Initialize with N Random cases (#33)

* Initialize with N Random cases

* document new parameters

docs/source/usage/how_to_run.rst

@@ -40,10 +40,15 @@ In addition to the ExaEpi inputs, there are also a number of runtime options tha
     The path to the ``*.bin`` file containing worker flow information.
     Must be provided if ``ic_type`` is ``"census"``. Examples of these data files are provided
     in ``ExaEpi/data/CensusData``.
+* ``agent.initial_case_type`` (`string`)
+    Either ``random`` or ``file``. If ``random``, ``agent.num_initial_cases`` must be set.
+    If ``file``, ``agent.case_filename`` must be set. Must be provided if ``ic_type`` is ``"census"``.
 * ``agent.case_filename`` (`string`)
     The path to the ``*.cases`` file containing the initial case data to use.
-    Must be provided if ``ic_type`` is ``"census"``. Examples of these data files are provided
+    Must be provided if ``initial_case_type`` is ``"file"``. Examples of these data files are provided
     in ``ExaEpi/data/CaseData``.
+* ``agent.num_initial_cases`` (int)
+    The number of initial cases to seed. Must be provided if ``initial_case_type`` is ``"random"``.
 * ``agent.nsteps`` (`integer`)
     The number of time steps to simulate. Currently, time steps are fixed at 12 hours, so to
     run for 30 days, input `60`.

examples/inputs.ca

@@ -1,13 +1,14 @@
 agent.ic_type = "census"
 agent.census_filename = "../../data/CensusData/CA.dat"
 agent.workerflow_filename = "../../data/CensusData/CA-wf.bin"
+agent.initial_case_type = "file"
 agent.case_filename = "../../data/CaseData/July4.cases"
 
-agent.nsteps = 10
-agent.plot_int = 168
+agent.nsteps = 120
+agent.plot_int = 10
 agent.random_travel_int = 24
 
-agent.aggregated_diag_int = 168
+agent.aggregated_diag_int = -1
 agent.aggregated_diag_prefix = "cases"
 
 contact.pSC  = 0.2
@@ -17,8 +18,9 @@ contact.pWO  = 0.5
 contact.pFA  = 1.0
 contact.pBAR = -1.
 
-disease.nstrain = 2
-disease.p_trans = 0.20 0.30
-disease.p_asymp = 0.40 0.40
-disease.reduced_inf = 0.75 0.75
-disease.reinfect_prob = 0.0
+disease.nstrain = 1
+disease.p_trans = 0.20
+disease.p_asymp = 0.40
+disease.reduced_inf = 0.75
+
+disease.symptomdev_length_mean = 3.0

examples/inputs_random_ca

@@ -0,0 +1,26 @@
+agent.ic_type = "census"
+agent.census_filename = "../../data/CensusData/CA.dat"
+agent.workerflow_filename = "../../data/CensusData/CA-wf.bin"
+agent.initial_case_type = "random"
+agent.num_initial_cases = 5
+
+agent.nsteps = 180
+agent.plot_int = 10
+agent.random_travel_int = 24
+
+agent.aggregated_diag_int = -1
+agent.aggregated_diag_prefix = "cases"
+
+contact.pSC  = 0.2
+contact.pCO  = 1.45
+contact.pNH  = 1.45
+contact.pWO  = 0.5
+contact.pFA  = 1.0
+contact.pBAR = -1.
+
+disease.nstrain = 1
+disease.p_trans = 0.20
+disease.p_asymp = 0.40
+disease.reduced_inf = 0.75
+
+disease.symptomdev_length_mean = 3.0

src/AgentContainer.H

@@ -29,8 +29,8 @@ struct RealIdx
         treatment_timer,        /*!< Timer since hospital admission */
         prob,                   /*!< Probability of infection */
         incubation_period,      /*!< Time until infectious */
-        infectious_period,       /*!< Length of time infectious */
-        symptomdev_period,       /*!< Time until symptoms would develop */
+        infectious_period,      /*!< Length of time infectious */
+        symptomdev_period,      /*!< Time until symptoms would develop */
         nattribs                /*!< number of real-type attribute*/
     };
 };

src/Initialization.H

@@ -23,10 +23,13 @@ namespace Initialization
                           const amrex::iMultiFab& comm_mf,
                           AgentContainer& pc);
 
