From 76a3a9dcaf24638e6615cdc61a4f500715da0201 Mon Sep 17 00:00:00 2001
From: Adam Smelko <adamsmelko1@gmail.com>
Date: Fri, 16 Jan 2026 10:20:05 +0000
Subject: [PATCH] fix: add biofvm into reactions_diffusion namespace

Fixes #91
---
 reactions-diffusion/biofvm/examples/diffuse.cpp              | 2 +-
 reactions-diffusion/biofvm/include/biofvm/agent.h            | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/agent_container.h  | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/agent_data.h       | 2 +-
 .../biofvm/include/biofvm/agent_data_generic_storage.h       | 4 ++--
 .../biofvm/include/biofvm/agent_generic_storage.h            | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/agent_interface.h  | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/bulk_functor.h     | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/mesh.h             | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/microenvironment.h | 4 ++--
 .../biofvm/include/biofvm/microenvironment_builder.h         | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/serializer.h       | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/solver.h           | 4 ++--
 reactions-diffusion/biofvm/include/biofvm/solver_registry.h  | 4 ++--
 .../biofvm/kernels/openmp_solver/examples/benchmark.cpp      | 4 ++--
 .../openmp_solver/include/openmp_solver/register_solver.h    | 2 +-
 .../biofvm/kernels/openmp_solver/src/bulk_solver.cpp         | 4 ++--
 .../biofvm/kernels/openmp_solver/src/bulk_solver.h           | 4 ++--
 .../biofvm/kernels/openmp_solver/src/cell_solver.cpp         | 4 ++--
 .../biofvm/kernels/openmp_solver/src/cell_solver.h           | 4 ++--
 .../biofvm/kernels/openmp_solver/src/diffusion_solver.cpp    | 2 +-
 .../biofvm/kernels/openmp_solver/src/diffusion_solver.h      | 4 ++--
 .../biofvm/kernels/openmp_solver/src/dirichlet_solver.cpp    | 4 ++--
 .../biofvm/kernels/openmp_solver/src/dirichlet_solver.h      | 4 ++--
 .../biofvm/kernels/openmp_solver/src/openmp_solver.cpp       | 2 +-
 .../biofvm/kernels/openmp_solver/src/openmp_solver.h         | 4 ++--
 .../biofvm/kernels/openmp_solver/src/problem.h               | 4 ++--
 .../biofvm/kernels/openmp_solver/src/register_solver.cpp     | 5 +++--
 .../biofvm/kernels/openmp_solver/tests/test_bulk_solver.cpp  | 4 ++--
 .../biofvm/kernels/openmp_solver/tests/test_cell_solver.cpp  | 4 ++--
 .../kernels/openmp_solver/tests/test_diffusion_solver.cpp    | 4 ++--
 .../kernels/openmp_solver/tests/test_dirichlet_solver.cpp    | 4 ++--
 .../biofvm/kernels/thrust_solver/examples/benchmark.cpp      | 4 ++--
 .../thrust_solver/include/thrust_solver/register_solver.h    | 4 ++--
 .../biofvm/kernels/thrust_solver/src/bulk_functor.h          | 4 ++--
 .../biofvm/kernels/thrust_solver/src/bulk_solver.cpp         | 2 +-
 .../biofvm/kernels/thrust_solver/src/bulk_solver.h           | 4 ++--
 .../biofvm/kernels/thrust_solver/src/cell_solver.cpp         | 4 ++--
 .../biofvm/kernels/thrust_solver/src/cell_solver.h           | 4 ++--
 .../biofvm/kernels/thrust_solver/src/data_manager.cpp        | 2 +-
 .../biofvm/kernels/thrust_solver/src/data_manager.h          | 4 ++--
 .../biofvm/kernels/thrust_solver/src/diffusion_solver.cpp    | 2 +-
 .../biofvm/kernels/thrust_solver/src/diffusion_solver.h      | 4 ++--
 .../biofvm/kernels/thrust_solver/src/dirichlet_solver.cpp    | 4 ++--
 .../biofvm/kernels/thrust_solver/src/dirichlet_solver.h      | 4 ++--
 .../biofvm/kernels/thrust_solver/src/register_solver.cpp     | 4 ++--
 .../biofvm/kernels/thrust_solver/src/thrust_solver.cpp       | 2 +-
 .../biofvm/kernels/thrust_solver/src/thrust_solver.h         | 4 ++--
 .../biofvm/kernels/thrust_solver/tests/test_bulk_solver.cpp  | 4 ++--
 .../biofvm/kernels/thrust_solver/tests/test_cell_solver.cpp  | 4 ++--
 .../kernels/thrust_solver/tests/test_diffusion_solver.cpp    | 4 ++--
 .../kernels/thrust_solver/tests/test_dirichlet_solver.cpp    | 4 ++--
 reactions-diffusion/biofvm/src/mesh.cpp                      | 2 +-
 reactions-diffusion/biofvm/src/microenvironment.cpp          | 2 +-
 reactions-diffusion/biofvm/src/microenvironment_builder.cpp  | 2 +-
 reactions-diffusion/biofvm/src/solver_registry.cpp           | 2 +-
 reactions-diffusion/biofvm/src/vtk_agents_serializer.cpp     | 2 +-
 reactions-diffusion/biofvm/src/vtk_agents_serializer.h       | 4 ++--
 reactions-diffusion/biofvm/src/vtk_serializer.cpp            | 2 +-
 reactions-diffusion/biofvm/src/vtk_serializer.h              | 4 ++--
 reactions-diffusion/biofvm/src/vtk_serializer_base.cpp       | 2 +-
 reactions-diffusion/biofvm/src/vtk_serializer_base.h         | 4 ++--
 reactions-diffusion/biofvm/tests/test_agent.cpp              | 2 +-
 reactions-diffusion/biofvm/tests/test_agent_container.cpp    | 2 +-
 reactions-diffusion/biofvm/tests/test_agent_data.cpp         | 2 +-
 reactions-diffusion/biofvm/tests/test_config_reader.cpp      | 2 +-
 .../biofvm/tests/test_dirichlet_modification.cpp             | 2 +-
 .../biofvm/tests/test_microenvironment_builder.cpp           | 2 +-
 reactions-diffusion/biofvm/tests/test_solver_registry.cpp    | 2 +-
 .../biofvm/tests/test_vtk_agents_serializer.cpp              | 2 +-
 reactions-diffusion/biofvm/tests/test_vtk_serializer.cpp     | 2 +-
 71 files changed, 118 insertions(+), 117 deletions(-)

