Updated outputs: fixed switched Ventilator/ICU label and changed runn…

…ing program stdout details.
AMReX-Codes · Nov 2, 2024 · 70ed0ac · 70ed0ac
1 parent 1a391bb
commit 70ed0ac
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Showing 4 changed files with 14 additions and 10 deletions.
diff --git a/src/AgentContainer.cpp b/src/AgentContainer.cpp
@@ -768,6 +768,9 @@ void AgentContainer::generateCellData (MultiFab& mf /*!< MultiFab with at least
 
     Returns a vector with 5 components corresponding to each value of #Status; each element is
     the total number of agents at a step with the corresponding #Status (in that order).
+
+    Status list: 0 - never, 1 - infected, 2 - immune, 3 - susceptible, 4 - dead, 5 - exposed, 6 - asymptomatic,
+                 7 - presymptomatic, 8 - symptomatic
 */
 std::array<Long, 9> AgentContainer::getTotals (const int a_d /*!< disease index */) {
     BL_PROFILE("getTotals");
@@ -779,6 +782,7 @@ std::array<Long, 9> AgentContainer::getTotals (const int a_d /*!< disease index
                   int s[9] = {0, 0, 0, 0, 0, 0, 0, 0, 0};
                   auto status = ptd.m_runtime_idata[i0(a_d)+IntIdxDisease::status][i];
 
+
                   AMREX_ALWAYS_ASSERT(status >= 0);
                   AMREX_ALWAYS_ASSERT(status <= 4);
 

diff --git a/src/DiseaseParm.H b/src/DiseaseParm.H
@@ -139,8 +139,7 @@ struct DiseaseParm
         a_t_hosp = 0.0;
         a_ICU = 0;
         a_ventilator = 0;
-        Real p_hosp = m_CHR[a_age_group];
-        if (amrex::Random(a_reng) < p_hosp) {
+        if (amrex::Random(a_reng) < m_CHR[a_age_group]) {
             if (a_age_group == AgeGroups::o65) a_t_hosp = m_t_hosp[AgeGroups_Hosp::o65];
             else if (a_age_group == AgeGroups::a50to64) a_t_hosp = m_t_hosp[AgeGroups_Hosp::a50to64];
             else a_t_hosp = m_t_hosp[AgeGroups_Hosp::u50];

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 (flag_hosp_ptr[i] == 1) {
-                    AMREX_ALWAYS_ASSERT(!isHospitalized(i, ptd));
-                    assign_hospital( i, hosp_i_ptr, hosp_j_ptr, ptd);
+                    // could have already been assignedto a hospital from another disease
+                    if (!isHospitalized(i, ptd)) assign_hospital( i, hosp_i_ptr, hosp_j_ptr, ptd);
                 }
             });
 

diff --git a/src/main.cpp b/src/main.cpp
@@ -160,8 +160,8 @@ void runAgent ()
                  << std::setw(12) << "Recovered"
                  << std::setw(12) << "Deaths"
                  << std::setw(15) << "Hospitalized"
-                 << std::setw(15) << "Ventilated"
-                 << std::setw(12) << "ICU"
+                 << std::setw(15) << "ICU"
+                 << std::setw(12) << "Ventilated"
                  << std::setw(12) << "Exposed"
                  << std::setw(15) << "Asymptomatic"
                  << std::setw(15) << "Presymptomatic"
@@ -425,12 +425,13 @@ void runAgent ()
 
             std::chrono::duration<double> elapsed_time = std::chrono::high_resolution_clock::now() - start_time;
 
-            Print() << "[Day " << cur_time <<  " " << std::fixed << std::setprecision(1) << elapsed_time.count() << "s] ";
+            Print() << "[Day " << cur_time <<  " " << std::fixed << std::setprecision(1) << elapsed_time.count() << "s] infected: ";
             for (int d = 0; d < params.num_diseases; d++) {
-                if (d > 0) Print() << "; ";
-                Print() << params.disease_names[d] << ": " << num_infected[d] << " infected, " << cumulative_deaths[d] << " deaths";
+                if (d > 0) Print() << ", ";
+                Print() << params.disease_names[d] << " " << num_infected[d];
             }
-            Print() << "\n";
+            // the cumulative deaths are not tracked separately for each disease
+            Print() << "; deaths: " << cumulative_deaths[0] << "\n";
 
             cur_time += 1.0_rt; // time step is one day
         }