Move mean_immune_time and immune_time_spread to 'disease' rather than…

… 'agent'. (#52)

* Move mean_immune_time and immune_time_spread to 'disease' rather than 'agent'

* also update docs

docs/source/usage/how_to_run.rst

@@ -73,10 +73,6 @@ In addition to the ExaEpi inputs, there are also a number of runtime options tha
     Whether or not to have symptomatic agents withdraw.
 * ``agent.symptomatic_withdraw_compliance`` (`float`, default: 0.95)
     Compliance rate for agents withdrawing when they have symptoms. Should be 0.0 to 1.0.
-* ``agent.mean_immune_time`` (`float`, default: 180)
-    The mean amount of time *in days* agents are immune post-infection
-* ``agent.immune_time_spread`` (`float`, default: 60)
-    The spread associated with the above mean, each agent will draw uniformly from mean +/- spread
 * ``agent.shelter_compliance`` (`float`)
     Fraction of agents that comply with shelter-in-place order.
 * ``contact.pSC`` (`float`, default: 0.2)
@@ -105,6 +101,10 @@ 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.mean_immune_time`` (`float`, default: 180)
+    The mean amount of time *in days* agents are immune post-infection
+* ``disease.immune_time_spread`` (`float`, default: 60)
+    The spread associated with the above mean, each agent will draw uniformly from mean +/- spread
 * ``disease.incubation_length_mean`` (`float`, default: ``3.0``)
     Mean length of the incubation period in days. Before this, agents have no symptoms and are not infectious.
 * ``disease.infectious_length_mean`` (`float`, default: ``6.0``)

src/AgentContainer.H

@@ -76,8 +76,6 @@ public:
             pp.query("symptomatic_withdraw", m_symptomatic_withdraw);
             pp.query("shelter_compliance", m_shelter_compliance);
             pp.query("symptomatic_withdraw_compliance", m_symptomatic_withdraw_compliance);
-            pp.query("mean_immune_time", m_mean_immune_time);
-            pp.query("immune_time_spread", m_immune_time_spread);
         }
 
         {
@@ -130,6 +128,9 @@ public:
             pp.query("incubation_length_std", h_parm->incubation_length_std);
             pp.query("infectious_length_std", h_parm->infectious_length_std);
             pp.query("symptomdev_length_std", h_parm->symptomdev_length_std);
+
+            pp.query("mean_immune_time", h_parm->mean_immune_time);
+            pp.query("immune_time_spread", h_parm->immune_time_spread);
         }
 
         h_parm->Initialize();
@@ -218,9 +219,6 @@ protected:
     amrex::Real m_shelter_compliance = 0.95_rt;
     amrex::Real m_symptomatic_withdraw_compliance = 0.95_rt;
 
-    amrex::Real m_mean_immune_time = 30*6;  /*! six months in days*/
-    amrex::Real m_immune_time_spread = 30*2;  /*! two months in days*/
-
     DiseaseParm* h_parm;    /*!< Disease parameters */
     DiseaseParm* d_parm;    /*!< Disease parameters (GPU device) */
 

src/AgentContainer.cpp

@@ -831,8 +831,8 @@ void AgentContainer::updateStatus (MultiFab& disease_stats /*!< Community-wise d
             auto symptomatic_withdraw = m_symptomatic_withdraw;
             auto symptomatic_withdraw_compliance = m_symptomatic_withdraw_compliance;
 
-            auto mean_immune_time = m_mean_immune_time;
-            auto immune_time_spread = m_immune_time_spread;
+            auto mean_immune_time = h_parm->mean_immune_time;
+            auto immune_time_spread = h_parm->immune_time_spread;
 
             // Track hospitalization, ICU, ventilator, and fatalities
             Real CHR[] = {.0104_rt, .0104_rt, .070_rt, .28_rt, 1.0_rt};  // sick -> hospital probabilities

src/DiseaseParm.H

@@ -79,6 +79,9 @@ struct DiseaseParm
     amrex::Real infectious_length_std = 1.0;   /*!< std dev (in days) for the above */
     amrex::Real symptomdev_length_std = 1.0;   /*!< std dev (in days) for the above */
 
+    amrex::Real mean_immune_time = 30*6;  /*! mean immunity time in days*/
+    amrex::Real immune_time_spread = 30*2;  /*! spread in immunity time in days*/
+
     void Initialize ();
 
     void printMatrix ();