diff --git a/reactions-diffusion/biofvm/examples/diffuse.cpp b/reactions-diffusion/biofvm/examples/diffuse.cpp
index f45bced7..e591b62d 100644
--- a/reactions-diffusion/biofvm/examples/diffuse.cpp
+++ b/reactions-diffusion/biofvm/examples/diffuse.cpp
@@ -10,7 +10,7 @@
 #include <biofvm/microenvironment.h>
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 int main()
 {
diff --git a/reactions-diffusion/biofvm/include/biofvm/agent.h b/reactions-diffusion/biofvm/include/biofvm/agent.h
index 35b9e6c5..67e3d32d 100644
--- a/reactions-diffusion/biofvm/include/biofvm/agent.h
+++ b/reactions-diffusion/biofvm/include/biofvm/agent.h
@@ -3,8 +3,8 @@
 #include "agent_data.h"
 #include "agent_generic_storage.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using agent = agent_generic_storage<base_agent_data, agent_data>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/agent_container.h b/reactions-diffusion/biofvm/include/biofvm/agent_container.h
index e1dac8b7..be55c8e8 100644
--- a/reactions-diffusion/biofvm/include/biofvm/agent_container.h
+++ b/reactions-diffusion/biofvm/include/biofvm/agent_container.h
@@ -5,10 +5,10 @@
 
 #include "agent.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using agent_container = physicore::generic_agent_and_data_container<base_agent, agent>;
 using agent_container_interface = physicore::generic_agent_interface_container<agent_interface>;
 using container_ptr = std::shared_ptr<agent_container_interface>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/agent_data.h b/reactions-diffusion/biofvm/include/biofvm/agent_data.h
index 71de0da7..e93b9634 100644
--- a/reactions-diffusion/biofvm/include/biofvm/agent_data.h
+++ b/reactions-diffusion/biofvm/include/biofvm/agent_data.h
@@ -2,7 +2,7 @@
 
 #include "agent_data_generic_storage.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using agent_data = agent_data_generic_storage<std::vector>;
 
diff --git a/reactions-diffusion/biofvm/include/biofvm/agent_data_generic_storage.h b/reactions-diffusion/biofvm/include/biofvm/agent_data_generic_storage.h
index 9aa67b08..295157ee 100644
--- a/reactions-diffusion/biofvm/include/biofvm/agent_data_generic_storage.h
+++ b/reactions-diffusion/biofvm/include/biofvm/agent_data_generic_storage.h
@@ -5,7 +5,7 @@
 #include <common/base_agent_data.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 template <template <typename...> typename ContainerType = std::vector>
 struct agent_data_generic_storage
@@ -109,4 +109,4 @@ void agent_data_generic_storage<ContainerType>::remove_at(index_t position)
 	is_active.resize(agents_count);
 }
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/agent_generic_storage.h b/reactions-diffusion/biofvm/include/biofvm/agent_generic_storage.h
index d2f51378..dd954dcb 100644
--- a/reactions-diffusion/biofvm/include/biofvm/agent_generic_storage.h
+++ b/reactions-diffusion/biofvm/include/biofvm/agent_generic_storage.h
@@ -5,7 +5,7 @@
 
