change all coff to coeff

Xiangyu-Hu · Aug 1, 2023 · b3312e7 · b3312e7
1 parent 3111031
commit b3312e7
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Showing 12 changed files with 40 additions and 40 deletions.
diff --git a/src/shared/materials/diffusion_reaction.h b/src/shared/materials/diffusion_reaction.h
@@ -58,7 +58,7 @@ class BaseDiffusion : public BaseMaterial
     size_t gradient_species_index_;
 
     virtual Real getReferenceDiffusivity() = 0;
-    virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) = 0;
+    virtual Real getInterParticleDiffusionCoeff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) = 0;
 };
 
 /**
@@ -81,7 +81,7 @@ class IsotropicDiffusion : public BaseDiffusion
     virtual ~IsotropicDiffusion(){};
 
     virtual Real getReferenceDiffusivity() override { return diff_cf_; };
-    virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) override
+    virtual Real getInterParticleDiffusionCoeff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) override
     {
         return diff_cf_;
     };
@@ -117,8 +117,8 @@ class DirectionalDiffusion : public IsotropicDiffusion
         return SMAX(diff_cf_, diff_cf_ + bias_diff_cf_);
     };
 
-    virtual Real getInterParticleDiffusionCoff(size_t particle_index_i,
-                                               size_t particle_index_j, Vecd &inter_particle_direction) override
+    virtual Real getInterParticleDiffusionCoeff(size_t particle_index_i,
+                                               size_t particle_index_j, const Vecd &inter_particle_direction) override
     {
         Vecd grad_ij = transformed_diffusivity_ * inter_particle_direction;
         return 1.0 / grad_ij.squaredNorm();
@@ -147,7 +147,7 @@ class LocalDirectionalDiffusion : public DirectionalDiffusion
     virtual void registerReloadLocalParameters(BaseParticles *base_particles) override;
     virtual void initializeLocalParameters(BaseParticles *base_particles) override;
 
-    virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, Vecd &inter_particle_direction) override
+    virtual Real getInterParticleDiffusionCoeff(size_t particle_index_i, size_t particle_index_j, const Vecd &inter_particle_direction) override
     {
         Matd trans_diffusivity = getAverageValue(local_transformed_diffusivity_[particle_index_i], local_transformed_diffusivity_[particle_index_j]);
         Vecd grad_ij = trans_diffusivity * inter_particle_direction;
@@ -293,10 +293,10 @@ class DiffusionReaction : public BaseMaterialType
      */
     Real getDiffusionTimeStepSize(Real smoothing_length)
     {
-        Real diff_coff_max = 0.0;
+        Real diff_coeff_max = 0.0;
         for (size_t k = 0; k < all_diffusions_.size(); ++k)
-            diff_coff_max = SMAX(diff_coff_max, all_diffusions_[k]->getReferenceDiffusivity());
-        return 0.5 * smoothing_length * smoothing_length / diff_coff_max / Real(Dimensions);
+            diff_coeff_max = SMAX(diff_coeff_max, all_diffusions_[k]->getReferenceDiffusivity());
+        return 0.5 * smoothing_length * smoothing_length / diff_coeff_max / Real(Dimensions);
     };
 
     /** Initialize a diffusion material. */

diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp
@@ -75,11 +75,11 @@ void DiffusionRelaxationInner<ParticlesType, KernelGradientType>::
 {
     for (size_t m = 0; m < this->all_diffusions_.size(); ++m)
     {
-        Real diff_coff_ij =
-            this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_j, e_ij);
+        Real diff_coeff_ij =
+            this->all_diffusions_[m]->getInterParticleDiffusionCoeff(particle_i, particle_j, e_ij);
         StdLargeVec<Real> &gradient_species = *this->gradient_species_[m];
         Real phi_ij = gradient_species[particle_i] - gradient_species[particle_j];
-        (*this->diffusion_dt_[m])[particle_i] += diff_coff_ij * phi_ij * surface_area_ij;
+        (*this->diffusion_dt_[m])[particle_i] += diff_coeff_ij * phi_ij * surface_area_ij;
     }
 }
 //=================================================================================================//
@@ -164,10 +164,10 @@ void DiffusionRelaxationDirichlet<ParticlesType, ContactParticlesType, KernelGra
 {
     for (size_t m = 0; m < this->all_diffusions_.size(); ++m)
     {
-        Real diff_coff_ij =
-            this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_i, e_ij);
+        Real diff_coeff_ij =
+            this->all_diffusions_[m]->getInterParticleDiffusionCoeff(particle_i, particle_i, e_ij);
         Real phi_ij = (*this->gradient_species_[m])[particle_i] - (*gradient_species_k[m])[particle_j];
-        (*this->diffusion_dt_[m])[particle_i] += diff_coff_ij * phi_ij * surface_area_ij;
+        (*this->diffusion_dt_[m])[particle_i] += diff_coeff_ij * phi_ij * surface_area_ij;
     }
 }
 //=================================================================================================//

