diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ae02097b..160af43b 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,36 +1,25 @@
-# List of source files
+# Automatically detect source files in subdirectories
+# Find all subdirectories in src/
+file(GLOB _subdirs RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *)
+list(FILTER _subdirs INCLUDE REGEX "^[^.]+$")  # Exclude hidden files
+set(_subdir_sources "")
+
+# For each subdirectory, collect all .cpp and .H files
+foreach(_dir IN LISTS _subdirs)
+    if(IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${_dir})
+        file(GLOB_RECURSE _dir_sources
+            "${_dir}/*.cpp"
+            "${_dir}/*.H"
+        )
+        list(APPEND _subdir_sources ${_dir_sources})
+    endif()
+endforeach()
+
+# Main source file list includes main.cpp and all subdirectory sources
 set(_sources
     main.cpp
-    AgentDefinitions.H
-    AgentContainer.H
-    AgentContainer.cpp
-    AirTravelFlow.H
-    AirTravelFlow.cpp
-    CaseData.H
-    CaseData.cpp
-    DiseaseCoupling.H
-    CensusData.H
-    CensusData.cpp
-    DiseaseParm.H
-    DiseaseParm.cpp
-    DemographicData.H
-    DemographicData.cpp
-    IO.H
-    IO.cpp
-    InteractionModel.H
-    InteractionModHome.H
-    InteractionModHomeNborhood.H
-    InteractionModWorkNborhood.H
-    InteractionModSchool.H
-    InteractionModWork.H
-    InteractionModelLibrary.H
-    InitializeInfections.H
-    InitializeInfections.cpp
-    UrbanPopAgentStruct.H
-    UrbanPopData.H
-    UrbanPopData.cpp
-    Utils.H
-    Utils.cpp)
+    ${_subdir_sources}
+)
 
 # List of input files
 set(_input_files)
diff --git a/src/AgentContainer.H b/src/agents/AgentContainer.H
similarity index 99%
rename from src/AgentContainer.H
rename to src/agents/AgentContainer.H
index 97973912..bbd7b8ae 100644
--- a/src/AgentContainer.H
+++ b/src/agents/AgentContainer.H
@@ -24,7 +24,7 @@
 #include "DiseaseStatus.H"
 #include "HospitalModel.H"
 #include "InteractionModelLibrary.H"
-#include "Utils.H"
+#include "RuntimeParams.H"
 
 /*! \brief Derived class from ParticleContainer that defines agents and their functions */
 class AgentContainer : public amrex::ParticleContainer<0, 0, RealIdx::nattribs, IntIdx::nattribs> {
diff --git a/src/AgentContainer.cpp b/src/agents/AgentContainer.cpp
similarity index 100%
rename from src/AgentContainer.cpp
rename to src/agents/AgentContainer.cpp
diff --git a/src/AgentDefinitions.H b/src/agents/AgentDefinitions.H
similarity index 100%
rename from src/AgentDefinitions.H
rename to src/agents/AgentDefinitions.H
diff --git a/src/DiseaseCoupling.H b/src/disease/DiseaseCoupling.H
similarity index 100%
rename from src/DiseaseCoupling.H
rename to src/disease/DiseaseCoupling.H
diff --git a/src/DiseaseParm.H b/src/disease/DiseaseParm.H
similarity index 100%
rename from src/DiseaseParm.H
rename to src/disease/DiseaseParm.H
diff --git a/src/DiseaseParm.cpp b/src/disease/DiseaseParm.cpp
similarity index 100%
rename from src/DiseaseParm.cpp
rename to src/disease/DiseaseParm.cpp
diff --git a/src/DiseaseStatus.H b/src/disease/DiseaseStatus.H
similarity index 99%
rename from src/DiseaseStatus.H
rename to src/disease/DiseaseStatus.H
index 2c237ff6..00a2e10e 100644
--- a/src/DiseaseStatus.H
+++ b/src/disease/DiseaseStatus.H
@@ -43,10 +43,10 @@ template <typename AC,   /*!< agent container type */
 class DiseaseStatus {
   public:
     /*! \brief constructor */
-    DiseaseStatus<AC, ACT, ACTD, A>() {}
+    DiseaseStatus() {}
 
     /*! \brief default destructor */
-    virtual ~DiseaseStatus<AC, ACT, ACTD, A>() = default;
+    virtual ~DiseaseStatus() = default;
 
