From aad683e3aedf178f5cc6512db93e9f2944231aad Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Mon, 9 Sep 2024 12:12:28 -0700 Subject: [PATCH 01/16] Solid viscosity update and restructuring first pass. Added preliminary viscosity test. Compiles and runs, but all existing struct and ustruct tests fail. Also, fluid/carreau-yasuda 3-procs fails. --- Code/Source/svFSI/ComMod.h | 20 +- Code/Source/svFSI/Parameters.cpp | 235 ++++++++++++++---- Code/Source/svFSI/Parameters.h | 85 +++++-- Code/Source/svFSI/README.md | 2 +- Code/Source/svFSI/consts.cpp | 15 ++ Code/Source/svFSI/consts.h | 12 +- Code/Source/svFSI/distribute.cpp | 13 +- Code/Source/svFSI/distribute.h | 4 +- Code/Source/svFSI/fluid.cpp | 20 +- Code/Source/svFSI/mat_models_carray.h | 222 +++++++++++++++++ Code/Source/svFSI/read_files.cpp | 72 ++++-- Code/Source/svFSI/read_files.h | 4 +- Code/Source/svFSI/set_equation_props.h | 8 +- Code/Source/svFSI/set_viscosity_props.h | 85 +++++-- Code/Source/svFSI/stokes.cpp | 8 +- Code/Source/svFSI/sv_struct.cpp | 199 ++++++++------- Code/Source/svFSI/ustruct.cpp | 16 +- .../1-rigid-solution/svFSIplus.xml | 4 +- .../3-inflate-cmm/svFSIplus.xml | 4 +- .../pipe_3d/1-rigid-solution/svFSIplus.xml | 4 +- .../cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml | 4 +- .../pipe_3d/3b-prestress-cmm/svFSIplus.xml | 4 +- tests/cases/fluid/carreau_yasuda/README.md | 4 +- .../cases/fluid/carreau_yasuda/svFSIplus.xml | 4 +- tests/cases/fluid/casson/README.md | 4 +- tests/cases/fluid/casson/svFSIplus.xml | 4 +- .../fluid/driven_cavity_2d/svFSIplus.xml | 4 +- tests/cases/fluid/dye_AD/svFSIplus.xml | 4 +- tests/cases/fluid/iliac_artery/svFSIplus.xml | 4 +- tests/cases/fluid/newtonian/README.md | 4 +- tests/cases/fluid/newtonian/svFSIplus.xml | 4 +- tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml | 4 +- .../fluid/pipe_RCR_3d_petsc/svFSIplus.xml | 4 +- .../pipe_RCR_3d_trilinos_bj/svFSIplus.xml | 4 +- .../pipe_RCR_3d_trilinos_ilut/svFSIplus.xml | 4 +- .../cases/fluid/pipe_RCR_genBC/svFSIplus.xml | 4 +- tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml | 4 +- .../cases/fluid/quadratic_tet10/svFSIplus.xml | 4 +- tests/cases/fsi/pipe_3d/svFSIplus.xml | 4 +- tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml | 4 +- .../fsi/pipe_3d_trilinos_bj/svFSIplus.xml | 4 +- .../fsi/pipe_3d_trilinos_ml/svFSIplus.xml | 4 +- .../P1P1/N004/svFSIplus.xml | 4 +- .../P1P1/N008/svFSIplus.xml | 4 +- .../P1P1/N016/svFSIplus.xml | 4 +- .../P1P1/N032/svFSIplus.xml | 4 +- .../P1P1/N064/svFSIplus.xml | 4 +- .../P1P1/N128/svFSIplus.xml | 4 +- .../P1P1/N256/svFSIplus.xml | 4 +- .../P2P1/N004/svFSIplus.xml | 4 +- .../P2P1/N008/svFSIplus.xml | 4 +- .../P2P1/N016/svFSIplus.xml | 4 +- .../P2P1/N032/svFSIplus.xml | 4 +- .../P2P1/N064/svFSIplus.xml | 4 +- .../P2P1/N128/svFSIplus.xml | 4 +- .../struct/LV_Holzapfel_passive/svFSIplus.xml | 4 +- .../LV_NeoHookean_passive/svFSIplus.xml | 4 +- .../LV_NeoHookean_passive_genBC/svFSIplus.xml | 4 +- .../LV_NeoHookean_passive_sv0D/svFSIplus.xml | 4 +- .../README.md | 14 ++ .../generate_load.py | 30 +++ .../load.dat | 3 + .../load.png | 3 + .../mesh/mesh-complete.mesh.vtu | 3 + .../mesh/mesh-surfaces/X0.vtp | 3 + .../mesh/mesh-surfaces/X1.vtp | 3 + .../mesh/mesh-surfaces/Y0.vtp | 3 + .../mesh/mesh-surfaces/Y1.vtp | 3 + .../mesh/mesh-surfaces/Z0.vtp | 3 + .../mesh/mesh-surfaces/Z1.vtp | 3 + .../svFSIplus.xml | 120 +++++++++ .../LV_NeoHookean_passive_genBC/svFSIplus.xml | 4 +- .../LV_NeoHookean_passive_sv0D/svFSIplus.xml | 4 +- tests/test_struct.py | 4 + 74 files changed, 1074 insertions(+), 317 deletions(-) create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-complete.mesh.vtu create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X0.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X1.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y0.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y1.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z0.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml diff --git a/Code/Source/svFSI/ComMod.h b/Code/Source/svFSI/ComMod.h index 8ca9e7bb..f5bb6403 100644 --- a/Code/Source/svFSI/ComMod.h +++ b/Code/Source/svFSI/ComMod.h @@ -386,7 +386,7 @@ class stModelType /// @brief Fluid viscosity model type // -class viscModelType +class fluidViscModelType { public: @@ -409,6 +409,19 @@ class viscModelType double n = 0.0; }; +/// @brief Fluid viscosity model type +// +class solidViscModelType +{ + public: + + // Type of constitutive model for fluid viscosity + consts::SolidViscosityModelType viscType = consts::SolidViscosityModelType::viscType_NA; + + // Viscosity value + double mu = 0.0; +}; + /// @brief Domain type is to keep track with element belong to which domain /// and also different physical quantities // @@ -439,7 +452,10 @@ class dmnType stModelType stM; // Viscosity model for fluids - viscModelType visc; + fluidViscModelType fluid_visc; + + // Viscosity model for solids + solidViscModelType solid_visc; }; /// @brief Mesh adjacency (neighboring element for each element) diff --git a/Code/Source/svFSI/Parameters.cpp b/Code/Source/svFSI/Parameters.cpp index 95ccb340..64eeeeb1 100644 --- a/Code/Source/svFSI/Parameters.cpp +++ b/Code/Source/svFSI/Parameters.cpp @@ -1069,43 +1069,43 @@ void VariableWallPropsParameters::set_values(tinyxml2::XMLElement* xml_elem) } ////////////////////////////////////////////////////////// -// ViscosityParameters // +// FluidViscosityParameters // ////////////////////////////////////////////////////////// -/// @brief Process parameters for various viscosity models. +/// @brief Process parameters for various fluid viscosity models. /// /// Define the XML element name for viscosiity parameters. -const std::string ViscosityParameters::xml_element_name_ = "Viscosity"; +const std::string FluidViscosityParameters::xml_element_name_ = "Fluid_viscosity"; -const std::string ViscosityParameters::CONSTANT_MODEL = "Constant"; -const std::string ViscosityParameters::CARREAU_YASUDA_MODEL = "Carreau-Yasuda"; -const std::string ViscosityParameters::CASSONS_MODEL = "Cassons"; +const std::string FluidViscosityParameters::CONSTANT_MODEL = "Constant"; +const std::string FluidViscosityParameters::CARREAU_YASUDA_MODEL = "Carreau-Yasuda"; +const std::string FluidViscosityParameters::CASSONS_MODEL = "Cassons"; -const std::set ViscosityParameters::model_names = { - ViscosityParameters::CONSTANT_MODEL, - ViscosityParameters::CARREAU_YASUDA_MODEL, - ViscosityParameters::CASSONS_MODEL +const std::set FluidViscosityParameters::model_names = { + FluidViscosityParameters::CONSTANT_MODEL, + FluidViscosityParameters::CARREAU_YASUDA_MODEL, + FluidViscosityParameters::CASSONS_MODEL }; -/// @brief Define a map to set parameters for each viscosity model. -using VpType = ViscosityParameters*; +/// @brief Define a map to set parameters for each fluid viscosity model. +using FVpType = FluidViscosityParameters*; using XmlType = tinyxml2::XMLElement*; -using SetViscosityParamMapType = std::map>; -SetViscosityParamMapType SetViscosityModelParamsMap = { - {ViscosityParameters::CARREAU_YASUDA_MODEL, [](VpType vp, XmlType params) -> void { vp->carreau_yasuda_model.set_values(params); }}, - {ViscosityParameters::CASSONS_MODEL, [](VpType vp, XmlType params) -> void { vp->cassons_model.set_values(params); }}, - {ViscosityParameters::CONSTANT_MODEL, [](VpType vp, XmlType params) -> void { vp->newtonian_model.set_values(params); }}, +using SetFluidViscosityParamMapType = std::map>; +SetFluidViscosityParamMapType SetFluidViscosityModelParamsMap = { + {FluidViscosityParameters::CARREAU_YASUDA_MODEL, [](FVpType vp, XmlType params) -> void { vp->carreau_yasuda_model.set_values(params); }}, + {FluidViscosityParameters::CASSONS_MODEL, [](FVpType vp, XmlType params) -> void { vp->cassons_model.set_values(params); }}, + {FluidViscosityParameters::CONSTANT_MODEL, [](FVpType vp, XmlType params) -> void { vp->newtonian_model.set_values(params); }}, }; -/// @brief Define a map to print parameters for each viscosity model. -using PrintViscosityParamaMapType = std::map>; -PrintViscosityParamaMapType PrintViscosityModelParamsMap = { - {ViscosityParameters::CARREAU_YASUDA_MODEL, [](VpType vp) -> void { vp->carreau_yasuda_model.print_parameters(); }}, - {ViscosityParameters::CASSONS_MODEL, [](VpType vp) -> void { vp->cassons_model.print_parameters(); }}, - {ViscosityParameters::CONSTANT_MODEL, [](VpType vp) -> void { vp->newtonian_model.print_parameters(); }}, +/// @brief Define a map to print parameters for each fluid viscosity model. +using PrintFluidViscosityParamaMapType = std::map>; +PrintFluidViscosityParamaMapType PrintFluidViscosityModelParamsMap = { + {FluidViscosityParameters::CARREAU_YASUDA_MODEL, [](FVpType vp) -> void { vp->carreau_yasuda_model.print_parameters(); }}, + {FluidViscosityParameters::CASSONS_MODEL, [](FVpType vp) -> void { vp->cassons_model.print_parameters(); }}, + {FluidViscosityParameters::CONSTANT_MODEL, [](FVpType vp) -> void { vp->newtonian_model.print_parameters(); }}, }; -ViscosityNewtonianParameters::ViscosityNewtonianParameters() +FluidViscosityNewtonianParameters::FluidViscosityNewtonianParameters() { // A parameter that must be defined. bool required = true; @@ -1113,24 +1113,24 @@ ViscosityNewtonianParameters::ViscosityNewtonianParameters() set_parameter("Value", 0.0, !required, constant_value); } -void ViscosityNewtonianParameters::print_parameters() +void FluidViscosityNewtonianParameters::print_parameters() { std::cout << constant_value.name_ << ": " << constant_value.value_ << std::endl; } -void ViscosityNewtonianParameters::set_values(tinyxml2::XMLElement* xml_elem) +void FluidViscosityNewtonianParameters::set_values(tinyxml2::XMLElement* xml_elem) { std::string error_msg = "Unknown Constitutive_model type=Newtonian XML element '"; using std::placeholders::_1; using std::placeholders::_2; std::function ftpr = - std::bind( &ViscosityNewtonianParameters::set_parameter_value, *this, _1, _2); + std::bind( &FluidViscosityNewtonianParameters::set_parameter_value, *this, _1, _2); xml_util_set_parameters(ftpr, xml_elem, error_msg); } -ViscosityCarreauYasudaParameters::ViscosityCarreauYasudaParameters() +FluidViscosityCarreauYasudaParameters::FluidViscosityCarreauYasudaParameters() { // A parameter that must be defined. bool required = true; @@ -1144,7 +1144,7 @@ ViscosityCarreauYasudaParameters::ViscosityCarreauYasudaParameters() set_parameter("Shear_rate_tensor_exponent", 0.0, !required, shear_rate_tensor_exponent); } -void ViscosityCarreauYasudaParameters::print_parameters() +void FluidViscosityCarreauYasudaParameters::print_parameters() { std::cout << limiting_high_shear_rate_viscosity.name_ << ": " << limiting_high_shear_rate_viscosity.value_ << std::endl; std::cout << limiting_low_shear_rate_viscosity.name_ << ": " << limiting_low_shear_rate_viscosity.value_ << std::endl; @@ -1153,18 +1153,18 @@ void ViscosityCarreauYasudaParameters::print_parameters() std::cout << shear_rate_tensor_multipler.name_ << ": " << shear_rate_tensor_multipler.value_ << std::endl; } -void ViscosityCarreauYasudaParameters::set_values(tinyxml2::XMLElement* xml_elem) +void FluidViscosityCarreauYasudaParameters::set_values(tinyxml2::XMLElement* xml_elem) { std::string error_msg = "Unknown Constitutive_model type=CarreauYasuda XML element '"; using std::placeholders::_1; using std::placeholders::_2; std::function ftpr = - std::bind( &ViscosityCarreauYasudaParameters::set_parameter_value, *this, _1, _2); + std::bind( &FluidViscosityCarreauYasudaParameters::set_parameter_value, *this, _1, _2); xml_util_set_parameters(ftpr, xml_elem, error_msg); } -ViscosityCassonsParameters::ViscosityCassonsParameters() +FluidViscosityCassonsParameters::FluidViscosityCassonsParameters() { // A parameter that must be defined. bool required = true; @@ -1174,35 +1174,35 @@ ViscosityCassonsParameters::ViscosityCassonsParameters() set_parameter("Yield_stress_parameter", 0.0, !required, yield_stress); } -void ViscosityCassonsParameters::print_parameters() +void FluidViscosityCassonsParameters::print_parameters() { std::cout << asymptotic_viscosity.name_ << ": " << asymptotic_viscosity.value_ << std::endl; std::cout << low_shear_rate_threshold.name_ << ": " << low_shear_rate_threshold.value_ << std::endl; std::cout << yield_stress.name_ << ": " << yield_stress.value_ << std::endl; } -void ViscosityCassonsParameters::set_values(tinyxml2::XMLElement* xml_elem) +void FluidViscosityCassonsParameters::set_values(tinyxml2::XMLElement* xml_elem) { std::string error_msg = "Unknown Constitutive_model type=Cassons XML element '"; using std::placeholders::_1; using std::placeholders::_2; std::function ftpr = - std::bind( &ViscosityCassonsParameters::set_parameter_value, *this, _1, _2); + std::bind( &FluidViscosityCassonsParameters::set_parameter_value, *this, _1, _2); xml_util_set_parameters(ftpr, xml_elem, error_msg); } -ViscosityParameters::ViscosityParameters() +FluidViscosityParameters::FluidViscosityParameters() { // A parameter that must be defined. bool required = true; - // Stores model from the XML element + // Stores model from the XML element model = Parameter("model", "", required); } -void ViscosityParameters::print_parameters() +void FluidViscosityParameters::print_parameters() { std::cout << std::endl; std::cout << "--------------------" << std::endl; @@ -1210,11 +1210,11 @@ void ViscosityParameters::print_parameters() std::cout << "--------------------" << std::endl; std::cout << model.name() << ": '" << model.value() << "'" << std::endl; - // Print parameters for the given viscosity model. - PrintViscosityModelParamsMap[model.value_](this); + // Print parameters for the given fluid_viscosity model. + PrintFluidViscosityModelParamsMap[model.value_](this); } -void ViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) +void FluidViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) { using namespace tinyxml2; @@ -1222,18 +1222,143 @@ void ViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) auto result = xml_elem->QueryStringAttribute("model", &smodel); if (smodel == nullptr) { - throw std::runtime_error("No MODEL given in the XML element."); + throw std::runtime_error("No MODEL given in the XML element."); } model.set(std::string(smodel)); - // Check viscosity model name. + // Check fluid_viscosity model name. if (model_names.count(model.value()) == 0) { - throw std::runtime_error("Unknown viscosity model '" + model.value() + + throw std::runtime_error("Unknown fluid viscosity model '" + model.value() + " in '" + xml_elem->Name() + "'."); } - // Set parameters for the given viscosity model. - SetViscosityModelParamsMap[model.value()](this, xml_elem); + // Set parameters for the given fluid_viscosity model. + SetFluidViscosityModelParamsMap[model.value()](this, xml_elem); +} + +////////////////////////////////////////////////////////// +// SolidViscosityParameters // +////////////////////////////////////////////////////////// + +/// @brief Process parameters for various solid viscosity models. +/// +/// Define the XML element name for viscosiity parameters. +const std::string SolidViscosityParameters::xml_element_name_ = "Solid_viscosity"; + +const std::string SolidViscosityParameters::NEWTONIAN_MODEL = "Newtonian"; +const std::string SolidViscosityParameters::POTENTIAL_MODEL = "Potential"; + +const std::set SolidViscosityParameters::model_names = { + SolidViscosityParameters::NEWTONIAN_MODEL, + SolidViscosityParameters::POTENTIAL_MODEL +}; + +/// @brief Define a map to set parameters for each solid viscosity model. +using SVpType = SolidViscosityParameters*; +using XmlType = tinyxml2::XMLElement*; +using SetSolidViscosityParamMapType = std::map>; +SetSolidViscosityParamMapType SetSolidViscosityModelParamsMap = { + {SolidViscosityParameters::NEWTONIAN_MODEL, [](SVpType vp, XmlType params) -> void { vp->newtonian_model.set_values(params); }}, + {SolidViscosityParameters::POTENTIAL_MODEL, [](SVpType vp, XmlType params) -> void { vp->potential_model.set_values(params); }}, +}; + +/// @brief Define a map to print parameters for each solid viscosity model. +using PrintSolidViscosityParamaMapType = std::map>; +PrintSolidViscosityParamaMapType PrintSolidViscosityModelParamsMap = { + {SolidViscosityParameters::NEWTONIAN_MODEL, [](SVpType vp) -> void { vp->newtonian_model.print_parameters(); }}, + {SolidViscosityParameters::POTENTIAL_MODEL, [](SVpType vp) -> void { vp->potential_model.print_parameters(); }}, +}; + +SolidViscosityNewtonianParameters::SolidViscosityNewtonianParameters() +{ + // A parameter that must be defined. + bool required = true; + + set_parameter("Value", 0.0, !required, constant_value); +} + +void SolidViscosityNewtonianParameters::print_parameters() +{ + std::cout << constant_value.name_ << ": " << constant_value.value_ << std::endl; +} + +void SolidViscosityNewtonianParameters::set_values(tinyxml2::XMLElement* xml_elem) +{ + std::string error_msg = "Unknown Constitutive_model type=Newtonian XML element '"; + + using std::placeholders::_1; + using std::placeholders::_2; + std::function ftpr = + std::bind( &SolidViscosityNewtonianParameters::set_parameter_value, *this, _1, _2); + + xml_util_set_parameters(ftpr, xml_elem, error_msg); +} + +SolidViscosityPotentialParameters::SolidViscosityPotentialParameters() +{ + // A parameter that must be defined. + bool required = true; + + set_parameter("Value", 0.0, !required, constant_value); +} + +void SolidViscosityPotentialParameters::print_parameters() +{ + std::cout << constant_value.name_ << ": " << constant_value.value_ << std::endl; +} + +void SolidViscosityPotentialParameters::set_values(tinyxml2::XMLElement* xml_elem) +{ + std::string error_msg = "Unknown Constitutive_model type=Potential XML element '"; + using std::placeholders::_1; + using std::placeholders::_2; + std::function ftpr = + std::bind( &SolidViscosityPotentialParameters::set_parameter_value, *this, _1, _2); + + xml_util_set_parameters(ftpr, xml_elem, error_msg); +} + +SolidViscosityParameters::SolidViscosityParameters() +{ + // A parameter that must be defined. + bool required = true; + + // Stores model from the XML element + model = Parameter("model", "", required); +} + +void SolidViscosityParameters::print_parameters() +{ + std::cout << std::endl; + std::cout << "--------------------" << std::endl; + std::cout << "Viscosity Parameters" << std::endl; + std::cout << "--------------------" << std::endl; + std::cout << model.name() << ": '" << model.value() << "'" << std::endl; + + // Print parameters for the given Solid_viscosity model. + PrintSolidViscosityModelParamsMap[model.value_](this); +} + +void SolidViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) +{ + using namespace tinyxml2; + + const char* smodel; + auto result = xml_elem->QueryStringAttribute("model", &smodel); + + if (smodel == nullptr) { + throw std::runtime_error("No MODEL given in the XML element."); + } + model.set(std::string(smodel)); + + // Check solid viscosity model name. + if (model_names.count(model.value()) == 0) { + throw std::runtime_error("Unknown solid viscosity model '" + model.value() + + " in '" + xml_elem->Name() + "'."); + } + + // Set parameters for the given solid viscosity model. + SetSolidViscosityModelParamsMap[model.value()](this, xml_elem); } ////////////////////////////////////////////////////////// @@ -1299,7 +1424,7 @@ DomainParameters::DomainParameters() set_parameter("Relative_tolerance", 1e-4, !required, relative_tolerance); set_parameter("Shell_thickness", 0.0, !required, shell_thickness); set_parameter("Solid_density", 0.5, !required, solid_density); - set_parameter("Solid_viscosity", 0.9, !required, solid_viscosity); + //set_parameter("Solid_viscosity", 0.9, !required, solid_viscosity); set_parameter("Source_term", 0.0, !required, source_term); set_parameter("Time_step_for_integration", 0.0, !required, time_step_for_integration); } @@ -1323,7 +1448,7 @@ void DomainParameters::print_parameters() stimulus.print_parameters(); - viscosity.print_parameters(); + fluid_viscosity.print_parameters(); } void DomainParameters::set_values(tinyxml2::XMLElement* domain_elem) @@ -1354,8 +1479,11 @@ void DomainParameters::set_values(tinyxml2::XMLElement* domain_elem) } else if (name == StimulusParameters::xml_element_name_) { stimulus.set_values(item); - } else