diff --git a/tests/2d_examples/test_0d_regression_test/regression_test.cpp b/tests/2d_examples/test_0d_regression_test/regression_test.cpp
@@ -19,8 +19,8 @@ BoundingBox system_domain_bounds(Vec2d(-BW, -BW), Vec2d(L + BW, H + BW));
 //----------------------------------------------------------------------
 //	Global parameters on material properties
 //----------------------------------------------------------------------
-Real diffusion_coff = 1.0e-3;
-Real bias_coff = 0.0;
+Real diffusion_coeff = 1.0e-3;
+Real bias_coeff = 0.0;
 Real alpha = Pi / 4.0;
 Vec2d bias_direction(cos(alpha), sin(alpha));
 Real initial_temperature = 0.0;
@@ -103,7 +103,7 @@ class DiffusionMaterial : public DiffusionReaction<Solid>
   public:
     DiffusionMaterial() : DiffusionReaction<Solid>({"Phi"}, SharedPtr<NoReaction>())
     {
-        initializeAnDiffusion<DirectionalDiffusion>("Phi", "Phi", diffusion_coff, bias_coff, bias_direction);
+        initializeAnDiffusion<DirectionalDiffusion>("Phi", "Phi", diffusion_coeff, bias_coeff, bias_direction);
     };
 };
 //----------------------------------------------------------------------

diff --git a/tests/2d_examples/test_2d_depolarization/depolarization.cpp b/tests/2d_examples/test_2d_depolarization/depolarization.cpp
@@ -18,8 +18,8 @@ StdVec<Vecd> observation_location = {Vecd(0.3, 0.7)};
 //----------------------------------------------------------------------
 //	Basic parameters for material properties.
 //----------------------------------------------------------------------
-Real diffusion_coff = 1.0;
-Real bias_coff = 0.0;
+Real diffusion_coeff = 1.0;
+Real bias_coeff = 0.0;
 Vec2d fiber_direction(1.0, 0.0);
 Real c_m = 1.0;
 Real k = 8.0;
@@ -83,7 +83,7 @@ int main()
 	SolidBody muscle_body(system, makeShared<MuscleBlock>("MuscleBlock"));
 	SharedPtr<AlievPanfilowModel> muscle_reaction_model_ptr = makeShared<AlievPanfilowModel>(k_a, c_m, k, a, b, mu_1, mu_2, epsilon);
 	muscle_body.defineParticlesAndMaterial<ElectroPhysiologyParticles, MonoFieldElectroPhysiology>(
-		muscle_reaction_model_ptr, TypeIdentity<DirectionalDiffusion>(), diffusion_coff, bias_coff, fiber_direction);
+		muscle_reaction_model_ptr, TypeIdentity<DirectionalDiffusion>(), diffusion_coeff, bias_coeff, fiber_direction);
 	muscle_body.generateParticles<ParticleGeneratorLattice>();
 
 	ObserverBody voltage_observer(system, "VoltageObserver");

diff --git a/tests/2d_examples/test_2d_diffusion/diffusion.cpp b/tests/2d_examples/test_2d_diffusion/diffusion.cpp
@@ -15,8 +15,8 @@ BoundingBox system_domain_bounds(Vec2d(0.0, 0.0), Vec2d(L, H));
 //----------------------------------------------------------------------
 //	Basic parameters for material properties.
 //----------------------------------------------------------------------
-Real diffusion_coff = 1.0e-4;
-Real bias_coff = 0.0;
+Real diffusion_coeff = 1.0e-4;
+Real bias_coeff = 0.0;
 Real alpha = Pi / 6.0;
 Vec2d bias_direction(cos(alpha), sin(alpha));
 //----------------------------------------------------------------------
@@ -44,7 +44,7 @@ class DiffusionMaterial : public DiffusionReaction<Solid>
   public:
     DiffusionMaterial() : DiffusionReaction<Solid>({"Phi"}, SharedPtr<NoReaction>())
     {
-        initializeAnDiffusion<DirectionalDiffusion>("Phi", "Phi", diffusion_coff, bias_coff, bias_direction);
+        initializeAnDiffusion<DirectionalDiffusion>("Phi", "Phi", diffusion_coeff, bias_coeff, bias_direction);
     };
 };
 using DiffusionParticles = DiffusionReactionParticles<SolidParticles, DiffusionMaterial>;

