From b1db9baf3a0519ab912866cfe4a008c6c79a7ec8 Mon Sep 17 00:00:00 2001
From: "jonathan.froehlich" <jonathan.froehlich@kit.edu>
Date: Thu, 26 Jan 2023 15:10:00 +0100
Subject: [PATCH] Renamed elphy solver methods
---
src/coupled/solvers/CellModelSolver.cpp | 2 +-
src/coupled/solvers/SegregatedSolver.cpp | 2 +-
src/electrophysiology/MainMonodomain.cpp | 2 +-
src/electrophysiology/MainOneCell.cpp | 2 +-
.../solvers/DiffusionSolver.cpp | 4 ++--
.../solvers/DiffusionSolver.hpp | 4 ++--
src/electrophysiology/solvers/ElphySolver.cpp | 6 +++---
src/electrophysiology/solvers/ElphySolver.hpp | 8 ++++----
.../solvers/LinearImplicitSolver.cpp | 16 ++++++++--------
.../solvers/LinearImplicitSolver.hpp | 10 +++++-----
.../solvers/SplittingSolver.hpp | 2 +-
test/coupled/TestCoupledConsistency.cpp | 6 +++---
12 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/src/coupled/solvers/CellModelSolver.cpp b/src/coupled/solvers/CellModelSolver.cpp
index ec0f46e0b..e2af47122 100644
--- a/src/coupled/solvers/CellModelSolver.cpp
+++ b/src/coupled/solvers/CellModelSolver.cpp
@@ -19,7 +19,7 @@ void CellModelSolver::Solve(Vector &potential, Vector &stretch) {
int step=elphyA.Step()+1;
//if (verbose == 1)
mout << "Solving Step " << step << " at time " << elphyA.Time() << "." << endl;
- elphySolver.SolveStep(elphyA, uNew);
+ elphySolver.Step(elphyA, uNew);
if (verbose > 0) {
PlotValues(uNew, step);
diff --git a/src/coupled/solvers/SegregatedSolver.cpp b/src/coupled/solvers/SegregatedSolver.cpp
index 83c0f78c5..84363b3cd 100644
--- a/src/coupled/solvers/SegregatedSolver.cpp
+++ b/src/coupled/solvers/SegregatedSolver.cpp
@@ -181,7 +181,7 @@ void SegregatedSolver::Step(IElphyAssemble &elphyAssemble, IElasticity &mechAsse
<< elphyAssemble.LastTStep()
<< "] - step " << elphyAssemble.Step() + 1 << " at time " << elphyAssemble.Time() << "."
<< endl;
- elphySolver->SolveStep(elphyAssemble, elphyValues);
+ elphySolver->Step(elphyAssemble, elphyValues);
}
// Projects stretch from elphy to mech
diff --git a/src/electrophysiology/MainMonodomain.cpp b/src/electrophysiology/MainMonodomain.cpp
index be66533d3..c77729dbb 100644
--- a/src/electrophysiology/MainMonodomain.cpp
+++ b/src/electrophysiology/MainMonodomain.cpp
@@ -53,7 +53,7 @@ void MainMonodomain::Initialize() {
Vector &MainMonodomain::Run() {
auto elphySolver = GetElphySolver(modelName, *cellModel, elphyA->ExcitationData());
- elphySolver->Solve(*elphyA, *potential);
+ elphySolver->Method(*elphyA, *potential);
elphyA->PrintActivationTime();
diff --git a/src/electrophysiology/MainOneCell.cpp b/src/electrophysiology/MainOneCell.cpp
index 83989471e..58a5811d8 100644
--- a/src/electrophysiology/MainOneCell.cpp
+++ b/src/electrophysiology/MainOneCell.cpp
@@ -37,7 +37,7 @@ Vector &MainOneCell::Run() {
} else {
elphyA = std::make_unique<MonodomainSplitting>(*problem, 0);
IBTSplittingSolver eSolver(ONLYODE);
- eSolver.Solve(*elphyA, *potential);
+ eSolver.Method(*elphyA, *potential);
}
