                                                 lparm->xmit_comm[ptd.m_idata[IntIdx::age_group][i]] * scale;
+                                                                 lparm->xmit_comm[ptd.m_idata[IntIdx::age_group][i]] *
+                                                                 weather_scale;
                         prob_ptr[i] *= static_cast<ParticleReal>(std::pow(comm_prob, num_infected_community));
                         prob_ptr[i] *= static_cast<ParticleReal>(std::pow(comm_prob_asymp, num_infected_community_asymp));
 
-                        Real nborhood_prob = 1.0_prt - infect * lparm->xmit_hood[ptd.m_idata[IntIdx::age_group][i]] * scale;
+                        Real nborhood_prob =
+                                1.0_prt - infect * lparm->xmit_hood[ptd.m_idata[IntIdx::age_group][i]] * weather_scale;
                         Real nborhood_prob_asymp = 1.0_prt - lparm->asymp_relative_inf * infect *
-                                                                     lparm->xmit_hood[ptd.m_idata[IntIdx::age_group][i]] * scale;
+                                                                     lparm->xmit_hood[ptd.m_idata[IntIdx::age_group][i]] *
+                                                                     weather_scale;
                         prob_ptr[i] *= static_cast<ParticleReal>(std::pow(nborhood_prob, num_infected_nborhood));
                         prob_ptr[i] *= static_cast<ParticleReal>(std::pow(nborhood_prob_asymp, num_infected_nborhood_asymp));
                     }

diff --git a/src/InteractionModSchool.H b/src/InteractionModSchool.H
@@ -170,7 +170,10 @@ void InteractionModSchool<PCType, PTDType, PType>::fastInteractSchool (PCType& a
                     auto prob_ptr = soa.GetRealData(RealIdx::nattribs + r0(d) + RealIdxDisease::prob).data();
                     auto lparm = agents.getDiseaseParameters_d(d);
                     auto lparm_h = agents.getDiseaseParameters_h(d);
-                    Real scale = 1.0_rt; // TODO this should vary based on cell
+                    auto weatherIdxPtr = soa.GetIntData(IntIdx::weatherLookup).data();
+                    auto varVec = agents.awd != nullptr ? agents.awd->varVec.data() : nullptr;
+                    auto weather_model = agents.m_weather_model;
+                    int a_weather_int = agents.m_weather_int;
                     Real infect = (1.0_rt - lparm_h->vac_eff);
                     auto d_ptr = getCommunityIndex.comm_to_local_index_d.data();
 
@@ -205,17 +208,23 @@ void InteractionModSchool<PCType, PTDType, PType>::fastInteractSchool (PCType& a
                             auto tidx = getTileIndex(iv, valid_box, true, bin_size, tbx);
                             auto community = d_ptr[tidx];
                             int pos = (community * max_school_id + school_id_ptr[i]) * max_school_grade + school_grade_ptr[i];
+                            Real weather_scale = 1.0_rt;
+                            if (a_weather_int > 0 && varVec != nullptr && weatherIdxPtr[i] >= 0) {
+                                weatherVars wvar = varVec[weatherIdxPtr[i]];
+                                weather_scale = weather_model(wvar);
+                            }
                             if (getSchoolType(school_grade_ptr[i]) == SchoolType::daycare) {
                                 if (adults && age_group_ptr[i] > AgeGroups::a5to17) { // adults-adults interaction accounted for
                                                                                       // in InteractionModWork.H
                                     // do nothing!
                                 } else {
                                     int num_infected_daycare = infected_daycare_d_ptr[pos];
-                                    Real daycare_prob = 1.0_rt - infect * lparm->xmit_school[SchoolType::daycare] * scale;
+                                    Real daycare_prob = 1.0_rt - infect * lparm->xmit_school[SchoolType::daycare] * weather_scale;
                                     prob_ptr[i] *= static_cast<ParticleReal>(std::pow(daycare_prob, num_infected_daycare));
                                     int num_infected_daycare_asymp = infected_daycare_asymp_d_ptr[pos];
                                     Real daycare_prob_asymp = 1.0_rt - lparm->asymp_relative_inf * infect *
-                                                                               lparm->xmit_school[SchoolType::daycare] * scale;
+                                                                               lparm->xmit_school[SchoolType::daycare] *
+                                                                               weather_scale;
                                     prob_ptr[i] *=
                                             static_cast<ParticleReal>(std::pow(daycare_prob_asymp, num_infected_daycare_asymp));
                                 }
@@ -238,9 +247,9 @@ void InteractionModSchool<PCType, PTDType, PType>::fastInteractSchool (PCType& a
                                         xmit = lparm->xmit_school_c2a[getSchoolType(school_grade_ptr[i])];
                                     }
                                 }
-                                Real school_prob = 1.0_rt - infect * xmit * scale;
+                                Real school_prob = 1.0_rt - infect * xmit * weather_scale;
                                 prob_ptr[i] *= static_cast<ParticleReal>(std::pow(school_prob, num_infected_school));
-                                Real school_prob_asymp = 1.0_rt - lparm->asymp_relative_inf * infect * xmit * scale;
+                                Real school_prob_asymp = 1.0_rt - lparm->asymp_relative_inf * infect * xmit * weather_scale;
                                 prob_ptr[i] *= static_cast<ParticleReal>(std::pow(school_prob_asymp, num_infected_school_asymp));
                             }
                         }