 #include "agent_interface.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 #ifdef _MSC_VER
 	#pragma warning(push)
@@ -79,4 +79,4 @@ class agent_generic_storage : public physicore::base_agent_generic_storage<BaseA
 	#pragma warning(pop)
 #endif
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/agent_interface.h b/reactions-diffusion/biofvm/include/biofvm/agent_interface.h
index 7450d82d..1bad467e 100644
--- a/reactions-diffusion/biofvm/include/biofvm/agent_interface.h
+++ b/reactions-diffusion/biofvm/include/biofvm/agent_interface.h
@@ -3,7 +3,7 @@
 #include <common/base_agent_interface.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class agent_interface : public virtual base_agent_interface
 {
@@ -27,4 +27,4 @@ class agent_interface : public virtual base_agent_interface
 	virtual uint8_t& is_active() = 0;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/bulk_functor.h b/reactions-diffusion/biofvm/include/biofvm/bulk_functor.h
index b257fa3f..b699956d 100644
--- a/reactions-diffusion/biofvm/include/biofvm/bulk_functor.h
+++ b/reactions-diffusion/biofvm/include/biofvm/bulk_functor.h
@@ -3,7 +3,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 struct BIOFVM_EXPORT bulk_functor
 {
@@ -13,4 +13,4 @@ struct BIOFVM_EXPORT bulk_functor
 	virtual ~bulk_functor() = default;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/mesh.h b/reactions-diffusion/biofvm/include/biofvm/mesh.h
index 43e16e36..4043cc0f 100644
--- a/reactions-diffusion/biofvm/include/biofvm/mesh.h
+++ b/reactions-diffusion/biofvm/include/biofvm/mesh.h
@@ -6,7 +6,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 struct BIOFVM_EXPORT cartesian_mesh
 {
@@ -31,4 +31,4 @@ struct BIOFVM_EXPORT cartesian_mesh
 	std::array<real_t, 3> voxel_center(std::array<index_t, 3> position) const;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/microenvironment.h b/reactions-diffusion/biofvm/include/biofvm/microenvironment.h
index d9002d00..b6a86207 100644
--- a/reactions-diffusion/biofvm/include/biofvm/microenvironment.h
+++ b/reactions-diffusion/biofvm/include/biofvm/microenvironment.h
@@ -15,7 +15,7 @@
 #include "serializer.h"
 #include "solver.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class BIOFVM_EXPORT microenvironment : public timestep_executor
 {
@@ -81,4 +81,4 @@ class BIOFVM_EXPORT microenvironment : public timestep_executor
 	bool compute_internalized_substrates = false;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/microenvironment_builder.h b/reactions-diffusion/biofvm/include/biofvm/microenvironment_builder.h
index 9476e5b1..8a86f77a 100644
--- a/reactions-diffusion/biofvm/include/biofvm/microenvironment_builder.h
+++ b/reactions-diffusion/biofvm/include/biofvm/microenvironment_builder.h
@@ -9,7 +9,7 @@
 #include "mesh.h"
 #include "microenvironment.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class BIOFVM_EXPORT microenvironment_builder
 {
@@ -77,4 +77,4 @@ class BIOFVM_EXPORT microenvironment_builder
 	std::unique_ptr<microenvironment> build();
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/serializer.h b/reactions-diffusion/biofvm/include/biofvm/serializer.h
index ac1e247c..5fca7367 100644
--- a/reactions-diffusion/biofvm/include/biofvm/serializer.h
+++ b/reactions-diffusion/biofvm/include/biofvm/serializer.h
@@ -4,7 +4,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class microenvironment;
 
@@ -18,4 +18,4 @@ class BIOFVM_EXPORT serializer
 
 using serializer_ptr = std::unique_ptr<serializer>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/solver.h b/reactions-diffusion/biofvm/include/biofvm/solver.h
index e3ad274c..0b375b6b 100644
--- a/reactions-diffusion/biofvm/include/biofvm/solver.h
+++ b/reactions-diffusion/biofvm/include/biofvm/solver.h
@@ -5,7 +5,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class microenvironment;
 
@@ -38,4 +38,4 @@ class BIOFVM_EXPORT solver
 
 using solver_ptr = std::unique_ptr<solver>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/include/biofvm/solver_registry.h b/reactions-diffusion/biofvm/include/biofvm/solver_registry.h
index 69bb5433..c1842d9b 100644
--- a/reactions-diffusion/biofvm/include/biofvm/solver_registry.h
+++ b/reactions-diffusion/biofvm/include/biofvm/solver_registry.h
@@ -8,7 +8,7 @@
 