diff --git a/src/electrophysiology/solvers/DiffusionSolver.cpp b/src/electrophysiology/solvers/DiffusionSolver.cpp
index 01b9d4eb6..b27b848e2 100644
--- a/src/electrophysiology/solvers/DiffusionSolver.cpp
+++ b/src/electrophysiology/solvers/DiffusionSolver.cpp
@@ -26,7 +26,7 @@ void DiffusionSolver::Initialize(IElphyAssemble &A, Vector &v) {
A.SetInitialValue(v);
}
-void DiffusionSolver::Solve(IElphyAssemble &A, Vector &potential) {
+void DiffusionSolver::Method(IElphyAssemble &A, Vector &potential) {
//mout.StartBlock("Elphy");
Initialize(A, potential);
@@ -103,6 +103,6 @@ bool DiffusionSolver::AssemblesOnce() const {
return assembleOnce;
}
-void DiffusionSolver::SolveStep(IElphyAssemble &A, Vectors &values) {
+void DiffusionSolver::Step(IElphyAssemble &A, Vectors &values) {
SolveStep(A, values[0]);
}
diff --git a/src/electrophysiology/solvers/DiffusionSolver.hpp b/src/electrophysiology/solvers/DiffusionSolver.hpp
index 110a6a9cb..2dc37c60e 100644
--- a/src/electrophysiology/solvers/DiffusionSolver.hpp
+++ b/src/electrophysiology/solvers/DiffusionSolver.hpp
@@ -21,9 +21,9 @@ public:
void SolveStep(IElphyAssemble &A, Vector &potential);
- void SolveStep(IElphyAssemble &A, Vectors &values) override;
+ void Step(IElphyAssemble &A, Vectors &values) override;
- void Solve(IElphyAssemble &A, Vector &potential);
+ void Method(IElphyAssemble &A, Vector &potential);
void assembleStep(IElphyAssemble &A, Vector &v);
diff --git a/src/electrophysiology/solvers/ElphySolver.cpp b/src/electrophysiology/solvers/ElphySolver.cpp
index bb2b687a4..3bb8e6069 100644
--- a/src/electrophysiology/solvers/ElphySolver.cpp
+++ b/src/electrophysiology/solvers/ElphySolver.cpp
@@ -8,7 +8,7 @@ ElphySolver::ElphySolver() {
Config::Get("IextInPDE", iextInPDE);
}
-void ElphySolver::Solve(IElphyAssemble &A, Vector &potential) {
+void ElphySolver::Method(IElphyAssemble &A, Vector &potential) {
//mout.StartBlock("Elphy");
Initialize(A, potential);
Vectors uNew(1, potential);
@@ -17,10 +17,10 @@ void ElphySolver::Solve(IElphyAssemble &A, Vector &potential) {
A.PlotIteration(uNew[0]);
A.PrintIteration(uNew[0]);
- vout(1) << "Solving Step " << A.Step() + 1 << " at time " << A.Time() << "." << endl;
+ vout(1) << "Solving Step " << A.Step() + 1 << " at time " << A.Time() << "." << endl;
vout(10).StartBlock("Godunov Splitting Step");
- SolveStep(A, uNew);
+ Step(A, uNew);
A.NextTimeStep();
diff --git a/src/electrophysiology/solvers/ElphySolver.hpp b/src/electrophysiology/solvers/ElphySolver.hpp
index 1605e4d22..214612e62 100644
--- a/src/electrophysiology/solvers/ElphySolver.hpp
+++ b/src/electrophysiology/solvers/ElphySolver.hpp
@@ -14,13 +14,15 @@ protected:
public:
explicit ElphySolver();
+ virtual void Initialize(IElphyAssemble &A, Vector &potential) {};
+
/**
* Solves purely electrophysiolical problem over the course of the timeSeries
* @param potential
* @param timeSeries
* The solution is stored in potential
*/
- virtual void Solve(IElphyAssemble &A, Vector &potential);
+ virtual void Method(IElphyAssemble &A, Vector &potential);
/**