if (name == ViscosityParameters::xml_element_name_) { - viscosity.set_values(item); + } else if (name == FluidViscosityParameters::xml_element_name_) { + fluid_viscosity.set_values(item); + + } else if (name == SolidViscosityParameters::xml_element_name_) { + solid_viscosity.set_values(item); } else if (item->GetText() != nullptr) { auto value = item->GetText(); @@ -1768,8 +1896,11 @@ void EquationParameters::set_values(tinyxml2::XMLElement* eq_elem) } else if (name == StimulusParameters::xml_element_name_) { default_domain->stimulus.set_values(item); - } else if (name == ViscosityParameters::xml_element_name_) { - default_domain->viscosity.set_values(item); + } else if (name == FluidViscosityParameters::xml_element_name_) { + default_domain->fluid_viscosity.set_values(item); + + } else if (name == SolidViscosityParameters::xml_element_name_) { + default_domain->solid_viscosity.set_values(item); } else if (name == ECGLeadsParameters::xml_element_name_) { ecg_leads.set_values(item); diff --git a/Code/Source/svFSI/Parameters.h b/Code/Source/svFSI/Parameters.h index 25f1d79b..2781eba8 100644 --- a/Code/Source/svFSI/Parameters.h +++ b/Code/Source/svFSI/Parameters.h @@ -791,25 +791,25 @@ class VariableWallPropsParameters : public ParameterLists ////////////////////////////////////////////////////////// -// Viscosity // +// FluidViscosity // ////////////////////////////////////////////////////////// // The following classes are used to store parameters for -// various viscosity models. +// various fluid viscosity models. -class ViscosityNewtonianParameters : public ParameterLists +class FluidViscosityNewtonianParameters : public ParameterLists { public: - ViscosityNewtonianParameters(); + FluidViscosityNewtonianParameters(); void print_parameters(); void set_values(tinyxml2::XMLElement* equation_params); Parameter constant_value; }; -class ViscosityCarreauYasudaParameters : public ParameterLists +class FluidViscosityCarreauYasudaParameters : public ParameterLists { public: - ViscosityCarreauYasudaParameters(); + FluidViscosityCarreauYasudaParameters(); void print_parameters(); void set_values(tinyxml2::XMLElement* xml_elem); @@ -820,10 +820,10 @@ class ViscosityCarreauYasudaParameters : public ParameterLists Parameter shear_rate_tensor_exponent; }; -class ViscosityCassonsParameters : public ParameterLists +class FluidViscosityCassonsParameters : public ParameterLists { public: - ViscosityCassonsParameters(); + FluidViscosityCassonsParameters(); void print_parameters(); void set_values(tinyxml2::XMLElement* xml_elem); Parameter asymptotic_viscosity; @@ -831,10 +831,10 @@ class ViscosityCassonsParameters : public ParameterLists Parameter low_shear_rate_threshold; }; -class ViscosityParameters : public ParameterLists +class FluidViscosityParameters : public ParameterLists { public: - ViscosityParameters(); + FluidViscosityParameters(); static const std::string xml_element_name_; @@ -848,11 +848,57 @@ class ViscosityParameters : public ParameterLists Parameter model; - ViscosityNewtonianParameters newtonian_model; - ViscosityCarreauYasudaParameters carreau_yasuda_model; - ViscosityCassonsParameters cassons_model; + FluidViscosityNewtonianParameters newtonian_model; + FluidViscosityCarreauYasudaParameters carreau_yasuda_model; + FluidViscosityCassonsParameters cassons_model; }; +////////////////////////////////////////////////////////// +// SolidViscosity // +////////////////////////////////////////////////////////// + +// The following classes are used to store parameters for +// various solid viscosity models. + +class SolidViscosityNewtonianParameters : public ParameterLists +{ + public: + SolidViscosityNewtonianParameters(); + void print_parameters(); + void set_values(tinyxml2::XMLElement* equation_params); + Parameter constant_value; +}; + +class SolidViscosityPotentialParameters : public ParameterLists +{ + public: + SolidViscosityPotentialParameters(); + void print_parameters(); + void set_values(tinyxml2::XMLElement* equation_params); + Parameter constant_value; +}; + +class SolidViscosityParameters : public ParameterLists +{ + public: + SolidViscosityParameters(); + + static const std::string xml_element_name_; + + static const std::string NEWTONIAN_MODEL; + static const std::string POTENTIAL_MODEL; + static const std::set model_names; + + void print_parameters(); + void set_values(tinyxml2::XMLElement* xml_elem); + + Parameter model; + + SolidViscosityNewtonianParameters newtonian_model; + SolidViscosityPotentialParameters potential_model; +}; + + /// @brief The LinearAlgebraParameters class stores parameters for /// the 'Linear_algebra' XML element. class LinearAlgebraParameters : public ParameterLists @@ -991,9 +1037,9 @@ class FiberReinforcementStressParameters : public ParameterLists /// /// fluid /// 1.06 -/// +/// /// 0.04 -/// +/// /// 0.2 /// /// \endcode @@ -1011,7 +1057,8 @@ class DomainParameters : public ParameterLists ConstitutiveModelParameters constitutive_model; FiberReinforcementStressParameters fiber_reinforcement_stress; StimulusParameters stimulus; - ViscosityParameters viscosity; + FluidViscosityParameters fluid_viscosity; + SolidViscosityParameters solid_viscosity; // Attributes. Parameter id; @@ -1060,7 +1107,7 @@ class DomainParameters : public ParameterLists Parameter shell_thickness; Parameter solid_density; - Parameter solid_viscosity; + //Parameter solid_viscosity; Parameter source_term; Parameter time_step_for_integration; }; @@ -1199,7 +1246,9 @@ class EquationParameters : public ParameterLists VariableWallPropsParameters variable_wall_properties; - ViscosityParameters viscosity; + FluidViscosityParameters fluid_viscosity; + + SolidViscosityParameters solid_viscosity; ECGLeadsParameters ecg_leads; }; diff --git a/Code/Source/svFSI/README.md b/Code/Source/svFSI/README.md index c9f84a50..e1b4b622 100644 --- a/Code/Source/svFSI/README.md +++ b/Code/Source/svFSI/README.md @@ -1048,7 +1048,7 @@ Distribute boundary condition data to all processors. -

dist_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, viscModelType& lVis)

+

dist_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, fluidViscModelType& lVis)

[distribute.cpp](https://github.com/ktbolt/svFSI/blob/Implement-svFSI-using-cpp_19/Code/Source/svFSI_cinterface/distribute.cpp) diff --git a/Code/Source/svFSI/consts.cpp b/Code/Source/svFSI/consts.cpp index 0ee1f2cf..bd2e521c 100644 --- a/Code/Source/svFSI/consts.cpp +++ b/Code/Source/svFSI/consts.cpp @@ -126,6 +126,21 @@ const std::map fluid_viscosity_model_name_t }; +/// @brief Map for solid viscosity model string to SolidViscosityModelType. +// +const std::map solid_viscosity_model_name_to_type +{ + {"Newtonian", SolidViscosityModelType::viscType_Newtonian}, + {"newtonian", SolidViscosityModelType::viscType_Newtonian}, + {"Newt", SolidViscosityModelType::viscType_Newtonian}, + {"newt", SolidViscosityModelType::viscType_Newtonian}, + + {"Potential", SolidViscosityModelType::viscType_Potential}, + {"potential", SolidViscosityModelType::viscType_Potential}, + {"Pot", SolidViscosityModelType::viscType_Potential}, + {"pot", SolidViscosityModelType::viscType_Potential}, +}; + /// @brief Map number of element nodes to element type. /// diff --git a/Code/Source/svFSI/consts.h b/Code/Source/svFSI/consts.h index 8d7e9720..0d8964c5 100644 --- a/Code/Source/svFSI/consts.h +++ b/Code/Source/svFSI/consts.h @@ -398,7 +398,7 @@ enum class PhysicalProperyType NA = 0, fluid_density = 1, solid_density = 2, - solid_viscosity = 3, + //solid_viscosity = 3, elasticity_modulus = 4, poisson_ratio = 5, conductivity = 6, @@ -460,6 +460,16 @@ enum class FluidViscosityModelType /// Map for fluid viscosity model string to FluidViscosityModelType. extern const std::map fluid_viscosity_model_name_to_type; +enum class SolidViscosityModelType +{ + viscType_NA = 695, + viscType_Newtonian = 694, + viscType_Potential = 693 +}; + +/// Map for solid viscosity model string to SolidViscosityModelType. +extern const std::map solid_viscosity_model_name_to_type; + /// Template for printing enum class types as an int. template std::ostream& operator<<(typename std::enable_if::value, std::ostream>::type& stream, const T& e) diff --git a/Code/Source/svFSI/distribute.cpp b/Code/Source/svFSI/distribute.cpp index d67f0f84..93532359 100644 --- a/Code/Source/svFSI/distribute.cpp +++ b/Code/Source/svFSI/distribute.cpp @@ -1061,12 +1061,13 @@ void dist_eq(ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, const std:: if ((dmn.phys == EquationType::phys_struct) || (dmn.phys == EquationType::phys_ustruct)) { dist_mat_consts(com_mod, cm_mod, cm, dmn.stM); + dist_solid_visc_model(com_mod, cm_mod, cm, dmn.solid_visc); } if ((dmn.phys == EquationType::phys_fluid) || (dmn.phys == EquationType::phys_stokes) || (dmn.phys == EquationType::phys_CMM && !com_mod.cmmInit)) { - dist_visc_model(com_mod, cm_mod, cm, dmn.visc); + dist_fluid_visc_model(com_mod, cm_mod, cm, dmn.fluid_visc); } } @@ -1224,7 +1225,7 @@ void dist_mat_consts(const ComMod& com_mod, const CmMod& cm_mod, const cmType& c } -void dist_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, viscModelType& lVis) +void dist_fluid_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, fluidViscModelType& lVis) { using namespace consts; @@ -1236,6 +1237,14 @@ void dist_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& c cm.bcast(cm_mod, &lVis.n); } +void dist_solid_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, solidViscModelType& lVis) +{ + using namespace consts; + + cm.bcast_enum(cm_mod, &lVis.viscType); + cm.bcast(cm_mod, &lVis.mu); +} + void part_face(Simulation* simulation, mshType& lM, faceType& lFa, faceType& gFa, Vector& gmtl) { diff --git a/Code/Source/svFSI/distribute.h b/Code/Source/svFSI/distribute.h index bd831f79..33cfabd2 100644 --- a/Code/Source/svFSI/distribute.h +++ b/Code/Source/svFSI/distribute.h @@ -45,7 +45,9 @@ void dist_eq(ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, const std:: void dist_mat_consts(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, stModelType& lStM); -void dist_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, viscModelType& lVis); +void dist_fluid_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, fluidViscModelType& lVis); + +void dist_solid_visc_model(const ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, solidViscModelType& lVis); void part_face(Simulation* simulation, mshType& lM, faceType& lFa, faceType& gFa, Vector& gmtl); diff --git a/Code/Source/svFSI/fluid.cpp b/Code/Source/svFSI/fluid.cpp index 2318e665..c9e35109 100644 --- a/Code/Source/svFSI/fluid.cpp +++ b/Code/Source/svFSI/fluid.cpp @@ -1950,20 +1950,20 @@ void get_viscosity(const ComMod& com_mod, const dmnType& lDmn, double& gamma, do double mu_i, mu_o, lam, a, n, T1, T2; - switch (lDmn.visc.viscType) { + switch (lDmn.fluid_visc.viscType) { case FluidViscosityModelType::viscType_Const: - mu = lDmn.visc.mu_i; + mu = lDmn.fluid_visc.mu_i; mu_s = mu; mu_x = 0.0; break; case FluidViscosityModelType::viscType_CY: - mu_i = lDmn.visc.mu_i; - mu_o = lDmn.visc.mu_o; - lam = lDmn.visc.lam; - a = lDmn.visc.a; - n = lDmn.visc.n; + mu_i = lDmn.fluid_visc.mu_i; + mu_o = lDmn.fluid_visc.mu_o; + lam = lDmn.fluid_visc.lam; + a = lDmn.fluid_visc.a; + n = lDmn.fluid_visc.n; T1 = 1.0 + pow(lam*gamma, a); T2 = pow(T1,((n-1.0)/a)); @@ -1976,9 +1976,9 @@ void get_viscosity(const ComMod& com_mod, const dmnType& lDmn, double& gamma, do break; case FluidViscosityModelType::viscType_Cass: - mu_i = lDmn.visc.mu_i; - mu_o = lDmn.visc.mu_o; - lam = lDmn.visc.lam; + mu_i = lDmn.fluid_visc.mu_i; + mu_o = lDmn.fluid_visc.mu_o; + lam = lDmn.fluid_visc.lam; if (gamma < lam) { mu_o = mu_o / sqrt(lam); diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index 8946fcd6..cc6bfcba 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -1134,6 +1134,228 @@ void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn cc_to_voigt_carray(CC, Dm); } + +/** + * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid + * with a viscous pseudo-potential model. + * + * @tparam nsd Number of spatial dimensions + * @param mu Solid viscosity parameter + * @param eNoN Number of nodes in an element + * @param Nx Shape function gradient matrix + * @param vx Velocity gradient matrix + * @param F Deformation gradient matrix + * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix + * @param Kvis_u Viscous tangent matrix contribution due to displacement + * @param Kvis_v Visous tangent matrix contribution due to velocity + */ +template +void get_visc_stress_pot(const double mu, const int eNoN, const Array& Nx, const double vx[nsd][nsd], const double F[nsd][nsd], + Array& Svis, Array3& Kvis_u, Array3& Kvis_v) { + + std::cout << "get_visc_stress_pot: " << std::endl; + std::cout << "mu: " << mu << std::endl; + + // Initialize Svis, Kvis_u, Kvis_v to zero + for (int i = 0; i < nsd; i++) { + for (int j = 0; j < nsd; j++) { + Svis(i,j) = 0.0; + for (int a = 0; a < eNoN; a++) { + for (int b = 0; b < eNoN; b++) { + Kvis_u(i*nsd+j,a,b) = 0.0; + Kvis_v(i*nsd+j,a,b) = 0.0; + } + } + } + } + + + // Required intermediate terms for stress and tangent + double Ft[nsd][nsd] = {0}, vxt[nsd][nsd] = {0}, F_Ft[nsd][nsd] = {0}, Ft_vx[nsd][nsd] = {0}, F_vxt[nsd][nsd] = {0}; + mat_fun_carray::transpose(F, Ft); + mat_fun_carray::mat_mul(F, Ft, F_Ft); + mat_fun_carray::mat_mul(Ft, vx, Ft_vx); + mat_fun_carray::transpose(vx, vxt); + mat_fun_carray::mat_mul(F, vxt, F_vxt); + + //double F_Nx[nsd][eNoN] = {0}, vx_Nx[nsd][eNoN] = {0}; + Array F_Nx(nsd,eNoN), vx_Nx(nsd,eNoN); + + for (int a = 0; a < eNoN; ++a) { + for (int i = 0; i < nsd; ++i) { + for (int j = 0; j < nsd; ++j) { + F_Nx(i,a) = F[i][j] * Nx(j,a); + vx_Nx(i,a) = vx[i][j] * Nx(j,a); + } + } + } + + // 2nd Piola-Kirchhoff stress due to viscosity + double Ft_vx_symm[nsd][nsd] = {0}; + mat_fun_carray::mat_symm(Ft_vx, Ft_vx_symm); + for (int i = 0; i < nsd; i++) { + for (int j = 0; j < nsd; j++) { + Svis(i,j) = mu * Ft_vx_symm[i][j]; + } + } + //Svis = mu * Ft_vx_symm; + + // Tangent matrix contributions due to viscosity + for (int b = 0; b < eNoN; ++b) { + for (int a = 0; a < eNoN; ++a) { + double Nx_Nx = 0.0; + for (int i = 0; i < nsd; ++i) { + Nx_Nx += Nx(i,a) * Nx(i,b); + } + + for (int i = 0; i < nsd; ++i) { + for (int j = 0; j < nsd; ++j) { + int ii = i * nsd + j; + Kvis_u(ii,a,b) = 0.5 * mu * (F_Nx(i,b) * vx_Nx(j,a) + Nx_Nx * F_vxt[i][j]); + Kvis_v(ii,a,b) = 0.5 * mu * (Nx_Nx * F_Ft[i][j] + F_Nx(i,b) * F_Nx(j,a)); + } + } + } + } +} + +/** + * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid + * with a Newtonian fluid-like viscosity model. + * + * @tparam nsd Number of spatial dimensions + * @param mu Solid viscosity parameter + * @param eNoN Number of nodes in an element + * @param Nx Shape function gradient matrix + * @param vx Velocity gradient matrix + * @param F Deformation gradient matrix + * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix + * @param Kvis_u Viscous tangent matrix contribution due to displacement + * @param Kvis_v Visous tangent matrix contribution due to velocity + */ +template +void get_visc_stress_newt(const double mu, const int eNoN, const Array& Nx, const double vx[nsd][nsd], const double F[nsd][nsd], + Array& Svis, Array3& Kvis_u, Array3& Kvis_v) { + + std::cout << "get_visc_stress_newt: " << std::endl; + std::cout << "mu: " << mu << std::endl; + + // Initialize Svis, Kvis_u, Kvis_v to zero + for (int i = 0; i < nsd; i++) { + for (int j = 0; j < nsd; j++) { + Svis(i,j) = 0.0; + for (int a = 0; a < eNoN; a++) { + for (int b = 0; b < eNoN; b++) { + Kvis_u(i*nsd+j,a,b) = 0.0; + Kvis_v(i*nsd+j,a,b) = 0.0; + } + } + } + } + + // Get identity matrix, Jacobian, and F^-1 + double Idm[nsd][nsd] = {0}; + mat_fun_carray::mat_id(Idm); + double J = mat_fun_carray::mat_det(F); + double Fi[nsd][nsd] = {0}; + mat_fun_carray::mat_inv(F, Fi); + + // Required intermediate terms for stress and tangent + double vx_Fi[nsd][nsd] = {0}, vx_Fi_symm[nsd][nsd] = {0}, ddev[nsd][nsd] = {0}; + // vx_Fi: Velocity gradient in current configuration + mat_fun_carray::mat_mul(vx, Fi, vx_Fi); + mat_fun_carray::mat_symm(vx_Fi, vx_Fi_symm); + // ddev: Deviatoric part of rate of strain tensor + mat_fun_carray::mat_dev(vx_Fi_symm, ddev); + //double Nx_Fi[nsd][eNoN] = {0}, ddev_Nx_Fi[nsd][eNoN] = {0}, vx_Fi_Nx_Fi[nsd][eNoN] = {0}; + Array Nx_Fi(nsd,eNoN), ddev_Nx_Fi(nsd,eNoN), vx_Fi_Nx_Fi(nsd,eNoN); + for (int a = 0; a < eNoN; ++a) { + for (int i = 0; i < nsd; ++i) { + for (int j = 0; j < nsd; ++j) { + Nx_Fi(i,a) += Nx(j,a) * Fi[j][i]; + } + } + for (int i = 0; i < nsd; ++i) { + for (int j = 0; j < nsd; ++j) { + ddev_Nx_Fi(i,a) += ddev[i][j] * Nx_Fi(j,a); + vx_Fi_Nx_Fi(i,a) += vx_Fi[i][j] * Nx_Fi(j,a); + } + } + } + + // 2nd Piola-Kirchhoff stress due to viscosity + double Fit[nsd][nsd] = {0}; + mat_fun_carray::transpose(Fi, Fit); + double ddev_Fit[nsd][nsd] = {0}; + mat_fun_carray::mat_mul(ddev, Fit, ddev_Fit); + double Fi_ddev_Fit[nsd][nsd] = {0}; + mat_fun_carray::mat_mul(Fi, ddev_Fit, Fi_ddev_Fit); + for (int i = 0; i < nsd; i++) { + for (int j = 0; j < nsd; j++) { + Svis(i,j) = 2.0 * mu * J * Fi_ddev_Fit[i][j]; + } + } + //Svis = 2.0 * mu * J * Fi_ddev_Fit; + + // Tangent matrix contributions due to viscosity + double r2d = 2.0 / nsd; + for (int b = 0; b < eNoN; ++b) { + for (int a = 0; a < eNoN; ++a) { + double Nx_Fi_Nx_Fi = 0.0; + for (int i = 0; i < nsd; ++i) { + Nx_Fi_Nx_Fi += Nx_Fi(i,a) * Nx_Fi(i,b); + } + + for (int i = 0; i < nsd; ++i) { + for (int j = 0; j < nsd; ++j) { + int ii = i * nsd + j; + + // Derivative of the residual w.r.t displacement + Kvis_u(ii,a,b) = mu * J * (2.0 * + (ddev_Nx_Fi(i,a) * Nx_Fi(j,b) - ddev_Nx_Fi(i,b) * Nx_Fi(j,a)) - + (Nx_Fi_Nx_Fi * vx_Fi[i][j] + Nx_Fi(i,b) * vx_Fi_Nx_Fi(j,a) - + r2d * Nx_Fi(i,a) * vx_Fi_Nx_Fi(j,b))); + + // Derivative of the residual w.r.t velocity + Kvis_v(ii,a,b) = mu * J * (Nx_Fi_Nx_Fi * Idm[i][j] + + Nx_Fi(i,b) * Nx_Fi(j,a) - r2d * Nx_Fi(i,a) * Nx_Fi(j,b)); + } + } + } + } +} + + +/** + * @brief Get the solid viscous PK2 stress and corresponding tangent matrix contributions + * Calls the appropriate function based on the viscosity type, either viscous + * pseudo-potential or Newtonian viscosity model. + * + * @tparam nsd Number of spatial dimensions + * @param[in] lDmn Domain object + * @param[in] eNoN Number of nodes in an element + * @param[in] Nx Shape function gradient matrix + * @param[in] vx Velocity gradient matrix + * @param[in] F Deformation gradient matrix + * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix + * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement + * @param[out] Kvis_v Viscous tangent matrix contribution due to velocity + */ +template +void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Array& Nx, const double vx[nsd][nsd], const double F[nsd][nsd], + Array& Svis, Array3& Kvis_u, Array3& Kvis_v) { + + switch (lDmn.solid_visc.viscType) { + case consts::SolidViscosityModelType::viscType_Newtonian: + get_visc_stress_newt(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v); + break; + + case consts::SolidViscosityModelType::viscType_Potential: + get_visc_stress_pot(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v); + break; + } +} + }; #endif diff --git a/Code/Source/svFSI/read_files.cpp b/Code/Source/svFSI/read_files.cpp index ad02588d..cce6cf79 100644 --- a/Code/Source/svFSI/read_files.cpp +++ b/Code/Source/svFSI/read_files.cpp @@ -1299,9 +1299,9 @@ void read_domain(Simulation* simulation, EquationParameters* eq_params, eqType& } break; - case PhysicalProperyType::solid_viscosity: - rtmp = domain_params->solid_viscosity.value(); - break; + // case PhysicalProperyType::solid_viscosity: + // rtmp = domain_params->solid_viscosity.value(); + // break; case PhysicalProperyType::source_term: rtmp = domain_params->source_term.value(); @@ -1333,7 +1333,13 @@ void read_domain(Simulation* simulation, EquationParameters* eq_params, eqType& if ((lEq.dmn[iDmn].phys == EquationType::phys_fluid) || (lEq.dmn[iDmn].phys == EquationType::phys_stokes) || (lEq.dmn[iDmn].phys == EquationType::phys_CMM && !com_mod.cmmInit)) { - read_visc_model(simulation, eq_params, domain_params, lEq.dmn[iDmn]); + read_fluid_visc_model(simulation, eq_params, domain_params, lEq.dmn[iDmn]); + } + + // Set parameters for a fluid