reorganize source code into subdirectories (#689)

### Description The code used to be simple, but now it's not. I've reorganized all of the source code files under `src/` into subdirectories (one level only). Unfortunately, virtually every file had to be changed in order to update header include paths. No other changes were made to the code (other than file renaming). The new `src/` directory layout is as follows: ```console $ tree -d . . ├── chemistry ├── cooling ├── hydro ├── io ├── linear_advection ├── math ├── particles ├── problems │ ├── Advection │ ├── Advection2D │ ├── AdvectionSemiellipse │ ├── BinaryOrbitCIC │ ├── Cooling │ ├── FCQuantities │ ├── HydroBlast2D │ ├── HydroBlast3D │ ├── HydroContact │ ├── HydroHighMach │ ├── HydroKelvinHelmholz │ ├── HydroLeblanc │ ├── HydroQuirk │ ├── HydroRichtmeyerMeshkov │ ├── HydroShocktube │ ├── HydroShocktubeCMA │ ├── HydroShuOsher │ ├── HydroSMS │ ├── HydroVacuum │ ├── HydroWave │ ├── NSCBC │ ├── ODEIntegration │ ├── PassiveScalar │ ├── PopIII │ ├── PrimordialChem │ ├── RadBeam │ ├── RadForce │ ├── RadhydroBB │ ├── RadhydroPulse │ ├── RadhydroPulseDyn │ ├── RadhydroPulseGrey │ ├── RadhydroPulseMGconst │ ├── RadhydroPulseMGint │ ├── RadhydroShell │ ├── RadhydroShock │ ├── RadhydroShockCGS │ ├── RadhydroShockMultigroup │ ├── RadhydroUniformAdvecting │ ├── RadMarshak │ ├── RadMarshakAsymptotic │ ├── RadMarshakCGS │ ├── RadMarshakVaytet │ ├── RadMatterCoupling │ ├── RadMatterCouplingRSLA │ ├── RadPulse │ ├── RadShadow │ ├── RadStreaming │ ├── RadStreamingY │ ├── RadSuOlson │ ├── RadTophat │ ├── RadTube │ ├── RandomBlast │ ├── RayleighTaylor2D │ ├── RayleighTaylor3D │ ├── ShockCloud │ ├── SphericalCollapse │ └── StarCluster ├── radiation ├── turbulence └── util ``` ### Related issues N/A ### Checklist _Before this pull request can be reviewed, all of these tasks should be completed. Denote completed tasks with an `x` inside the square brackets `[ ]` in the Markdown source below:_ - [x] I have added a description (see above). - [x] I have added a link to any related issues see (see above). - [x] I have read the [Contributing Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md). - [ ] I have added tests for any new physics that this PR adds to the code. - [x] I have tested this PR on my local computer and all tests pass. - [x] I have manually triggered the GPU tests with the magic comment `/azp run`. - [x] I have requested a reviewer for this PR. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
quokka-astro · Jul 29, 2024 · c37cfb2 · c37cfb2
1 parent da1931a
commit c37cfb2
Show file tree

Hide file tree

Showing 248 changed files with 469 additions and 469 deletions.
diff --git a/src/AdvectionSimulation.cpp b/src/AdvectionSimulation.cpp
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -24,7 +24,7 @@ if(QUOKKA_OPENPMD)
   add_subdirectory(${QuokkaCode_SOURCE_DIR}/extern/openPMD-api ${QuokkaCode_BINARY_DIR}/openPMD-api)
   include_directories(${OpenPMD_INCLUDE_DIRS_RET})
   link_libraries(openPMD::openPMD)
-  set(openPMDSources "${CMAKE_CURRENT_SOURCE_DIR}/openPMD.cpp")
+  set(openPMDSources "${CMAKE_CURRENT_SOURCE_DIR}/io/openPMD.cpp")
   message(STATUS "WARNING: OpenPMD plotfiles are ENABLED. Face-centered variables will only be available as cell-centered averages in plotfiles!")
 else()
   set(openPMDSources "")
@@ -129,75 +129,16 @@ link_libraries(yaml-cpp::yaml-cpp)
 include(CTest)
 