-    void setInitialCases (AgentContainer& pc, const amrex::iMultiFab& unit_mf,
-                          const amrex::iMultiFab& FIPS_mf, const amrex::iMultiFab& comm_mf,
-                          const CaseData& cases, const DemographicData& demo);
+    void setInitialCasesFromFile (AgentContainer& pc, const amrex::iMultiFab& unit_mf,
+                                  const amrex::iMultiFab& FIPS_mf, const amrex::iMultiFab& comm_mf,
+                                  const CaseData& cases, const DemographicData& demo);
 
+    void setInitialCasesRandom (AgentContainer& pc, const amrex::iMultiFab& unit_mf,
+                                const amrex::iMultiFab& FIPS_mf, const amrex::iMultiFab& comm_mf,
+                                int num_cases, const DemographicData& demo);
 }
 }
 

src/Initialization.cpp

@@ -232,15 +232,20 @@ namespace Initialization
                                   const amrex::iMultiFab& comm_mf, /*!< MultiFab with community number at each grid cell */
                                   std::map<std::pair<int, int>,
                                   amrex::DenseBins<AgentContainer::ParticleType> >& bin_map, /*!< Map of dense bins with agents */
-                                  const CaseData& /*cases*/, /*!< Case data */
                                   const DemographicData& demo, /*!< Demographic data */
                                   int unit, /*!< Unit number to infect */
                                   int ninfect /*!< Target number of agents to infect */ ) {
-        // chose random community in unit
-        int ncomms = demo.Start[unit+1] - demo.Start[unit];
+        // chose random community
+        int ncomms = demo.Ncommunity;
+        int comm_offset = 0;
+        if (unit > 0) {
+            ncomms = demo.Start[unit+1] - demo.Start[unit];
+            comm_offset = demo.Start[unit];
+        }
+
         int random_comm = -1;
         if (ParallelDescriptor::IOProcessor()) {
-            random_comm = amrex::Random_int(ncomms) + demo.Start[unit];
+            random_comm = amrex::Random_int(ncomms) + comm_offset;
         }
         ParallelDescriptor::Bcast(&random_comm, 1);
 
@@ -348,15 +353,15 @@ namespace Initialization
           number of infected agents is equal or greater than the number of infections for this
           FIPS code. See #ExaEpi::Initialization::infect_random_community().
     */
-    void setInitialCases( AgentContainer&         pc,       /*!< Agent container (particle container) */
-                          const amrex::iMultiFab& unit_mf,  /*!< MultiFab with unit number at each grid cell */
-                          const amrex::iMultiFab& FIPS_mf,  /*!< FIPS code (component 0) and
+    void setInitialCasesFromFile (AgentContainer&         pc,       /*!< Agent container (particle container) */
+                                  const amrex::iMultiFab& unit_mf,  /*!< MultiFab with unit number at each grid cell */
+                                  const amrex::iMultiFab& FIPS_mf,  /*!< FIPS code (component 0) and
                                                                  census tract number (component 1) */
-                          const amrex::iMultiFab& comm_mf,  /*!< MultiFab with community number at each grid cell */
-                          const CaseData&         cases,    /*!< Case data */
-                          const DemographicData& demo       /*!< demographic data */ )
+                                  const amrex::iMultiFab& comm_mf,  /*!< MultiFab with community number at each grid cell */
+                                  const CaseData&         cases,    /*!< Case data */
+                                  const DemographicData& demo       /*!< demographic data */ )
     {
-        BL_PROFILE("setInitialCases");
+        BL_PROFILE("setInitialCasesFromFile");
 
         std::map<std::pair<int, int>, amrex::DenseBins<AgentContainer::ParticleType> > bin_map;
 