viscosity model. + if ((lEq.dmn[iDmn].phys == EquationType::phys_struct) || + (lEq.dmn[iDmn].phys == EquationType::phys_ustruct)) { + read_solid_visc_model(simulation, eq_params, domain_params, lEq.dmn[iDmn]); } } } @@ -2830,11 +2836,11 @@ void read_rmsh(Simulation* simulation, EquationParameters* eq_param) } //----------------- -// read_visc_model +// read_fluid_visc_model //----------------- -// Set the viscosity material model parameters for the given domain. +// Set the fluid viscosity material model parameters for the given domain. // -void read_visc_model(Simulation* simulation, EquationParameters* eq_params, DomainParameters* domain_params, dmnType& lDmn) +void read_fluid_visc_model(Simulation* simulation, EquationParameters* eq_params, DomainParameters* domain_params, dmnType& lDmn) { using namespace consts; @@ -2843,14 +2849,14 @@ void read_visc_model(Simulation* simulation, EquationParameters* eq_params, Doma FluidViscosityModelType vmodel_type; std::string vmodel_str; - if (domain_params->viscosity.model.defined()) { - vmodel_str = domain_params->viscosity.model.value(); + if (domain_params->fluid_viscosity.model.defined()) { + vmodel_str = domain_params->fluid_viscosity.model.value(); std::transform(vmodel_str.begin(), vmodel_str.end(), vmodel_str.begin(), ::tolower); try { vmodel_type = fluid_viscosity_model_name_to_type.at(vmodel_str); } catch (const std::out_of_range& exception) { - throw std::runtime_error("Unknown viscosity model '" + vmodel_str + "'."); + throw std::runtime_error("Unknown fluid viscosity model '" + vmodel_str + "'."); } } else { vmodel_type = FluidViscosityModelType::viscType_Const; @@ -2858,19 +2864,57 @@ void read_visc_model(Simulation* simulation, EquationParameters* eq_params, Doma // Set the parameters for the given viscosity model. // - auto& viscosity_params = domain_params->viscosity; + auto& viscosity_params = domain_params->fluid_viscosity; try { - set_viscosity_props[vmodel_type](simulation, viscosity_params, lDmn); + set_fluid_viscosity_props[vmodel_type](simulation, viscosity_params, lDmn); } catch (const std::bad_function_call& exception) { - throw std::runtime_error("[read_visc_model] Viscosity model '" + vmodel_str + "' is not supported."); + throw std::runtime_error("[read_fluid_visc_model] Viscosity model '" + vmodel_str + "' is not supported."); } - if ((lDmn.phys == EquationType::phys_stokes) && (lDmn.visc.viscType != FluidViscosityModelType::viscType_Const)) { + if ((lDmn.phys == EquationType::phys_stokes) && (lDmn.fluid_visc.viscType != FluidViscosityModelType::viscType_Const)) { throw std::runtime_error("Only constant viscosity is allowed for Stokes flow."); } } +//----------------- +// read_solid_visc_model +//----------------- +// Set the solid viscosity material model parameters for the given domain. +// +void read_solid_visc_model(Simulation* simulation, EquationParameters* eq_params, DomainParameters* domain_params, dmnType& lDmn) +{ + using namespace consts; + + // Get viscosity model. + // + SolidViscosityModelType vmodel_type; + std::string vmodel_str; + + if (domain_params->solid_viscosity.model.defined()) { + vmodel_str = domain_params->solid_viscosity.model.value(); + std::transform(vmodel_str.begin(), vmodel_str.end(), vmodel_str.begin(), ::tolower); + + try { + vmodel_type = solid_viscosity_model_name_to_type.at(vmodel_str); + } catch (const std::out_of_range& exception) { + throw std::runtime_error("Unknown solid viscosity model '" + vmodel_str + "'."); + } + } else { + vmodel_type = SolidViscosityModelType::viscType_Newtonian; + } + + // Set the parameters for the given viscosity model. + // + auto& viscosity_params = domain_params->solid_viscosity; + + try { + set_solid_viscosity_props[vmodel_type](simulation, viscosity_params, lDmn); + } catch (const std::bad_function_call& exception) { + throw std::runtime_error("[read_solid_visc_model] Viscosity model '" + vmodel_str + "' is not supported."); + } +} + //-------------------- // read_wall_props_ff //-------------------- diff --git a/Code/Source/svFSI/read_files.h b/Code/Source/svFSI/read_files.h index 16cdc07a..656b190c 100644 --- a/Code/Source/svFSI/read_files.h +++ b/Code/Source/svFSI/read_files.h @@ -86,7 +86,9 @@ namespace read_files_ns { void read_trac_bcff(ComMod& com_mod, MBType& lMB, faceType& lFa, const std::string& file_name); - void read_visc_model(Simulation* simulation, EquationParameters* eq_params, DomainParameters* domain_params, dmnType& lDmn); + void read_fluid_visc_model(Simulation* simulation, EquationParameters* eq_params, DomainParameters* domain_params, dmnType& lDmn); + + void read_solid_visc_model(Simulation* simulation, EquationParameters* eq_params, DomainParameters* domain_params, dmnType& lDmn); void read_wall_props_ff(ComMod& com_mod, const std::string& file_path, const int iM, const int iFa); diff --git a/Code/Source/svFSI/set_equation_props.h b/Code/Source/svFSI/set_equation_props.h index c9bc5279..f20b2627 100644 --- a/Code/Source/svFSI/set_equation_props.h +++ b/Code/Source/svFSI/set_equation_props.h @@ -330,7 +330,7 @@ SetEquationPropertiesMapType set_equation_props = { propL[1][n] = PhysicalProperyType::elasticity_modulus; propL[2][n] = PhysicalProperyType::poisson_ratio; propL[3][n] = PhysicalProperyType::damping; - propL[4][n] = PhysicalProperyType::solid_viscosity; + //propL[4][n] = PhysicalProperyType::solid_viscosity; propL[5][n] = PhysicalProperyType::f_x; propL[6][n] = PhysicalProperyType::f_y; if (simulation->com_mod.nsd == 3) { @@ -342,7 +342,7 @@ SetEquationPropertiesMapType set_equation_props = { propL[0][n] = PhysicalProperyType::solid_density; propL[1][n] = PhysicalProperyType::elasticity_modulus; propL[2][n] = PhysicalProperyType::poisson_ratio; - propL[3][n] = PhysicalProperyType::solid_viscosity; + //propL[3][n] = PhysicalProperyType::solid_viscosity; propL[4][n] = PhysicalProperyType::ctau_M; propL[5][n] = PhysicalProperyType::ctau_C; propL[6][n] = PhysicalProperyType::f_x; @@ -570,7 +570,7 @@ SetEquationPropertiesMapType set_equation_props = { propL[1][0] = PhysicalProperyType::damping; propL[2][0] = PhysicalProperyType::elasticity_modulus; propL[3][0] = PhysicalProperyType::poisson_ratio; - propL[4][0] = PhysicalProperyType::solid_viscosity; + //propL[4][0] = PhysicalProperyType::solid_viscosity; propL[5][0] = PhysicalProperyType::f_x; propL[6][0] = PhysicalProperyType::f_y; if (simulation->com_mod.nsd == 3) { @@ -614,7 +614,7 @@ SetEquationPropertiesMapType set_equation_props = { propL[0][0] = PhysicalProperyType::solid_density; propL[1][0] = PhysicalProperyType::elasticity_modulus; propL[2][0] = PhysicalProperyType::poisson_ratio; - propL[3][0] = PhysicalProperyType::solid_viscosity; + //propL[3][0] = PhysicalProperyType::solid_viscosity; propL[4][0] = PhysicalProperyType::ctau_M; propL[5][0] = PhysicalProperyType::ctau_C; propL[6][0] = PhysicalProperyType::f_x; diff --git a/Code/Source/svFSI/set_viscosity_props.h b/Code/Source/svFSI/set_viscosity_props.h index 7e03fe68..0730471e 100644 --- a/Code/Source/svFSI/set_viscosity_props.h +++ b/Code/Source/svFSI/set_viscosity_props.h @@ -32,49 +32,51 @@ // S e t V i s c o s i t y P r o p e r t i e s // /////////////////////////////////////////////////////////// // -// The 'set_viscosity_props ' map defined here sets fluid +// The 'set_fluid_viscosity_props ' map defined here sets fluid +// viscosity properties from values read in from a file. +// The 'set_solid_viscosity_props ' map defined here sets solid // viscosity properties from values read in from a file. -using SetViscosityPropertiesMapType = std::map>; -SetViscosityPropertiesMapType set_viscosity_props = { +SetFluidViscosityPropertiesMapType set_fluid_viscosity_props = { //---------------------------// // viscType_Const // //---------------------------// // -{consts::FluidViscosityModelType::viscType_Const, [](Simulation* simulation, ViscosityParameters& params, dmnType& lDmn) -> void +{consts::FluidViscosityModelType::viscType_Const, [](Simulation* simulation, FluidViscosityParameters& params, dmnType& lDmn) -> void { using namespace consts; auto& com_mod = simulation->get_com_mod(); - lDmn.visc.viscType = FluidViscosityModelType::viscType_Const; - lDmn.visc.mu_i = params.newtonian_model.constant_value.value(); + lDmn.fluid_visc.viscType = FluidViscosityModelType::viscType_Const; + lDmn.fluid_visc.mu_i = params.newtonian_model.constant_value.value(); } }, //---------------------------// // viscType_CY // //---------------------------// // -{consts::FluidViscosityModelType::viscType_CY, [](Simulation* simulation, ViscosityParameters& params, dmnType& lDmn) -> void +{consts::FluidViscosityModelType::viscType_CY, [](Simulation* simulation, FluidViscosityParameters& params, dmnType& lDmn) -> void { using namespace consts; auto& com_mod = simulation->get_com_mod(); auto& model_params = params.carreau_yasuda_model; - lDmn.visc.viscType = FluidViscosityModelType::viscType_CY; + lDmn.fluid_visc.viscType = FluidViscosityModelType::viscType_CY; - lDmn.visc.mu_i = model_params.limiting_high_shear_rate_viscosity.value(); - lDmn.visc.mu_o = model_params.limiting_low_shear_rate_viscosity.value(); - lDmn.visc.lam = model_params.shear_rate_tensor_multipler.value(); - lDmn.visc.a = model_params.shear_rate_tensor_exponent.value(); - lDmn.visc.n = model_params.power_law_index.value(); + lDmn.fluid_visc.mu_i = model_params.limiting_high_shear_rate_viscosity.value(); + lDmn.fluid_visc.mu_o = model_params.limiting_low_shear_rate_viscosity.value(); + lDmn.fluid_visc.lam = model_params.shear_rate_tensor_multipler.value(); + lDmn.fluid_visc.a = model_params.shear_rate_tensor_exponent.value(); + lDmn.fluid_visc.n = model_params.power_law_index.value(); - if (lDmn.visc.mu_i > lDmn.visc.mu_o) { + if (lDmn.fluid_visc.mu_i > lDmn.fluid_visc.mu_o) { throw std::runtime_error("Unexpected inputs for Carreau-Yasuda model. " - "High shear-rate viscosity value (" + std::to_string(lDmn.visc.mu_i) + - " should be larger than low shear-rate value " + std::to_string(lDmn.visc.mu_i) + "."); + "High shear-rate viscosity value (" + std::to_string(lDmn.fluid_visc.mu_i) + + " should be larger than low shear-rate value " + std::to_string(lDmn.fluid_visc.mu_i) + "."); } } }, @@ -83,22 +85,61 @@ SetViscosityPropertiesMapType set_viscosity_props = { // viscType_Cass // //---------------------------// // -{consts::FluidViscosityModelType::viscType_Cass, [](Simulation* simulation, ViscosityParameters& params, dmnType& lDmn) -> void +{consts::FluidViscosityModelType::viscType_Cass, [](Simulation* simulation, FluidViscosityParameters& params, dmnType& lDmn) -> void { using namespace consts; auto& com_mod = simulation->get_com_mod(); auto& model_params = params.cassons_model; - lDmn.visc.viscType = FluidViscosityModelType::viscType_Cass; - lDmn.visc.mu_i = model_params.asymptotic_viscosity(); - lDmn.visc.mu_o = model_params.yield_stress(); + lDmn.fluid_visc.viscType = FluidViscosityModelType::viscType_Cass; + lDmn.fluid_visc.mu_i = model_params.asymptotic_viscosity(); + lDmn.fluid_visc.mu_o = model_params.yield_stress(); if (model_params.low_shear_rate_threshold.defined()) { - lDmn.visc.lam = model_params.low_shear_rate_threshold(); + lDmn.fluid_visc.lam = model_params.low_shear_rate_threshold(); } else { - lDmn.visc.lam = 0.5; + lDmn.fluid_visc.lam = 0.5; } } }, }; + + + + + +using SetSolidViscosityPropertiesMapType = std::map>; + +SetSolidViscosityPropertiesMapType set_solid_viscosity_props = { + +//---------------------------// +// viscType_Newtonian // +//---------------------------// +// +{consts::SolidViscosityModelType::viscType_Newtonian, [](Simulation* simulation, SolidViscosityParameters& params, dmnType& lDmn) -> void +{ + using namespace consts; + auto& com_mod = simulation->get_com_mod(); + + lDmn.solid_visc.viscType = SolidViscosityModelType::viscType_Newtonian; + lDmn.solid_visc.mu = params.newtonian_model.constant_value.value(); +} }, + +//---------------------------// +// viscType_Potential // +//---------------------------// +// +{consts::SolidViscosityModelType::viscType_Potential, [](Simulation* simulation, SolidViscosityParameters& params, dmnType& lDmn) -> void +{ + using namespace consts; + auto& com_mod = simulation->get_com_mod(); + + lDmn.solid_visc.viscType = SolidViscosityModelType::viscType_Potential; + lDmn.solid_visc.mu = params.potential_model.constant_value.value(); +} }, + +}; + + diff --git a/Code/Source/svFSI/stokes.cpp b/Code/Source/svFSI/stokes.cpp index 5b9f96ba..a90949cf 100644 --- a/Code/Source/svFSI/stokes.cpp +++ b/Code/Source/svFSI/stokes.cpp @@ -255,7 +255,7 @@ void stokes_2d_c(ComMod& com_mod, const int lStab, const int eNoNw, const int eN int cDmn = com_mod.cDmn; auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double mu = dmn.visc.mu_i; + double mu = dmn.fluid_visc.mu_i; double ctM = dmn.prop[PhysicalProperyType::ctau_M]; Vector fb(2); @@ -378,7 +378,7 @@ void stokes_2d_m(ComMod& com_mod, const int eNoNw, const int eNoNq, const double auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double mu = dmn.visc.mu_i; + double mu = dmn.fluid_visc.mu_i; Vector fb(2); fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; @@ -488,7 +488,7 @@ void stokes_3d_c(ComMod& com_mod, const int lStab, const int eNoNw, const int eN int cDmn = com_mod.cDmn; auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double mu = dmn.visc.mu_i; + double mu = dmn.fluid_visc.mu_i; double ctM = dmn.prop[PhysicalProperyType::ctau_M]; Vector fb(3); @@ -604,7 +604,7 @@ void stokes_3d_m(ComMod& com_mod, const int eNoNw, const int eNoNq, const double auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double mu = dmn.visc.mu_i; + double mu = dmn.fluid_visc.mu_i; Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; diff --git a/Code/Source/svFSI/sv_struct.cpp b/Code/Source/svFSI/sv_struct.cpp index f9755d60..d5733099 100644 --- a/Code/Source/svFSI/sv_struct.cpp +++ b/Code/Source/svFSI/sv_struct.cpp @@ -387,7 +387,7 @@ void struct_2d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, // Set parameters // double rho = dmn.prop.at(PhysicalProperyType::solid_density); - double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); + //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); double dmp = dmn.prop.at(PhysicalProperyType::damping); Vector fb({dmn.prop.at(PhysicalProperyType::f_x), dmn.prop.at(PhysicalProperyType::f_y)}); double afu = eq.af * eq.beta*dt*dt; @@ -445,6 +445,9 @@ void struct_2d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, S0(1,0) = S0(0,1); + // TODO: Update solid viscosity contribution below + double mu = 0.0; + double Jac = mat_det(F, 2); auto Fi = mat_inv(F, 2); @@ -616,7 +619,7 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in // Set parameters // double rho = dmn.prop.at(PhysicalProperyType::solid_density); - double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); + //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); double dmp = dmn.prop.at(PhysicalProperyType::damping); double fb[3]{dmn.prop.at(PhysicalProperyType::f_x), dmn.prop.at(PhysicalProperyType::f_y), @@ -691,38 +694,38 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in S0[2][1] = S0[1][2]; S0[0][2] = S0[2][0]; - double Jac = mat_fun_carray::mat_det<3>(F); + // double Jac = mat_fun_carray::mat_det<3>(F); - double Fi[3][3]; - mat_fun_carray::mat_inv<3>(F, Fi); + // double Fi[3][3]; + // mat_fun_carray::mat_inv<3>(F, Fi); - // Viscous contribution - // Velocity gradient in current configuration - double VxFi[3][3]; - mat_fun_carray::mat_mul(vx, Fi, VxFi); + // // Viscous contribution + // // Velocity gradient in current configuration + // double VxFi[3][3]; + // mat_fun_carray::mat_mul(vx, Fi, VxFi); - // Deviatoric strain tensor - double VxFi_sym[3][3]; - mat_fun_carray::mat_symm<3>(VxFi,VxFi_sym); + // // Deviatoric strain tensor + // double VxFi_sym[3][3]; + // mat_fun_carray::mat_symm<3>(VxFi,VxFi_sym); - double ddev[3][3]; - mat_fun_carray::mat_dev<3>(VxFi_sym, ddev); + // double ddev[3][3]; + // mat_fun_carray::mat_dev<3>(VxFi_sym, ddev); - // 2nd Piola-Kirchhoff stress due to viscosity - double Fi_transp[3][3]; - mat_fun_carray::transpose<3>(Fi, Fi_transp); + // // 2nd Piola-Kirchhoff stress due to viscosity + // double Fi_transp[3][3]; + // mat_fun_carray::transpose<3>(Fi, Fi_transp); - double Svis[3][3]; - mat_fun_carray::mat_mul<3>(ddev, Fi_transp, Svis); + // double Svis[3][3]; + // mat_fun_carray::mat_mul<3>(ddev, Fi_transp, Svis); - double Fi_Svis_m[3][3]; - mat_fun_carray::mat_mul<3>(Fi, Svis, Fi_Svis_m); + // double Fi_Svis_m[3][3]; + // mat_fun_carray::mat_mul<3>(Fi, Svis, Fi_Svis_m); - for (int i = 0; i < 3; i++) { - for (int j = 0; j < 3; j++) { - Svis[i][j] = 2.0 * mu * Jac * Fi_Svis_m[i][j]; - } - } + // for (int i = 0; i < 3; i++) { + // for (int j = 0; j < 3; j++) { + // Svis[i][j] = 2.0 * mu * Jac * Fi_Svis_m[i][j]; + // } + // } // Initialize tensor indexing. mat_fun_carray::ten_init(3); @@ -735,10 +738,18 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in mat_models_carray::get_pk2cc<3>(com_mod, cep_mod, dmn, F, nFn, fN, ya_g, S, Dm); + + // Viscous 2nd Piola-Kirchhoff stress and tangent contributions + Array Svis(3,3); + Array3 Kvis_u(9, eNoN, eNoN); + Array3 Kvis_v(9, eNoN, eNoN); + + mat_models_carray::get_visc_stress_and_tangent<3>(dmn, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v); + // Elastic + Viscous stresses for (int i = 0; i < 3; i++) { for (int j = 0; j < 3; j++) { - S[i][j] += Svis[i][j]; + S[i][j] += Svis(i,j); } } @@ -807,31 +818,31 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(5,2,a) = (Nx(2,a)*F[2][0] + F[2][2]*Nx(0,a)); } - // Below quantities are used for viscous stress contribution - // Shape function gradients in the current configuration - // - Array NxFi(3,eNoN), DdNx(3,eNoN), VxNx(3,eNoN); + // // Below quantities are used for viscous stress contribution + // // Shape function gradients in the current configuration + // // + // Array NxFi(3,eNoN), DdNx(3,eNoN), VxNx(3,eNoN); - for (int a = 0; a < eNoN; a++) { - NxFi(0,a) = Nx(0,a)*Fi[0][0] + Nx(1,a)*Fi[1][0] + Nx(2,a)*Fi[2][0]; - NxFi(1,a) = Nx(0,a)*Fi[0][1] + Nx(1,a)*Fi[1][1] + Nx(2,a)*Fi[2][1]; - NxFi(2,a) = Nx(0,a)*Fi[0][2] + Nx(1,a)*Fi[1][2] + Nx(2,a)*Fi[2][2]; + // for (int a = 0; a < eNoN; a++) { + // NxFi(0,a) = Nx(0,a)*Fi[0][0] + Nx(1,a)*Fi[1][0] + Nx(2,a)*Fi[2][0]; + // NxFi(1,a) = Nx(0,a)*Fi[0][1] + Nx(1,a)*Fi[1][1] + Nx(2,a)*Fi[2][1]; + // NxFi(2,a) = Nx(0,a)*Fi[0][2] + Nx(1,a)*Fi[1][2] + Nx(2,a)*Fi[2][2]; - DdNx(0,a) = ddev[0][0]*NxFi(0,a) + ddev[0][1]*NxFi(1,a) + ddev[0][2]*NxFi(2,a); - DdNx(1,a) = ddev[1][0]*NxFi(0,a) + ddev[1][1]*NxFi(1,a) + ddev[1][2]*NxFi(2,a); - DdNx(2,a) = ddev[2][0]*NxFi(0,a) + ddev[2][1]*NxFi(1,a) + ddev[2][2]*NxFi(2,a); + // DdNx(0,a) = ddev[0][0]*NxFi(0,a) + ddev[0][1]*NxFi(1,a) + ddev[0][2]*NxFi(2,a); + // DdNx(1,a) = ddev[1][0]*NxFi(0,a) + ddev[1][1]*NxFi(1,a) + ddev[1][2]*NxFi(2,a); + // DdNx(2,a) = ddev[2][0]*NxFi(0,a) + ddev[2][1]*NxFi(1,a) + ddev[2][2]*NxFi(2,a); - VxNx(0,a) = VxFi[0][0]*NxFi(0,a) + VxFi[1][0]*NxFi(1,a) + VxFi[2][0]*NxFi(2,a); - VxNx(1,a) = VxFi[0][1]*NxFi(0,a) + VxFi[1][1]*NxFi(1,a) + VxFi[2][1]*NxFi(2,a); - VxNx(2,a) = VxFi[0][2]*NxFi(0,a) + VxFi[1][2]*NxFi(1,a) + VxFi[2][2]*NxFi(2,a); - } + // VxNx(0,a) = VxFi[0][0]*NxFi(0,a) + VxFi[1][0]*NxFi(1,a) + VxFi[2][0]*NxFi(2,a); + // VxNx(1,a) = VxFi[0][1]*NxFi(0,a) + VxFi[1][1]*NxFi(1,a) + VxFi[2][1]*NxFi(2,a); + // VxNx(2,a) = VxFi[0][2]*NxFi(0,a) + VxFi[1][2]*NxFi(1,a) + VxFi[2][2]*NxFi(2,a); + // } // Local stiffness tensor double r13 = 1.0 / 3.0; double r23 = 2.0 / 3.0; - double rmu = afu * mu * Jac; - double rmv = afv * mu * Jac; - double NxSNx, T1, NxNx, BmDBm, Tv; + // double rmu = afu * mu * Jac; + // double rmv = afv * mu * Jac; + double NxSNx, T1, NxNx, BmDBm; Array DBm(6,3); @@ -850,7 +861,7 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in // Material Stiffness (Bt*D*B) mat_fun_carray::mat_mul6x3<3>(Dm, Bm.rslice(b), DBm); - NxNx = NxFi(0,a)*NxFi(0,b) + NxFi(1,a)*NxFi(1,b) + NxFi(2,a)*NxFi(2,b); + // NxNx = NxFi(0,a)*NxFi(0,b) + NxFi(1,a)*NxFi(1,b) + NxFi(2,a)*NxFi(2,b); // dM1/du1 // Material stiffness: Bt*D*B @@ -858,11 +869,11 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,0,a)*DBm(2,0) + Bm(3,0,a)*DBm(3,0) + Bm(4,0,a)*DBm(4,0) + Bm(5,0,a)*DBm(5,0); - // Viscous