 #include "solver.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class solver_registry
 {
@@ -38,4 +38,4 @@ struct registry_adder
 	}
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/examples/benchmark.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/examples/benchmark.cpp
index fce0b94f..9c1b6116 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/examples/benchmark.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/examples/benchmark.cpp
@@ -10,8 +10,8 @@
 #include "dirichlet_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 void make_agents(microenvironment& m, index_t count, bool conflict)
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/include/openmp_solver/register_solver.h b/reactions-diffusion/biofvm/kernels/openmp_solver/include/openmp_solver/register_solver.h
index ff16bcd4..d6962c4f 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/include/openmp_solver/register_solver.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/include/openmp_solver/register_solver.h
@@ -1,6 +1,6 @@
 #pragma once
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 void attach_to_registry();
 
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.cpp
index c4a67eba..9efd1d9c 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.cpp
@@ -3,8 +3,8 @@
 #include <noarr/structures_extended.hpp>
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 void bulk_solver::initialize(microenvironment& m) { fnc = std::move(m.bulk_fnc); }
 
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.h b/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.h
index 8a3ed62f..42542e72 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.h
@@ -15,7 +15,7 @@ D = (D + dt*S*T)/(1 + dt*(U+S))
 where D is a voxel substrate density vector
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class bulk_solver
 {
@@ -27,4 +27,4 @@ class bulk_solver
 	void solve(const microenvironment& m, diffusion_solver& d_solver);
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.cpp
index 3e290150..312a1de9 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.cpp
@@ -5,8 +5,8 @@
 #include <noarr/structures_extended.hpp>
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 
 namespace {
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.h b/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.h
index edddce3c..f8795fd5 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.h
@@ -38,7 +38,7 @@ F = fraction released at death
 D = D + I*F/v
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class cell_solver : private generic_agent_solver<agent>
 {
@@ -68,4 +68,4 @@ class cell_solver : private generic_agent_solver<agent>
 	void release_internalized_substrates(const microenvironment& m, diffusion_solver& d_solver, index_t index);
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.cpp
index 1b412dbf..b2d55c4a 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.cpp
@@ -8,7 +8,7 @@
 #include "solver_utils.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 auto get_diagonal_layout(const problem_t& problem, index_t n)
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.h b/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.h
index f4a7176d..fbf452fc 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.h
@@ -39,7 +39,7 @@ d_i'' == (d_i' + c_i*d_(i+1)'')*b_i'                          n >  i >= 1
 y/z dimensions are solved alongside tiled xs dimension
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class diffusion_solver
 {
@@ -92,4 +92,4 @@ class diffusion_solver
 	void solve();
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.cpp
index 3eba1c8f..9690b54f 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.cpp
@@ -4,8 +4,8 @@
 #include "omp_helper.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 auto fix_dims(const index_t* voxel_index, index_t dims)
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.h b/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.h
index 659f96b1..e07953a2 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.h
@@ -12,7 +12,7 @@ m.dirichlet_conditions - array of bools specifying if a substrate of a dirichlet
 m.dirichlet_values - array of dirichlet values for each substrate with a dirichlet condition
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class dirichlet_solver
 {
@@ -20,4 +20,4 @@ class dirichlet_solver
 	static void solve(microenvironment& m, diffusion_solver& d_solver);
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.cpp
index 173091a3..ff2b3d57 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.cpp
@@ -3,7 +3,7 @@
 #include "dirichlet_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 void openmp_solver::initialize(biofvm::microenvironment& m)
 {
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.h b/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.h
index 92958616..7c5fb356 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.h
@@ -6,7 +6,7 @@
 #include "cell_solver.h"
 #include "diffusion_solver.h"
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class openmp_solver : public solver
 {
@@ -26,4 +26,4 @@ class openmp_solver : public solver
 	void recompute_positional_data(microenvironment& m) override;
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/problem.h b/reactions-diffusion/biofvm/kernels/openmp_solver/src/problem.h
index a7cb26a7..f04680e7 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/problem.h
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/problem.h
@@ -4,7 +4,7 @@
 
 #include <biofvm/microenvironment.h>
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 struct problem_t
 {
@@ -46,4 +46,4 @@ struct problem_t
 	}
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/src/register_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/src/register_solver.cpp
index 97b34f6f..78e5071c 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/src/register_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/src/register_solver.cpp
@@ -4,7 +4,8 @@
 
 #include "openmp_solver.h"
 