@@ -374,17 +379,41 @@ namespace Initialization
                     int u=0;
                     int i=0;
                     while (i < cases.Size_hubs[ihub]) {
-                        int nSuccesses= infect_random_community(pc, unit_mf, FIPS_mf, comm_mf, bin_map, cases, demo, units[u], ntry);
+                        int nSuccesses= infect_random_community(pc, unit_mf, FIPS_mf, comm_mf, bin_map, demo, units[u], ntry);
                         ninf += nSuccesses;
                         i+= nSuccesses;
                         u=(u+1)%units.size(); //sometimes we infect fewer than ntry, but switch to next unit anyway
                     }
-                    amrex::Print() << "Infected " << i<< " total " << ninf << " after processing FIPS " << FIPS<< " \n";
+                    amrex::Print() << "Infected " << i<< " total " << ninf << " after processing FIPS " << FIPS << " \n";
                 }
             }
         }
         amrex::ignore_unused(ninf);
     }
 
+    void setInitialCasesRandom (AgentContainer&         pc,       /*!< Agent container (particle container) */
+                                const amrex::iMultiFab& unit_mf,  /*!< MultiFab with unit number at each grid cell */
+                                const amrex::iMultiFab& FIPS_mf,  /*!< FIPS code (component 0) and
+                                                                 census tract number (component 1) */
+                                const amrex::iMultiFab& comm_mf,  /*!< MultiFab with community number at each grid cell */
+                                int num_cases,
+                                const DemographicData& demo       /*!< demographic data */ )
+    {
+        BL_PROFILE("setInitialCasesRandom");
+
+        std::map<std::pair<int, int>, amrex::DenseBins<AgentContainer::ParticleType> > bin_map;
+
+        int ninf = 0;
+        for (int ihub = 0; ihub < num_cases; ++ihub) {
+            int i = 0;
+            while (i < 1) {
+                int nSuccesses= infect_random_community(pc, unit_mf, FIPS_mf, comm_mf, bin_map, demo, -1, 1);
+                ninf += nSuccesses;
+                i+= nSuccesses;
+            }
+        }
+        amrex::ignore_unused(ninf);
+    }
+
 }
 }

src/Utils.H

@@ -52,6 +52,9 @@ struct TestParams
     */
     std::string workerflow_filename;
 
+    std::string initial_case_type;
+    int num_initial_cases;
+
     /*! Initial cases filename (CaseData::InitFromFile):
         The case data file is an ASCII text file with three columns of numbers:
         FIPS code, current number of cases, and cumulative number of cases till date.

src/Utils.cpp

@@ -47,7 +47,14 @@ void ExaEpi::Utils::get_test_params (   TestParams& params,         /*!< Test pa
         params.ic_type = ICType::Census;
         pp.get("census_filename", params.census_filename);
         pp.get("workerflow_filename", params.workerflow_filename);
-        pp.get("case_filename", params.case_filename);
+        pp.get("initial_case_type", params.initial_case_type);
+        if (params.initial_case_type == "file") {
+            pp.get("case_filename", params.case_filename);
+        } else if (params.initial_case_type == "random") {
+            pp.get("num_initial_cases", params.num_initial_cases);
+        } else {
+            amrex::Abort("initial case type not recognized");
+        }
     } else {
         amrex::Abort("ic type not recognized");
     }

src/main.cpp

@@ -99,7 +99,9 @@ void runAgent ()
     if (params.ic_type == ICType::Census) { demo.InitFromFile(params.census_filename); }
 
     CaseData cases;
-    if (params.ic_type == ICType::Census) { cases.InitFromFile(params.case_filename); }
+    if (params.ic_type == ICType::Census && params.initial_case_type == "file") {
+        cases.InitFromFile(params.case_filename);
+    }
 
     Geometry geom = ExaEpi::Utils::get_geometry(demo, params);
 
@@ -152,7 +154,13 @@ void runAgent ()
         } else if (params.ic_type == ICType::Census) {
             pc.initAgentsCensus(num_residents, unit_mf, FIPS_mf, comm_mf, demo);
             ExaEpi::Initialization::read_workerflow(demo, params, unit_mf, comm_mf, pc);
-            ExaEpi::Initialization::setInitialCases(pc, unit_mf, FIPS_mf, comm_mf, cases, demo);
+            if (params.initial_case_type == "file") {
+                ExaEpi::Initialization::setInitialCasesFromFile(pc, unit_mf, FIPS_mf, comm_mf,
+                                                        cases, demo);
+            } else {
+                ExaEpi::Initialization::setInitialCasesRandom(pc, unit_mf, FIPS_mf, comm_mf,
+                                                              params.num_initial_cases, demo);
+            }
         }
     }