From fed549e5c135973c56b8068256f8c4de51f313b3 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sun, 3 May 2026 09:26:52 +0000 Subject: [PATCH 1/5] Initial plan From cec147a0e48042e3c5a8e723dbde4898ddec67a6 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sun, 3 May 2026 09:29:40 +0000 Subject: [PATCH 2/5] Replace GeneralisedLinearSpringForce with LinearSpringForce/PathmanathanInteractionForce Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/900d25b2-02ee-49b4-a57c-9484fa59c3e8 Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com> --- test/TestCylindricalCryptLiteratePaper.hpp | 6 ++++-- test/TestDeltaNotchLiteratePaper.hpp | 7 ++++--- test/TestMorphogenMonolayerLiteratePaper.hpp | 7 ++++--- 3 files changed, 12 insertions(+), 8 deletions(-) diff --git a/test/TestCylindricalCryptLiteratePaper.hpp b/test/TestCylindricalCryptLiteratePaper.hpp index 4251564..7246476 100644 --- a/test/TestCylindricalCryptLiteratePaper.hpp +++ b/test/TestCylindricalCryptLiteratePaper.hpp @@ -48,6 +48,8 @@ #include "NagaiHondaForce.hpp" #include "RepulsionForce.hpp" +#include "LinearSpringForce.hpp" +#include "PathmanathanInteractionForce.hpp" #include "DiffusionCaUpdateRule.hpp" #include "VolumeConstraintPottsUpdateRule.hpp" #include "AdhesionPottsUpdateRule.hpp" @@ -329,7 +331,7 @@ class TestCylindricalCryptLiteratePaper : public AbstractCellBasedWithTimingsTes simulator.AddSimulationModifier(p_modifier); // Create a force law and pass it to the simulation - MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force); + MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force); p_linear_force->SetMeinekeSpringStiffness(50.0); p_linear_force->SetCutOffLength(cut_off_length); simulator.AddForce(p_linear_force); @@ -407,7 +409,7 @@ class TestCylindricalCryptLiteratePaper : public AbstractCellBasedWithTimingsTes simulator.AddSimulationModifier(p_modifier); // Create a force law and pass it to the simulation - MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force); + MAKE_PTR(LinearSpringForce<2>, p_linear_force); p_linear_force->SetMeinekeSpringStiffness(50.0); simulator.AddForce(p_linear_force); diff --git a/test/TestDeltaNotchLiteratePaper.hpp b/test/TestDeltaNotchLiteratePaper.hpp index 89c8ad2..0ba1e89 100644 --- a/test/TestDeltaNotchLiteratePaper.hpp +++ b/test/TestDeltaNotchLiteratePaper.hpp @@ -43,7 +43,8 @@ #include "HoneycombMeshGenerator.hpp" #include "DiffusionForce.hpp" #include "RepulsionForce.hpp" -#include "GeneralisedLinearSpringForce.hpp" +#include "LinearSpringForce.hpp" +#include "PathmanathanInteractionForce.hpp" #include "OnLatticeSimulation.hpp" #include "DeltaNotchTrackingModifier.hpp" @@ -314,7 +315,7 @@ class TestDeltaNotchLiteratePaper: public AbstractCellBasedWithTimingsTestSuite simulator.AddSimulationModifier(p_differentiation_modifier); // Create a force law and pass it to the simulation - MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force); + MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force); p_linear_force->SetMeinekeSpringStiffness(50.0); p_linear_force->SetCutOffLength(cut_off_length); simulator.AddForce(p_linear_force); @@ -378,7 +379,7 @@ class TestDeltaNotchLiteratePaper: public AbstractCellBasedWithTimingsTestSuite simulator.AddSimulationModifier(p_differentiation_modifier); // Create a force law and pass it to the simulation - MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force); + MAKE_PTR(LinearSpringForce<2>, p_linear_force); p_linear_force->SetMeinekeSpringStiffness(50.0); p_linear_force->SetCutOffLength(1.5); simulator.AddForce(p_linear_force); diff --git a/test/TestMorphogenMonolayerLiteratePaper.hpp b/test/TestMorphogenMonolayerLiteratePaper.hpp index d801af4..5c3c0ec 100644 --- a/test/TestMorphogenMonolayerLiteratePaper.hpp +++ b/test/TestMorphogenMonolayerLiteratePaper.hpp @@ -44,7 +44,8 @@ #include "MeshBasedCellPopulationWithGhostNodes.hpp" #include "HoneycombMeshGenerator.hpp" -#include "GeneralisedLinearSpringForce.hpp" +#include "LinearSpringForce.hpp" +#include "PathmanathanInteractionForce.hpp" #include "NodeBasedCellPopulation.hpp" #include "RepulsionForce.hpp" @@ -341,7 +342,7 @@ class TestMorphogenMonolayerLiteratePaper : public AbstractCellBasedWithTimingsT simulator.SetOutputDivisionLocations(true); // Create a force law and pass it to the simulation - MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force); + MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force); p_linear_force->SetMeinekeSpringStiffness(50.0); p_linear_force->SetCutOffLength(cut_off_length); simulator.AddForce(p_linear_force); @@ -416,7 +417,7 @@ class TestMorphogenMonolayerLiteratePaper : public AbstractCellBasedWithTimingsT simulator.SetOutputDivisionLocations(true); - MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force); + MAKE_PTR(LinearSpringForce<2>, p_linear_force); p_linear_force->SetMeinekeSpringStiffness(50.0); p_linear_force->SetCutOffLength(1.5); simulator.AddForce(p_linear_force); From 87c1aeb7583ea5adc94f6316367b6aeadb2d1de4 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sun, 3 May 2026 09:34:39 +0000 Subject: [PATCH 3/5] Also replace DifferentialAdhesionGeneralisedLinearSpringForce and RepulsionForce Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/5b619335-e853-4cb5-b76a-ee1e7e6c54a5 Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com> --- test/TestCellSortingLiteratePaper.hpp | 6 +++--- test/TestCylindricalCryptLiteratePaper.hpp | 2 +- test/TestDeltaNotchLiteratePaper.hpp | 2 +- test/TestMorphogenMonolayerLiteratePaper.hpp | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/test/TestCellSortingLiteratePaper.hpp b/test/TestCellSortingLiteratePaper.hpp index c1ce94d..65b518b 100644 --- a/test/TestCellSortingLiteratePaper.hpp +++ b/test/TestCellSortingLiteratePaper.hpp @@ -43,7 +43,7 @@ #include "MeshBasedCellPopulationWithGhostNodes.hpp" #include "HoneycombMeshGenerator.hpp" -#include "DifferentialAdhesionGeneralisedLinearSpringForce.hpp" +#include "DifferentialAdhesionLinearSpringForce.hpp" #include "OnLatticeSimulation.hpp" #include "CellPopulationAdjacencyMatrixWriter.hpp" @@ -311,7 +311,7 @@ class TestCellSortingLiteratePaper : public AbstractCellBasedWithTimingsTestSuit simulator.SetEndTime(M_TIME_TO_STEADY_STATE); // Create a force law and pass it to the simulation - MAKE_PTR(DifferentialAdhesionGeneralisedLinearSpringForce<2>, p_differential_adhesion_force); + MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force); p_differential_adhesion_force->SetMeinekeSpringStiffness(50.0); p_differential_adhesion_force->SetHomotypicLabelledSpringConstantMultiplier(1.0); p_differential_adhesion_force->SetHeterotypicSpringConstantMultiplier(0.1); @@ -384,7 +384,7 @@ class TestCellSortingLiteratePaper : public AbstractCellBasedWithTimingsTestSuit