 set (QuokkaSourcesNoEOS "${CMAKE_CURRENT_SOURCE_DIR}/main.cpp"
-                        "${CMAKE_CURRENT_SOURCE_DIR}/DiagBase.cpp" 
-                        "${CMAKE_CURRENT_SOURCE_DIR}/DiagFilter.cpp" 
-                        "${CMAKE_CURRENT_SOURCE_DIR}/DiagFramePlane.cpp" 
-                        "${CMAKE_CURRENT_SOURCE_DIR}/DiagPDF.cpp" 
-                        "${CMAKE_CURRENT_SOURCE_DIR}/GrackleLikeCooling.cpp" 
-                        "${CMAKE_CURRENT_SOURCE_DIR}/GrackleDataReader.cpp"
-                        "${CMAKE_CURRENT_SOURCE_DIR}/TabulatedCooling.cpp" 
-                        "${CMAKE_CURRENT_SOURCE_DIR}/CloudyDataReader.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/io/DiagBase.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/io/DiagFilter.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/io/DiagFramePlane.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/io/DiagPDF.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/cooling/GrackleLikeCooling.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/cooling/GrackleDataReader.cpp"
+                        "${CMAKE_CURRENT_SOURCE_DIR}/cooling/TabulatedCooling.cpp" 
+                        "${CMAKE_CURRENT_SOURCE_DIR}/cooling/CloudyDataReader.cpp" 
                         "${openPMDSources}")
 
 set (QuokkaObjSources "${QuokkaSourcesNoEOS}" "${gamma_law_sources}")
 
-add_subdirectory(Advection)
-add_subdirectory(Advection2D)
-add_subdirectory(AdvectionSemiellipse)
-
-add_subdirectory(HydroBlast2D)
-add_subdirectory(HydroBlast3D)
-add_subdirectory(HydroContact)
-add_subdirectory(HydroKelvinHelmholz)
-add_subdirectory(HydroLeblanc)
-add_subdirectory(HydroRichtmeyerMeshkov)
-add_subdirectory(HydroShocktube)
-add_subdirectory(HydroShocktubeCMA)
-add_subdirectory(HydroShuOsher)
-add_subdirectory(HydroSMS)
-add_subdirectory(HydroVacuum)
-add_subdirectory(HydroWave)
-add_subdirectory(HydroQuirk)
-add_subdirectory(HydroHighMach)
-add_subdirectory(RayleighTaylor2D)
-add_subdirectory(RayleighTaylor3D)
-add_subdirectory(RadBeam)
-add_subdirectory(RadForce)
-add_subdirectory(RadMarshak)
-add_subdirectory(RadMarshakCGS)
-add_subdirectory(RadMarshakAsymptotic)
-add_subdirectory(RadMarshakVaytet)
-add_subdirectory(RadMatterCoupling)
-add_subdirectory(RadMatterCouplingRSLA)
-add_subdirectory(RadPulse)
-add_subdirectory(RadShadow)
-add_subdirectory(RadStreaming)
-add_subdirectory(RadStreamingY)
-add_subdirectory(RadSuOlson)
-add_subdirectory(RadTophat)
-add_subdirectory(RadTube)
-
-add_subdirectory(RadhydroShell)
-add_subdirectory(RadhydroShock)
-add_subdirectory(RadhydroShockCGS)
-add_subdirectory(RadhydroShockMultigroup)
-add_subdirectory(RadhydroUniformAdvecting)
-add_subdirectory(RadhydroPulse)
-add_subdirectory(RadhydroPulseDyn)
-add_subdirectory(RadhydroPulseGrey)
-add_subdirectory(RadhydroPulseMGconst)
-add_subdirectory(RadhydroPulseMGint)
-add_subdirectory(RadhydroBB)
-
-add_subdirectory(BinaryOrbitCIC)
-add_subdirectory(Cooling)
-add_subdirectory(FCQuantities)
-add_subdirectory(NSCBC)
-add_subdirectory(ODEIntegration)
-add_subdirectory(PassiveScalar)
-add_subdirectory(RandomBlast)
-add_subdirectory(PrimordialChem)
-add_subdirectory(PopIII)
-add_subdirectory(ShockCloud)
-add_subdirectory(StarCluster)
-add_subdirectory(SphericalCollapse)
+add_subdirectory(problems)
diff --git a/src/RadhydroSimulation.hpp b/src/RadhydroSimulation.hpp
@@ -48,16 +48,16 @@
 #include <conduit_node.hpp>
 #endif
 
-#include "Chemistry.hpp"
-#include "GrackleLikeCooling.hpp"
 #include "SimulationData.hpp"
-#include "TabulatedCooling.hpp"
+#include "chemistry/Chemistry.hpp"
+#include "cooling/GrackleLikeCooling.hpp"
+#include "cooling/TabulatedCooling.hpp"
 #include "eos.H"
-#include "hydro_system.hpp"
+#include "hydro/hydro_system.hpp"
 #include "hyperbolic_system.hpp"
 #include "physics_info.hpp"
 #include "physics_numVars.hpp"
-#include "radiation_system.hpp"
+#include "radiation/radiation_system.hpp"
 #include "simulation.hpp"
 