-void physicore::biofvm::kernels::openmp_solver::attach_to_registry()
+void physicore::reactions_diffusion::biofvm::kernels::openmp_solver::attach_to_registry()
 {
-	static const physicore::biofvm::registry_adder<openmp_solver> openmp_solver_adder("openmp_solver");
+	static const physicore::reactions_diffusion::biofvm::registry_adder<openmp_solver> openmp_solver_adder(
+		"openmp_solver");
 }
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_bulk_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_bulk_solver.cpp
index f0b336a0..41c36580 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_bulk_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_bulk_solver.cpp
@@ -6,9 +6,9 @@
 #include "diffusion_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_cell_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_cell_solver.cpp
index ab38ae7b..09b96543 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_cell_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_cell_solver.cpp
@@ -8,9 +8,9 @@
 #include "diffusion_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh, bool compute_interalized)
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_diffusion_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_diffusion_solver.cpp
index 68d81e8b..9bb0ca3c 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_diffusion_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_diffusion_solver.cpp
@@ -4,9 +4,9 @@
 #include "diffusion_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)
diff --git a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_dirichlet_solver.cpp b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_dirichlet_solver.cpp
index 1a48c4b5..9844416e 100644
--- a/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_dirichlet_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_dirichlet_solver.cpp
@@ -7,9 +7,9 @@
 #include "dirichlet_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/examples/benchmark.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/examples/benchmark.cpp
index 0e631fc9..0da3ba8b 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/examples/benchmark.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/examples/benchmark.cpp
@@ -10,8 +10,8 @@
 #include "namespace_config.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 void make_agents(microenvironment& m, index_t count, bool conflict)
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/include/thrust_solver/register_solver.h b/reactions-diffusion/biofvm/kernels/thrust_solver/include/thrust_solver/register_solver.h
index a5bbae17..d0a4a152 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/include/thrust_solver/register_solver.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/include/thrust_solver/register_solver.h
@@ -1,10 +1,10 @@
 #pragma once
 
 // Forward declarations for both TBB and CUDA thrust solver backends
-namespace physicore::biofvm::kernels::tbb_thrust_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::tbb_thrust_solver {
 void attach_to_registry();
 }
 
-namespace physicore::biofvm::kernels::cuda_thrust_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::cuda_thrust_solver {
 void attach_to_registry();
 }
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_functor.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_functor.h
index 70230470..733be7f5 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_functor.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_functor.h
@@ -3,7 +3,7 @@
 #include "data_manager.h"
 #include "namespace_config.h"
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 struct device_bulk_functor
 {
@@ -13,4 +13,4 @@ struct device_bulk_functor
 	PHYSICORE_THRUST_DEVICE_FN virtual ~device_bulk_functor() = default;
 };
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.cpp
index 60753963..d5c35cc5 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.cpp
@@ -9,7 +9,7 @@
 #include "namespace_config.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 template <typename density_layout_t>
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.h
index 271dc4b4..28c6563f 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/bulk_solver.h
@@ -18,7 +18,7 @@ D = (D + dt*S*T)/(1 + dt*(U+S))
 where D is a voxel substrate density vector
 */
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 class bulk_solver
 {
@@ -36,4 +36,4 @@ class bulk_solver
 	~bulk_solver();
 };
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.cpp
index 0c6f086b..d8856755 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.cpp
@@ -19,8 +19,8 @@
 #endif
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 constexpr index_t no_ballot = std::numeric_limits<index_t>::max();
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.h
index 50a74008..97918d42 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/cell_solver.h
@@ -36,7 +36,7 @@ F = fraction released at death
 D = D + I*F/v
 */
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 class cell_solver
 {
@@ -75,4 +75,4 @@ class cell_solver
 	~cell_solver();
 };
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.cpp
index 5cc4df26..99565972 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.cpp
@@ -6,7 +6,7 @@
 #include "namespace_config.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 void data_manager::initialize(const microenvironment& m, diffusion_solver& d_solver)
 {
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.h
index 0144d5bc..f44b1530 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/data_manager.h
@@ -19,7 +19,7 @@
 	#define PHYSICORE_THRUST_STD std
 #endif
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 class diffusion_solver;
 
@@ -74,4 +74,4 @@ class data_manager : private generic_agent_solver<agent>
 };
 