     /*! \brief Updates disease status of each agent at a given step and
      *   also updates a MultiFab that tracks disease statistics (hospitalization,
diff --git a/src/HospitalModel.H b/src/disease/HospitalModel.H
similarity index 99%
rename from src/HospitalModel.H
rename to src/disease/HospitalModel.H
index 22ed9998..17023904 100644
--- a/src/HospitalModel.H
+++ b/src/disease/HospitalModel.H
@@ -8,7 +8,7 @@
 #include "AgentDefinitions.H"
 #include "DiseaseParm.H"
 #include "InteractionModel.H"
-#include "Utils.H"
+#include "RuntimeParams.H"
 
 using namespace amrex;
 
diff --git a/src/Utils.H b/src/init/RuntimeParams.H
similarity index 98%
rename from src/Utils.H
rename to src/init/RuntimeParams.H
index fbaaef3d..5a71c065 100644
--- a/src/Utils.H
+++ b/src/init/RuntimeParams.H
@@ -1,9 +1,9 @@
-/*! @file Utils.H
+/*! @file RuntimeParams.H
     \brief Defines the #ExaEpi::Utils namespace
 */
 
-#ifndef UTILS_H_
-#define UTILS_H_
+#ifndef RUNTIME_PARAMS_H_
+#define RUNTIME_PARAMS_H_
 
 #include <AMReX_Geometry.H>
 #include <AMReX_IntVect.H>
diff --git a/src/Utils.cpp b/src/init/RuntimeParams.cpp
similarity index 98%
rename from src/Utils.cpp
rename to src/init/RuntimeParams.cpp
index ee389584..eff1311b 100644
--- a/src/Utils.cpp
+++ b/src/init/RuntimeParams.cpp
@@ -1,4 +1,4 @@
-/*! @file Utils.cpp
+/*! @file RuntimeParams.cpp
     \brief Contains function implementations for the #ExaEpi::Utils namespace
 */
 
@@ -11,7 +11,7 @@
 #include <AMReX_RealBox.H>
 
 #include "DemographicData.H"
-#include "Utils.H"
+#include "RuntimeParams.H"
 
 #include <cmath>
 #include <string>
diff --git a/src/CensusData.H b/src/init/census/CensusData.H
similarity index 99%
rename from src/CensusData.H
rename to src/init/census/CensusData.H
index 98bc4bf4..fd5ab7c1 100644
--- a/src/CensusData.H
+++ b/src/init/census/CensusData.H
@@ -13,7 +13,7 @@
 #include "AgentContainer.H"
 #include "CaseData.H"
 #include "DemographicData.H"
-#include "Utils.H"
+#include "RuntimeParams.H"
 
 /*! \brief A class encapsulating all data relevant to the ICType Census */
 struct CensusData {
diff --git a/src/CensusData.cpp b/src/init/census/CensusData.cpp
similarity index 100%
rename from src/CensusData.cpp
rename to src/init/census/CensusData.cpp
diff --git a/src/DemographicData.H b/src/init/census/DemographicData.H
similarity index 100%
rename from src/DemographicData.H
rename to src/init/census/DemographicData.H
diff --git a/src/DemographicData.cpp b/src/init/census/DemographicData.cpp
similarity index 100%
rename from src/DemographicData.cpp
rename to src/init/census/DemographicData.cpp
diff --git a/src/CaseData.H b/src/init/infections/CaseData.H
similarity index 100%
rename from src/CaseData.H
rename to src/init/infections/CaseData.H
diff --git a/src/CaseData.cpp b/src/init/infections/CaseData.cpp
similarity index 100%
rename from src/CaseData.cpp
rename to src/init/infections/CaseData.cpp
diff --git a/src/InitializeInfections.H b/src/init/infections/InitializeInfections.H
similarity index 96%
rename from src/InitializeInfections.H
rename to src/init/infections/InitializeInfections.H
index f64b553c..899f476e 100644
--- a/src/InitializeInfections.H
+++ b/src/init/infections/InitializeInfections.H
@@ -13,7 +13,7 @@
 #include "AgentContainer.H"
 #include "CaseData.H"
 #include "DemographicData.H"
-#include "Utils.H"
+#include "RuntimeParams.H"
 
 void setInitialCasesFromFile(AgentContainer& pc, CaseData& cases, const std::string& name, int d_idx,
                              const Vector<int>& FIPS_codes, const Vector<int>& unit_community_start, iMultiFab& comm_mf,
diff --git a/src/InitializeInfections.cpp b/src/init/infections/InitializeInfections.cpp
similarity index 100%
rename from src/InitializeInfections.cpp
rename to src/init/infections/InitializeInfections.cpp
diff --git a/src/UrbanPopAgentStruct.H b/src/init/urbanpop/UrbanPopAgentStruct.H
similarity index 100%
rename from src/UrbanPopAgentStruct.H
rename to src/init/urbanpop/UrbanPopAgentStruct.H
diff --git a/src/UrbanPopData.H b/src/init/urbanpop/UrbanPopData.H
similarity index 98%
rename from src/UrbanPopData.H
rename to src/init/urbanpop/UrbanPopData.H
index 1ed3b201..338c81da 100644
--- a/src/UrbanPopData.H
+++ b/src/init/urbanpop/UrbanPopData.H
@@ -12,7 +12,7 @@
 