diff --git a/tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.h b/tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.h
@@ -20,7 +20,7 @@ BoundingBox system_domain_bounds(Vec2d(-BW, -BW), Vec2d(L + BW, H + BW));
 //----------------------------------------------------------------------
 //	Basic parameters for material properties.
 //----------------------------------------------------------------------
-Real diffusion_coff = 1;
+Real diffusion_coeff = 1;
 std::array<std::string, 1> species_name_list{"Phi"};
 //----------------------------------------------------------------------
 //	Initial and boundary conditions.
@@ -95,7 +95,7 @@ class DiffusionMaterial : public DiffusionReaction<Solid>
   public:
     DiffusionMaterial() : DiffusionReaction<Solid>({"Phi"}, SharedPtr<NoReaction>())
     {
-        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coff);
+        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coeff);
     }
 };
 using DiffusionParticles = DiffusionReactionParticles<SolidParticles, DiffusionMaterial>;

diff --git a/tests/2d_examples/test_2d_heat_transfer/heat_transfer.cpp b/tests/2d_examples/test_2d_heat_transfer/heat_transfer.cpp
@@ -20,7 +20,7 @@ StdVec<Vecd> observation_location = {Vecd(0.0, DH * 0.5)};
 //----------------------------------------------------------------------
 //	Global parameters on the material properties
 //----------------------------------------------------------------------
-Real diffusion_coff = 1.0e-3;
+Real diffusion_coeff = 1.0e-3;
 Real rho0_f = 1.0;                  /**< Density. */
 Real U_f = 1.0;                     /**< Characteristic velocity. */
 Real c_f = 10.0 * U_f;              /**< Speed of sound. */
@@ -101,7 +101,7 @@ class ThermofluidBodyMaterial : public DiffusionReaction<WeaklyCompressibleFluid
     ThermofluidBodyMaterial()
         : DiffusionReaction<WeaklyCompressibleFluid>({"Phi"}, SharedPtr<NoReaction>(), rho0_f, c_f, mu_f)
     {
-        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coff);
+        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coeff);
     };
 };
 using DiffusionBaseParticles = DiffusionReactionParticles<BaseParticles, ThermofluidBodyMaterial>;

diff --git a/tests/3d_examples/test_3d_heart_electromechanics/excitation-contraction.cpp b/tests/3d_examples/test_3d_heart_electromechanics/excitation-contraction.cpp
@@ -36,8 +36,8 @@ Real poisson = 0.4995;
 Real bulk_modulus = 2.0 * a0[0] * (1.0 + poisson) / (3.0 * (1.0 - 2.0 * poisson));
 /** Electrophysiology parameters. */
 std::array<std::string, 1> species_name_list{"Phi"};
-Real diffusion_coff = 0.8;
-Real bias_coff = 0.0;
+Real diffusion_coeff = 0.8;
+Real bias_coeff = 0.0;
 /** Electrophysiology parameters. */
 Real c_m = 1.0;
 Real k = 8.0;
@@ -72,7 +72,7 @@ class FiberDirectionDiffusion : public DiffusionReaction<LocallyOrthotropicMuscl
                                     {"Phi"}, SharedPtr<NoReaction>(),
                                     rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0)
     {
-        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coff);
+        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coeff);
     };
 };
 using FiberDirectionDiffusionParticles = DiffusionReactionParticles<ElasticSolidParticles, FiberDirectionDiffusion>;
@@ -363,7 +363,7 @@ int main(int ac, char *av[])
     SharedPtr<AlievPanfilowModel> muscle_reaction_model_ptr = makeShared<AlievPanfilowModel>(k_a, c_m, k, a, b, mu_1, mu_2, epsilon);
     physiology_heart.defineParticlesAndMaterial<
         ElectroPhysiologyParticles, MonoFieldElectroPhysiology>(
-        muscle_reaction_model_ptr, TypeIdentity<LocalDirectionalDiffusion>(), diffusion_coff, bias_coff, fiber_direction);
+        muscle_reaction_model_ptr, TypeIdentity<LocalDirectionalDiffusion>(), diffusion_coeff, bias_coeff, fiber_direction);
     (!system.RunParticleRelaxation() && system.ReloadParticles())
         ? physiology_heart.generateParticles<ParticleGeneratorReload>(io_environment, "HeartModel")
         : physiology_heart.generateParticles<ParticleGeneratorLattice>();

diff --git a/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.cpp b/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.cpp
@@ -114,7 +114,7 @@ int main(int ac, char *av[])
     SharedPtr<AlievPanfilowModel> muscle_reaction_model_ptr = makeShared<AlievPanfilowModel>(k_a, c_m, k, a, b, mu_1, mu_2, epsilon);
     physiology_heart.defineParticlesAndMaterial<
         ElectroPhysiologyParticles, MonoFieldElectroPhysiology>(
-        muscle_reaction_model_ptr, TypeIdentity<LocalDirectionalDiffusion>(), diffusion_coff, bias_coff, fiber_direction);
+        muscle_reaction_model_ptr, TypeIdentity<LocalDirectionalDiffusion>(), diffusion_coeff, bias_coeff, fiber_direction);
     (!system.RunParticleRelaxation() && system.ReloadParticles())
         ? physiology_heart.generateParticles<ParticleGeneratorReload>(io_environment, "HeartModel")
         : physiology_heart.generateParticles<ParticleGeneratorLattice>();