* Solves a single electrophysiolgical time step with the given parameters
@@ -29,9 +31,7 @@ public:
* @param t
* @param dt
*/
- virtual void SolveStep(IElphyAssemble &A, Vectors &values) = 0;
-
- virtual void Initialize(IElphyAssemble &A, Vector &potential) {};
+ virtual void Step(IElphyAssemble &A, Vectors &values) = 0;
virtual void Finalize(Vectors &values) {};
};
diff --git a/src/electrophysiology/solvers/LinearImplicitSolver.cpp b/src/electrophysiology/solvers/LinearImplicitSolver.cpp
index e702d82ff..3429cdbd8 100644
--- a/src/electrophysiology/solvers/LinearImplicitSolver.cpp
+++ b/src/electrophysiology/solvers/LinearImplicitSolver.cpp
@@ -20,7 +20,7 @@ void LinearImplicitSolver::Initialize(IElphyAssemble &A, Vector &V) {
A.SetInitialValue(V);
}
-void LinearImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
+void LinearImplicitSolver::Method(IElphyAssemble &A, Vector &V) {
Vectors vNew(M.Type() == TENSION ? 3 : 1, V);
Initialize(A, vNew[0]);
if (M.Type() == TENSION) {
@@ -35,7 +35,7 @@ void LinearImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
<< A.NextTimeStep(false) << " (" << A.StepSize() << ")" << endl;
vout(10).StartBlock("LinearImplicit Step");
- SolveStep(A, vNew);
+ Step(A, vNew);
vout(10).EndBlock();
@@ -47,7 +47,7 @@ void LinearImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
A.PrintIteration(V);
}
-void LinearImplicitSolver::SolveStep(IElphyAssemble &A, Vectors &values) {
+void LinearImplicitSolver::Step(IElphyAssemble &A, Vectors &values) {
A.Initialize(values[0]);
A.updateExternalCurrent(values[0]);
A.updateIionVecs(*gating);
@@ -173,7 +173,7 @@ void LinearImplicitSolver::PrintMaxMinGating() {
}
-void ImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
+void ImplicitSolver::Method(IElphyAssemble &A, Vector &V) {
Vectors vNew(M.Type() == TENSION ? 3 : 1, V);
Initialize(A, vNew[0]);
if (M.Type() == TENSION) {
@@ -191,7 +191,7 @@ void ImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
<< A.NextTimeStep(false) << " (" << A.StepSize() << ")" << endl;
vout(10).StartBlock("Implicit step");
- SolveStep(A, vNew);
+ Step(A, vNew);
vout(10).EndBlock();
@@ -204,7 +204,7 @@ void ImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
}
-void ImplicitSolver::SolveStep(IElphyAssemble &A, Vectors &values) {
+void ImplicitSolver::Step(IElphyAssemble &A, Vectors &values) {
A.NextTimeStep();
A.Initialize(values[0]);
A.updateExternalCurrent(values[0]);
@@ -230,7 +230,7 @@ bool ImplicitSolver::SolvePDE(IElphyAssemble &A, Vectors &values) {
}
-void SemiImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
+void SemiImplicitSolver::Method(IElphyAssemble &A, Vector &V) {
Vectors vNew(M.Type() == TENSION ? 3 : 1, V);
Initialize(A, vNew[0]);
if (M.Type() == TENSION) {
@@ -246,7 +246,7 @@ void SemiImplicitSolver::Solve(IElphyAssemble &A, Vector &V) {
<< A.NextTimeStep(false) << " (" << A.StepSize() << ")" << endl;
vout(10).StartBlock("Semi Implicit Step");
- SolveStep(A, vNew);
+ Step(A, vNew);
vout(10).EndBlock();
}