diff --git a/src/InteractionModWork.H b/src/InteractionModWork.H
@@ -137,7 +137,10 @@ void InteractionModWork<PCType, PTDType, PType>::fastInteractWork (PCType& agent
                 auto prob_ptr = soa.GetRealData(RealIdx::nattribs + r0(d) + RealIdxDisease::prob).data();
                 auto lparm = agents.getDiseaseParameters_d(d);
                 auto lparm_h = agents.getDiseaseParameters_h(d);
-                Real scale = 1.0_rt; // TODO this should vary based on cell
+                auto weatherIdxPtr = soa.GetIntData(IntIdx::weatherLookup).data();
+                auto varVec = agents.awd != nullptr ? agents.awd->varVec.data() : nullptr;
+                auto weather_model = agents.m_weather_model;
+                int a_weather_int = agents.m_weather_int;
                 Real infect = 1.0_rt - lparm_h->vac_eff;
                 auto d_ptr = getCommunityIndex.comm_to_local_index_d.data();
 
@@ -165,10 +168,16 @@ void InteractionModWork<PCType, PTDType, PType>::fastInteractWork (PCType& agent
                         auto community = d_ptr[tidx];
                         int wgroup_i = (community * max_workgroup + workgroup_ptr[i]) * max_naics + naics_ptr[i];
                         int num_infected_workgroup = infected_workgroup_d_ptr[wgroup_i];
-                        Real workgroup_prob = 1.0_prt - infect * lparm->xmit_work * scale;
+                        Real weather_scale = 1.0_rt;
+                        if (a_weather_int > 0 && varVec != nullptr && weatherIdxPtr[i] >= 0) {
+                            weatherVars wvar = varVec[weatherIdxPtr[i]];
+                            weather_scale = weather_model(wvar);
+                        }
+                        Real workgroup_prob = 1.0_prt - infect * lparm->xmit_work * weather_scale;
                         prob_ptr[i] *= static_cast<ParticleReal>(std::pow(workgroup_prob, num_infected_workgroup));
                         int num_infected_workgroup_asymp = infected_workgroup_asymp_d_ptr[wgroup_i];
-                        Real workgroup_prob_asymp = 1.0_prt - lparm->asymp_relative_inf * infect * lparm->xmit_work * scale;
+                        Real workgroup_prob_asymp =
+                                1.0_prt - lparm->asymp_relative_inf * infect * lparm->xmit_work * weather_scale;
                         prob_ptr[i] *= static_cast<ParticleReal>(std::pow(workgroup_prob_asymp, num_infected_workgroup_asymp));
                     }
                 });