diff --git a/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h b/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h
@@ -39,8 +39,8 @@ Real poisson = 0.4995;
 Real bulk_modulus = 2.0 * a0[0] * (1.0 + poisson) / (3.0 * (1.0 - 2.0 * poisson));
 /** Electrophysiology parameters. */
 std::array<std::string, 1> species_name_list{"Phi"};
-Real diffusion_coff = 0.8;
-Real bias_coff = 0.0;
+Real diffusion_coeff = 0.8;
+Real bias_coeff = 0.0;
 /** Electrophysiology parameters. */
 Real c_m = 1.0;
 Real k = 8.0;
@@ -74,7 +74,7 @@ class FiberDirectionDiffusion : public DiffusionReaction<LocallyOrthotropicMuscl
                                     {"Phi"}, SharedPtr<NoReaction>(),
                                     rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0)
     {
-        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coff);
+        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coeff);
     };
 };
 using FiberDirectionDiffusionParticles = DiffusionReactionParticles<ElasticSolidParticles, FiberDirectionDiffusion>;

diff --git a/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.cpp b/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.cpp
@@ -129,7 +129,7 @@ int main(int ac, char *av[])
     SharedPtr<AlievPanfilowModel> muscle_reaction_model_ptr = makeShared<AlievPanfilowModel>(k_a, c_m, k, a, b, mu_1, mu_2, epsilon);
     physiology_heart.defineParticlesAndMaterial<
         ElectroPhysiologyParticles, MonoFieldElectroPhysiology>(
-        muscle_reaction_model_ptr, TypeIdentity<LocalDirectionalDiffusion>(), diffusion_coff, bias_coff, fiber_direction);
+        muscle_reaction_model_ptr, TypeIdentity<LocalDirectionalDiffusion>(), diffusion_coeff, bias_coeff, fiber_direction);
     (!system.RunParticleRelaxation() && system.ReloadParticles())
         ? physiology_heart.generateParticles<ParticleGeneratorReload>(io_environment, "HeartModel")
         : physiology_heart.generateParticles<ParticleGeneratorLattice>();
@@ -147,7 +147,7 @@ int main(int ac, char *av[])
     SharedPtr<AlievPanfilowModel> pkj_reaction_model_ptr = makeShared<AlievPanfilowModel>(k_a, c_m, k, a, b, mu_1, mu_2, epsilon);
     pkj_body.defineParticlesAndMaterial<
         ElectroPhysiologyReducedParticles, MonoFieldElectroPhysiology>(
-        pkj_reaction_model_ptr, TypeIdentity<DirectionalDiffusion>(), diffusion_coff * acceleration_factor, bias_coff, fiber_direction);
+        pkj_reaction_model_ptr, TypeIdentity<DirectionalDiffusion>(), diffusion_coeff * acceleration_factor, bias_coeff, fiber_direction);
     pkj_body.generateParticles<NetworkGeneratorWithExtraCheck>(starting_point, second_point, 50, 1.0);
     TreeTerminates pkj_leaves(pkj_body);
     //----------------------------------------------------------------------

diff --git a/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h b/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h
@@ -64,8 +64,8 @@ Real poisson = 0.4995;
 Real bulk_modulus = 2.0 * a0[0] * (1.0 + poisson) / (3.0 * (1.0 - 2.0 * poisson));
 /** Electrophysiology parameters. */
 Real acceleration_factor = 27.5; /** Acceleration factor for fast diffusion on purkinje network. */
-Real diffusion_coff = 0.8;
-Real bias_coff = 0.0;
+Real diffusion_coeff = 0.8;
+Real bias_coeff = 0.0;
 /** Electrophysiology parameters. */
 std::array<std::string, 1> species_name_list{"Phi"};
 Real c_m = 1.0;
@@ -104,7 +104,7 @@ class FiberDirectionDiffusion : public DiffusionReaction<LocallyOrthotropicMuscl
               {"Phi"}, SharedPtr<NoReaction>(),
               rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0)
     {
-        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coff);
+        initializeAnDiffusion<IsotropicDiffusion>("Phi", "Phi", diffusion_coeff);
     };
 };
 using FiberDirectionDiffusionParticles = DiffusionReactionParticles<ElasticSolidParticles, FiberDirectionDiffusion>;