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.cpp
index b17dc858..ea95422e 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.cpp
@@ -11,7 +11,7 @@
 #include "namespace_config.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.h
index 963c91d9..901080a8 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/diffusion_solver.h
@@ -30,7 +30,7 @@ d_n'' == d_n'/b_n'
 d_i'' == (d_i' - c_i*d_(i+1)'')*b_i'                          n >  i >= 1
 */
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 class diffusion_solver
 {
@@ -81,4 +81,4 @@ class diffusion_solver
 	~diffusion_solver();
 };
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.cpp
index 0c96d9c3..ff2fd9cb 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.cpp
@@ -6,8 +6,8 @@
 #include "namespace_config.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 constexpr auto fix_dims(const index_t* voxel_index, index_t dims)
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.h
index 86ff0508..faf88597 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/dirichlet_solver.h
@@ -15,7 +15,7 @@ m.dirichlet_conditions - array of bools specifying if a substrate of a dirichlet
 m.dirichlet_values - array of dirichlet values for each substrate with a dirichlet condition
 */
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 class dirichlet_solver
 {
@@ -33,4 +33,4 @@ class dirichlet_solver
 	void solve(microenvironment& m, diffusion_solver& d_solver);
 };
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/register_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/register_solver.cpp
index 16f4352e..54c38d78 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/register_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/register_solver.cpp
@@ -5,8 +5,8 @@
 #include "namespace_config.h"
 #include "thrust_solver.h"
 
-void physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE::attach_to_registry()
+void physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE::attach_to_registry()
 {
-	static const physicore::biofvm::registry_adder<thrust_solver> thrust_solver_adder(
+	static const physicore::reactions_diffusion::biofvm::registry_adder<thrust_solver> thrust_solver_adder(
 		PHYSICORE_THRUST_SOLVER_REGISTRY_NAME);
 }
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.cpp
index bc25117e..0fda1739 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.cpp
@@ -2,7 +2,7 @@
 
 #include "namespace_config.h"
 using namespace physicore;
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 void thrust_solver::initialize(biofvm::microenvironment& m)
 {
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.h b/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.h
index 0a8adad6..69095de0 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.h
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/src/thrust_solver.h
@@ -9,7 +9,7 @@
 #include "dirichlet_solver.h"
 #include "namespace_config.h"
 
-namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
+namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE {
 
 class thrust_solver : public solver
 {
@@ -34,4 +34,4 @@ class thrust_solver : public solver
 	void recompute_positional_data(microenvironment& m) override;
 };
 
-} // namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
+} // namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_bulk_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_bulk_solver.cpp
index 39c4e34b..82634d3c 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_bulk_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_bulk_solver.cpp
@@ -15,9 +15,9 @@
 #endif
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_cell_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_cell_solver.cpp
index 7cf202bc..6ff426e9 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_cell_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_cell_solver.cpp
@@ -17,9 +17,9 @@
 #endif
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh, bool compute_interalized)
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_diffusion_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_diffusion_solver.cpp
index 062d6d6b..dbb6947f 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_diffusion_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_diffusion_solver.cpp
@@ -11,9 +11,9 @@
 #endif
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)
diff --git a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_dirichlet_solver.cpp b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_dirichlet_solver.cpp
index 863003fc..6a28e249 100644
--- a/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_dirichlet_solver.cpp
+++ b/reactions-diffusion/biofvm/kernels/thrust_solver/tests/test_dirichlet_solver.cpp
@@ -14,9 +14,9 @@
 #endif
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
+using namespace physicore::reactions_diffusion::biofvm::kernels::PHYSICORE_THRUST_SOLVER_NAMESPACE;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)
diff --git a/reactions-diffusion/biofvm/src/mesh.cpp b/reactions-diffusion/biofvm/src/mesh.cpp
index a6d1fc3c..ca37aa7f 100644
--- a/reactions-diffusion/biofvm/src/mesh.cpp
+++ b/reactions-diffusion/biofvm/src/mesh.cpp
@@ -3,7 +3,7 @@
 #include <cassert>
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 cartesian_mesh::cartesian_mesh(index_t dims, std::array<sindex_t, 3> bounding_box_mins,
 							   std::array<sindex_t, 3> bounding_box_maxs, std::array<index_t, 3> voxel_shape)
diff --git a/reactions-diffusion/biofvm/src/microenvironment.cpp b/reactions-diffusion/biofvm/src/microenvironment.cpp
index df85b2ae..a4893380 100644
--- a/reactions-diffusion/biofvm/src/microenvironment.cpp
+++ b/reactions-diffusion/biofvm/src/microenvironment.cpp
@@ -9,7 +9,7 @@
 #include "microenvironment_builder.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 microenvironment::microenvironment(const cartesian_mesh& mesh, index_t substrates_count, real_t timestep)
 	: diffusion_timestep(timestep), mesh(mesh), substrates_count(substrates_count)
diff --git a/reactions-diffusion/biofvm/src/microenvironment_builder.cpp b/reactions-diffusion/biofvm/src/microenvironment_builder.cpp
index 498f92e7..c433660e 100644
--- a/reactions-diffusion/biofvm/src/microenvironment_builder.cpp
+++ b/reactions-diffusion/biofvm/src/microenvironment_builder.cpp
@@ -8,7 +8,7 @@
 #include "vtk_agents_serializer.h"
 #include "vtk_serializer.h"
 