 // Simulation class should be initialized only once per program (i.e., is a singleton)

diff --git a/src/Chemistry.cpp → src/chemistry/Chemistry.cpp b/src/Chemistry.cpp → src/chemistry/Chemistry.cpp
@@ -7,7 +7,7 @@
 /// \brief Implements methods for primordial chemistry using Microphysics
 ///
 
-#include "Chemistry.hpp"
+#include "chemistry/Chemistry.hpp"
 #include "burn_type.H"
 #include "burner.H"
 

diff --git a/src/Chemistry.hpp → src/chemistry/Chemistry.hpp b/src/Chemistry.hpp → src/chemistry/Chemistry.hpp
@@ -14,8 +14,8 @@
 #include "AMReX.H"
 #include "AMReX_GpuQualifiers.H"
 
-#include "hydro_system.hpp"
-#include "radiation_system.hpp"
+#include "hydro/hydro_system.hpp"
+#include "radiation/radiation_system.hpp"
 
 #ifdef PRIMORDIAL_CHEM
 #include "actual_eos_data.H"

diff --git a/src/CloudyDataReader.cpp → src/cooling/CloudyDataReader.cpp b/src/CloudyDataReader.cpp → src/cooling/CloudyDataReader.cpp
@@ -26,7 +26,7 @@
 #include "fmt/core.h"
 
 #include "CloudyDataReader.hpp"
-#include "FastMath.hpp"
+#include "math/FastMath.hpp"
 
 namespace quokka::TabulatedCooling
 {

diff --git a/src/CloudyDataReader.hpp → src/cooling/CloudyDataReader.hpp b/src/CloudyDataReader.hpp → src/cooling/CloudyDataReader.hpp
diff --git a/src/GrackleDataReader.cpp → src/cooling/GrackleDataReader.cpp b/src/GrackleDataReader.cpp → src/cooling/GrackleDataReader.cpp
@@ -23,8 +23,8 @@
 #include "AMReX_BLassert.H"
 #include "AMReX_Print.H"
 #include "AMReX_TableData.H"
-#include "FastMath.hpp"
 #include "fmt/core.h"
+#include "math/FastMath.hpp"
 
 namespace quokka::GrackleLikeCooling
 {

diff --git a/src/GrackleDataReader.hpp → src/cooling/GrackleDataReader.hpp b/src/GrackleDataReader.hpp → src/cooling/GrackleDataReader.hpp
diff --git a/src/GrackleLikeCooling.cpp → src/cooling/GrackleLikeCooling.cpp b/src/GrackleLikeCooling.cpp → src/cooling/GrackleLikeCooling.cpp
@@ -8,7 +8,7 @@
 /// tables.
 ///
 
-#include "GrackleLikeCooling.hpp"
+#include "cooling/GrackleLikeCooling.hpp"
 
 namespace quokka::GrackleLikeCooling
 {

diff --git a/src/GrackleLikeCooling.hpp → src/cooling/GrackleLikeCooling.hpp b/src/GrackleLikeCooling.hpp → src/cooling/GrackleLikeCooling.hpp
@@ -14,15 +14,15 @@
 #include "AMReX_GpuQualifiers.H"
 #include "AMReX_iMultiFab.H"
 
-#include "FastMath.hpp"
 #include "GrackleDataReader.hpp"
-#include "Interpolate2D.hpp"
-#include "ODEIntegrate.hpp"
 #include "fmt/core.h"
 #include "fundamental_constants.H"
-#include "hydro_system.hpp"
-#include "radiation_system.hpp"
-#include "root_finding.hpp"
+#include "hydro/hydro_system.hpp"
+#include "math/FastMath.hpp"
+#include "math/Interpolate2D.hpp"
+#include "math/ODEIntegrate.hpp"
+#include "math/root_finding.hpp"
+#include "radiation/radiation_system.hpp"
 
 namespace quokka::GrackleLikeCooling
 {

diff --git a/src/TabulatedCooling.cpp → src/cooling/TabulatedCooling.cpp b/src/TabulatedCooling.cpp → src/cooling/TabulatedCooling.cpp
@@ -8,7 +8,7 @@
 /// tables.
 ///
 