terms contribution - Tv = (2.0*(DdNx(0,a)*NxFi(0,b) - DdNx(0,b)*NxFi(0,a)) - (NxNx*VxFi[0][0] + NxFi(0,b)*VxNx(0,a) - - r23*NxFi(0,a)*VxNx(0,b))) * rmu + (r13*NxFi(0,a)*NxFi(0,b) + NxNx) * rmv; + // // Viscous terms contribution + // Tv = (2.0*(DdNx(0,a)*NxFi(0,b) - DdNx(0,b)*NxFi(0,a)) - (NxNx*VxFi[0][0] + NxFi(0,b)*VxNx(0,a) - + // r23*NxFi(0,a)*VxNx(0,b))) * rmu + (r13*NxFi(0,a)*NxFi(0,b) + NxNx) * rmv; - lK(0,a,b) = lK(0,a,b) + w*(T1 + afu*BmDBm + Tv); + lK(0,a,b) = lK(0,a,b) + w*( T1 + afu*(BmDBm + Kvis_u(0,a,b)) + afv*Kvis_v(0,a,b) ); // dM1/du2 // Material stiffness: Bt*D*B @@ -870,13 +881,13 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,0,a)*DBm(2,1) + Bm(3,0,a)*DBm(3,1) + Bm(4,0,a)*DBm(4,1) + Bm(5,0,a)*DBm(5,1); - // Viscous terms contribution - Tv = (2.0*(DdNx(0,a)*NxFi(1,b) - DdNx(0,b)*NxFi(1,a)) - - (NxNx*VxFi[0][1] + NxFi(0,b)*VxNx(1,a) - - r23*NxFi(0,a)*VxNx(1,b))) * rmu - + (NxFi(1,a)*NxFi(0,b) - r23*NxFi(0,a)*NxFi(1,b)) * rmv; + // // Viscous terms contribution + // Tv = (2.0*(DdNx(0,a)*NxFi(1,b) - DdNx(0,b)*NxFi(1,a)) + // - (NxNx*VxFi[0][1] + NxFi(0,b)*VxNx(1,a) + // - r23*NxFi(0,a)*VxNx(1,b))) * rmu + // + (NxFi(1,a)*NxFi(0,b) - r23*NxFi(0,a)*NxFi(1,b)) * rmv; - lK(1,a,b) = lK(1,a,b) + w*(afu*BmDBm + Tv); + lK(1,a,b) = lK(1,a,b) + w*( afu*(BmDBm + Kvis_u(1,a,b)) + afv*(Kvis_v(1,a,b)) ); // dM1/du3 // Material stiffness: Bt*D*B @@ -885,12 +896,12 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(4,0,a)*DBm(4,2) + Bm(5,0,a)*DBm(5,2); // Viscous terms contribution - Tv = (2.0*(DdNx(0,a)*NxFi(2,b) - DdNx(0,b)*NxFi(2,a)) - - (NxNx*VxFi[0][2] + NxFi(0,b)*VxNx(2,a) - - r23*NxFi(0,a)*VxNx(2,b))) * rmu + - (NxFi(2,a)*NxFi(0,b) - r23*NxFi(0,a)*NxFi(2,b)) * rmv; + // Tv = (2.0*(DdNx(0,a)*NxFi(2,b) - DdNx(0,b)*NxFi(2,a)) - + // (NxNx*VxFi[0][2] + NxFi(0,b)*VxNx(2,a) - + // r23*NxFi(0,a)*VxNx(2,b))) * rmu + + // (NxFi(2,a)*NxFi(0,b) - r23*NxFi(0,a)*NxFi(2,b)) * rmv; - lK(2,a,b) = lK(2,a,b) + w*(afu*BmDBm + Tv); + lK(2,a,b) = lK(2,a,b) + w*( afu*(BmDBm + Kvis_u(2,a,b)) + afv*Kvis_v(2,a,b) ); // dM2/du1 // Material stiffness: Bt*D*B @@ -899,12 +910,12 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(4,1,a)*DBm(4,0) + Bm(5,1,a)*DBm(5,0); // Viscous terms contribution - Tv = (2.0*(DdNx(1,a)*NxFi(0,b) - DdNx(1,b)*NxFi(0,a)) - - (NxNx*VxFi[1][0] + NxFi(1,b)*VxNx(0,a) - - r23*NxFi(1,a)*VxNx(0,b))) * rmu + - (NxFi(0,a)*NxFi(1,b) - r23*NxFi(1,a)*NxFi(0,b)) * rmv; + // Tv = (2.0*(DdNx(1,a)*NxFi(0,b) - DdNx(1,b)*NxFi(0,a)) - + // (NxNx*VxFi[1][0] + NxFi(1,b)*VxNx(0,a) - + // r23*NxFi(1,a)*VxNx(0,b))) * rmu + + // (NxFi(0,a)*NxFi(1,b) - r23*NxFi(1,a)*NxFi(0,b)) * rmv; - lK(dof+0,a,b) = lK(dof+0,a,b) + w*(afu*BmDBm + Tv); + lK(dof+0,a,b) = lK(dof+0,a,b) + w*( afu*(BmDBm + Kvis_u(dof+0,a,b)) + afv*Kvis_v(dof+0,a,b) ); // dM2/du2 // Material stiffness: Bt*D*B @@ -913,12 +924,12 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(4,1,a)*DBm(4,1) + Bm(5,1,a)*DBm(5,1); // Viscous terms contribution - Tv = (2.0*(DdNx(1,a)*NxFi(1,b) - DdNx(1,b)*NxFi(1,a)) - - (NxNx*VxFi[1][1] + NxFi(1,b)*VxNx(1,a) - - r23*NxFi(1,a)*VxNx(1,b))) * rmu + - (r13*NxFi(1,a)*NxFi(1,b) + NxNx) * rmv; + // Tv = (2.0*(DdNx(1,a)*NxFi(1,b) - DdNx(1,b)*NxFi(1,a)) - + // (NxNx*VxFi[1][1] + NxFi(1,b)*VxNx(1,a) - + // r23*NxFi(1,a)*VxNx(1,b))) * rmu + + // (r13*NxFi(1,a)*NxFi(1,b) + NxNx) * rmv; - lK(dof+1,a,b) = lK(dof+1,a,b) + w*(T1 + afu*BmDBm + Tv); + lK(dof+1,a,b) = lK(dof+1,a,b) + w*(T1 + afu*(BmDBm + Kvis_u(dof+1,a,b)) + afv*Kvis_v(dof+1,a,b) ); // dM2/du3 // Material stiffness: Bt*D*B @@ -927,12 +938,12 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(4,1,a)*DBm(4,2) + Bm(5,1,a)*DBm(5,2); // Viscous terms contribution - Tv = (2.0*(DdNx(1,a)*NxFi(2,b) - DdNx(1,b)*NxFi(2,a)) - - (NxNx*VxFi[1][2] + NxFi(1,b)*VxNx(2,a) - - r23*NxFi(1,a)*VxNx(2,b))) * rmu + (NxFi(2,a)*NxFi(1,b) - - r23*NxFi(1,a)*NxFi(2,b)) * rmv; + // Tv = (2.0*(DdNx(1,a)*NxFi(2,b) - DdNx(1,b)*NxFi(2,a)) - + // (NxNx*VxFi[1][2] + NxFi(1,b)*VxNx(2,a) - + // r23*NxFi(1,a)*VxNx(2,b))) * rmu + (NxFi(2,a)*NxFi(1,b) - + // r23*NxFi(1,a)*NxFi(2,b)) * rmv; - lK(dof+2,a,b) = lK(dof+2,a,b) + w*(afu*BmDBm + Tv); + lK(dof+2,a,b) = lK(dof+2,a,b) + w*( afu*(BmDBm + Kvis_u(dof+2,a,b)) + afv*Kvis_v(dof+2,a,b) ); // dM3/du1 // Material stiffness: Bt*D*B @@ -941,12 +952,12 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(4,2,a)*DBm(4,0) + Bm(5,2,a)*DBm(5,0); // Viscous terms contribution - Tv = (2.0*(DdNx(2,a)*NxFi(0,b) - DdNx(2,b)*NxFi(0,a)) - - (NxNx*VxFi[2][0] + NxFi(2,b)*VxNx(0,a) - - r23*NxFi(2,a)*VxNx(0,b))) * rmu + (NxFi(0,a)*NxFi(2,b) - - r23*NxFi(2,a)*NxFi(0,b)) * rmv; + // Tv = (2.0*(DdNx(2,a)*NxFi(0,b) - DdNx(2,b)*NxFi(0,a)) - + // (NxNx*VxFi[2][0] + NxFi(2,b)*VxNx(0,a) - + // r23*NxFi(2,a)*VxNx(0,b))) * rmu + (NxFi(0,a)*NxFi(2,b) - + // r23*NxFi(2,a)*NxFi(0,b)) * rmv; - lK(2*dof+0,a,b) = lK(2*dof+0,a,b) + w*(afu*BmDBm + Tv); + lK(2*dof+0,a,b) = lK(2*dof+0,a,b) + w*( afu*(BmDBm + Kvis_u(2*dof+0,a,b)) + afv*Kvis_v(2*dof+0,a,b) ); // dM3/du2 // Material stiffness: Bt*D*B @@ -955,12 +966,12 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(4,2,a)*DBm(4,1) + Bm(5,2,a)*DBm(5,1); // Viscous terms contribution - Tv = (2.0*(DdNx(2,a)*NxFi(1,b) - DdNx(2,b)*NxFi(1,a)) - - (NxNx*VxFi[2][1] + NxFi(2,b)*VxNx(1,a) - - r23*NxFi(2,a)*VxNx(1,b))) * rmu + (NxFi(1,a)*NxFi(2,b) - - r23*NxFi(2,a)*NxFi(1,b)) * rmv; + // Tv = (2.0*(DdNx(2,a)*NxFi(1,b) - DdNx(2,b)*NxFi(1,a)) - + // (NxNx*VxFi[2][1] + NxFi(2,b)*VxNx(1,a) - + // r23*NxFi(2,a)*VxNx(1,b))) * rmu + (NxFi(1,a)*NxFi(2,b) - + // r23*NxFi(2,a)*NxFi(1,b)) * rmv; - lK(2*dof+1,a,b) = lK(2*dof+1,a,b) + w*(afu*BmDBm + Tv); + lK(2*dof+1,a,b) = lK(2*dof+1,a,b) + w*( afu*(BmDBm + Kvis_u(2*dof+1,a,b)) + afv*Kvis_v(2*dof+1,a,b) ); // dM3/du3 // Material stiffness: Bt*D*B @@ -968,13 +979,13 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,2,a)*DBm(2,2) + Bm(3,2,a)*DBm(3,2) + Bm(4,2,a)*DBm(4,2) + Bm(5,2,a)*DBm(5,2); - // Viscous terms contribution - Tv = (2.0*(DdNx(2,a)*NxFi(2,b) - DdNx(2,b)*NxFi(2,a)) - - (NxNx*VxFi[2][2] + NxFi(2,b)*VxNx(2,a) - - r23*NxFi(2,a)*VxNx(2,b))) * rmu + - (r13*NxFi(2,a)*NxFi(2,b) + NxNx) * rmv; + // // Viscous terms contribution + // Tv = (2.0*(DdNx(2,a)*NxFi(2,b) - DdNx(2,b)*NxFi(2,a)) - + // (NxNx*VxFi[2][2] + NxFi(2,b)*VxNx(2,a) - + // r23*NxFi(2,a)*VxNx(2,b))) * rmu + + // (r13*NxFi(2,a)*NxFi(2,b) + NxNx) * rmv; - lK(2*dof+2,a,b) = lK(2*dof+2,a,b) + w*(T1 + afu*BmDBm + Tv); + lK(2*dof+2,a,b) = lK(2*dof+2,a,b) + w*( T1 + afu*(BmDBm + Kvis_u(2*dof+2,a,b)) + afv*Kvis_v(2*dof+2,a,b) ); } } @@ -1009,7 +1020,9 @@ void struct_3d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, // Set parameters // double rho = dmn.prop.at(PhysicalProperyType::solid_density); - double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); + //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); + // TODO: Do I need to update solid viscosity implementation here? + double mu = 0; double dmp = dmn.prop.at(PhysicalProperyType::damping); Vector fb({dmn.prop.at(PhysicalProperyType::f_x), dmn.prop.at(PhysicalProperyType::f_y), diff --git a/Code/Source/svFSI/ustruct.cpp b/Code/Source/svFSI/ustruct.cpp index 25ab4162..d49e030e 100644 --- a/Code/Source/svFSI/ustruct.cpp +++ b/Code/Source/svFSI/ustruct.cpp @@ -450,7 +450,9 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; double ctV = 36.0; - double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + // TODO: Update solid viscosity implementation here + double mu = 0; Vector fb(2); fb[0] = dmn.prop[PhysicalProperyType::f_x]; @@ -667,7 +669,9 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; double ctV = 36.0; - double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + // TODO: Update solid viscosity implementation here + double mu = 0; Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; @@ -931,7 +935,9 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; - double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + // TODO: Update solid viscosity implementation here + double mu = 0; double am = eq.am; double af = eq.af * eq.gam * dt; double afm = af / am; @@ -1228,7 +1234,9 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // Define parameters // - double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; + // TODO: Update solid viscosity implementation here + double mu = 0; Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; diff --git a/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml b/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml index ea9dec2c..bb627f16 100755 --- a/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml +++ b/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml @@ -48,9 +48,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml b/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml index bb68a5eb..87db25da 100755 --- a/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml +++ b/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml @@ -57,9 +57,9 @@ 1e-12 1.06 - + 0.04 - + 1.0 0.5 diff --git a/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml b/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml index ac825aa4..6e96ddb3 100755 --- a/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml +++ b/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml @@ -44,9 +44,9 @@ 1.06 - + 0.04 - + true 3 10 diff --git a/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml b/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml index d7407b2a..9e287d27 100644 --- a/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml +++ b/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml @@ -53,9 +53,9 @@ 1e-12 1.06 - + 0.04 - + 1.0 0.5 0.2 diff --git a/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml b/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml index 0ec907cb..4bcaec1f 100644 --- a/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml +++ b/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml @@ -54,9 +54,9 @@ 1.06 - + 0.04 - + 1.0 0.5 0.2 diff --git a/tests/cases/fluid/carreau_yasuda/README.md b/tests/cases/fluid/carreau_yasuda/README.md index 7ef7b6f5..0a348e15 100755 --- a/tests/cases/fluid/carreau_yasuda/README.md +++ b/tests/cases/fluid/carreau_yasuda/README.md @@ -25,13 +25,13 @@ where The model parameters are specified in the `Viscosity` sub-section ``` - + 0.022 0.22 0.11 0.644 0.392 - + ``` diff --git a/tests/cases/fluid/carreau_yasuda/svFSIplus.xml b/tests/cases/fluid/carreau_yasuda/svFSIplus.xml index 3432fbae..ad8dc11b 100644 --- a/tests/cases/fluid/carreau_yasuda/svFSIplus.xml +++ b/tests/cases/fluid/carreau_yasuda/svFSIplus.xml @@ -51,13 +51,13 @@ 1.06 - + 0.022 0.22 0.11 0.644 0.392 - + true diff --git a/tests/cases/fluid/casson/README.md b/tests/cases/fluid/casson/README.md index 87e10ca7..5528f21f 100755 --- a/tests/cases/fluid/casson/README.md +++ b/tests/cases/fluid/casson/README.md @@ -11,11 +11,11 @@ where $k_0(c)$ and $k_1(c)$ are functions of the hematocrit $c$. The model parameters are specified in the `Viscosity` sub-section ``` - + 0.3953 0.22803 0.5 - + ``` diff --git a/tests/cases/fluid/casson/svFSIplus.xml b/tests/cases/fluid/casson/svFSIplus.xml index 8856084a..be7ea31c 100644 --- a/tests/cases/fluid/casson/svFSIplus.xml +++ b/tests/cases/fluid/casson/svFSIplus.xml @@ -51,11 +51,11 @@ 1.06 - + 0.3953 0.22803 0.5 - + true diff --git a/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml b/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml index ea01561a..02efbf98 100755 --- a/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml +++ b/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml @@ -53,9 +53,9 @@ 0.0 100 - + 10 - + true diff --git a/tests/cases/fluid/dye_AD/svFSIplus.xml b/tests/cases/fluid/dye_AD/svFSIplus.xml index 72938238..896c8aa1 100644 --- a/tests/cases/fluid/dye_AD/svFSIplus.xml +++ b/tests/cases/fluid/dye_AD/svFSIplus.xml @@ -49,9 +49,9 @@ 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/iliac_artery/svFSIplus.xml b/tests/cases/fluid/iliac_artery/svFSIplus.xml index 06b1db1a..3ceb995f 100644 --- a/tests/cases/fluid/iliac_artery/svFSIplus.xml +++ b/tests/cases/fluid/iliac_artery/svFSIplus.xml @@ -53,9 +53,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/newtonian/README.md b/tests/cases/fluid/newtonian/README.md index 06386b07..0f98fd1c 100755 --- a/tests/cases/fluid/newtonian/README.md +++ b/tests/cases/fluid/newtonian/README.md @@ -6,7 +6,7 @@ Simulation of a 3D pipe flow problem using a Newtonian viscosity model. The model parameters are specified in the `Viscosity` sub-section ``` - + 0.04 - + ``` diff --git a/tests/cases/fluid/newtonian/svFSIplus.xml b/tests/cases/fluid/newtonian/svFSIplus.xml index 4cb18417..aa292b00 100644 --- a/tests/cases/fluid/newtonian/svFSIplus.xml +++ b/tests/cases/fluid/newtonian/svFSIplus.xml @@ -51,9 +51,9 @@ 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml index 9e2f9512..0c27eebc 100755 --- a/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml index 3d55be4f..d8ad9e1a 100755 --- a/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml index 11c6c7fd..8ebcabaa 100755 --- a/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml index bf9eea56..9a56223b 100755 --- a/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml index 2668aee4..ee6a0905 100644 --- a/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml index a9e762d6..09aa3366 100644 --- a/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/quadratic_tet10/svFSIplus.xml b/tests/cases/fluid/quadratic_tet10/svFSIplus.xml index 0be4a7b6..d578ee3f 100755 --- a/tests/cases/fluid/quadratic_tet10/svFSIplus.xml +++ b/tests/cases/fluid/quadratic_tet10/svFSIplus.xml @@ -48,9 +48,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fsi/pipe_3d/svFSIplus.xml b/tests/cases/fsi/pipe_3d/svFSIplus.xml index fb8f03c5..8b96e124 100755 --- a/tests/cases/fsi/pipe_3d/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml b/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml index 30ed00bb..7a5de1e0 100755 --- a/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml b/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml index 7232e927..58174209 100755 --- a/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml b/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml index 83a619a7..0118c347 100755 --- a/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml index 6c841099..53568c1a 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml index 9f7c24e5..330eafd0 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml index a2337808..be1c9150 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml index 77e5a9ee..09af1117 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml index 601115cb..3f05e908 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml @@ -53,9 +53,9 @@ false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml index ff3cd9cc..84ef7e11 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml @@ -53,9 +53,9 @@ false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml index 48712fbf..be491440 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml @@ -53,9 +53,9 @@ false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml index 815e63f3..c617c204 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml index 0238139f..71400ef3 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml index 54288f9b..f1e18a41 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml index f2fbdd7b..988ce0c3 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml index 60fac398..23f98e0a 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml index ff2a7758..517a754a 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/struct/LV_Holzapfel_passive/svFSIplus.xml b/tests/cases/struct/LV_Holzapfel_passive/svFSIplus.xml index d3d7007c..24ee9550 100644 --- a/tests/cases/struct/LV_Holzapfel_passive/svFSIplus.xml +++ b/tests/cases/struct/LV_Holzapfel_passive/svFSIplus.xml @@ -58,9 +58,9 @@ 1.0 1.0e6 0.483333 - + 0.0 - + 590.0 diff --git a/tests/cases/struct/LV_NeoHookean_passive/svFSIplus.xml b/tests/cases/struct/LV_NeoHookean_passive/svFSIplus.xml index 529b4c10..15f2023d 100644 --- a/tests/cases/struct/LV_NeoHookean_passive/svFSIplus.xml +++ b/tests/cases/struct/LV_NeoHookean_passive/svFSIplus.xml @@ -59,9 +59,9 @@ ST91 - + 0.0 - + diff --git a/tests/cases/struct/LV_NeoHookean_passive_genBC/svFSIplus.xml b/tests/cases/struct/LV_NeoHookean_passive_genBC/svFSIplus.xml index 4ce3b646..0e2aa36e 100644 --- a/tests/cases/struct/LV_NeoHookean_passive_genBC/svFSIplus.xml +++ b/tests/cases/struct/LV_NeoHookean_passive_genBC/svFSIplus.xml @@ -59,9 +59,9 @@ ST91 - + 0.0 - + diff --git a/tests/cases/struct/LV_NeoHookean_passive_sv0D/svFSIplus.xml b/tests/cases/struct/LV_NeoHookean_passive_sv0D/svFSIplus.xml index d8e48dbc..368f9eb2 100644 --- a/tests/cases/struct/LV_NeoHookean_passive_sv0D/svFSIplus.xml +++ b/tests/cases/struct/LV_NeoHookean_passive_sv0D/svFSIplus.xml @@ -59,9 +59,9 @@ ST91 - + 0.0 - + diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md new file mode 100644 index 00000000..76920dcd --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md @@ -0,0 +1,14 @@ +This test case simulates prescribed extension and compression of a slab of material +described by the Neohookean material model and a Newtonian solid viscosity model. + +The load profile is sinusoidal over a period of 1 second with an amplitude +of 100 dynes/cm^2. The load is applied on the Z1 face in the z-direction. + +![Load Profile](load.png) + +The load data is defined in `load.dat`, which can be generated with +`load.py` + +The resulting deformation is shown in the video below: +![Deformation](movie.gif) + diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py new file mode 100644 index 00000000..6bca358b --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py @@ -0,0 +1,30 @@ +import numpy as np +import os + +# Go to directory of this script +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Number of timesteps and number of Fourier modes +n_timesteps = 1001 +n_modes = 256 + +# Generate time values from 0 to 1 +time = np.linspace(0, 1, n_timesteps) + +# Generate sinusoidal load values with an amplitude of 100 +amplitude = 100 +load = amplitude * np.sin(2 * np.pi * time) + +# Write the time and load values to a text file +with open("load.dat", "w") as file: + file.write(f"{n_timesteps} {n_modes}\n") + for t, s in zip(time, load): + file.write(f"{t:.3f} {s:.3f}\n") + +# # Plot the load values +# import matplotlib.pyplot as plt +# plt.plot(time, load) +# plt.xlabel("Time (s)") +# plt.ylabel("load (dynes/cm^2)") +# plt.title("Active load") +# plt.savefig("load.png") \ No newline at end of file diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat new file mode 100644 index 00000000..76a138a2 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5f05379dd385ff0155468f2ee4cd3e75b9214f951c354f7c4110d4fc789253c6 +size 13461 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png new file mode 100644 index 00000000..16ce1650 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:03536faaa1e7d9990a6fea2c7bb95bf3dd405c46b9b882be732aa2f8f970805a +size 28380 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-complete.mesh.vtu b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-complete.mesh.vtu new file mode 100644 index 00000000..f09242eb --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-complete.mesh.