Should be incubation period, not latent period.

Check if agent is in hospital before assigning hospital. This can happen in multiple diseases.
AMReX-Codes · Nov 6, 2024 · 04511a5 · 04511a5
1 parent 627ca7c
commit 04511a5
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Showing 3 changed files with 9 additions and 10 deletions.
diff --git a/examples/inputs.nm b/examples/inputs.nm
@@ -10,11 +10,12 @@ agent.urbanpop_filename = "../UrbanPop/NM_35/urbanpop_nm"
 agent.nsteps = 70
 #agent.seed = 11
 
-agent.number_of_diseases = 2
-agent.disease_names = "covid" "flu"
 # disease.initial_case_type = "file"
 # disease.case_filename = "../CaseData/nm-july4.cases"
 
+agent.number_of_diseases = 2
+agent.disease_names = "covid" "flu"
+
 disease.initial_case_type = "random" "random"
 disease.num_initial_cases = 1000
 
@@ -31,4 +32,4 @@ disease_flu.num_initial_cases = 100
 disease_flu.p_trans = 0.3
 disease_flu.latent_length_mean = 3.0
 disease_flu.infectious_length_mean = 3.0
-disease_flu.incution_length_mean = 3.0
+disease_flu.incubation_length_mean = 3.0
diff --git a/src/DiseaseStatus.H b/src/DiseaseStatus.H
@@ -201,8 +201,8 @@ void DiseaseStatus<AC,ACT,ACTD,A>::updateAgents(AC& a_agents, /*!< Agent contain
 
             ParallelFor( np, [=] AMREX_GPU_DEVICE (int i) noexcept
             {
-                if (marked_for_hosp_ptr[i] == 1) {
-                    AMREX_ALWAYS_ASSERT(!inHospital(i, ptd));
+                if (marked_for_hosp_ptr[i] == 1 && !inHospital(i, ptd)) {
+                    //AMREX_ALWAYS_ASSERT(!inHospital(i, ptd));
                     assign_hospital( i, hosp_i_ptr, hosp_j_ptr, ptd);
                 }
             });

diff --git a/src/HospitalModel.H b/src/HospitalModel.H
@@ -86,13 +86,13 @@ void HospitalModel<PCType, PTDType, PType>::treatAgents(PCType& a_agents, /*!< A
             int r_RT = RealIdx::nattribs;
 
             GpuArray<int*,ExaEpi::max_num_diseases> status_ptrs, symptomatic_ptrs;
-            GpuArray<ParticleReal*,ExaEpi::max_num_diseases> counter_ptrs, timer_ptrs, latent_per_ptrs;
+            GpuArray<ParticleReal*,ExaEpi::max_num_diseases> counter_ptrs, timer_ptrs, incubation_per_ptrs;
             for (int d = 0; d < n_disease; d++) {
                 status_ptrs[d] = soa.GetIntData(i_RT+i0(d)+IntIdxDisease::status).data();
                 symptomatic_ptrs[d] = soa.GetIntData(i_RT+i0(d)+IntIdxDisease::symptomatic).data();
                 counter_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::disease_counter).data();
                 timer_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::treatment_timer).data();
-                latent_per_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::latent_period).data();
+                incubation_per_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
             }
 
             Gpu::DeviceVector<int> is_alive(np);
@@ -134,9 +134,7 @@ void HospitalModel<PCType, PTDType, PType>::treatAgents(PCType& a_agents, /*!< A
                         // agent is not in hospital
                         return;
                     }
-                    // Should this be:?
-                    // if (counter_ptrs[d][i] == Math::floor(incubation_per_ptrs[d][i]))
-                    if (counter_ptrs[d][i] == Math::ceil(latent_per_ptrs[d][i])) {
+                    if (counter_ptrs[d][i] == Math::floor(incubation_per_ptrs[d][i])) {
                         // agent just started treatment
                         return;
                     }