-#include "TabulatedCooling.hpp"
+#include "cooling/TabulatedCooling.hpp"
 #include "CloudyDataReader.hpp"
 
 namespace quokka::TabulatedCooling

diff --git a/src/TabulatedCooling.hpp → src/cooling/TabulatedCooling.hpp b/src/TabulatedCooling.hpp → src/cooling/TabulatedCooling.hpp
@@ -14,13 +14,13 @@
 #include "AMReX_iMultiFab.H"
 #include "fmt/core.h"
 
-#include "FastMath.hpp"
-#include "Interpolate2D.hpp"
-#include "ODEIntegrate.hpp"
 #include "fundamental_constants.H"
-#include "hydro_system.hpp"
-#include "radiation_system.hpp"
-#include "root_finding.hpp"
+#include "hydro/hydro_system.hpp"
+#include "math/FastMath.hpp"
+#include "math/Interpolate2D.hpp"
+#include "math/ODEIntegrate.hpp"
+#include "math/root_finding.hpp"
+#include "radiation/radiation_system.hpp"
 
 namespace quokka::TabulatedCooling
 {

diff --git a/src/EOS.hpp → src/hydro/EOS.hpp b/src/EOS.hpp → src/hydro/EOS.hpp
diff --git a/src/HLLC.hpp → src/hydro/HLLC.hpp b/src/HLLC.hpp → src/hydro/HLLC.hpp
@@ -6,10 +6,10 @@
 #include <AMReX.H>
 #include <AMReX_REAL.H>
 
-#include "ArrayView.hpp"
-#include "EOS.hpp"
-#include "HydroState.hpp"
-#include "valarray.hpp"
+#include "hydro/EOS.hpp"
+#include "hydro/HydroState.hpp"
+#include "util/ArrayView.hpp"
+#include "util/valarray.hpp"
 
 namespace quokka::Riemann
 {

diff --git a/src/HLLD.hpp → src/hydro/HLLD.hpp b/src/HLLD.hpp → src/hydro/HLLD.hpp
@@ -6,9 +6,9 @@
 #include <AMReX.H>
 #include <AMReX_REAL.H>
 
-#include "ArrayView.hpp"
-#include "HydroState.hpp"
-#include "valarray.hpp"
+#include "hydro/HydroState.hpp"
+#include "util/ArrayView.hpp"
+#include "util/valarray.hpp"
 
 namespace quokka::Riemann
 {

diff --git a/src/HydroState.hpp → src/hydro/HydroState.hpp b/src/HydroState.hpp → src/hydro/HydroState.hpp
diff --git a/src/LLF.hpp → src/hydro/LLF.hpp b/src/LLF.hpp → src/hydro/LLF.hpp
@@ -6,8 +6,8 @@
 #include <AMReX.H>
 #include <AMReX_REAL.H>
 
-#include "HydroState.hpp"
-#include "valarray.hpp"
+#include "hydro/HydroState.hpp"
+#include "util/valarray.hpp"
 
 namespace quokka::Riemann
 {

diff --git a/src/NSCBC_inflow.hpp → src/hydro/NSCBC_inflow.hpp b/src/NSCBC_inflow.hpp → src/hydro/NSCBC_inflow.hpp
@@ -12,9 +12,9 @@
 
 #include "AMReX_GpuQualifiers.H"
 #include "AMReX_REAL.H"
-#include "EOS.hpp"
-#include "hydro_system.hpp"
-#include "valarray.hpp"
+#include "hydro/EOS.hpp"
+#include "hydro/hydro_system.hpp"
+#include "util/valarray.hpp"
 
 namespace NSCBC
 {

diff --git a/src/NSCBC_outflow.hpp → src/hydro/NSCBC_outflow.hpp b/src/NSCBC_outflow.hpp → src/hydro/NSCBC_outflow.hpp
@@ -11,9 +11,9 @@
 
 #include "AMReX_GpuQualifiers.H"
 #include "AMReX_REAL.H"
-#include "EOS.hpp"
-#include "hydro_system.hpp"
-#include "valarray.hpp"
+#include "hydro/EOS.hpp"
+#include "hydro/hydro_system.hpp"
+#include "util/valarray.hpp"
 
 namespace NSCBC
 {

diff --git a/src/hydro_system.cpp → src/hydro/hydro_system.cpp b/src/hydro_system.cpp → src/hydro/hydro_system.cpp
@@ -7,4 +7,4 @@
 /// \brief Implements methods for solving the (1d) Euler equations.
 ///
 