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d74418f571657908b5c4e73f7cc5ce040fd300ac444b1c893ab23001bb6e09ae +size 7499 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X0.vtp b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X0.vtp new file mode 100644 index 00000000..904401ad --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3f71480fecee6f177719ab68b14bb2b61bbbce8fc745c87576fd51f3fb0b3ef8 +size 3655 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X1.vtp b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X1.vtp new file mode 100644 index 00000000..20b2d0e5 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bd46bcf90705c0e062aa658846aacb9091334a56fffac81715631628cd1f097f +size 3669 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y0.vtp b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y0.vtp new file mode 100644 index 00000000..19c7f008 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1ef44a9a441563692f58baccf576b3c10e6df4277046d1054db5ab821d498bf0 +size 4795 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y1.vtp b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y1.vtp new file mode 100644 index 00000000..7ac40cb0 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4d2ad3c14f29583d9d2015b0c0ba681b66c0d2380e4b8851ca30a2cb81773183 +size 4629 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z0.vtp b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z0.vtp new file mode 100644 index 00000000..49112c41 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6ee78716770c3ed486e5e81d32f90226e215bc095b5cda4f5c708218b84ee407 +size 3188 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp new file mode 100644 index 00000000..22122b6f --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2bdc7813853e641c5a71c20f1cea215c9c0215523f51272c5650077614dcb29 +size 3245 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml new file mode 100644 index 00000000..8dc1e35c --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml @@ -0,0 +1,120 @@ + + + + + 0 + 3 + 1000 + 0.001 + 0.50 + STOP_SIM + + 1 + result + 2 + 1 + + 100 + 0 + + 1 + 0 + 0 + + + + + + + mesh/mesh-complete.mesh.vtu + + + mesh/mesh-surfaces/X0.vtp + + + + mesh/mesh-surfaces/X1.vtp + + + + mesh/mesh-surfaces/Y0.vtp + + + + mesh/mesh-surfaces/Y1.vtp + + + + mesh/mesh-surfaces/Z0.vtp + + + + mesh/mesh-surfaces/Z1.vtp + + + + + + + + + + + true + 1 + 4 + 1e-9 + + 1.0 + 1.0e3 + 0.48333 + + + + + 100.0 + + + ST91 + + + true + true + true + true + true + true + true + true + + + + + fsils + + 1e-9 + 400 + + + + Dir + 0.0 + (0, 0, 1) + true + false + + + + Neu + Unsteady + load.dat + (0, 0, 1) + true + false + + + + + + + diff --git a/tests/cases/ustruct/LV_NeoHookean_passive_genBC/svFSIplus.xml b/tests/cases/ustruct/LV_NeoHookean_passive_genBC/svFSIplus.xml index ec7758a8..f0209966 100644 --- a/tests/cases/ustruct/LV_NeoHookean_passive_genBC/svFSIplus.xml +++ b/tests/cases/ustruct/LV_NeoHookean_passive_genBC/svFSIplus.xml @@ -59,9 +59,9 @@ ST91 - + 0.0 - + diff --git a/tests/cases/ustruct/LV_NeoHookean_passive_sv0D/svFSIplus.xml b/tests/cases/ustruct/LV_NeoHookean_passive_sv0D/svFSIplus.xml index 223fc1f7..c9ae2b1a 100644 --- a/tests/cases/ustruct/LV_NeoHookean_passive_sv0D/svFSIplus.xml +++ b/tests/cases/ustruct/LV_NeoHookean_passive_sv0D/svFSIplus.xml @@ -59,9 +59,9 @@ ST91 - + 0.0 - + diff --git a/tests/test_struct.py b/tests/test_struct.py index 4fda6376..7d5b714b 100644 --- a/tests/test_struct.py +++ b/tests/test_struct.py @@ -68,3 +68,7 @@ def test_LV_NeoHookean_passive_sv0D(n_proc): def test_tensile_adventitia_Guccione_active(n_proc): test_folder = "tensile_adventitia_Guccione_active" run_with_reference(base_folder, test_folder, fields, n_proc, t_max=2) + +def test_tensile_adventitia_Newtonian_viscosity(n_proc): + test_folder = "tensile_adventitia_Newtonian_viscosity" + run_with_reference(base_folder, test_folder, fields, n_proc, t_max=2) From 603bcb1926bdfe219f1c820bdcafb81ed814176e Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Tue, 10 Sep 2024 12:24:27 -0700 Subject: [PATCH 02/16] Add useful comments --- Code/Source/svFSI/mat_models_carray.h | 19 +++++++++---------- Code/Source/svFSI/nn.cpp | 13 +++++++++++++ Code/Source/svFSI/sv_struct.cpp | 2 ++ 3 files changed, 24 insertions(+), 10 deletions(-) diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index cc6bfcba..8bd07c78 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -1142,8 +1142,8 @@ void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn * @tparam nsd Number of spatial dimensions * @param mu Solid viscosity parameter * @param eNoN Number of nodes in an element - * @param Nx Shape function gradient matrix - * @param vx Velocity gradient matrix + * @param Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX) + * @param vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX) * @param F Deformation gradient matrix * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix * @param Kvis_u Viscous tangent matrix contribution due to displacement @@ -1153,8 +1153,6 @@ template void get_visc_stress_pot(const double mu, const int eNoN, const Array& Nx, const double vx[nsd][nsd], const double F[nsd][nsd], Array& Svis, Array3& Kvis_u, Array3& Kvis_v) { - std::cout << "get_visc_stress_pot: " << std::endl; - std::cout << "mu: " << mu << std::endl; // Initialize Svis, Kvis_u, Kvis_v to zero for (int i = 0; i < nsd; i++) { @@ -1191,6 +1189,9 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N } // 2nd Piola-Kirchhoff stress due to viscosity + // S = mu * E_dot + // = mu * 1/2 * F^T * (dv/dx + dv/dx^T) * F + // = mu * 1/2 * ( F^T * dv/dX + (F^T * dv/dX)^T ) double Ft_vx_symm[nsd][nsd] = {0}; mat_fun_carray::mat_symm(Ft_vx, Ft_vx_symm); for (int i = 0; i < nsd; i++) { @@ -1226,8 +1227,8 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N * @tparam nsd Number of spatial dimensions * @param mu Solid viscosity parameter * @param eNoN Number of nodes in an element - * @param Nx Shape function gradient matrix - * @param vx Velocity gradient matrix + * @param Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX) + * @param vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX) * @param F Deformation gradient matrix * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix * @param Kvis_u Viscous tangent matrix contribution due to displacement @@ -1237,8 +1238,6 @@ template void get_visc_stress_newt(const double mu, const int eNoN, const Array& Nx, const double vx[nsd][nsd], const double F[nsd][nsd], Array& Svis, Array3& Kvis_u, Array3& Kvis_v) { - std::cout << "get_visc_stress_newt: " << std::endl; - std::cout << "mu: " << mu << std::endl; // Initialize Svis, Kvis_u, Kvis_v to zero for (int i = 0; i < nsd; i++) { @@ -1334,8 +1333,8 @@ void get_visc_stress_newt(const double mu, const int eNoN, const Array& * @tparam nsd Number of spatial dimensions * @param[in] lDmn Domain object * @param[in] eNoN Number of nodes in an element - * @param[in] Nx Shape function gradient matrix - * @param[in] vx Velocity gradient matrix + * @param[in] Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX) + * @param[in] vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX) * @param[in] F Deformation gradient matrix * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement diff --git a/Code/Source/svFSI/nn.cpp b/Code/Source/svFSI/nn.cpp index d0e5e862..13596cd1 100644 --- a/Code/Source/svFSI/nn.cpp +++ b/Code/Source/svFSI/nn.cpp @@ -439,6 +439,19 @@ void get_xi(const int nsd, consts::ElementType eType, const int eNoN, const Arra xi = xiK; } +/** + * @brief Get shape function gradient w.r.t reference configuration coordinates. + * dN/dX = dN/dxi * dxi/dX, where xi is the parametric coordinates of the parent element + * + * @param eNoN Number of nodes in the element + * @param nsd Number of spatial dimensions + * @param insd + * @param Nxi Shape function gradient w.r.t. parametric coordinates of the parent element + * @param x Element node positions in reference configuration + * @param Nx Shape function gradient w.r.t reference configuration coordinates + * @param Jac Jacobian of element in reference configuration + * @param ks Matrix where each component is (dxi/dX)^2 + */ void gnn(const int eNoN, const int nsd, const int insd, Array& Nxi, Array& x, Array& Nx, double& Jac, Array& ks) { diff --git a/Code/Source/svFSI/sv_struct.cpp b/Code/Source/svFSI/sv_struct.cpp index d5733099..91f49121 100644 --- a/Code/Source/svFSI/sv_struct.cpp +++ b/Code/Source/svFSI/sv_struct.cpp @@ -659,6 +659,7 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in ud[1] += N(a)*(rho*(al(j,a)-bfl(1,a)) + dmp*yl(j,a)); ud[2] += N(a)*(rho*(al(k,a)-bfl(2,a)) + dmp*yl(k,a)); + // Velocity gradient tensor w.r.t. reference coordinates (dv/dX) vx[0][0] += Nx(0,a)*yl(i,a); vx[0][1] += Nx(1,a)*yl(i,a); vx[0][2] += Nx(2,a)*yl(i,a); @@ -669,6 +670,7 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in vx[2][1] += Nx(1,a)*yl(k,a); vx[2][2] += Nx(2,a)*yl(k,a); + // Deformation gradient tensor (I + du/dX) F[0][0] += Nx(0,a)*dl(i,a); F[0][1] += Nx(1,a)*dl(i,a); F[0][2] += Nx(2,a)*dl(i,a); From ddc1dfb4c21d73ab803e465aeb99a307511c5603 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Wed, 11 Sep 2024 06:53:42 -0700 Subject: [PATCH 03/16] Update comments for solid visc models --- Code/Source/svFSI/mat_models_carray.h | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index 8bd07c78..f785e459 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -1138,6 +1138,13 @@ void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn /** * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid * with a viscous pseudo-potential model. + * This is defined by a viscous pseuo-potential + * Psi = mu/2 * tr(E_dot^2) + * The viscous 2nd Piola-Kirchhoff stress is given by + * Svis = dPsi/dE_dot + * = mu * E_dot + * = mu * 1/2 * F^T * (grad(v) + grad(v)^T) * F + * = mu * 1/2 * ( (F^T * Grad(v)) + (F^T * Grad(v))^T ) * * @tparam nsd Number of spatial dimensions * @param mu Solid viscosity parameter @@ -1189,9 +1196,7 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N } // 2nd Piola-Kirchhoff stress due to viscosity - // S = mu * E_dot - // = mu * 1/2 * F^T * (dv/dx + dv/dx^T) * F - // = mu * 1/2 * ( F^T * dv/dX + (F^T * dv/dX)^T ) + // Svis = mu * 1/2 * ( (F^T * dv/dX) + (F^T * dv/dX)^T ) double Ft_vx_symm[nsd][nsd] = {0}; mat_fun_carray::mat_symm(Ft_vx, Ft_vx_symm); for (int i = 0; i < nsd; i++) { @@ -1199,7 +1204,6 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N Svis(i,j) = mu * Ft_vx_symm[i][j]; } } - //Svis = mu * Ft_vx_symm; // Tangent matrix contributions due to viscosity for (int b = 0; b < eNoN; ++b) { @@ -1223,6 +1227,11 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N /** * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid * with a Newtonian fluid-like viscosity model. + * The viscous deviatoric Cauchy stress is given by + * sigma_vis_dev = 2 * mu * d_dev + * where d_dev = 1/2 * (grad(v) + grad(v)^T) - 1/3 * (div(v)) * I + * The viscous 2nd Piola-Kirchhoff stress is given by a pull-back operation + * Svis = 2 * mu * J * F^-1 * d_dev * F^-T * * @tparam nsd Number of spatial dimensions * @param mu Solid viscosity parameter @@ -1283,6 +1292,7 @@ void get_visc_stress_newt(const double mu, const int eNoN, const Array& } // 2nd Piola-Kirchhoff stress due to viscosity + // Svis = 2 * mu * J * F^-1 * d_dev * F^-T double Fit[nsd][nsd] = {0}; mat_fun_carray::transpose(Fi, Fit); double ddev_Fit[nsd][nsd] = {0}; @@ -1294,7 +1304,6 @@ void get_visc_stress_newt(const double mu, const int eNoN, const Array& Svis(i,j) = 2.0 * mu * J * Fi_ddev_Fit[i][j]; } } - //Svis = 2.0 * mu * J * Fi_ddev_Fit; // Tangent matrix contributions due to viscosity double r2d = 2.0 / nsd; From 03d71c2ab31ca12eceada97fbe81176e6ad4683a Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Wed, 11 Sep 2024 11:06:38 -0700 Subject: [PATCH 04/16] Updating solid viscosity for ustruct. Removing solid viscosity stabilization in ustruct_xd_c() following Vijay's svFSI fork --- Code/Source/svFSI/mat_models_carray.h | 41 +++++ Code/Source/svFSI/ustruct.cpp | 206 +++++++------------------- Code/Source/svFSI/ustruct.h | 4 +- 3 files changed, 96 insertions(+), 155 deletions(-) diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index f785e459..611d66e4 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -39,6 +39,7 @@ #include "Tensor4.h" #include "mat_fun.h" +#include "mat_fun_carray.h" namespace mat_models_carray { @@ -1364,6 +1365,46 @@ void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Arra } } +/** + * @brief Get the solid viscous PK2 stress and corresponding tangent matrix contributions + * Calls the appropriate function based on the viscosity type, either viscous + * pseudo-potential or Newtonian viscosity model. + * + * Same as above, except takes vx and F as Array objects instead of C-style arrays. + * + * @tparam nsd Number of spatial dimensions + * @param[in] lDmn Domain object + * @param[in] eNoN Number of nodes in an element + * @param[in] Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX) + * @param[in] vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX) + * @param[in] F Deformation gradient matrix + * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix + * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement + * @param[out] Kvis_v Viscous tangent matrix contribution due to velocity + */ +template +void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Array& Nx, Array& vx_Array, Array& F_Array, + Array& Svis, Array3& Kvis_u, Array3& Kvis_v) { + + // Convert vx_Array and F_Array to C-style arrays + double vx[nsd][nsd], F[nsd][nsd]; + for (int i = 0; i < nsd; i++) { + for (int j = 0; j < nsd; j++) { + vx[i][j] = vx_Array(i,j); + F[i][j] = F_Array(i,j); + } + } + switch (lDmn.solid_visc.viscType) { + case consts::SolidViscosityModelType::viscType_Newtonian: + get_visc_stress_newt(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v); + break; + + case consts::SolidViscosityModelType::viscType_Potential: + get_visc_stress_pot(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v); + break; + } +} + }; #endif diff --git a/Code/Source/svFSI/ustruct.cpp b/Code/Source/svFSI/ustruct.cpp index d49e030e..cf8602f9 100644 --- a/Code/Source/svFSI/ustruct.cpp +++ b/Code/Source/svFSI/ustruct.cpp @@ -52,6 +52,7 @@ #include "fs.h" #include "mat_fun.h" #include "mat_models.h" +#include "mat_models_carray.h" #include "nn.h" #include "utils.h" @@ -384,13 +385,13 @@ void construct_usolid(ComMod& com_mod, CepMod& cep_mod, const mshType& lM, const auto N0 = fs[0].N.col(g); auto N1 = fs[1].N.col(g); ustruct_3d_c(com_mod, cep_mod, vmsStab, fs[0].eNoN, fs[1].eNoN, w, Jac, N0, N1, Nwx, - Nqx, al, yl, dl, bfl, ksix, lR, lK, lKd); + Nqx, al, yl, dl, bfl, lR, lK, lKd); } else if (nsd == 2) { auto N0 = fs[0].N.col(g); auto N1 = fs[1].N.col(g); ustruct_2d_c(com_mod, cep_mod, vmsStab, fs[0].eNoN, fs[1].eNoN, w, Jac, N0, N1, Nwx, - Nqx, al, yl, dl, bfl, ksix, lR, lK, lKd); + Nqx, al, yl, dl, bfl, lR, lK, lKd); } } // for g = 0 to fs[1].nG @@ -427,7 +428,7 @@ int get_col_ptr(ComMod& com_mod, const int rowN, const int colN) void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd) { using namespace consts; @@ -449,10 +450,6 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in int cDmn = com_mod.cDmn; auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double ctV = 36.0; - //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; - // TODO: Update solid viscosity implementation here - double mu = 0; Vector fb(2); fb[0] = dmn.prop[PhysicalProperyType::f_x]; @@ -529,21 +526,10 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double tauM = 0.0; double tauC = 0.0; - Array Kx(2,2); if (vmsFlag) { mat_models::get_tau(com_mod, eq.dmn[cDmn], Jac, Je, tauM, tauC); - // Stabilization parameter for solid viscosity - Kx = mat_mul(Kxi, Fi); - Kx = mat_mul(transpose(Fi), Kx); - - double tauV = Kx(0,0)*Kx(0,0) + Kx(1,0)*Kx(1,0) + - Kx(0,1)*Kx(0,1) + Kx(1,1)*Kx(1,1); - - tauV = ctV * mu * mu * tauV; - tauM = 1.0 / sqrt( tauV + pow(1.0/tauM,2.0)); - } else { tauM = 0.0; tauC = 0.0; @@ -646,7 +632,7 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd) { using namespace consts; @@ -668,10 +654,6 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in int cDmn = com_mod.cDmn; auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double ctV = 36.0; - //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; - // TODO: Update solid viscosity implementation here - double mu = 0; Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; @@ -767,22 +749,10 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double tauM = 0.0; double tauC = 0.0; - Array Kx(3,3); if (vmsFlag) { mat_models::get_tau(com_mod, eq.dmn[cDmn], Jac, Je, tauM, tauC); - // Stabilization parameter for solid viscosity - Kx = mat_mul(Kxi, Fi); - Kx = mat_mul(transpose(Fi), Kx); - - double tauV = Kx(0,0)*Kx(0,0) + Kx(1,0)*Kx(1,0) + Kx(2,0)*Kx(2,0) + - Kx(0,1)*Kx(0,1) + Kx(1,1)*Kx(1,1) + Kx(2,1)*Kx(2,1) + - Kx(0,2)*Kx(0,2) + Kx(1,2)*Kx(1,2) + Kx(2,2)*Kx(2,2); - - tauV = ctV * mu * mu * tauV; - tauM = 1.0 / sqrt( tauV + pow(1.0/tauM,2.0)); - } else { tauM = 0.0; tauC = 0.0; @@ -935,9 +905,6 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; - //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; - // TODO: Update solid viscosity implementation here - double mu = 0; double am = eq.am; double af = eq.af * eq.gam * dt; double afm = af / am; @@ -1003,16 +970,12 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in double Ja = 0; mat_models::get_pk2cc_dev(com_mod, cep_mod, eq.dmn[cDmn], F, nFn, fN, ya_g, Siso, Dm, Ja); - // Viscous contribution - // Velocity gradient in current configuration - auto VxFi = mat_mul(vx, Fi); - - // Deviatoric strain tensor - auto ddev = mat_dev(mat_symm(VxFi,2), 2); - - // 2nd Piola-Kirchhoff stress due to viscosity - auto Svis = mat_mul(ddev, transpose(Fi)); - Svis = 2.0*mu*Jac*mat_mul(Fi, Svis); + // Viscous 2nd Piola-Kirchhoff stress and tangent contributions + Array Svis(2,2); + Array3 Kvis_u(4, eNoNw, eNoNw); + Array3 Kvis_v(4, eNoNw, eNoNw); + + mat_models_carray::get_visc_stress_and_tangent<2>(dmn, eNoNw, Nwx, vx, F, Svis, Kvis_u, Kvis_v); // Compute rho and beta depending on the volumetric penalty model // @@ -1033,7 +996,7 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in tauC = 0.0; } - // Total isochoric 2nd Piola-Kirchhoff stress + // Total isochoric 2nd Piola-Kirchhoff stress (Elastic + Viscous) Siso = Siso + Svis; // Deviatoric 1st Piola-Kirchhoff tensor (P) @@ -1050,6 +1013,8 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in NxFi(1,a) = Nwx(0,a)*Fi(0,1) + Nwx(1,a)*Fi(1,1); } + // Velocity gradient in current configuration + auto VxFi = mat_mul(vx, Fi); double rC = beta*pd + VxFi(1,1) + VxFi(2,2); double rCl = -p + tauC*rC; @@ -1082,19 +1047,16 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in Bm(2,1,a) = Nwx(2,a)*F(1,2) + F(1,0)*Nwx(1,a); } - Array VxNx(2,eNoNw), DdNx(2,eNoNw); + Array VxNx(2,eNoNw); for (int a = 0; a < eNoNw; a++) { - DdNx(0,a) = ddev(0,0)*NxFi(0,a) + ddev(0,1)*NxFi(1,a); - DdNx(1,a) = ddev(1,0)*NxFi(0,a) + ddev(1,1)*NxFi(1,a); - VxNx(0,a) = VxFi(0,0)*NxFi(0,a) + VxFi(1,0)*NxFi(1,a); VxNx(1,a) = VxFi(0,1)*NxFi(0,a) + VxFi(1,1)*NxFi(1,a); } // Tangent (stiffness) matrices // - double NxSNx{0.0}, NxNx{0.0}, BtDB{0.0}, + double NxSNx{0.0}, BtDB{0.0}, T1{0.0}, T2{0.0}, T3{0.0}, Tv{0.0}, Ku{0.0}; @@ -1116,23 +1078,19 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in DBm(2,0) = Dm(2,0)*Bm(0,0,b) + Dm(2,1)*Bm(1,0,b) + Dm(2,2)*Bm(2,0,b); DBm(2,1) = Dm(2,0)*Bm(0,1,b) + Dm(2,1)*Bm(1,1,b) + Dm(2,2)*Bm(2,1,b); - NxNx = NxFi(0,a)*NxFi(0,b) + NxFi(1,a)*NxFi(1,b); // dM1_dV1 + af/am *dM_1/dU_1 // BtDB = Bm(0,0,a)*DBm(0,0) + Bm(1,0,a)*DBm(1,0) + Bm(2,0,a)*DBm(2,0); T1 = Jac*rho*vd(0)*Nw(a)*NxFi(0,b); T2 = -tauC*Jac*NxFi(0,a)*VxNx(0,b); - Tv = (1.0*(DdNx(0,a)*NxFi(0,b) - DdNx(0,b)*NxFi(0,a)) - - (NxNx*VxFi(0,0) + NxFi(0,b)*VxNx(0,a) - - NxFi(0,a)*VxNx(0,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + Tv + BtDB + NxSNx); + Ku = w*af*(T1 + T2 + BtDB + NxSNx + Kvis_u(0,a,b)); lKd(0,a,b) = lKd(0,a,b) + Ku; T1 = am*Jac*rho*Nw(a)*Nw(b); T2 = T1 + af*Jac*tauC*rho*NxFi(0,a)*NxFi(0,b); - Tv = af*mu*Jac*NxNx; + Tv = af*Kvis_v(0,a,b); lK(0,a,b) = lK(0,a,b) + w*(T2 + Tv) + afm*Ku; // dM_1/dV_2 + af/am *dM_1/dU_2 @@ -1141,16 +1099,12 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(0)*Nw(a)*NxFi(1,b); T2 = -tauC*Jac*NxFi(0,a)*VxNx(1,b); T3 = Jac*rCl*(NxFi(0,a)*NxFi(1,b) - NxFi(1,a)*NxFi(0,b)); - Tv = (1.0*(DdNx(0,a)*NxFi(1,b) - DdNx(0,b)*NxFi(1,a)) - - (NxNx*VxFi(0,1) + NxFi(0,b)*VxNx(1,a) - - NxFi(0,a)*VxNx(1,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(1,a,b)); lKd(1,a,b) = lKd(1,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(0,a)*NxFi(1,b); - Tv = af*mu*Jac*(NxFi(1,a)*NxFi(0,b) - - NxFi(0,a)*NxFi(1,b)); + Tv = af*Kvis_v(1,a,b); lK(1,a,b) = lK(1,a,b) + w*(T2 + Tv) + afm*Ku; // dM_2/dV_1 + af/am *dM_2/dU_1 @@ -1159,16 +1113,12 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(1)*Nw(a)*NxFi(0,b); T2 = -tauC*Jac*NxFi(1,a)*VxNx(0,b); T3 = Jac*rCl*(NxFi(1,a)*NxFi(0,b) - NxFi(0,a)*NxFi(1,b)); - Tv = (1.0*(DdNx(1,a)*NxFi(0,b) - DdNx(1,b)*NxFi(0,a)) - - (NxNx*VxFi(1,0) + NxFi(1,b)*VxNx(0,a) - - NxFi(1,a)*VxNx(0,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(2,a,b)); lKd(2,a,b) = lKd(2,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(1,a)*NxFi(0,b); - Tv = af*mu*Jac*(NxFi(0,a)*NxFi(1,b) - - NxFi(1,a)*NxFi(0,b)); + Tv = af*Kvis_v(2,a,b); lK(3,a,b) = lK(3,a,b) + w*(T2 + Tv) + afm*Ku; // dM_2/dV_2 + af/am *dM_2/dU_2 @@ -1176,16 +1126,13 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in BtDB = Bm(0,1,a)*DBm(0,1) + Bm(1,1,a)*DBm(1,1) + Bm(2,1,a)*DBm(2,1); T1 = Jac*rho*vd(1)*Nw(a)*NxFi(1,b); T2 = -tauC*Jac*NxFi(1,a)*VxNx(1,b); - Tv = (1.0*(DdNx(1,a)*NxFi(1,b) - DdNx(1,b)*NxFi(1,a)) - - (NxNx*VxFi(1,1) + NxFi(1,b)*VxNx(1,a) - - NxFi(1,a)*VxNx(1,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + Tv + BtDB + NxSNx); + Ku = w*af*(T1 + T2 + BtDB + NxSNx + Kvis_u(3,a,b)); lKd(3,a,b) = lKd(3,a,b) + Ku; T1 = am*Jac*rho*Nw(a)*Nw(b); T2 = T1 + af*Jac*tauC*rho*NxFi(1,a)*NxFi(1,b); - Tv = af*mu*Jac*NxNx; + Tv = af*Kvis_v(3,a,b); lK(4,a,b) = lK(4,a,b) + w*(T2 + Tv) + afm*Ku; } } @@ -1233,10 +1180,6 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in const double dt = com_mod.dt; // Define parameters - // - //double mu = dmn.prop[PhysicalProperyType::solid_viscosity]; - // TODO: Update solid viscosity implementation here - double mu = 0; Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; @@ -1328,17 +1271,13 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in double Ja = 0; mat_models::get_pk2cc_dev(com_mod, cep_mod, eq.dmn[cDmn], F, nFn, fN, ya_g, Siso, Dm, Ja); - // Viscous contribution - // - // Velocity gradient in current configuration - auto VxFi = mat_mul(vx, Fi); - - // Deviatoric strain tensor - auto ddev = mat_dev(mat_symm(VxFi,3), 3); + // Viscous 2nd Piola-Kirchhoff stress and tangent contributions + Array Svis(3,3); + Array3 Kvis_u(9, eNoNw, eNoNw); + Array3 Kvis_v(9, eNoNw, eNoNw); + + mat_models_carray::get_visc_stress_and_tangent<3>(dmn, eNoNw, Nwx, vx, F, Svis, Kvis_u, Kvis_v); - // 2nd Piola-Kirchhoff stress due to viscosity - auto Svis = mat_mul(ddev, transpose(Fi)); - Svis = 2.0 * mu * Jac * mat_mul(Fi, Svis); // Compute rho and beta depending on the volumetric penalty model // @@ -1359,7 +1298,7 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in tauC = 0.0; } - // Total isochoric 2nd Piola-Kirchhoff stress + // Total isochoric 2nd Piola-Kirchhoff stress (Elastic + Viscous) Siso = Siso + Svis; // Deviatoric 1st Piola-Kirchhoff tensor (P) @@ -1376,6 +1315,8 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in NxFi(2,a) = Nwx(0,a)*Fi(0,2) + Nwx(1,a)*Fi(1,2) + Nwx(2,a)*Fi(2,2); } + // Velocity gradient in current configuration + auto VxFi = mat_mul(vx, Fi); double rC = beta*pd + VxFi(0,0) + VxFi(1,1) + VxFi(2,2); double rCl = -p + tauC*rC; @@ -1430,13 +1371,9 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in Bm(5,2,a) = (Nwx(2,a)*F(2,0) + F(2,2)*Nwx(0,a)); } - Array VxNx(3,eNoNw), DdNx(3,eNoNw); + Array VxNx(3,eNoNw); for (int a = 0; a < eNoNw; a++) { - DdNx(0,a) = ddev(0,0)*NxFi(0,a) + ddev(0,1)*NxFi(1,a) + ddev(0,2)*NxFi(2,a); - DdNx(1,a) = ddev(1,0)*NxFi(0,a) + ddev(1,1)*NxFi(1,a) + ddev(1,2)*NxFi(2,a); - DdNx(2,a) = ddev(2,0)*NxFi(0,a) + ddev(2,1)*NxFi(1,a) + ddev(2,2)*NxFi(2,a); - VxNx(0,a) = VxFi(0,0)*NxFi(0,a) + VxFi(1,0)*NxFi(1,a) + VxFi(2,0)*NxFi(2,a); VxNx(1,a) = VxFi(0,1)*NxFi(0,a) + VxFi(1,1)*NxFi(1,a) + VxFi(2,1)*NxFi(2,a); VxNx(2,a) = VxFi(0,2)*NxFi(0,a) + VxFi(1,2)*NxFi(1,a) + VxFi(2,2)*NxFi(2,a); @@ -1446,7 +1383,7 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double r13 = 1.0 / 3.0; double r23 = 2.0 / 3.0; - double NxSNx{0.0}, BtDB{0.0}, NxNx{0.0}; + double NxSNx{0.0}, BtDB{0.0}; double Tv{0.0}, Ku{0.0}; for (int b = 0; b < eNoNw; b++) { @@ -1458,7 +1395,6 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in + Nwx(2,a)*Siso(2,1)*Nwx(1,b) + Nwx(2,a)*Siso(2,2)*Nwx(2,b); auto DBm = mat_mul(Dm, Bm.rslice(b)); - NxNx = NxFi(0,a)*NxFi(0,b) + NxFi(1,a)*NxFi(1,b) + NxFi(2,a)*NxFi(2,b); // dM1_dV1 + af/am *dM_1/dU_1 BtDB = Bm(0,0,a)*DBm(0,0) + Bm(1,0,a)*DBm(1,0) + @@ -1466,16 +1402,13 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in Bm(4,0,a)*DBm(4,0) + Bm(5,0,a)*DBm(5,0); T1 = Jac*rho*vd(0)*Nw(a)*NxFi(0,b); T2 = -tauC*Jac*NxFi(0,a)*VxNx(0,b); - Tv = (2.0*(DdNx(0,a)*NxFi(0,b) - DdNx(0,b)*NxFi(0,a)) - - (NxNx*VxFi(0,0) + NxFi(0,b)*VxNx(0,a) - - r23*NxFi(0,a)*VxNx(0,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + Tv + BtDB + NxSNx); + Ku = w*af*(T1 + T2 + BtDB + NxSNx + Kvis_u(0,a,b)); lKd(0,a,b) = lKd(0,a,b) + Ku; T1 = am*Jac*rho*Nw(a)*Nw(b); T2 = T1 + af*Jac*tauC*rho*NxFi(0,a)*NxFi(0,b); - Tv = af*mu*Jac*(r13*NxFi(0,a)*NxFi(0,b) + NxNx); + Tv = af*Kvis_v(0,a,b); lK(0,a,b) = lK(0,a,b) + w*(T2 + Tv) + afm*Ku; // dM_1/dV_2 + af/am *dM_1/dU_2 @@ -1485,16 +1418,12 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(0)*Nw(a)*NxFi(1,b); T2 = -tauC*Jac*NxFi(0,a)*VxNx(1,b); T3 = Jac*rCl*(NxFi(0,a)*NxFi(1,b) - NxFi(1,a)*NxFi(0,b)); - Tv = (2.0*(DdNx(0,a)*NxFi(1,b) - DdNx(0,b)*NxFi(1,a)) - - (NxNx*VxFi(0,1) + NxFi(0,b)*VxNx(1,a) - - r23*NxFi(0,a)*VxNx(1,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(1,a,b)); lKd(1,a,b) = lKd(1,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(0,a)*NxFi(1,b); - Tv = af*mu*Jac*(NxFi(1,a)*NxFi(0,b) - - r23*NxFi(0,a)*NxFi(1,b)); + Tv = af*Kvis_v(1,a,b); lK(1,a,b) = lK(1,a,b) + w*(T2 + Tv) + afm*Ku; // dM_1/dV_3 + af/am *dM_1/dU_3 @@ -1505,16 +1434,12 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(0)*Nw(a)*NxFi(2,b); T2 = -tauC*Jac*NxFi(0,a)*VxNx(2,b); T3 = Jac*rCl*(NxFi(0,a)*NxFi(2,b) - NxFi(2,a)*NxFi(0,b)); - Tv = (2.0*(DdNx(0,a)*NxFi(2,b) - DdNx(0,b)*NxFi(2,a)) - - (NxNx*VxFi(0,2) + NxFi(0,b)*VxNx(2,a) - - r23*NxFi(0,a)*VxNx(2,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(2,a,b)); lKd(2,a,b) = lKd(2,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(0,a)*NxFi(2,b); - Tv = af*mu*Jac*(NxFi(2,a)*NxFi(0,b) - - r23*NxFi(0,a)*NxFi(2,b)); + Tv = af*Kvis_v(2,a,b); lK(2,a,b) = lK(2,a,b) + w*(T2 + Tv) + afm*Ku; // dM_2/dV_1 + af/am *dM_2/dU_1 @@ -1526,16 +1451,12 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(1)*Nw(a)*NxFi(0,b); T2 = -tauC*Jac*NxFi(1,a)*VxNx(0,b); T3 = Jac*rCl*(NxFi(1,a)*NxFi(0,b) - NxFi(0,a)*NxFi(1,b)); - Tv = (2.0*(DdNx(1,a)*NxFi(0,b) - DdNx(1,b)*NxFi(0,a)) - - (NxNx*VxFi(1,0) + NxFi(1,b)*VxNx(0,a) - - r23*NxFi(1,a)*VxNx(0,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(3,a,b)); lKd(3,a,b) = lKd(3,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(1,a)*NxFi(0,b); - Tv = af*mu*Jac*(NxFi(0,a)*NxFi(1,b) - - r23*NxFi(1,a)*NxFi(0,b)); + Tv = af*Kvis_v(3,a,b); lK(4,a,b) = lK(4,a,b) + w*(T2 + Tv) + afm*Ku; @@ -1549,16 +1470,13 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T2 = -tauC*Jac*NxFi(1,a)*VxNx(1,b); - Tv = (2.0*(DdNx(1,a)*NxFi(1,b) - DdNx(1,b)*NxFi(1,a)) - - (NxNx*VxFi(1,1) + NxFi(1,b)*VxNx(1,a) - - r23*NxFi(1,a)*VxNx(1,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + Tv + BtDB + NxSNx); + Ku = w*af*(T1 + T2 + BtDB + NxSNx + Kvis_u(4,a,b)); lKd(4,a,b) = lKd(4,a,b) + Ku; T1 = am*Jac*rho*Nw(a)*Nw(b); T2 = T1 + af*Jac*tauC*rho*NxFi(1,a)*NxFi(1,b); - Tv = af*mu*Jac*(r13*NxFi(1,a)*NxFi(1,b) + NxNx); + Tv = af*Kvis_v(4,a,b); lK(5,a,b) = lK(5,a,b) + w*(T2 + Tv) + afm*Ku; @@ -1572,16 +1490,12 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T2 = -tauC*Jac*NxFi(1,a)*VxNx(2,b); T3 = Jac*rCl*(NxFi(1,a)*NxFi(2,b) - NxFi(2,a)*NxFi(1,b)); - Tv = (2.0*(DdNx(1,a)*NxFi(2,b) - DdNx(1,b)*NxFi(2,a)) - - (NxNx*VxFi(1,2) + NxFi(1,b)*VxNx(2,a) - - r23*NxFi(1,a)*VxNx(2,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(5,a,b)); lKd(5,a,b) = lKd(5,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(1,a)*NxFi(2,b); - Tv = af*mu*Jac*(NxFi(2,a)*NxFi(1,b) - - r23*NxFi(1,a)*NxFi(2,b)); + Tv = af*Kvis_v(5,a,b); lK(6,a,b) = lK(6,a,b) + w*(T2 + Tv) + afm*Ku; // dM_3/dV_1 + af/am *dM_3/dU_1 @@ -1593,17 +1507,12 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(2)*Nw(a)*NxFi(0,b); T2 = -tauC*Jac*NxFi(2,a)*VxNx(0,b); T3 = Jac*rCl*(NxFi(2,a)*NxFi(0,b) - NxFi(0,a)*NxFi(2,b)); - - Tv = (2.0*(DdNx(2,a)*NxFi(0,b) - DdNx(2,b)*NxFi(0,a)) - - (NxNx*VxFi(2,0) + NxFi(2,b)*VxNx(0,a) - - r23*NxFi(2,a)*VxNx(0,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(6,a,b)); lKd(6,a,b) = lKd(6,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(2,a)*NxFi(0,b); - Tv = af*mu*Jac*(NxFi(0,a)*NxFi(2,b) - - r23*NxFi(2,a)*NxFi(0,b)); + Tv = af*Kvis_v(6,a,b); lK(8,a,b) = lK(8,a,b) + w*(T2 + Tv) + afm*Ku; // dM_3/dV_2 + af/am *dM_3/dU_2 @@ -1615,17 +1524,12 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(2)*Nw(a)*NxFi(1,b); T2 = -tauC*Jac*NxFi(2,a)*VxNx(1,b); T3 = Jac*rCl*(NxFi(2,a)*NxFi(1,b) - NxFi(1,a)*NxFi(2,b)); - - Tv = (2.0*(DdNx(2,a)*NxFi(1,b) - DdNx(2,b)*NxFi(1,a)) - - (NxNx*VxFi(2,1) + NxFi(2,b)*VxNx(1,a) - - r23*NxFi(2,a)*VxNx(1,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + T3 + Tv + BtDB); + Ku = w*af*(T1 + T2 + T3 + BtDB + Kvis_u(7,a,b)); lKd(7,a,b) = lKd(7,a,b) + Ku; T2 = af*Jac*tauC*rho*NxFi(2,a)*NxFi(1,b); - Tv = af*mu*Jac*(NxFi(1,a)*NxFi(2,b) - - r23*NxFi(2,a)*NxFi(1,b)); + Tv = af*Kvis_v(7,a,b); lK(9,a,b) = lK(9,a,b) + w*(T2 + Tv) + afm*Ku; @@ -1637,17 +1541,13 @@ void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in T1 = Jac*rho*vd(2)*Nw(a)*NxFi(2,b); T2 = -tauC*Jac*NxFi(2,a)*VxNx(2,b); - - Tv = (2.0*(DdNx(2,a)*NxFi(2,b) - DdNx(2,b)*NxFi(2,a)) - - (NxNx*VxFi(2,2) + NxFi(2,b)*VxNx(2,a) - - r23*NxFi(2,a)*VxNx(2,b)))*mu*Jac; - Ku = w*af*(T1 + T2 + Tv + BtDB + NxSNx); + Ku = w*af*(T1 + T2 + BtDB + NxSNx + Kvis_u(8,a,b)); lKd(8,a,b) = lKd(8,a,b) + Ku; T1 = am*Jac*rho*Nw(a)*Nw(b); T2 = T1 + af*Jac*tauC*rho*NxFi(2,a)*NxFi(2,b); - Tv = af*mu*Jac*(r13*NxFi(2,a)*NxFi(2,b) + NxNx); + Tv = af*Kvis_v(8,a,b); lK(10,a,b) = lK(10,a,b) + w*(T2 + Tv) + afm*Ku; } diff --git a/Code/Source/svFSI/ustruct.h b/Code/Source/svFSI/ustruct.h index 972e88a0..71698323 100644 --- a/Code/Source/svFSI/ustruct.h +++ b/Code/Source/svFSI/ustruct.h @@ -51,7 +51,7 @@ int get_col_ptr(ComMod& com_mod, const int rowN, const int colN); void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd); void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, @@ -63,7 +63,7 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd); void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, From 693611960d1f28edb98818b1098ea21669af9b7c Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Wed, 11 Sep 2024 11:12:31 -0700 Subject: [PATCH 05/16] Solid viscosity update for struct_2d(). Cleanup comments in struct_3d_carray() --- Code/Source/svFSI/sv_struct.cpp | 173 +++----------------------------- 1 file changed, 14 insertions(+), 159 deletions(-) diff --git a/Code/Source/svFSI/sv_struct.cpp b/Code/Source/svFSI/sv_struct.cpp index 91f49121..085007e6 100644 --- a/Code/Source/svFSI/sv_struct.cpp +++ b/Code/Source/svFSI/sv_struct.cpp @@ -445,26 +445,17 @@ void struct_2d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, S0(1,0) = S0(0,1); - // TODO: Update solid viscosity contribution below - double mu = 0.0; - - double Jac = mat_det(F, 2); - auto Fi = mat_inv(F, 2); - - // Viscous contribution - // Velocity gradient in current configuration - auto VxFi = mat_mul(vx, Fi); - - // Deviatoric strain tensor - auto ddev = mat_dev(mat_symm(VxFi,2), 2); - - // 2nd Piola-Kirchhoff stress due to viscosity - auto Svis = mat_mul(ddev, transpose(Fi)); - Svis = 2.0 * mu * Jac * mat_mul(Fi, Svis); - + // 2nd Piola-Kirchhoff stress (S) and material stiffness tensor in Voight notation (Dm) Array S(2,2), Dm(3,3); mat_models::get_pk2cc(com_mod, cep_mod, dmn, F, nFn, fN, ya_g, S, Dm); + // Viscous 2nd Piola-Kirchhoff stress and tangent contributions + Array Svis(2,2); + Array3 Kvis_u(4, eNoN, eNoN); + Array3 Kvis_v(4, eNoN, eNoN); + + mat_models_carray::get_visc_stress_and_tangent<2>(dmn, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v); + // Elastic + Viscous stresses S = S + Svis; @@ -507,22 +498,9 @@ void struct_2d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, Array NxFi(2,eNoN), DdNx(2,eNoN), VxNx(2,eNoN); - for (int a = 0; a < eNoN; a++) { - NxFi(0,a) = Nx(0,a)*Fi(0,0) + Nx(1,a)*Fi(1,0); - NxFi(1,a) = Nx(0,a)*Fi(0,1) + Nx(1,a)*Fi(1,1); - - DdNx(0,a) = ddev(0,0)*NxFi(0,a) + ddev(0,1)*NxFi(1,a); - DdNx(1,a) = ddev(1,0)*NxFi(0,a) + ddev(1,1)*NxFi(1,a); - - VxNx(0,a) = VxFi(0,0)*NxFi(0,a) + VxFi(1,0)*NxFi(1,a); - VxNx(1,a) = VxFi(0,1)*NxFi(0,a) + VxFi(1,1)*NxFi(1,a); - } // Local stiffness tensor - // - double rmu = afu*mu*Jac; - double rmv = afv*mu*Jac; - double T1, Tv, NxNx, NxSNx, BmDBm; + double T1, NxNx, NxSNx, BmDBm; for (int b = 0; b < eNoN; b++) { for (int a = 0; a < eNoN; a++) { @@ -542,51 +520,30 @@ void struct_2d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, DBm(2,0) = Dm(2,0)*Bm(0,0,b) + Dm(2,1)*Bm(1,0,b) + Dm(2,2)*Bm(2,0,b); DBm(2,1) = Dm(2,0)*Bm(0,1,b) + Dm(2,1)*Bm(1,1,b) + Dm(2,2)*Bm(2,1,b); - NxNx = NxFi(0,a)*NxFi(0,b) + NxFi(1,a)*NxFi(1,b); // dM1/du1 // Material stiffness: Bt*D*B BmDBm = Bm(0,0,a)*DBm(0,0) + Bm(1,0,a)*DBm(1,0) + Bm(2,0,a)*DBm(2,0); - // Viscous terms contribution - Tv = (2.0*(DdNx(0,a)*NxFi(0,b) - DdNx(0,b)*NxFi(0,a)) - (NxNx*VxFi(0,0) + NxFi(0,b)*VxNx(0,a) - - NxFi(0,a)*VxNx(0,b))) * rmu + (NxNx) * rmv; - - lK(0,a,b) = lK(0,a,b) + w*(T1 + afu*BmDBm + Tv); + lK(0,a,b) = lK(0,a,b) + w*( T1 + afu*(BmDBm + Kvis_u(0,a,b)) + afv*Kvis_v(0,a,b) ); // dM1/du2 // Material stiffness: Bt*D*B BmDBm = Bm(0,0,a)*DBm(0,1) + Bm(1,0,a)*DBm(1,1) + Bm(2,0,a)*DBm(2,1); - // Viscous terms contribution - Tv = (2.0*(DdNx(0,a)*NxFi(1,b) - DdNx(0,b)*NxFi(1,a)) - - (NxNx*VxFi(0,1) + NxFi(0,b)*VxNx(1,a) - - NxFi(0,a)*VxNx(1,b))) * rmu + (NxFi(1,a)*NxFi(0,b) - - NxFi(0,a)*NxFi(1,b)) * rmv; - - lK(1,a,b) = lK(1,a,b) + w*(afu*BmDBm + Tv); + lK(1,a,b) = lK(1,a,b) + w*( afu*(BmDBm + Kvis_u(1,a,b)) + afv*Kvis_v(1,a,b) ); // dM2/du1 // Material stiffness: Bt*D*B BmDBm = Bm(0,1,a)*DBm(0,0) + Bm(1,1,a)*DBm(1,0) + Bm(2,1,a)*DBm(2,0); - // Viscous terms contribution - Tv = (2.0*(DdNx(1,a)*NxFi(0,b) - DdNx(1,b)*NxFi(0,a)) - - (NxNx*VxFi(1,0) + NxFi(1,b)*VxNx(0,a) - - NxFi(1,a)*VxNx(0,b))) * rmu + (NxFi(0,a)*NxFi(1,b) - - NxFi(1,a)*NxFi(0,b)) * rmv; - - lK(dof+0,a,b) = lK(dof+0,a,b) + w*(afu*BmDBm + Tv); + lK(dof+0,a,b) = lK(dof+0,a,b) + w*( afu*(BmDBm + Kvis_u(dof+0,a,b)) + afv*Kvis_v(dof+0,a,b) ); // dM2/du2 // Material stiffness: Bt*D*B BmDBm = Bm(0,1,a)*DBm(0,1) + Bm(1,1,a)*DBm(1,1) + Bm(2,1,a)*DBm(2,1); - // Viscous terms contribution - Tv = (2.0*(DdNx(1,a)*NxFi(1,b) - DdNx(1,b)*NxFi(1,a)) - (NxNx*VxFi(1,1) + NxFi(1,b)*VxNx(1,a) - - NxFi(1,a)*VxNx(1,b))) * rmu + (NxNx) * rmv; - - lK(dof+1,a,b) = lK(dof+1,a,b) + w*(T1 + afu*BmDBm + Tv); + lK(dof+1,a,b) = lK(dof+1,a,b) + w*( T1 + afu*(BmDBm + Kvis_u(dof+1,a,b)) + afv*Kvis_v(dof+1,a,b) ); } } } @@ -696,39 +653,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in S0[2][1] = S0[1][2]; S0[0][2] = S0[2][0]; - // double Jac = mat_fun_carray::mat_det<3>(F); - - // double Fi[3][3]; - // mat_fun_carray::mat_inv<3>(F, Fi); - - // // Viscous contribution - // // Velocity gradient in current configuration - // double VxFi[3][3]; - // mat_fun_carray::mat_mul(vx, Fi, VxFi); - - // // Deviatoric strain tensor - // double VxFi_sym[3][3]; - // mat_fun_carray::mat_symm<3>(VxFi,VxFi_sym); - - // double ddev[3][3]; - // mat_fun_carray::mat_dev<3>(VxFi_sym, ddev); - - // // 2nd Piola-Kirchhoff stress due to viscosity - // double Fi_transp[3][3]; - // mat_fun_carray::transpose<3>(Fi, Fi_transp); - - // double Svis[3][3]; - // mat_fun_carray::mat_mul<3>(ddev, Fi_transp, Svis); - - // double Fi_Svis_m[3][3]; - // mat_fun_carray::mat_mul<3>(Fi, Svis, Fi_Svis_m); - - // for (int i = 0; i < 3; i++) { - // for (int j = 0; j < 3; j++) { - // Svis[i][j] = 2.0 * mu * Jac * Fi_Svis_m[i][j]; - // } - // } - // Initialize tensor indexing. mat_fun_carray::ten_init(3); @@ -820,30 +744,7 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(5,2,a) = (Nx(2,a)*F[2][0] + F[2][2]*Nx(0,a)); } - // // Below quantities are used for viscous stress contribution - // // Shape function gradients in the current configuration - // // - // Array NxFi(3,eNoN), DdNx(3,eNoN), VxNx(3,eNoN); - - // for (int a = 0; a < eNoN; a++) { - // NxFi(0,a) = Nx(0,a)*Fi[0][0] + Nx(1,a)*Fi[1][0] + Nx(2,a)*Fi[2][0]; - // NxFi(1,a) = Nx(0,a)*Fi[0][1] + Nx(1,a)*Fi[1][1] + Nx(2,a)*Fi[2][1]; - // NxFi(2,a) = Nx(0,a)*Fi[0][2] + Nx(1,a)*Fi[1][2] + Nx(2,a)*Fi[2][2]; - - // DdNx(0,a) = ddev[0][0]*NxFi(0,a) + ddev[0][1]*NxFi(1,a) + ddev[0][2]*NxFi(2,a); - // DdNx(1,a) = ddev[1][0]*NxFi(0,a) + ddev[1][1]*NxFi(1,a) + ddev[1][2]*NxFi(2,a); - // DdNx(2,a) = ddev[2][0]*NxFi(0,a) + ddev[2][1]*NxFi(1,a) + ddev[2][2]*NxFi(2,a); - - // VxNx(0,a) = VxFi[0][0]*NxFi(0,a) + VxFi[1][0]*NxFi(1,a) + VxFi[2][0]*NxFi(2,a); - // VxNx(1,a) = VxFi[0][1]*NxFi(0,a) + VxFi[1][1]*NxFi(1,a) + VxFi[2][1]*NxFi(2,a); - // VxNx(2,a) = VxFi[0][2]*NxFi(0,a) + VxFi[1][2]*NxFi(1,a) + VxFi[2][2]*NxFi(2,a); - // } - // Local stiffness tensor - double r13 = 1.0 / 3.0; - double r23 = 2.0 / 3.0; - // double rmu = afu * mu * Jac; - // double rmv = afv * mu * Jac; double NxSNx, T1, NxNx, BmDBm; Array DBm(6,3); @@ -863,7 +764,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in // Material Stiffness (Bt*D*B) mat_fun_carray::mat_mul6x3<3>(Dm, Bm.rslice(b), DBm); - // NxNx = NxFi(0,a)*NxFi(0,b) + NxFi(1,a)*NxFi(1,b) + NxFi(2,a)*NxFi(2,b); // dM1/du1 // Material stiffness: Bt*D*B @@ -871,10 +771,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,0,a)*DBm(2,0) + Bm(3,0,a)*DBm(3,0) + Bm(4,0,a)*DBm(4,0) + Bm(5,0,a)*DBm(5,0); - // // Viscous terms contribution - // Tv = (2.0*(DdNx(0,a)*NxFi(0,b) - DdNx(0,b)*NxFi(0,a)) - (NxNx*VxFi[0][0] + NxFi(0,b)*VxNx(0,a) - - // r23*NxFi(0,a)*VxNx(0,b))) * rmu + (r13*NxFi(0,a)*NxFi(0,b) + NxNx) * rmv; - lK(0,a,b) = lK(0,a,b) + w*( T1 + afu*(BmDBm + Kvis_u(0,a,b)) + afv*Kvis_v(0,a,b) ); // dM1/du2 @@ -883,11 +779,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,0,a)*DBm(2,1) + Bm(3,0,a)*DBm(3,1) + Bm(4,0,a)*DBm(4,1) + Bm(5,0,a)*DBm(5,1); - // // Viscous terms contribution - // Tv = (2.0*(DdNx(0,a)*NxFi(1,b) - DdNx(0,b)*NxFi(1,a)) - // - (NxNx*VxFi[0][1] + NxFi(0,b)*VxNx(1,a) - // - r23*NxFi(0,a)*VxNx(1,b))) * rmu - // + (NxFi(1,a)*NxFi(0,b) - r23*NxFi(0,a)*NxFi(1,b)) * rmv; lK(1,a,b) = lK(1,a,b) + w*( afu*(BmDBm + Kvis_u(1,a,b)) + afv*(Kvis_v(1,a,b)) ); @@ -897,11 +788,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,0,a)*DBm(2,2) + Bm(3,0,a)*DBm(3,2) + Bm(4,0,a)*DBm(4,2) + Bm(5,0,a)*DBm(5,2); - // Viscous terms contribution - // Tv = (2.0*(DdNx(0,a)*NxFi(2,b) - DdNx(0,b)*NxFi(2,a)) - - // (NxNx*VxFi[0][2] + NxFi(0,b)*VxNx(2,a) - - // r23*NxFi(0,a)*VxNx(2,b))) * rmu + - // (NxFi(2,a)*NxFi(0,b) - r23*NxFi(0,a)*NxFi(2,b)) * rmv; lK(2,a,b) = lK(2,a,b) + w*( afu*(BmDBm + Kvis_u(2,a,b)) + afv*Kvis_v(2,a,b) ); @@ -911,11 +797,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,1,a)*DBm(2,0) + Bm(3,1,a)*DBm(3,0) + Bm(4,1,a)*DBm(4,0) + Bm(5,1,a)*DBm(5,0); - // Viscous terms contribution - // Tv = (2.0*(DdNx(1,a)*NxFi(0,b) - DdNx(1,b)*NxFi(0,a)) - - // (NxNx*VxFi[1][0] + NxFi(1,b)*VxNx(0,a) - - // r23*NxFi(1,a)*VxNx(0,b))) * rmu + - // (NxFi(0,a)*NxFi(1,b) - r23*NxFi(1,a)*NxFi(0,b)) * rmv; lK(dof+0,a,b) = lK(dof+0,a,b) + w*( afu*(BmDBm + Kvis_u(dof+0,a,b)) + afv*Kvis_v(dof+0,a,b) ); @@ -925,11 +806,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,1,a)*DBm(2,1) + Bm(3,1,a)*DBm(3,1) + Bm(4,1,a)*DBm(4,1) + Bm(5,1,a)*DBm(5,1); - // Viscous terms contribution - // Tv = (2.0*(DdNx(1,a)*NxFi(1,b) - DdNx(1,b)*NxFi(1,a)) - - // (NxNx*VxFi[1][1] + NxFi(1,b)*VxNx(1,a) - - // r23*NxFi(1,a)*VxNx(1,b))) * rmu + - // (r13*NxFi(1,a)*NxFi(1,b) + NxNx) * rmv; lK(dof+1,a,b) = lK(dof+1,a,b) + w*(T1 + afu*(BmDBm + Kvis_u(dof+1,a,b)) + afv*Kvis_v(dof+1,a,b) ); @@ -939,11 +815,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,1,a)*DBm(2,2) + Bm(3,1,a)*DBm(3,2) + Bm(4,1,a)*DBm(4,2) + Bm(5,1,a)*DBm(5,2); - // Viscous terms contribution - // Tv = (2.0*(DdNx(1,a)*NxFi(2,b) - DdNx(1,b)*NxFi(2,a)) - - // (NxNx*VxFi[1][2] + NxFi(1,b)*VxNx(2,a) - - // r23*NxFi(1,a)*VxNx(2,b))) * rmu + (NxFi(2,a)*NxFi(1,b) - - // r23*NxFi(1,a)*NxFi(2,b)) * rmv; lK(dof+2,a,b) = lK(dof+2,a,b) + w*( afu*(BmDBm + Kvis_u(dof+2,a,b)) + afv*Kvis_v(dof+2,a,b) ); @@ -953,11 +824,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,2,a)*DBm(2,0) + Bm(3,2,a)*DBm(3,0) + Bm(4,2,a)*DBm(4,0) + Bm(5,2,a)*DBm(5,0); - // Viscous terms contribution - // Tv = (2.0*(DdNx(2,a)*NxFi(0,b) - DdNx(2,b)*NxFi(0,a)) - - // (NxNx*VxFi[2][0] + NxFi(2,b)*VxNx(0,a) - - // r23*NxFi(2,a)*VxNx(0,b))) * rmu + (NxFi(0,a)*NxFi(2,b) - - // r23*NxFi(2,a)*NxFi(0,b)) * rmv; lK(2*dof+0,a,b) = lK(2*dof+0,a,b) + w*( afu*(BmDBm + Kvis_u(2*dof+0,a,b)) + afv*Kvis_v(2*dof+0,a,b) ); @@ -967,11 +833,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,2,a)*DBm(2,1) + Bm(3,2,a)*DBm(3,1) + Bm(4,2,a)*DBm(4,1) + Bm(5,2,a)*DBm(5,1); - // Viscous terms contribution - // Tv = (2.0*(DdNx(2,a)*NxFi(1,b) - DdNx(2,b)*NxFi(1,a)) - - // (NxNx*VxFi[2][1] + NxFi(2,b)*VxNx(1,a) - - // r23*NxFi(2,a)*VxNx(1,b))) * rmu + (NxFi(1,a)*NxFi(2,b) - - // r23*NxFi(2,a)*NxFi(1,b)) * rmv; lK(2*dof+1,a,b) = lK(2*dof+1,a,b) + w*( afu*(BmDBm + Kvis_u(2*dof+1,a,b)) + afv*Kvis_v(2*dof+1,a,b) ); @@ -981,12 +842,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in Bm(2,2,a)*DBm(2,2) + Bm(3,2,a)*DBm(3,2) + Bm(4,2,a)*DBm(4,2) + Bm(5,2,a)*DBm(5,2); - // // Viscous terms contribution - // Tv = (2.0*(DdNx(2,a)*NxFi(2,b) - DdNx(2,b)*NxFi(2,a)) - - // (NxNx*VxFi[2][2] + NxFi(2,b)*VxNx(2,a) - - // r23*NxFi(2,a)*VxNx(2,b))) * rmu + - // (r13*NxFi(2,a)*NxFi(2,b) + NxNx) * rmv; - lK(2*dof+2,a,b) = lK(2*dof+2,a,b) + w*( T1 + afu*(BmDBm + Kvis_u(2*dof+2,a,b)) + afv*Kvis_v(2*dof+2,a,b) ); } } @@ -995,6 +850,7 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in /// @brief Reproduces Fortran 'STRUCT3D' subroutine. // +// DEPRECATED: This function is deprecated and will be removed in the future. void struct_3d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, const double w, const Vector& N, const Array& Nx, const Array& al, const Array& yl, const Array& dl, const Array& bfl, const Array& fN, const Array& pS0l, @@ -1023,7 +879,6 @@ void struct_3d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, // double rho = dmn.prop.at(PhysicalProperyType::solid_density); //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); - // TODO: Do I need to update solid viscosity implementation here? double mu = 0; double dmp = dmn.prop.at(PhysicalProperyType::damping); Vector fb({dmn.prop.at(PhysicalProperyType::f_x), From 864f51df06df3997d95de1bdf9119f501f15857f Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Thu, 12 Sep 2024 09:21:55 -0700 Subject: [PATCH 06/16] Adding back viscosity-based stabilization in ustruct_xd_c(). PROBABLY REMOVE LATER. Also, print solid_viscosity parameters --- Code/Source/svFSI/Parameters.cpp | 2 ++ Code/Source/svFSI/ustruct.cpp | 38 ++++++++++++++++++++++++++++---- Code/Source/svFSI/ustruct.h | 4 ++-- 3 files changed, 38 insertions(+), 6 deletions(-) diff --git a/Code/Source/svFSI/Parameters.cpp b/Code/Source/svFSI/Parameters.cpp index 64eeeeb1..afc70e4d 100644 --- a/Code/Source/svFSI/Parameters.cpp +++ b/Code/Source/svFSI/Parameters.cpp @@ -1449,6 +1449,8 @@ void DomainParameters::print_parameters() stimulus.print_parameters(); fluid_viscosity.print_parameters(); + + solid_viscosity.print_parameters(); } void DomainParameters::set_values(tinyxml2::XMLElement* domain_elem) diff --git a/Code/Source/svFSI/ustruct.cpp b/Code/Source/svFSI/ustruct.cpp index cf8602f9..c430502e 100644 --- a/Code/Source/svFSI/ustruct.cpp +++ b/Code/Source/svFSI/ustruct.cpp @@ -385,13 +385,13 @@ void construct_usolid(ComMod& com_mod, CepMod& cep_mod, const mshType& lM, const auto N0 = fs[0].N.col(g); auto N1 = fs[1].N.col(g); ustruct_3d_c(com_mod, cep_mod, vmsStab, fs[0].eNoN, fs[1].eNoN, w, Jac, N0, N1, Nwx, - Nqx, al, yl, dl, bfl, lR, lK, lKd); + Nqx, al, yl, dl, bfl, ksix, lR, lK, lKd); } else if (nsd == 2) { auto N0 = fs[0].N.col(g); auto N1 = fs[1].N.col(g); ustruct_2d_c(com_mod, cep_mod, vmsStab, fs[0].eNoN, fs[1].eNoN, w, Jac, N0, N1, Nwx, - Nqx, al, yl, dl, bfl, lR, lK, lKd); + Nqx, al, yl, dl, bfl, ksix, lR, lK, lKd); } } // for g = 0 to fs[1].nG @@ -428,7 +428,7 @@ int get_col_ptr(ComMod& com_mod, const int rowN, const int colN) void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, Array3& lKd) { using namespace consts; @@ -451,6 +451,9 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; + double ctV = 36.0; + double mu = dmn.solid_visc.mu; + Vector fb(2); fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; @@ -526,10 +529,22 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double tauM = 0.0; double tauC = 0.0; + Array Kx(3,3); if (vmsFlag) { mat_models::get_tau(com_mod, eq.dmn[cDmn], Jac, Je, tauM, tauC); + // Stabilization parameter for solid viscosity + Kx = mat_mul(Kxi, Fi); + Kx = mat_mul(transpose(Fi), Kx); + + double tauV = Kx(0,0)*Kx(0,0) + Kx(1,0)*Kx(1,0) + Kx(2,0)*Kx(2,0) + + Kx(0,1)*Kx(0,1) + Kx(1,1)*Kx(1,1) + Kx(2,1)*Kx(2,1) + + Kx(0,2)*Kx(0,2) + Kx(1,2)*Kx(1,2) + Kx(2,2)*Kx(2,2); + + tauV = ctV * mu * mu * tauV; + tauM = 1.0 / sqrt( tauV + pow(1.0/tauM,2.0)); + } else { tauM = 0.0; tauC = 0.0; @@ -632,7 +647,7 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, Array3& lKd) { using namespace consts; @@ -655,6 +670,9 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; + double ctV = 36.0; + double mu = dmn.solid_visc.mu; + Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; @@ -749,10 +767,22 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double tauM = 0.0; double tauC = 0.0; + Array Kx(3,3); if (vmsFlag) { mat_models::get_tau(com_mod, eq.dmn[cDmn], Jac, Je, tauM, tauC); + // Stabilization parameter for solid viscosity + Kx = mat_mul(Kxi, Fi); + Kx = mat_mul(transpose(Fi), Kx); + + double tauV = Kx(0,0)*Kx(0,0) + Kx(1,0)*Kx(1,0) + Kx(2,0)*Kx(2,0) + + Kx(0,1)*Kx(0,1) + Kx(1,1)*Kx(1,1) + Kx(2,1)*Kx(2,1) + + Kx(0,2)*Kx(0,2) + Kx(1,2)*Kx(1,2) + Kx(2,2)*Kx(2,2); + + tauV = ctV * mu * mu * tauV; + tauM = 1.0 / sqrt( tauV + pow(1.0/tauM,2.0)); + } else { tauM = 0.0; tauC = 0.0; diff --git a/Code/Source/svFSI/ustruct.h b/Code/Source/svFSI/ustruct.h index 71698323..f331b82a 100644 --- a/Code/Source/svFSI/ustruct.h +++ b/Code/Source/svFSI/ustruct.h @@ -51,7 +51,7 @@ int get_col_ptr(ComMod& com_mod, const int rowN, const int colN); void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, Array3& lKd); void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, @@ -63,7 +63,7 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, Array3& lKd); void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, From 84a492e648b3d58754489be64917a3b37eaad288 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Thu, 12 Sep 2024 12:45:16 -0700 Subject: [PATCH 07/16] Modifying viscosity test case and documentation --- .../README.md | 7 +- .../generate_load.py | 24 +-- .../load.dat | 4 +- .../load.png | 4 +- .../movie.avi | 3 + .../movie.gif | 3 + .../plot_z1_face_displacement.py | 145 ++++++++++++++++++ .../result_002.vtu | 3 + .../svFSIplus.xml | 29 ++-- .../z1_face_displacement.dat | 3 + .../z1_face_displacement.png | 3 + .../z1_face_displacement_no_viscosity.dat | 3 + 12 files changed, 203 insertions(+), 28 deletions(-) create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md index 76920dcd..2e2b5462 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md @@ -1,8 +1,8 @@ This test case simulates prescribed extension and compression of a slab of material described by the Neohookean material model and a Newtonian solid viscosity model. -The load profile is sinusoidal over a period of 1 second with an amplitude -of 100 dynes/cm^2. The load is applied on the Z1 face in the z-direction. +The load profile is a 0.5s ramp to 1e5 dynes/cm^2, then held for another 0.5s. +The load is applied on the Z1 face in the z-direction. ![Load Profile](load.png) @@ -12,3 +12,6 @@ The load data is defined in `load.dat`, which can be generated with The resulting deformation is shown in the video below: ![Deformation](movie.gif) +The z-displacement of the Z1 face is plotted below: +![Z1 Displacement](z1_face_displacement.png) + diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py index 6bca358b..88e2ac57 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/generate_load.py @@ -11,9 +11,13 @@ # Generate time values from 0 to 1 time = np.linspace(0, 1, n_timesteps) -# Generate sinusoidal load values with an amplitude of 100 -amplitude = 100 -load = amplitude * np.sin(2 * np.pi * time) +# Generate 0.25s ramp to max load, then hold for 0.25s, then 0.25s ramp down to 0, then hold for 0.25s +load = np.zeros(n_timesteps) +max_load= -1e2 +load[time < 0.25] = max_load * time[time < 0.25] / 0.25 +load[(time >= 0.25) & (time < 0.5)] = max_load +load[(time >= 0.5) & (time < 0.75)] = max_load * (1 - (time[(time >= 0.5) & (time < 0.75)] - 0.5) / 0.25) +load[time >= 0.75] = 0 # Write the time and load values to a text file with open("load.dat", "w") as file: @@ -21,10 +25,10 @@ for t, s in zip(time, load): file.write(f"{t:.3f} {s:.3f}\n") -# # Plot the load values -# import matplotlib.pyplot as plt -# plt.plot(time, load) -# plt.xlabel("Time (s)") -# plt.ylabel("load (dynes/cm^2)") -# plt.title("Active load") -# plt.savefig("load.png") \ No newline at end of file +# Plot the load values +import matplotlib.pyplot as plt +plt.plot(time, load) +plt.xlabel("Time (s)") +plt.ylabel("load (dynes/cm^2)") +plt.title("Active load") +plt.savefig("load.png") \ No newline at end of file diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat index 76a138a2..0e638709 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.dat @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:5f05379dd385ff0155468f2ee4cd3e75b9214f951c354f7c4110d4fc789253c6 -size 13461 +oid sha256:1baa9ed6cf748d42b962453326733347bb3f82c1bd9c49a653568896e15e1e6c +size 13723 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png index 16ce1650..5b70832a 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/load.png @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:03536faaa1e7d9990a6fea2c7bb95bf3dd405c46b9b882be732aa2f8f970805a -size 28380 +oid sha256:c58557b9830a4b793a2bb89cf130bdc4540104d8190db0c64dc59e0da1cf8d9b +size 22901 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi new file mode 100644 index 00000000..96e26e14 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef57cd8f936a0cf25e660b3d529771aab89290b89596d4263df53d30f2c02b2d +size 6623568 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif new file mode 100644 index 00000000..9e33a2be --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4edfb7f628141625b3cc440bf2da329cbb83d259c433e0a0921dc95df97395ba +size 6098624 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py new file mode 100644 index 00000000..609cb008 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py @@ -0,0 +1,145 @@ +''' +Plots the displacement of the z1 face of the mesh over time +''' + +import matplotlib.pyplot as plt +import numpy as np +import pyvista as pv +import os +import glob +import xml.etree.ElementTree as ET + +def get_timestep(result_file): + ''' + Extracts the timestep of a results_###.vtu file + ''' + # If file path is provided, get the file name + file_name = os.path.basename(result_file) + + # Get the ###.vtu part + s = file_name.split('_')[-1] + + # Get the ### part + s = s.split('.')[0] + + # Return as integer + return int(s) + +def get_start_end_step(results_folder): + """ + Automatically determine the start timestep, end timestep, and step size based on all + svFSI results file in results_folder. + + Args: + results_folder: A string of absolute file path of folder containing results of + svFSIplus simulation. This usually ends with 16-procs/ or other + number. + + Returns: + (start_timestep, end_timestep, step): A tuple of 3 integers, giving the first + timestep of results to process, the last timestep, and the step size. + + """ + + # Get list of all .vtu files in results_folder sorted by time step + list_of_files = sorted( filter( os.path.isfile, + glob.glob(os.path.join(results_folder, '*.vtu')) ), key = get_timestep) + + # Get start time from the first result file (list_of_files[0]) + start_file_name = os.path.basename(list_of_files[0]) + start_timestep = int("".join([i for i in start_file_name if i.isdigit()])) + print('Start timestep:', start_timestep) + + # Get end time from the last result file (list_of_files[-1]) + end_file_name = os.path.basename(list_of_files[-1]) + end_timestep = int("".join([i for i in end_file_name if i.isdigit()])) + print('End timestep:', end_timestep) + + # Get step size by looking at second time step + start_plus_one_file_name = os.path.basename(list_of_files[1]) + start_time_plus_one = int("".join([i for i in start_plus_one_file_name if i.isdigit()])) + step = start_time_plus_one - start_timestep + print('Step:', step) + + return (start_timestep, end_timestep, step) + +def get_timestep_size(svfsiplus_xml_file): + ''' + Reads the timestep size from an svFSIplus XML file. + + Args: + svfsiplus_xml_file: The file path to the svFSIplus XML input file + + Returns: + timestep_size: The size of the timestep in the input file + ''' + # Parse the XML file + tree = ET.parse(svfsiplus_xml_file) + root = tree.getroot() + + # Find the element containing the Time_step_size + timestep_size = None + for elem in root.iter(): + if elem.tag == 'Time_step_size': + timestep_size = float(elem.text) + break + + return timestep_size + + +# Move to this script's directory +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Load the z1 face +mesh = pv.read("mesh/mesh-surfaces/Z1.vtp") + +# Get the start timestep, end timestep, and step size +start_timestep, end_timestep, step = get_start_end_step("4-procs/") + +# Get the timestep size +timestep_size = get_timestep_size("svFSIPlus.xml") + +# Get the time values +time = np.arange(start_timestep, end_timestep + 1, step) * timestep_size + +# Loop over the results files +displacements = [] +for n in range(start_timestep, end_timestep + 1, step): + # Load the results file + result_file = f"4-procs/result_{n:03d}.vtu" + result = pv.read(result_file) + + # Sample displacement at the z1 face + displacement = mesh.sample(result).point_data['Displacement'][:, 2].mean() + + # Append to the list + displacements.append(displacement) + +# Save the displacements to a text file +with open("z1_face_displacement.dat", "w") as file: + file.write(f"{len(time)}\n") + for t, s in zip(time, displacements): + file.write(f"{t:.3f} {s:.3f}\n") + + +# Plot the displacement +plt.plot(time, displacements, label="With viscosity") +plt.xlabel("Time (s)") +plt.ylabel("z Displacement (cm)") +plt.title("Z1 face displacement") + +# Plot the displacement with no viscosity +if os.path.exists("z1_face_displacement_no_viscosity.dat"): + with open("z1_face_displacement_no_viscosity.dat", "r") as file: + lines = file.readlines() + n = int(lines[0]) + time_no_viscosity = np.zeros(n) + displacements_no_viscosity = np.zeros(n) + for i, line in enumerate(lines[1:]): + time_no_viscosity[i], displacements_no_viscosity[i] = map(float, line.split()) + + plt.plot(time_no_viscosity, displacements_no_viscosity, label="Without viscosity") + + +plt.legend() +plt.savefig("z1_face_displacement.png") \ No newline at end of file diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu new file mode 100644 index 00000000..e825b3c5 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:44dbb51f4fe7314e1697e355406c3f504ca96bc1d49ee663781434752c4c6a47 +size 76298 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml index 8dc1e35c..0c6c7ee2 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml @@ -4,7 +4,7 @@ 0 3 - 1000 + 2 0.001 0.50 STOP_SIM @@ -52,6 +52,9 @@ mesh/mesh-surfaces/Z1.vtp + (0.0, 0.0, 1.0) + (1.0, 0.0, 0.0) + @@ -62,19 +65,24 @@ true 1 - 4 - 1e-9 + 12 + 1e-8 - 1.0 - 1.0e3 + 1.0e-2 + 1.0e5 0.48333 - - - 100.0 + 10.0 + + 100.0 + 8.0 + 6.0 + 12.0 + + ST91 @@ -92,14 +100,13 @@ fsils - 1e-9 + 1e-12 400 Dir 0.0 - (0, 0, 1) true false @@ -108,8 +115,6 @@ Neu Unsteady load.dat - (0, 0, 1) - true false diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat new file mode 100644 index 00000000..5dacbf61 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:855d728af95387dc3affd486650bc68c0d7916c48487e6339b521ff73517ed62 +size 1204 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png new file mode 100644 index 00000000..014ab90f --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:93ddda4b02c7b85dbc677a64d858642897904c09c222941acfc17ae054890d81 +size 44635 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat new file mode 100644 index 00000000..5eab0210 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e1d56d394cf534e922c22849b3c1f55d80419b592f7f87f638ad73e9eb4d6e93 +size 1218 From 05ff4b0d65b7962d90ade15e86da92cac2d46b25 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Thu, 12 Sep 2024 16:24:12 -0700 Subject: [PATCH 08/16] Removing viscosity-based stabilization in ustruct_xd_c(). According to Vijay, not important. Not included in Vijay's fork. This causes 2 ustruct tests (tensile_adventitia_HGO and LV_Guccione_active) to fail, because due to their larger momentum stabilization terms, they are slightly impacted by viscosity-based stabilization. --- Code/Source/svFSI/ustruct.cpp | 38 ++++------------------------------- Code/Source/svFSI/ustruct.h | 4 ++-- 2 files changed, 6 insertions(+), 36 deletions(-) diff --git a/Code/Source/svFSI/ustruct.cpp b/Code/Source/svFSI/ustruct.cpp index c430502e..cf8602f9 100644 --- a/Code/Source/svFSI/ustruct.cpp +++ b/Code/Source/svFSI/ustruct.cpp @@ -385,13 +385,13 @@ void construct_usolid(ComMod& com_mod, CepMod& cep_mod, const mshType& lM, const auto N0 = fs[0].N.col(g); auto N1 = fs[1].N.col(g); ustruct_3d_c(com_mod, cep_mod, vmsStab, fs[0].eNoN, fs[1].eNoN, w, Jac, N0, N1, Nwx, - Nqx, al, yl, dl, bfl, ksix, lR, lK, lKd); + Nqx, al, yl, dl, bfl, lR, lK, lKd); } else if (nsd == 2) { auto N0 = fs[0].N.col(g); auto N1 = fs[1].N.col(g); ustruct_2d_c(com_mod, cep_mod, vmsStab, fs[0].eNoN, fs[1].eNoN, w, Jac, N0, N1, Nwx, - Nqx, al, yl, dl, bfl, ksix, lR, lK, lKd); + Nqx, al, yl, dl, bfl, lR, lK, lKd); } } // for g = 0 to fs[1].nG @@ -428,7 +428,7 @@ int get_col_ptr(ComMod& com_mod, const int rowN, const int colN) void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd) { using namespace consts; @@ -451,9 +451,6 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double ctV = 36.0; - double mu = dmn.solid_visc.mu; - Vector fb(2); fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; @@ -529,22 +526,10 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double tauM = 0.0; double tauC = 0.0; - Array Kx(3,3); if (vmsFlag) { mat_models::get_tau(com_mod, eq.dmn[cDmn], Jac, Je, tauM, tauC); - // Stabilization parameter for solid viscosity - Kx = mat_mul(Kxi, Fi); - Kx = mat_mul(transpose(Fi), Kx); - - double tauV = Kx(0,0)*Kx(0,0) + Kx(1,0)*Kx(1,0) + Kx(2,0)*Kx(2,0) + - Kx(0,1)*Kx(0,1) + Kx(1,1)*Kx(1,1) + Kx(2,1)*Kx(2,1) + - Kx(0,2)*Kx(0,2) + Kx(1,2)*Kx(1,2) + Kx(2,2)*Kx(2,2); - - tauV = ctV * mu * mu * tauV; - tauM = 1.0 / sqrt( tauV + pow(1.0/tauM,2.0)); - } else { tauM = 0.0; tauC = 0.0; @@ -647,7 +632,7 @@ void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd) { using namespace consts; @@ -670,9 +655,6 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in auto& dmn = eq.dmn[cDmn]; const double dt = com_mod.dt; - double ctV = 36.0; - double mu = dmn.solid_visc.mu; - Vector fb(3); fb[0] = dmn.prop[PhysicalProperyType::f_x]; fb[1] = dmn.prop[PhysicalProperyType::f_y]; @@ -767,22 +749,10 @@ void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in // double tauM = 0.0; double tauC = 0.0; - Array Kx(3,3); if (vmsFlag) { mat_models::get_tau(com_mod, eq.dmn[cDmn], Jac, Je, tauM, tauC); - // Stabilization parameter for solid viscosity - Kx = mat_mul(Kxi, Fi); - Kx = mat_mul(transpose(Fi), Kx); - - double tauV = Kx(0,0)*Kx(0,0) + Kx(1,0)*Kx(1,0) + Kx(2,0)*Kx(2,0) + - Kx(0,1)*Kx(0,1) + Kx(1,1)*Kx(1,1) + Kx(2,1)*Kx(2,1) + - Kx(0,2)*Kx(0,2) + Kx(1,2)*Kx(1,2) + Kx(2,2)*Kx(2,2); - - tauV = ctV * mu * mu * tauV; - tauM = 1.0 / sqrt( tauV + pow(1.0/tauM,2.0)); - } else { tauM = 0.0; tauC = 0.0; diff --git a/Code/Source/svFSI/ustruct.h b/Code/Source/svFSI/ustruct.h index f331b82a..71698323 100644 --- a/Code/Source/svFSI/ustruct.h +++ b/Code/Source/svFSI/ustruct.h @@ -51,7 +51,7 @@ int get_col_ptr(ComMod& com_mod, const int rowN, const int colN); void ustruct_2d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd); void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, @@ -63,7 +63,7 @@ void ustruct_2d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const in void ustruct_3d_c(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector& Nw, const Vector& Nq, const Array& Nwx, const Array& Nqx, const Array& al, const Array& yl, - const Array& dl, const Array& bfl, const Array& Kxi, Array& lR, Array3& lK, + const Array& dl, const Array& bfl, Array& lR, Array3& lK, Array3& lKd); void ustruct_3d_m(ComMod& com_mod, CepMod& cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, From a824f50db18882ecddf98c4008e20da8e8323e32 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Mon, 16 Sep 2024 08:23:26 -0700 Subject: [PATCH 09/16] Potential viscosity bug fix (very important for convergence) --- Code/Source/svFSI/mat_models_carray.