Emplacing when copy agent

UofUEpiBio · Sep 26, 2023 · bf344f7 · bf344f7
1 parent 3fe5d6a
commit bf344f7
Show file tree

Hide file tree

Showing 7 changed files with 30 additions and 21 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -64,5 +64,6 @@
     "typeinfo": "cpp",
     "variant": "cpp",
     "semaphore": "cpp"
-  }
+  },
+  "intel-corporation.oneapi-analysis-configurator.binary-path": "/home/george/Documents/development/epiworld/tests/01c.o"
 }
diff --git a/Makefile b/Makefile
@@ -13,3 +13,9 @@ helloworld.o: helloworld.cpp epiworld.hpp
 	g++ -std=c++17 -O2 helloworld.cpp -o helloworld.o
 
 .PHONY: examples all-examples epiworld.hpp
+
+image=intel/oneapi-basekit:devel-ubuntu22.04
+# --device=/dev/dri enables the gpu (if available). May not be available in Linux VM or Windows
+oneapi:
+	docker run --cap-add=SYS_ADMIN --cap-add=SYS_PTRACE \
+		--device=/dev/dri -it "${image}"
diff --git a/epiworld.hpp b/epiworld.hpp
@@ -15269,6 +15269,9 @@ class ModelSIS : public epiworld::Model<TSeq>
 
 public:
 
+    static const int SUSCEPTIBLE = 0;
+    static const int INFECTED    = 1;
+
     ModelSIS() {};
 
     ModelSIS(
@@ -15310,7 +15313,7 @@ inline ModelSIS<TSeq>::ModelSIS(
 
     // Preparing the virus -------------------------------------------
     epiworld::Virus<TSeq> virus(vname);
-    virus.set_state(1,0,0);
+    virus.set_state(ModelSIS<TSeq>::INFECTED, ModelSIS<TSeq>::SUSCEPTIBLE, ModelSIS<TSeq>::SUSCEPTIBLE);
 
     virus.set_prob_infecting(&model("Transmission rate"));
     virus.set_prob_recovery(&model("Recovery rate"));
@@ -17193,14 +17196,12 @@ inline ModelSEIRD<TSeq>::ModelSEIRD(
 template<typename TSeq = EPI_DEFAULT_TSEQ>
 class ModelSIRDCONN : public epiworld::Model<TSeq>
 {
-private:
+public:
     static const int SUSCEPTIBLE = 0;
     static const int INFECTED    = 1;
-    static const int RECOVERED     = 2;
+    static const int RECOVERED   = 2;
     static const int DECEASED    = 3;
 
-public:
-
     ModelSIRDCONN() {
 
         // tracked_agents_infected.reserve(1e4);

diff --git a/include/epiworld/agent-meat.hpp b/include/epiworld/agent-meat.hpp
@@ -90,27 +90,27 @@ inline Agent<TSeq>::Agent(const Agent<TSeq> & p) :
     id     = p.id;
 
     // Dealing with the virus
-    viruses.resize(p.get_n_viruses(), nullptr);
+    viruses.reserve(p.get_n_viruses());
     n_viruses = viruses.size();
     for (size_t i = 0u; i < n_viruses; ++i)
     {
 
         // Will create a copy of the virus, with the exeption of
         // the virus code
-        viruses[i] = std::make_shared<Virus<TSeq>>(*p.viruses[i]);
-        viruses[i]->set_agent(this, i);
+        viruses.emplace_back(std::make_shared<Virus<TSeq>>(*p.viruses[i]));
+        viruses.back()->set_agent(this, i);
 
     }
 
-    tools.resize(p.get_n_tools(), nullptr);
+    tools.reserve(p.get_n_tools());
     n_tools = tools.size();
     for (size_t i = 0u; i < n_tools; ++i)
     {
 
         // Will create a copy of the virus, with the exeption of
         // the virus code
-        tools[i] = std::make_shared<Tool<TSeq>>(*p.tools[i]);
-        tools[i]->set_agent(this, i);
+        tools.emplace_back(std::make_shared<Tool<TSeq>>(*p.tools[i]));
+        tools.back()->set_agent(this, i);
 
     }
 

diff --git a/include/epiworld/models/sirdconnected.hpp b/include/epiworld/models/sirdconnected.hpp
@@ -4,14 +4,12 @@
 template<typename TSeq = EPI_DEFAULT_TSEQ>
 class ModelSIRDCONN : public epiworld::Model<TSeq>
 {
-private:
+public:
     static const int SUSCEPTIBLE = 0;
     static const int INFECTED    = 1;
-    static const int RECOVERED     = 2;
+    static const int RECOVERED   = 2;
     static const int DECEASED    = 3;
 
-public:
-
     ModelSIRDCONN() {
 
         // tracked_agents_infected.reserve(1e4);

diff --git a/include/epiworld/models/sis.hpp b/include/epiworld/models/sis.hpp
@@ -15,6 +15,9 @@ class ModelSIS : public epiworld::Model<TSeq>
 
 public:
 
+    static const int SUSCEPTIBLE = 0;
+    static const int INFECTED    = 1;
+
     ModelSIS() {};
 
     ModelSIS(
@@ -56,7 +59,7 @@ inline ModelSIS<TSeq>::ModelSIS(
 
     // Preparing the virus -------------------------------------------
     epiworld::Virus<TSeq> virus(vname);
-    virus.set_state(1,0,0);
+    virus.set_state(ModelSIS<TSeq>::INFECTED, ModelSIS<TSeq>::SUSCEPTIBLE, ModelSIS<TSeq>::SUSCEPTIBLE);
 
     virus.set_prob_infecting(&model("Transmission rate"));
     virus.set_prob_recovery(&model("Recovery rate"));

diff --git a/tests/01c-sir.cpp b/tests/01c-sir.cpp
@@ -24,18 +24,18 @@ EPIWORLD_TEST_CASE("SIR-omp", "[OMP-SIR]") {
         );
 
     model_0.seed(1231);
-    model_0.agents_smallworld(1000, 5, false, 0.01);
+    model_0.agents_smallworld(10000, 5, false, 0.01);
     model_0.verbose_off();
-    model_0.run_multiple(100, 10, 1231, saver_0, true, true, 1);
+    model_0.run_multiple(100, 100, 1231, saver_0, true, true, 1);
 
     epimodels::ModelSIR<> model_1(
         "a virus", 0.01, .9, .3
         );
 
     model_1.seed(1231);
-    model_1.agents_smallworld(1000, 5, false, 0.01);
+    model_1.agents_smallworld(10000, 5, false, 0.01);
     model_1.verbose_off();
-    model_1.run_multiple(100, 10, 1231, saver_1, true, true, 2);
+    model_1.run_multiple(100, 100, 1231, saver_1, true, true, 2);
 
     std::vector< std::string > files = {
         "reproductive.csv",