-#include "hydro_system.hpp"
+#include "hydro/hydro_system.hpp"
diff --git a/src/hydro_system.hpp → src/hydro/hydro_system.hpp b/src/hydro_system.hpp → src/hydro/hydro_system.hpp
@@ -20,15 +20,15 @@
 #include "AMReX_iMultiFab.H"
 
 // internal headers
-#include "ArrayView.hpp"
-#include "EOS.hpp"
 #include "HLLC.hpp"
 #include "HLLD.hpp"
 #include "LLF.hpp"
+#include "hydro/EOS.hpp"
 #include "hyperbolic_system.hpp"
 #include "physics_info.hpp"
-#include "radiation_system.hpp"
-#include "valarray.hpp"
+#include "radiation/radiation_system.hpp"
+#include "util/ArrayView.hpp"
+#include "util/valarray.hpp"
 
 // Microphysics headers
 #include "extern_parameters.H"

diff --git a/src/mhd_system.cpp → src/hydro/mhd_system.cpp b/src/mhd_system.cpp → src/hydro/mhd_system.cpp
diff --git a/src/mhd_system.hpp → src/hydro/mhd_system.hpp b/src/mhd_system.hpp → src/hydro/mhd_system.hpp
diff --git a/src/hyperbolic_system.hpp b/src/hyperbolic_system.hpp
@@ -24,8 +24,8 @@
 #include "AMReX_SPACE.H"
 
 // internal headers
-#include "ArrayView.hpp"
-#include "math_impl.hpp"
+#include "math/math_impl.hpp"
+#include "util/ArrayView.hpp"
 
 // #define MULTIDIM_EXTREMA_CHECK
 

diff --git a/src/DiagBase.H → src/io/DiagBase.H b/src/DiagBase.H → src/io/DiagBase.H
diff --git a/src/DiagBase.cpp → src/io/DiagBase.cpp b/src/DiagBase.cpp → src/io/DiagBase.cpp
diff --git a/src/DiagFilter.H → src/io/DiagFilter.H b/src/DiagFilter.H → src/io/DiagFilter.H
diff --git a/src/DiagFilter.cpp → src/io/DiagFilter.cpp b/src/DiagFilter.cpp → src/io/DiagFilter.cpp
diff --git a/src/DiagFramePlane.H → src/io/DiagFramePlane.H b/src/DiagFramePlane.H → src/io/DiagFramePlane.H
diff --git a/src/DiagFramePlane.cpp → src/io/DiagFramePlane.cpp b/src/DiagFramePlane.cpp → src/io/DiagFramePlane.cpp
diff --git a/src/DiagPDF.H → src/io/DiagPDF.H b/src/DiagPDF.H → src/io/DiagPDF.H
diff --git a/src/DiagPDF.cpp → src/io/DiagPDF.cpp b/src/DiagPDF.cpp → src/io/DiagPDF.cpp
diff --git a/src/openPMD.cpp → src/io/openPMD.cpp b/src/openPMD.cpp → src/io/openPMD.cpp
diff --git a/src/openPMD.hpp → src/io/openPMD.hpp b/src/openPMD.hpp → src/io/openPMD.hpp
diff --git a/src/linear_advection/AdvectionSimulation.cpp b/src/linear_advection/AdvectionSimulation.cpp
@@ -0,0 +1 @@
+#include "linear_advection/AdvectionSimulation.hpp"
diff --git a/src/AdvectionSimulation.hpp → src/linear_advection/AdvectionSimulation.hpp b/src/AdvectionSimulation.hpp → src/linear_advection/AdvectionSimulation.hpp
@@ -23,9 +23,9 @@
 #include "AMReX_YAFluxRegister.H"
 #include <AMReX_FluxRegister.H>
 
-#include "ArrayView.hpp"
-#include "linear_advection.hpp"
+#include "linear_advection/linear_advection.hpp"
 #include "simulation.hpp"
+#include "util/ArrayView.hpp"
 
 // Simulation class should be initialized only once per program (i.e., is a singleton)
 template <typename problem_t> class AdvectionSimulation : public AMRSimulation<problem_t>

diff --git a/src/linear_advection.cpp → src/linear_advection/linear_advection.cpp b/src/linear_advection.cpp → src/linear_advection/linear_advection.cpp
@@ -7,4 +7,4 @@
 /// \brief Implements methods for solving a scalar linear advection equation.
 ///
 