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 using namespace physicore;
 
 void microenvironment_builder::set_name(std::string_view name_) { this->name = name_; }
diff --git a/reactions-diffusion/biofvm/src/solver_registry.cpp b/reactions-diffusion/biofvm/src/solver_registry.cpp
index 99a6be20..6d728f28 100644
--- a/reactions-diffusion/biofvm/src/solver_registry.cpp
+++ b/reactions-diffusion/biofvm/src/solver_registry.cpp
@@ -8,7 +8,7 @@
 	#include "thrust_solver/register_solver.h"
 #endif
 
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 bool solver_registry::register_factory(std::string solver_name, solver_factory_func_t&& f)
 {
diff --git a/reactions-diffusion/biofvm/src/vtk_agents_serializer.cpp b/reactions-diffusion/biofvm/src/vtk_agents_serializer.cpp
index c6a0d8bb..d139d688 100644
--- a/reactions-diffusion/biofvm/src/vtk_agents_serializer.cpp
+++ b/reactions-diffusion/biofvm/src/vtk_agents_serializer.cpp
@@ -12,7 +12,7 @@
 #include "agent_container.h"
 #include "microenvironment.h"
 
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 vtk_agents_serializer::vtk_agents_serializer(std::string_view output_dir, const microenvironment& m)
 	: vtk_serializer_base(output_dir, "vtk_agents", "agents.pvd"), substrate_count(m.substrates_count)
diff --git a/reactions-diffusion/biofvm/src/vtk_agents_serializer.h b/reactions-diffusion/biofvm/src/vtk_agents_serializer.h
index 43397f36..ab8a49d5 100644
--- a/reactions-diffusion/biofvm/src/vtk_agents_serializer.h
+++ b/reactions-diffusion/biofvm/src/vtk_agents_serializer.h
@@ -12,7 +12,7 @@
 #include "serializer.h"
 #include "vtk_serializer_base.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class vtk_agents_serializer : public vtk_serializer_base, public serializer, private generic_agent_solver<agent>
 {
@@ -36,4 +36,4 @@ class vtk_agents_serializer : public vtk_serializer_base, public serializer, pri
 	void serialize(const microenvironment& m, real_t current_time) override;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/src/vtk_serializer.cpp b/reactions-diffusion/biofvm/src/vtk_serializer.cpp
index 248ef742..daf5c013 100644
--- a/reactions-diffusion/biofvm/src/vtk_serializer.cpp
+++ b/reactions-diffusion/biofvm/src/vtk_serializer.cpp
@@ -9,7 +9,7 @@
 
 #include "microenvironment.h"
 
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 vtk_serializer::vtk_serializer(std::string_view output_dir, microenvironment& m)
 	: vtk_serializer_base(output_dir, "vtk_microenvironment", "microenvironment.pvd")
diff --git a/reactions-diffusion/biofvm/src/vtk_serializer.h b/reactions-diffusion/biofvm/src/vtk_serializer.h
index b08c67e6..1921f4af 100644
--- a/reactions-diffusion/biofvm/src/vtk_serializer.h
+++ b/reactions-diffusion/biofvm/src/vtk_serializer.h
@@ -10,7 +10,7 @@
 #include "serializer.h"
 #include "vtk_serializer_base.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class vtk_serializer : public vtk_serializer_base, public serializer
 {
@@ -24,4 +24,4 @@ class vtk_serializer : public vtk_serializer_base, public serializer
 	void serialize(const microenvironment& m, real_t current_time) override;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/src/vtk_serializer_base.cpp b/reactions-diffusion/biofvm/src/vtk_serializer_base.cpp
index 6ad384bb..3632fef7 100644
--- a/reactions-diffusion/biofvm/src/vtk_serializer_base.cpp
+++ b/reactions-diffusion/biofvm/src/vtk_serializer_base.cpp
@@ -3,7 +3,7 @@
 #include <filesystem>
 #include <fstream>
 
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 vtk_serializer_base::vtk_serializer_base(std::string_view output_dir, std::string_view vtks_dir_name,
 										 std::string_view pvd_file_name)
diff --git a/reactions-diffusion/biofvm/src/vtk_serializer_base.h b/reactions-diffusion/biofvm/src/vtk_serializer_base.h
index 25ffe77c..efc2d15e 100644
--- a/reactions-diffusion/biofvm/src/vtk_serializer_base.h
+++ b/reactions-diffusion/biofvm/src/vtk_serializer_base.h
@@ -8,7 +8,7 @@
 
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using vtkRealArray = std::conditional_t<std::is_same_v<real_t, float>, vtkFloatArray, vtkDoubleArray>;
 