 #include "CaseData.H"
 #include "UrbanPopAgentStruct.H"
-#include "Utils.H"
+#include "RuntimeParams.H"
 
 struct AgentExtras {
     amrex::IntVect home_xy;
diff --git a/src/UrbanPopData.cpp b/src/init/urbanpop/UrbanPopData.cpp
similarity index 100%
rename from src/UrbanPopData.cpp
rename to src/init/urbanpop/UrbanPopData.cpp
diff --git a/src/InteractionModAirTravel.H b/src/interactions/InteractionModAirTravel.H
similarity index 100%
rename from src/InteractionModAirTravel.H
rename to src/interactions/InteractionModAirTravel.H
diff --git a/src/InteractionModHome.H b/src/interactions/InteractionModHome.H
similarity index 100%
rename from src/InteractionModHome.H
rename to src/interactions/InteractionModHome.H
diff --git a/src/InteractionModHomeNborhood.H b/src/interactions/InteractionModHomeNborhood.H
similarity index 100%
rename from src/InteractionModHomeNborhood.H
rename to src/interactions/InteractionModHomeNborhood.H
diff --git a/src/InteractionModSchool.H b/src/interactions/InteractionModSchool.H
similarity index 100%
rename from src/InteractionModSchool.H
rename to src/interactions/InteractionModSchool.H
diff --git a/src/InteractionModWork.H b/src/interactions/InteractionModWork.H
similarity index 100%
rename from src/InteractionModWork.H
rename to src/interactions/InteractionModWork.H
diff --git a/src/InteractionModWorkNborhood.H b/src/interactions/InteractionModWorkNborhood.H
similarity index 100%
rename from src/InteractionModWorkNborhood.H
rename to src/interactions/InteractionModWorkNborhood.H
diff --git a/src/InteractionModel.H b/src/interactions/InteractionModel.H
similarity index 98%
rename from src/InteractionModel.H
rename to src/interactions/InteractionModel.H
index a6f8a231..9045ca31 100644
--- a/src/InteractionModel.H
+++ b/src/interactions/InteractionModel.H
@@ -42,10 +42,10 @@ template <typename PCType,  /*!< agent container type */
 class InteractionModel {
   public:
     /*! \brief null constructor */
-    InteractionModel<PCType, PTDType, PType>(bool _fast_bin) : fast_bin(_fast_bin) {}
+    InteractionModel(bool _fast_bin) : fast_bin(_fast_bin) {}
 
     /*! \brief default destructor */
-    virtual ~InteractionModel<PCType, PTDType, PType>() = default;
+    virtual ~InteractionModel() = default;
 
     /*! \brief Interact agents for a model */
     virtual void interactAgents(PCType&, MultiFab&) = 0;
diff --git a/src/InteractionModelLibrary.H b/src/interactions/InteractionModelLibrary.H
similarity index 100%
rename from src/InteractionModelLibrary.H
rename to src/interactions/InteractionModelLibrary.H
diff --git a/src/IO.H b/src/io/IO.H
similarity index 100%
rename from src/IO.H
rename to src/io/IO.H
diff --git a/src/IO.cpp b/src/io/IO.cpp
similarity index 100%
rename from src/IO.cpp
rename to src/io/IO.cpp
diff --git a/src/main.cpp b/src/main.cpp
index 3b8a7bde..2037784b 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -16,8 +16,8 @@
 #include "DemographicData.H"
 #include "IO.H"
 #include "InitializeInfections.H"
+#include "RuntimeParams.H"
 #include "UrbanPopData.H"
-#include "Utils.H"
 
 #include "version.h"
 
diff --git a/src/AirTravelFlow.H b/src/travel/AirTravelFlow.H
similarity index 100%
rename from src/AirTravelFlow.H
rename to src/travel/AirTravelFlow.H
diff --git a/src/AirTravelFlow.cpp b/src/travel/AirTravelFlow.cpp
similarity index 100%
rename from src/AirTravelFlow.cpp
rename to src/travel/AirTravelFlow.cpp