Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into deve…

…lopment
AMReX-Agent · Jan 9, 2024 · c10aa5f · c10aa5f
2 parents d6e09b7 + 5d5c6d5
commit c10aa5f
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Showing 3 changed files with 17 additions and 23 deletions.
diff --git a/docs/source/install/cmake.rst b/docs/source/install/cmake.rst
@@ -57,4 +57,4 @@ or by adding arguments with ``-D<OPTION>=<VALUE>`` to the first CMake call, e.g.
 
 .. code-block:: bash
 
-   cmake -S . -B build -DAMReX_COMPUTE=CUDA
+   cmake -S . -B build -DAMReX_GPU_BACKEND=CUDA
diff --git a/etc/plot.py b/etc/plot.py
@@ -13,5 +13,5 @@
 print(ad["immune"].sum())
 print(ad["previously_infected"].sum())
 
-plt.pcolormesh(ad["total"].reshape(3000, 3000))
+plt.pcolormesh(ad["total"].reshape(ds.domain_dimensions[0:2]))
 plt.savefig("test")
diff --git a/src/Initialization.cpp b/src/Initialization.cpp
@@ -254,9 +254,9 @@ namespace Initialization
 
             Gpu::Device::streamSynchronize();
             num_infected += num_infected_d.dataValue();
-	    if(num_infected>=ninfect) { 
-		    break;
-	    }
+            if (num_infected >= ninfect) {
+                break;
+            }
         }
 
         ParallelDescriptor::ReduceIntSum(num_infected);
@@ -268,35 +268,29 @@ namespace Initialization
                           const CaseData& cases, const DemographicData& demo)
     {
         BL_PROFILE("setInitialCases");
-/*
-        amrex::Vector<int> FIPS_code_to_i(57000, -1);
-        for (int i = 0; i < demo.FIPS.size(); ++i) {
-            FIPS_code_to_i[demo.FIPS[i]] = i;
-	                            printf("Unit %d has FIPS %d and num Comm %d and population %d\n", i, demo.FIPS[i], demo.Start[i+1]-demo.Start[i], demo.Population[i]);
-        }
-*/
+
         std::map<std::pair<int, int>, amrex::DenseBins<AgentContainer::ParticleType> > bin_map;
 
         int ntry = 5;
         int ninf = 0;
         for (int ihub = 0; ihub < cases.N_hubs; ++ihub) {
             if (cases.Size_hubs[ihub] > 0) {
                 int FIPS = cases.FIPS_hubs[ihub];
-		std::vector<int> units;
-		units.resize(0);
-	        for (int i = 0; i < demo.Nunit; ++i) if(demo.FIPS[i]==FIPS)units.push_back(i);		
+                std::vector<int> units;
+                units.resize(0);
+                for (int i = 0; i < demo.Nunit; ++i) if(demo.FIPS[i]==FIPS)units.push_back(i);
                 //int unit = FIPS_code_to_i[FIPS];
                 if (units.size() > 0) {
-		    printf("Infecting %d people in FIPS %d\n", cases.Size_hubs[ihub], FIPS);
-		    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);
+                    printf("Infecting %d people in FIPS %d\n", cases.Size_hubs[ihub], FIPS);
+                    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);
                         ninf += nSuccesses;
-			i+= nSuccesses;
-			u=(u+1)%units.size(); //sometimes we infect fewer than ntry, but switch to next unit anyway
+                        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";
                 }
             }
         }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -57,4 +57,4 @@ or by adding arguments with ``-D<OPTION>=<VALUE>`` to the first CMake call, e.g.

		.. code-block:: bash

		cmake -S . -B build -DAMReX_COMPUTE=CUDA
		cmake -S . -B build -DAMReX_GPU_BACKEND=CUDA