expose the length of the incubation, infectious, and symptomatic stages

AMReX-Agent · Dec 2, 2023 · bac1fba · bac1fba
1 parent f14695e
commit bac1fba
Show file tree

Hide file tree

Showing 4 changed files with 21 additions and 5 deletions.
diff --git a/docs/source/usage/how_to_run.rst b/docs/source/usage/how_to_run.rst
@@ -93,6 +93,12 @@ In addition to the ExaEpi inputs, there are also a number of runtime options tha
     one entry for each disease strain.
 * ``disease.vac_eff`` (`float`, example: ``0.4``)
     The vaccine efficacy - the probability of transmission will be multiplied by this factor
+* ``disease.incubation_length`` (`int`, default: ``3``)
+    Length of the incubation period in days. Before this, agents have no symptoms and are not infectious.
+* ``disease.infectious_length`` (`int`, default: ``6``)
+    Length of the infectious period in days. This counter starts once the incubation phase is over. Before tihs, agents are symptomatic and can spread the disease.
+* ``disease.symptomatic_length`` (`int`, default: ``5``)
+    Length of the symptomatic-but-not-infectious stage in days. This counter starts once the infectious phase is complete. During this time agents are symptomatic and may self-withdraw, but they cannot spread the illness.
 
 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
@@ -267,6 +267,10 @@ public:
                 h_parm->p_asymp[i] = p_asymp[i];
                 h_parm->reduced_inf[i] = reduced_inf[i];
             }
+
+            pp.query("incubation_length", h_parm->incubation_length);
+            pp.query("infectious_length", h_parm->infectious_length);
+            pp.query("symptomatic_length", h_parm->symptomatic_length);
         }
 
         h_parm->Initialize();

diff --git a/src/AgentContainer.cpp b/src/AgentContainer.cpp
@@ -710,6 +710,8 @@ void AgentContainer::updateStatus (MultiFab& disease_stats)
                 };
             };
 
+            auto* lparm = d_parm;
+
             // Track hospitalization, ICU, ventilator, and fatalities
             Real CHR[] = {.0104, .0104, .070, .28, 1.0};  // sick -> hospital probabilities
             Real CIC[] = {.24, .24, .24, .36, .35};      // hospital -> ICU probabilities
@@ -725,7 +727,7 @@ void AgentContainer::updateStatus (MultiFab& disease_stats)
                 }
                 else if (status_ptr[i] == Status::infected) {
                     counter_ptr[i] += 1;
-                    if (counter_ptr[i] < 3) {
+                    if (counter_ptr[i] < lparm->incubation_length) {
                         // incubation phase
                         return;
                     }
@@ -812,8 +814,8 @@ void AgentContainer::updateStatus (MultiFab& disease_stats)
                                 }
                             }
                         }
-                        else { // not hospitalized, recover on day 9
-                            if (counter_ptr[i] == 9.0) {
+                        else { // not hospitalized, recover once not infectious
+                            if (counter_ptr[i] == lparm->incubation_length + lparm->infectious_length) {
                                 status_ptr[i] = Status::immune;
                             }
                         }
@@ -998,14 +1000,14 @@ void AgentContainer::interactAgentsHomeWork (MultiFab& /*mask_behavior*/, bool h
 
                 AMREX_ALWAYS_ASSERT( (Long) i < np);
                 if (status_ptr[i] == Status::immune) { return; }
-                if (status_ptr[i] == Status::infected && counter_ptr[i] < 3) { return; }  // incubation stage
+                if (status_ptr[i] == Status::infected && counter_ptr[i] < lparm->incubation_length) { return; }  // incubation stage
                 //amrex::Real i_mask = mask_arr(home_i_ptr[i], home_j_ptr[i], 0);
                 for (unsigned int jj = cell_start; jj < cell_stop; ++jj) {
                     auto j = inds[jj];
                     AMREX_ALWAYS_ASSERT( (Long) j < np);
                     //amrex::Real j_mask = mask_arr(home_i_ptr[j], home_j_ptr[j], 0);
                     if (status_ptr[j] == Status::immune) {continue;}
-                    if (status_ptr[i] == Status::infected && counter_ptr[j] < 3) { continue; }  // incubation stage
+                    if (status_ptr[i] == Status::infected && counter_ptr[j] < lparm->incubation_length) { continue; }  // incubation stage
 
                     if (status_ptr[i] == Status::infected && status_ptr[j] != Status::infected) {
                         // i can infect j

diff --git a/src/DiseaseParm.H b/src/DiseaseParm.H
@@ -48,6 +48,10 @@ struct DiseaseParm
 
     amrex::Real Child_compliance, Child_HH_closure;
 
+    int incubation_length  = 3;
+    int infectious_length  = 6;
+    int symptomatic_length = 5; // note, this does not affect the model yet
+
     void Initialize ();
 };
 #endif