@@ -28,4 +28,4 @@ class vtk_serializer_base
 	vtk_serializer_base(std::string_view output_dir, std::string_view vtks_dir_name, std::string_view pvd_file_name);
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm
diff --git a/reactions-diffusion/biofvm/tests/test_agent.cpp b/reactions-diffusion/biofvm/tests/test_agent.cpp
index 02b59373..2b24486b 100644
--- a/reactions-diffusion/biofvm/tests/test_agent.cpp
+++ b/reactions-diffusion/biofvm/tests/test_agent.cpp
@@ -5,7 +5,7 @@
 #include "agent_data.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 class AgentTest : public ::testing::Test
 {
diff --git a/reactions-diffusion/biofvm/tests/test_agent_container.cpp b/reactions-diffusion/biofvm/tests/test_agent_container.cpp
index b18ad1e5..0b132290 100644
--- a/reactions-diffusion/biofvm/tests/test_agent_container.cpp
+++ b/reactions-diffusion/biofvm/tests/test_agent_container.cpp
@@ -4,7 +4,7 @@
 #include "agent_container.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 namespace {
 agent_container make_agent_container()
diff --git a/reactions-diffusion/biofvm/tests/test_agent_data.cpp b/reactions-diffusion/biofvm/tests/test_agent_data.cpp
index ac5816b7..8c644170 100644
--- a/reactions-diffusion/biofvm/tests/test_agent_data.cpp
+++ b/reactions-diffusion/biofvm/tests/test_agent_data.cpp
@@ -3,7 +3,7 @@
 
 #include "agent_data.h"
 
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 using namespace physicore;
 
 namespace {
diff --git a/reactions-diffusion/biofvm/tests/test_config_reader.cpp b/reactions-diffusion/biofvm/tests/test_config_reader.cpp
index 9d10d05b..53980434 100644
--- a/reactions-diffusion/biofvm/tests/test_config_reader.cpp
+++ b/reactions-diffusion/biofvm/tests/test_config_reader.cpp
@@ -7,7 +7,7 @@
 #include "microenvironment.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 class ConfigReaderTest : public ::testing::Test
 {
diff --git a/reactions-diffusion/biofvm/tests/test_dirichlet_modification.cpp b/reactions-diffusion/biofvm/tests/test_dirichlet_modification.cpp
index 98102333..982d0a83 100644
--- a/reactions-diffusion/biofvm/tests/test_dirichlet_modification.cpp
+++ b/reactions-diffusion/biofvm/tests/test_dirichlet_modification.cpp
@@ -2,7 +2,7 @@
 #include <gtest/gtest.h>
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 TEST(DirichletModification, SetInteriorVoxel)
 {
diff --git a/reactions-diffusion/biofvm/tests/test_microenvironment_builder.cpp b/reactions-diffusion/biofvm/tests/test_microenvironment_builder.cpp
index e7a87533..49e084b9 100644
--- a/reactions-diffusion/biofvm/tests/test_microenvironment_builder.cpp
+++ b/reactions-diffusion/biofvm/tests/test_microenvironment_builder.cpp
@@ -11,7 +11,7 @@
 #include "microenvironment_builder.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 TEST(MicroenvironmentBuilder, SettersAndBuild)
 {
diff --git a/reactions-diffusion/biofvm/tests/test_solver_registry.cpp b/reactions-diffusion/biofvm/tests/test_solver_registry.cpp
index 4a0bea35..9c92a399 100644
--- a/reactions-diffusion/biofvm/tests/test_solver_registry.cpp
+++ b/reactions-diffusion/biofvm/tests/test_solver_registry.cpp
@@ -4,7 +4,7 @@
 #include "solver_registry.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 class mock_solver : public solver
 {
diff --git a/reactions-diffusion/biofvm/tests/test_vtk_agents_serializer.cpp b/reactions-diffusion/biofvm/tests/test_vtk_agents_serializer.cpp
index 9512f619..43dd6800 100644
--- a/reactions-diffusion/biofvm/tests/test_vtk_agents_serializer.cpp
+++ b/reactions-diffusion/biofvm/tests/test_vtk_agents_serializer.cpp
@@ -18,7 +18,7 @@
 #include "vtk_agents_serializer.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 class VtkAgentsSerializerTest : public ::testing::Test
 {
diff --git a/reactions-diffusion/biofvm/tests/test_vtk_serializer.cpp b/reactions-diffusion/biofvm/tests/test_vtk_serializer.cpp
index 4ac36ddf..5bd776ad 100644
--- a/reactions-diffusion/biofvm/tests/test_vtk_serializer.cpp
+++ b/reactions-diffusion/biofvm/tests/test_vtk_serializer.cpp
@@ -17,7 +17,7 @@
 #include "vtk_serializer.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 class VtkSerializerTest : public ::testing::Test
 {