-#include "linear_advection.hpp"
+#include "linear_advection/linear_advection.hpp"
diff --git a/src/linear_advection.hpp → src/linear_advection/linear_advection.hpp b/src/linear_advection.hpp → src/linear_advection/linear_advection.hpp
diff --git a/src/FastMath.hpp → src/math/FastMath.hpp b/src/FastMath.hpp → src/math/FastMath.hpp
diff --git a/src/Interpolate2D.cpp → src/math/Interpolate2D.cpp b/src/Interpolate2D.cpp → src/math/Interpolate2D.cpp
diff --git a/src/Interpolate2D.hpp → src/math/Interpolate2D.hpp b/src/Interpolate2D.hpp → src/math/Interpolate2D.hpp
diff --git a/src/ODEIntegrate.hpp → src/math/ODEIntegrate.hpp b/src/ODEIntegrate.hpp → src/math/ODEIntegrate.hpp
@@ -18,7 +18,7 @@
 #include "AMReX_GpuQualifiers.H"
 #include "AMReX_REAL.H"
 
-#include "valarray.hpp"
+#include "util/valarray.hpp"
 
 using Real = amrex::Real;
 

diff --git a/src/gauss.hpp → src/math/gauss.hpp b/src/gauss.hpp → src/math/gauss.hpp
diff --git a/src/interpolate.cpp → src/math/interpolate.cpp b/src/interpolate.cpp → src/math/interpolate.cpp
@@ -1,7 +1,7 @@
 #include <cassert>
 #include <cmath>
 
-#include "interpolate.hpp"
+#include "math/interpolate.hpp"
 
 #define LIKELY_IN_CACHE_SIZE 8
 

diff --git a/src/interpolate.hpp → src/math/interpolate.hpp b/src/interpolate.hpp → src/math/interpolate.hpp
diff --git a/src/math_impl.hpp → src/math/math_impl.hpp b/src/math_impl.hpp → src/math/math_impl.hpp
diff --git a/src/quadrature.hpp → src/math/quadrature.hpp b/src/quadrature.hpp → src/math/quadrature.hpp
diff --git a/src/root_finding.hpp → src/math/root_finding.hpp b/src/root_finding.hpp → src/math/root_finding.hpp
@@ -55,7 +55,7 @@
 
 #endif
 
-#include "math_impl.hpp"
+#include "math/math_impl.hpp"
 
 #ifdef BOOST_MATH_LOG_ROOT_ITERATIONS
 #define BOOST_MATH_LOGGER_INCLUDE <boost/math/tools/iteration_logger.hpp>

diff --git a/src/CICParticles.hpp → src/particles/CICParticles.hpp b/src/CICParticles.hpp → src/particles/CICParticles.hpp
diff --git a/src/Advection/CMakeLists.txt → src/problems/Advection/CMakeLists.txt b/src/Advection/CMakeLists.txt → src/problems/Advection/CMakeLists.txt
@@ -1,4 +1,4 @@
-add_executable(test_advection test_advection.cpp ../fextract.cpp ${QuokkaObjSources})
+add_executable(test_advection test_advection.cpp ../../util/fextract.cpp ${QuokkaObjSources})
 
 if(AMReX_GPU_BACKEND MATCHES "CUDA")
     setup_target_for_cuda_compilation(test_advection)

diff --git a/src/Advection/test_advection.cpp → src/problems/Advection/test_advection.cpp b/src/Advection/test_advection.cpp → src/problems/Advection/test_advection.cpp
@@ -19,9 +19,9 @@
 #include "AMReX_ParallelDescriptor.H"
 #include "AMReX_REAL.H"
 
-#include "AdvectionSimulation.hpp"
-#include "fextract.hpp"
+#include "linear_advection/AdvectionSimulation.hpp"
 #include "test_advection.hpp"
+#include "util/fextract.hpp"
 
 struct SawtoothProblem {
 };

diff --git a/src/Advection/test_advection.hpp → src/problems/Advection/test_advection.hpp b/src/Advection/test_advection.hpp → src/problems/Advection/test_advection.hpp
@@ -11,13 +11,13 @@
 
 // external headers
 #ifdef HAVE_PYTHON
-#include "matplotlibcpp.h"
+#include "util/matplotlibcpp.h"
 #endif
 #include <fmt/format.h>
 
 // internal headers
 
-#include "linear_advection.hpp"
+#include "linear_advection/linear_advection.hpp"
 
 // function definitions
 

diff --git a/src/Advection2D/CMakeLists.txt → src/problems/Advection2D/CMakeLists.txt b/src/Advection2D/CMakeLists.txt → src/problems/Advection2D/CMakeLists.txt