simulator.SetEndTime(M_TIME_TO_STEADY_STATE); // Create a force law and pass it to the simulation - MAKE_PTR(DifferentialAdhesionGeneralisedLinearSpringForce<2>, p_differential_adhesion_force); + MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force); p_differential_adhesion_force->SetMeinekeSpringStiffness(50.0); p_differential_adhesion_force->SetHomotypicLabelledSpringConstantMultiplier(1.0); p_differential_adhesion_force->SetHeterotypicSpringConstantMultiplier(0.1); diff --git a/test/TestCylindricalCryptLiteratePaper.hpp b/test/TestCylindricalCryptLiteratePaper.hpp index 7246476..7e502a5 100644 --- a/test/TestCylindricalCryptLiteratePaper.hpp +++ b/test/TestCylindricalCryptLiteratePaper.hpp @@ -47,7 +47,7 @@ #include "OnLatticeSimulation.hpp" #include "NagaiHondaForce.hpp" -#include "RepulsionForce.hpp" +#include "LogarithmicRepulsionForce.hpp" #include "LinearSpringForce.hpp" #include "PathmanathanInteractionForce.hpp" #include "DiffusionCaUpdateRule.hpp" diff --git a/test/TestDeltaNotchLiteratePaper.hpp b/test/TestDeltaNotchLiteratePaper.hpp index 0ba1e89..b17ac94 100644 --- a/test/TestDeltaNotchLiteratePaper.hpp +++ b/test/TestDeltaNotchLiteratePaper.hpp @@ -42,7 +42,7 @@ #include "MeshBasedCellPopulationWithGhostNodes.hpp" #include "HoneycombMeshGenerator.hpp" #include "DiffusionForce.hpp" -#include "RepulsionForce.hpp" +#include "LogarithmicRepulsionForce.hpp" #include "LinearSpringForce.hpp" #include "PathmanathanInteractionForce.hpp" diff --git a/test/TestMorphogenMonolayerLiteratePaper.hpp b/test/TestMorphogenMonolayerLiteratePaper.hpp index 5c3c0ec..ec770b6 100644 --- a/test/TestMorphogenMonolayerLiteratePaper.hpp +++ b/test/TestMorphogenMonolayerLiteratePaper.hpp @@ -48,7 +48,7 @@ #include "PathmanathanInteractionForce.hpp" #include "NodeBasedCellPopulation.hpp" -#include "RepulsionForce.hpp" +#include "LogarithmicRepulsionForce.hpp" #include "VertexBasedCellPopulation.hpp" #include "HoneycombVertexMeshGenerator.hpp" From 45fb0ecd2b00a7156b85a9d933e141b82be44f70 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sun, 3 May 2026 09:44:09 +0000 Subject: [PATCH 4/5] Apply review suggestions: DifferentialAdhesionPathmanathanInteractionForce for node-based, remove LogarithmicRepulsionForce includes Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/e5f2f4ab-5362-4bf4-b7fe-7e898948ccde Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com> --- test/TestCellSortingLiteratePaper.hpp | 3 ++- test/TestCylindricalCryptLiteratePaper.hpp | 1 - test/TestDeltaNotchLiteratePaper.hpp | 1 - test/TestMorphogenMonolayerLiteratePaper.hpp | 1 - 4 files changed, 2 insertions(+), 4 deletions(-) diff --git a/test/TestCellSortingLiteratePaper.hpp b/test/TestCellSortingLiteratePaper.hpp index 65b518b..a3eabbb 100644 --- a/test/TestCellSortingLiteratePaper.hpp +++ b/test/TestCellSortingLiteratePaper.hpp @@ -43,6 +43,7 @@ #include "MeshBasedCellPopulationWithGhostNodes.hpp" #include "HoneycombMeshGenerator.hpp" +#include "DifferentialAdhesionPathmanathanInteractionForce.hpp" #include "DifferentialAdhesionLinearSpringForce.hpp" #include "OnLatticeSimulation.hpp" @@ -311,7 +312,7 @@ class TestCellSortingLiteratePaper : public AbstractCellBasedWithTimingsTestSuit simulator.SetEndTime(M_TIME_TO_STEADY_STATE); // Create a force law and pass it to the simulation - MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force); + MAKE_PTR(DifferentialAdhesionPathmanathanInteractionForce<2>, p_differential_adhesion_force); p_differential_adhesion_force->SetMeinekeSpringStiffness(50.0); p_differential_adhesion_force->SetHomotypicLabelledSpringConstantMultiplier(1.0); p_differential_adhesion_force->SetHeterotypicSpringConstantMultiplier(0.1); diff --git a/test/TestCylindricalCryptLiteratePaper.hpp b/test/TestCylindricalCryptLiteratePaper.hpp index 7e502a5..050c63f 100644 --- a/test/TestCylindricalCryptLiteratePaper.hpp +++ b/test/TestCylindricalCryptLiteratePaper.hpp @@ -47,7 +47,6 @@ #include "OnLatticeSimulation.hpp" #include "NagaiHondaForce.hpp" -#include "LogarithmicRepulsionForce.hpp" #include "LinearSpringForce.hpp" #include "PathmanathanInteractionForce.hpp" #include "DiffusionCaUpdateRule.hpp" diff --git a/test/TestDeltaNotchLiteratePaper.hpp b/test/TestDeltaNotchLiteratePaper.hpp index b17ac94..1e61a0e 100644 --- a/test/TestDeltaNotchLiteratePaper.hpp +++ b/test/TestDeltaNotchLiteratePaper.hpp @@ -42,7 +42,6 @@ #include "MeshBasedCellPopulationWithGhostNodes.hpp" #include "HoneycombMeshGenerator.hpp" #include "DiffusionForce.hpp" -#include "LogarithmicRepulsionForce.hpp" #include "LinearSpringForce.hpp" #include "PathmanathanInteractionForce.hpp" diff --git a/test/TestMorphogenMonolayerLiteratePaper.hpp b/test/TestMorphogenMonolayerLiteratePaper.hpp index ec770b6..f9b9ca0 100644 --- a/test/TestMorphogenMonolayerLiteratePaper.hpp +++ b/test/TestMorphogenMonolayerLiteratePaper.hpp @@ -48,7 +48,6 @@ #include "PathmanathanInteractionForce.hpp" #include "NodeBasedCellPopulation.hpp" -#include "LogarithmicRepulsionForce.hpp" #include "VertexBasedCellPopulation.hpp" #include "HoneycombVertexMeshGenerator.hpp" From c9aadedfea339e1487aa390c3f5c60307d9aebe5 Mon Sep 17 00:00:00 2001 From: James Osborne Date: Sun, 3 May 2026 11:34:07 +0100 Subject: [PATCH 5/5] Updating User Project to Latest Force Hierachy Co-authored-by: Copilot --- test/TestCellSortingLiteratePaper.hpp | 4 ++-- test/TestCylindricalCryptLiteratePaper.hpp | 4 ++-- test/TestDeltaNotchLiteratePaper.hpp | 6 ++++-- test/TestMorphogenMonolayerLiteratePaper.hpp | 4 ++-- 4 files changed, 10 insertions(+), 8 deletions(-) diff --git a/test/TestCellSortingLiteratePaper.hpp b/test/TestCellSortingLiteratePaper.hpp index a3eabbb..8e75701 100644 --- a/test/TestCellSortingLiteratePaper.hpp +++ b/test/TestCellSortingLiteratePaper.hpp @@ -313,7 +313,7 @@ class TestCellSortingLiteratePaper : public AbstractCellBasedWithTimingsTestSuit // Create a force law and pass it to the simulation MAKE_PTR(DifferentialAdhesionPathmanathanInteractionForce<2>, p_differential_adhesion_force); - p_differential_adhesion_force->SetMeinekeSpringStiffness(50.0); + p_differential_adhesion_force->SetSpringStiffness(50.0); p_differential_adhesion_force->SetHomotypicLabelledSpringConstantMultiplier(1.0); p_differential_adhesion_force->SetHeterotypicSpringConstantMultiplier(0.1); p_differential_adhesion_force->SetCutOffLength(cut_off_length); @@ -386,7 +386,7 @@ class TestCellSortingLiteratePaper : public AbstractCellBasedWithTimingsTestSuit // Create a force law and pass it to the simulation MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force); - p_differential_adhesion_force->SetMeinekeSpringStiffness(50.0); + p_differential_adhesion_force->SetSpringStiffness(50.0); p_differential_adhesion_force->SetHomotypicLabelledSpringConstantMultiplier(1.0); p_differential_adhesion_force->SetHeterotypicSpringConstantMultiplier(0.1); simulator.AddForce(p_differential_adhesion_force); diff --git a/test/TestCylindricalCryptLiteratePaper.hpp b/test/TestCylindricalCryptLiteratePaper.hpp index 050c63f..e1a3094 100644 --- a/test/TestCylindricalCryptLiteratePaper.hpp +++ b/test/TestCylindricalCryptLiteratePaper.hpp @@ -331,7 +331,7 @@ class TestCylindricalCryptLiteratePaper : public AbstractCellBasedWithTimingsTes // Create a force law and pass it to the simulation MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force); - p_linear_force->SetMeinekeSpringStiffness(50.0); + p_linear_force->SetSpringStiffness(50.0); p_linear_force->SetCutOffLength(cut_off_length); simulator.AddForce(p_linear_force); @@ -409,7 +409,7 @@ class TestCylindricalCryptLiteratePaper : public AbstractCellBasedWithTimingsTes // Create a force law and pass it to the simulation MAKE_PTR(LinearSpringForce<2>, p_linear_force); - p_linear_force->SetMeinekeSpringStiffness(50.0); + p_linear_force->SetSpringStiffness(50.0); simulator.AddForce(p_linear_force); // Solid base boundary condition diff --git a/test/TestDeltaNotchLiteratePaper.hpp b/test/TestDeltaNotchLiteratePaper.hpp index 1e61a0e..5be3823 100644 --- a/test/TestDeltaNotchLiteratePaper.hpp +++ b/test/TestDeltaNotchLiteratePaper.hpp @@ -41,6 +41,8 @@ #include "MeshBasedCellPopulationWithGhostNodes.hpp" #include "HoneycombMeshGenerator.hpp" +#include "NodesOnlyMesh.hpp" +#include "NodeBasedCellPopulation.hpp" #include "DiffusionForce.hpp" #include "LinearSpringForce.hpp" #include "PathmanathanInteractionForce.hpp" @@ -315,7 +317,7 @@ class TestDeltaNotchLiteratePaper: public AbstractCellBasedWithTimingsTestSuite // Create a force law and pass it to the simulation MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force); - p_linear_force->SetMeinekeSpringStiffness(50.0); + p_linear_force->SetSpringStiffness(50.0); p_linear_force->SetCutOffLength(cut_off_length); simulator.AddForce(p_linear_force); @@ -379,7 +381,7 @@ class TestDeltaNotchLiteratePaper: public AbstractCellBasedWithTimingsTestSuite // Create a force law and pass it to the simulation MAKE_PTR(LinearSpringForce<2>, p_linear_force); - p_linear_force->SetMeinekeSpringStiffness(50.0); + p_linear_force->SetSpringStiffness(50.0); p_linear_force->SetCutOffLength(1.5); simulator.AddForce(p_linear_force); diff --git a/test/TestMorphogenMonolayerLiteratePaper.hpp b/test/TestMorphogenMonolayerLiteratePaper.hpp index f9b9ca0..60ae90b 100644 --- a/test/TestMorphogenMonolayerLiteratePaper.hpp +++ b/test/TestMorphogenMonolayerLiteratePaper.hpp @@ -342,7 +342,7 @@ class TestMorphogenMonolayerLiteratePaper : public AbstractCellBasedWithTimingsT // Create a force law and pass it to the simulation MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force); - p_linear_force->SetMeinekeSpringStiffness(50.0); + p_linear_force->SetSpringStiffness(50.0); p_linear_force->SetCutOffLength(cut_off_length); simulator.AddForce(p_linear_force); @@ -417,7 +417,7 @@ class TestMorphogenMonolayerLiteratePaper : public AbstractCellBasedWithTimingsT simulator.SetOutputDivisionLocations(true); MAKE_PTR(LinearSpringForce<2>, p_linear_force); - p_linear_force->SetMeinekeSpringStiffness(50.0); + p_linear_force->SetSpringStiffness(50.0); p_linear_force->SetCutOffLength(1.5); simulator.AddForce(p_linear_force);