diff --git a/src/electrophysiology/solvers/LinearImplicitSolver.hpp b/src/electrophysiology/solvers/LinearImplicitSolver.hpp
index e2474cfbd..85e0f463c 100644
--- a/src/electrophysiology/solvers/LinearImplicitSolver.hpp
+++ b/src/electrophysiology/solvers/LinearImplicitSolver.hpp
@@ -76,7 +76,7 @@ public:
virtual void Initialize(IElphyAssemble &A, Vector &potential);
- virtual void Solve(IElphyAssemble &A, Vector &V);
+ virtual void Method(IElphyAssemble &A, Vector &V);
void SolveConcentration(double t, double dt, const Vectors &values);
@@ -84,7 +84,7 @@ public:
virtual void SolvePDE(IElphyAssemble &A);
- void SolveStep(IElphyAssemble &A, Vectors &values) override;
+ void Step(IElphyAssemble &A, Vectors &values) override;
std::function<void(IElphyAssemble &A, const Vectors &values)> StaggeredStep;
@@ -112,9 +112,9 @@ public:
std::unique_ptr<LinearSolver>(GetLinearSolverByPrefix("Elphy"))
) {};
- void Solve(IElphyAssemble &A, Vector &V) override;
+ void Method(IElphyAssemble &A, Vector &V) override;
- void SolveStep(IElphyAssemble &A, Vectors &values) override;
+ void Step(IElphyAssemble &A, Vectors &values) override;
bool SolvePDE(IElphyAssemble &A, Vectors &values);
};
@@ -124,7 +124,7 @@ class SemiImplicitSolver : public LinearImplicitSolver {
public:
SemiImplicitSolver(MCellModel &cellModel) : LinearImplicitSolver(cellModel) {};
- void Solve(IElphyAssemble &A, Vector &V) override;
+ void Method(IElphyAssemble &A, Vector &V) override;
void SolvePDE(IElphyAssemble &A) override;
};
diff --git a/src/electrophysiology/solvers/SplittingSolver.hpp b/src/electrophysiology/solvers/SplittingSolver.hpp
index 48a73e095..2d085d6cd 100644
--- a/src/electrophysiology/solvers/SplittingSolver.hpp
+++ b/src/electrophysiology/solvers/SplittingSolver.hpp
@@ -118,7 +118,7 @@ public:
selectScheme(splitting);
}
- void SolveStep(IElphyAssemble &A, Vectors &values) override {
+ void Step(IElphyAssemble &A, Vectors &values) override {
solveSplittingStep(A, values);
}
diff --git a/test/coupled/TestCoupledConsistency.cpp b/test/coupled/TestCoupledConsistency.cpp
index 5fa53997b..e1ec4e592 100644
--- a/test/coupled/TestCoupledConsistency.cpp
+++ b/test/coupled/TestCoupledConsistency.cpp
@@ -120,8 +120,8 @@ TEST_P(CoupledConsistencyTest, CompareCellModels) {
tensionV[2] = 1.0; // Iota4
while (!elphyA->IsFinished()) {
- elphySolver->SolveStep(*elphyA, elphyV);
- tensionSolver->SolveStep(*coupledA, tensionV);
+ elphySolver->Step(*elphyA, elphyV);
+ tensionSolver->Step(*coupledA, tensionV);
EXPECT_EQ(elphyA->Time(), coupledA->Time());
ASSERT_MPPVECTOR_EQ(elphyV[0], tensionV[0]);
@@ -162,7 +162,7 @@ TEST_P(CoupledConsistencyTest, CompareSolvers) {
ASSERT_MPPVECTOR_EQ(elphyA->ExternalCurrent(), coupledA->ExternalCurrent());
while (!mechA->IsFinished()) {
- elphySolver->SolveStep(*elphyA, elphyV);
+ elphySolver->Step(*elphyA, elphyV);
coupledSolver.Step(*coupledA, *mechA, coupledV, coupledU);
EXPECT_EQ(elphyA->Time(), mechA->Time());
--
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