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index 611d66e4..79430eee 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -1190,8 +1190,8 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N for (int a = 0; a < eNoN; ++a) { for (int i = 0; i < nsd; ++i) { for (int j = 0; j < nsd; ++j) { - F_Nx(i,a) = F[i][j] * Nx(j,a); - vx_Nx(i,a) = vx[i][j] * Nx(j,a); + F_Nx(i,a) += F[i][j] * Nx(j,a); + vx_Nx(i,a) += vx[i][j] * Nx(j,a); } } } From 3d5000ddf01bc730a373c4c4fa397a0ea330de82 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Mon, 16 Sep 2024 10:48:38 -0700 Subject: [PATCH 10/16] Minor bug fix in Newtonian tangent. Doesn't seem to improve convergence. Probably still another bug in Newtonian tangent. --- Code/Source/svFSI/mat_models_carray.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index 79430eee..13b0c835 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -1287,7 +1287,7 @@ void get_visc_stress_newt(const double mu, const int eNoN, const Array& for (int i = 0; i < nsd; ++i) { for (int j = 0; j < nsd; ++j) { ddev_Nx_Fi(i,a) += ddev[i][j] * Nx_Fi(j,a); - vx_Fi_Nx_Fi(i,a) += vx_Fi[i][j] * Nx_Fi(j,a); + vx_Fi_Nx_Fi(i,a) += vx_Fi[j][i] * Nx_Fi(j,a); } } } From 466f9e621a5f59d62d7374bb985f776560db2aef Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Mon, 16 Sep 2024 11:08:17 -0700 Subject: [PATCH 11/16] Updating Newtonian viscosity test case, adding Potential viscosity test case --- .../README.md | 19 ++- .../movie.avi | 4 +- .../movie.gif | 4 +- .../result_001.vtu | 3 + .../result_002.vtu | 3 - .../svFSIplus.xml | 12 +- .../z1_face_displacement.dat | 2 +- .../z1_face_displacement.png | 4 +- .../z1_face_displacement_no_viscosity.dat | 4 +- .../README.md | 28 ++++ .../generate_load.py | 34 ++++ .../load.dat | 3 + .../load.png | 3 + .../mesh/mesh-complete.mesh.vtu | 3 + .../mesh/mesh-surfaces/X0.vtp | 3 + .../mesh/mesh-surfaces/X1.vtp | 3 + .../mesh/mesh-surfaces/Y0.vtp | 3 + .../mesh/mesh-surfaces/Y1.vtp | 3 + .../mesh/mesh-surfaces/Z0.vtp | 3 + .../mesh/mesh-surfaces/Z1.vtp | 3 + .../movie.avi | 3 + .../movie.gif | 3 + .../plot_z1_face_displacement.py | 145 ++++++++++++++++++ .../result_001.vtu | 3 + .../svFSIplus.xml | 125 +++++++++++++++ .../z1_face_displacement.dat | 3 + .../z1_face_displacement.png | 3 + .../z1_face_displacement_no_viscosity.dat | 3 + tests/test_struct.py | 6 +- 29 files changed, 417 insertions(+), 21 deletions(-) create mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_001.vtu delete mode 100644 tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/generate_load.py create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/load.dat create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/load.png create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.avi create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.gif create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/result_001.vtu create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png create mode 100644 tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md index 2e2b5462..9ff7b10c 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md @@ -1,5 +1,20 @@ -This test case simulates prescribed extension and compression of a slab of material -described by the Neohookean material model and a Newtonian solid viscosity model. +This test case simulates pulling and releasing a slab of material +described by the Guccione material model and a Newtonian solid viscosity model. +In this viscosity model, the viscous deviatoric Cauchy stress is identical to that +for a Newtonian fluid: + +$$ +\sigma^{dev}_{vis} = 2 \mu \mathbf{d}^{dev} +$$ +where +$$ +\mathbf{d}^{dev} = \frac{1}{2} (\nabla_x \mathbf{v} + (\nabla_x \mathbf{v})^T) - \frac{1}{3} (\nabla_x \cdot \mathbf{v}) \mathbf{I} +$$ + +The viscous part of the 2nd Piola-Kirchhoff stress is then given by a pull-back operation +$$ +\mathbf{S}_{vis} = 2 \mu J \mathbf{F}^{-1} \mathbf{d}^{dev} \mathbf{F}^{-T} +$$ The load profile is a 0.5s ramp to 1e5 dynes/cm^2, then held for another 0.5s. The load is applied on the Z1 face in the z-direction. diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi index 96e26e14..cc571072 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.avi @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ef57cd8f936a0cf25e660b3d529771aab89290b89596d4263df53d30f2c02b2d -size 6623568 +oid sha256:bb7fff34151f35d1e773ffa24943fc829e66b759ea05c0e7e06862fb36c297b0 +size 6689058 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif index 9e33a2be..bcb06b5a 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/movie.gif @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:4edfb7f628141625b3cc440bf2da329cbb83d259c433e0a0921dc95df97395ba -size 6098624 +oid sha256:8248b3481ce5c4614ab8c915c370b2d0f479b11a4ea4d6964c8ed09f7e726935 +size 915192 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_001.vtu b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_001.vtu new file mode 100644 index 00000000..05be8a51 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_001.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:88da8f9d0b6275eef0731efd4774edb3dd32acc2e8f3cde954c2c7b4f87e4c90 +size 76626 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu deleted file mode 100644 index e825b3c5..00000000 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/result_002.vtu +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:44dbb51f4fe7314e1697e355406c3f504ca96bc1d49ee663781434752c4c6a47 -size 76298 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml index 0c6c7ee2..007fb6b3 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml @@ -4,14 +4,14 @@ 0 3 - 2 - 0.001 + 1 + 0.01 0.50 STOP_SIM 1 result - 2 + 1 1 100 @@ -66,14 +66,14 @@ true 1 12 - 1e-8 + 1e-9 1.0e-2 1.0e5 0.48333 - 10.0 + 50.0 @@ -100,7 +100,7 @@ fsils - 1e-12 + 1e-10 400 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat index 5dacbf61..8536ab01 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:855d728af95387dc3affd486650bc68c0d7916c48487e6339b521ff73517ed62 +oid sha256:8b9be491d17fad5eac0f4f834a8e9f26be1d13f70937fd6b83ae34273ea4260a size 1204 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png index 014ab90f..1d22a601 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:93ddda4b02c7b85dbc677a64d858642897904c09c222941acfc17ae054890d81 -size 44635 +oid sha256:23fa1813c8c831ad04236a3ccaedce2119e510a3b99dd67e06b13a5f1dbc18c5 +size 45469 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat index 5eab0210..3ef76690 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e1d56d394cf534e922c22849b3c1f55d80419b592f7f87f638ad73e9eb4d6e93 -size 1218 +oid sha256:2c29c7f8626c2e0132ded468a36acc9c19f1a3142c49aac9168795d3398739ac +size 1219 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md b/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md new file mode 100644 index 00000000..43273587 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md @@ -0,0 +1,28 @@ +This test case simulates pulling and releasing a slab of material +described by the Guccione material model and a pseudo-potential solid viscosity model. +In this viscosity model, the so-called viscous pseudo-potential $\Psi_{vis}$ is +given by +$$ +\Psi_{vis} = \frac{\mu}{2} \text{tr}(\dot{\mathbf{E}}) +$$ +The viscous part of the 2nd Piola-Kirchhoff stress is then given by +$$ +S_{vis} = \frac{\partial \Psi_{vis}}{\partial \dot{\mathbf{E}}} = \mu \dot{\mathbf{E}} +$$ + + + +The load profile is a 0.5s ramp to 1e5 dynes/cm^2, then held for another 0.5s. +The load is applied on the Z1 face in the z-direction. + +![Load Profile](load.png) + +The load data is defined in `load.dat`, which can be generated with +`load.py` + +The resulting deformation is shown in the video below: +![Deformation](movie.gif) + +The z-displacement of the Z1 face is plotted below: +![Z1 Displacement](z1_face_displacement.png) + diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/generate_load.py b/tests/cases/struct/tensile_adventitia_Potential_viscosity/generate_load.py new file mode 100644 index 00000000..88e2ac57 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/generate_load.py @@ -0,0 +1,34 @@ +import numpy as np +import os + +# Go to directory of this script +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Number of timesteps and number of Fourier modes +n_timesteps = 1001 +n_modes = 256 + +# Generate time values from 0 to 1 +time = np.linspace(0, 1, n_timesteps) + +# Generate 0.25s ramp to max load, then hold for 0.25s, then 0.25s ramp down to 0, then hold for 0.25s +load = np.zeros(n_timesteps) +max_load= -1e2 +load[time < 0.25] = max_load * time[time < 0.25] / 0.25 +load[(time >= 0.25) & (time < 0.5)] = max_load +load[(time >= 0.5) & (time < 0.75)] = max_load * (1 - (time[(time >= 0.5) & (time < 0.75)] - 0.5) / 0.25) +load[time >= 0.75] = 0 + +# Write the time and load values to a text file +with open("load.dat", "w") as file: + file.write(f"{n_timesteps} {n_modes}\n") + for t, s in zip(time, load): + file.write(f"{t:.3f} {s:.3f}\n") + +# Plot the load values +import matplotlib.pyplot as plt +plt.plot(time, load) +plt.xlabel("Time (s)") +plt.ylabel("load (dynes/cm^2)") +plt.title("Active load") +plt.savefig("load.png") \ No newline at end of file diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/load.dat b/tests/cases/struct/tensile_adventitia_Potential_viscosity/load.dat new file mode 100644 index 00000000..0e638709 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/load.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1baa9ed6cf748d42b962453326733347bb3f82c1bd9c49a653568896e15e1e6c +size 13723 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/load.png b/tests/cases/struct/tensile_adventitia_Potential_viscosity/load.png new file mode 100644 index 00000000..5b70832a --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/load.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c58557b9830a4b793a2bb89cf130bdc4540104d8190db0c64dc59e0da1cf8d9b +size 22901 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu new file mode 100644 index 00000000..f09242eb --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d74418f571657908b5c4e73f7cc5ce040fd300ac444b1c893ab23001bb6e09ae +size 7499 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp new file mode 100644 index 00000000..904401ad --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3f71480fecee6f177719ab68b14bb2b61bbbce8fc745c87576fd51f3fb0b3ef8 +size 3655 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp new file mode 100644 index 00000000..20b2d0e5 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bd46bcf90705c0e062aa658846aacb9091334a56fffac81715631628cd1f097f +size 3669 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp new file mode 100644 index 00000000..19c7f008 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1ef44a9a441563692f58baccf576b3c10e6df4277046d1054db5ab821d498bf0 +size 4795 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp new file mode 100644 index 00000000..7ac40cb0 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4d2ad3c14f29583d9d2015b0c0ba681b66c0d2380e4b8851ca30a2cb81773183 +size 4629 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp new file mode 100644 index 00000000..49112c41 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6ee78716770c3ed486e5e81d32f90226e215bc095b5cda4f5c708218b84ee407 +size 3188 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp new file mode 100644 index 00000000..22122b6f --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2bdc7813853e641c5a71c20f1cea215c9c0215523f51272c5650077614dcb29 +size 3245 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.avi b/tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.avi new file mode 100644 index 00000000..31bbc25c --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.avi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ba4cd361b458769225571014243263bcfc0da4cd823f33f127504b6be3277c76 +size 6617286 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.gif b/tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.gif new file mode 100644 index 00000000..f5cfd62a --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/movie.gif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cd29195603702282ef78ddb057f52f9deebebe68d2e7333e218d8744aaac5236 +size 4112863 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py b/tests/cases/struct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py new file mode 100644 index 00000000..609cb008 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py @@ -0,0 +1,145 @@ +''' +Plots the displacement of the z1 face of the mesh over time +''' + +import matplotlib.pyplot as plt +import numpy as np +import pyvista as pv +import os +import glob +import xml.etree.ElementTree as ET + +def get_timestep(result_file): + ''' + Extracts the timestep of a results_###.vtu file + ''' + # If file path is provided, get the file name + file_name = os.path.basename(result_file) + + # Get the ###.vtu part + s = file_name.split('_')[-1] + + # Get the ### part + s = s.split('.')[0] + + # Return as integer + return int(s) + +def get_start_end_step(results_folder): + """ + Automatically determine the start timestep, end timestep, and step size based on all + svFSI results file in results_folder. + + Args: + results_folder: A string of absolute file path of folder containing results of + svFSIplus simulation. This usually ends with 16-procs/ or other + number. + + Returns: + (start_timestep, end_timestep, step): A tuple of 3 integers, giving the first + timestep of results to process, the last timestep, and the step size. + + """ + + # Get list of all .vtu files in results_folder sorted by time step + list_of_files = sorted( filter( os.path.isfile, + glob.glob(os.path.join(results_folder, '*.vtu')) ), key = get_timestep) + + # Get start time from the first result file (list_of_files[0]) + start_file_name = os.path.basename(list_of_files[0]) + start_timestep = int("".join([i for i in start_file_name if i.isdigit()])) + print('Start timestep:', start_timestep) + + # Get end time from the last result file (list_of_files[-1]) + end_file_name = os.path.basename(list_of_files[-1]) + end_timestep = int("".join([i for i in end_file_name if i.isdigit()])) + print('End timestep:', end_timestep) + + # Get step size by looking at second time step + start_plus_one_file_name = os.path.basename(list_of_files[1]) + start_time_plus_one = int("".join([i for i in start_plus_one_file_name if i.isdigit()])) + step = start_time_plus_one - start_timestep + print('Step:', step) + + return (start_timestep, end_timestep, step) + +def get_timestep_size(svfsiplus_xml_file): + ''' + Reads the timestep size from an svFSIplus XML file. + + Args: + svfsiplus_xml_file: The file path to the svFSIplus XML input file + + Returns: + timestep_size: The size of the timestep in the input file + ''' + # Parse the XML file + tree = ET.parse(svfsiplus_xml_file) + root = tree.getroot() + + # Find the element containing the Time_step_size + timestep_size = None + for elem in root.iter(): + if elem.tag == 'Time_step_size': + timestep_size = float(elem.text) + break + + return timestep_size + + +# Move to this script's directory +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Load the z1 face +mesh = pv.read("mesh/mesh-surfaces/Z1.vtp") + +# Get the start timestep, end timestep, and step size +start_timestep, end_timestep, step = get_start_end_step("4-procs/") + +# Get the timestep size +timestep_size = get_timestep_size("svFSIPlus.xml") + +# Get the time values +time = np.arange(start_timestep, end_timestep + 1, step) * timestep_size + +# Loop over the results files +displacements = [] +for n in range(start_timestep, end_timestep + 1, step): + # Load the results file + result_file = f"4-procs/result_{n:03d}.vtu" + result = pv.read(result_file) + + # Sample displacement at the z1 face + displacement = mesh.sample(result).point_data['Displacement'][:, 2].mean() + + # Append to the list + displacements.append(displacement) + +# Save the displacements to a text file +with open("z1_face_displacement.dat", "w") as file: + file.write(f"{len(time)}\n") + for t, s in zip(time, displacements): + file.write(f"{t:.3f} {s:.3f}\n") + + +# Plot the displacement +plt.plot(time, displacements, label="With viscosity") +plt.xlabel("Time (s)") +plt.ylabel("z Displacement (cm)") +plt.title("Z1 face displacement") + +# Plot the displacement with no viscosity +if os.path.exists("z1_face_displacement_no_viscosity.dat"): + with open("z1_face_displacement_no_viscosity.dat", "r") as file: + lines = file.readlines() + n = int(lines[0]) + time_no_viscosity = np.zeros(n) + displacements_no_viscosity = np.zeros(n) + for i, line in enumerate(lines[1:]): + time_no_viscosity[i], displacements_no_viscosity[i] = map(float, line.split()) + + plt.plot(time_no_viscosity, displacements_no_viscosity, label="Without viscosity") + + +plt.legend() +plt.savefig("z1_face_displacement.png") \ No newline at end of file diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/result_001.vtu b/tests/cases/struct/tensile_adventitia_Potential_viscosity/result_001.vtu new file mode 100644 index 00000000..d18a1ea6 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/result_001.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:238e6783fbe88d0453f5ea64cd615c7eff9225a63a545d468844f339895c31f2 +size 77010 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml b/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml new file mode 100644 index 00000000..e50e128f --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml @@ -0,0 +1,125 @@ + + + + + 0 + 3 + 1 + 0.01 + 0.50 + STOP_SIM + + 1 + result + 1 + 1 + + 100 + 0 + + 1 + 0 + 0 + + + + + + + mesh/mesh-complete.mesh.vtu + + + mesh/mesh-surfaces/X0.vtp + + + + mesh/mesh-surfaces/X1.vtp + + + + mesh/mesh-surfaces/Y0.vtp + + + + mesh/mesh-surfaces/Y1.vtp + + + + mesh/mesh-surfaces/Z0.vtp + + + + mesh/mesh-surfaces/Z1.vtp + + + (0.0, 0.0, 1.0) + (1.0, 0.0, 0.0) + + + + + + + + + + true + 1 + 12 + 1e-9 + + 1.0e-2 + 1.0e5 + 0.48333 + + + 50.0 + + + + 100.0 + 8.0 + 6.0 + 12.0 + + + ST91 + + + true + true + true + true + true + true + true + true + + + + + fsils + + 1e-10 + 400 + + + + Dir + 0.0 + true + false + + + + Neu + Unsteady + load.dat + false + + + + + + + diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat b/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat new file mode 100644 index 00000000..6bfbd991 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:edd0644b1495f7143f126d05761955e683c52b3629c7ecdbfe145536b2cdd496 +size 1204 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png b/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png new file mode 100644 index 00000000..fe2f4ae2 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6619455ecc4d4ea2dbcf3059ed3d547e13a41520d89ecd2a1dc7ed194ba2adc2 +size 44793 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat b/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat new file mode 100644 index 00000000..3ef76690 --- /dev/null +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2c29c7f8626c2e0132ded468a36acc9c19f1a3142c49aac9168795d3398739ac +size 1219 diff --git a/tests/test_struct.py b/tests/test_struct.py index 7d5b714b..9b02081a 100644 --- a/tests/test_struct.py +++ b/tests/test_struct.py @@ -71,4 +71,8 @@ def test_tensile_adventitia_Guccione_active(n_proc): def test_tensile_adventitia_Newtonian_viscosity(n_proc): test_folder = "tensile_adventitia_Newtonian_viscosity" - run_with_reference(base_folder, test_folder, fields, n_proc, t_max=2) + run_with_reference(base_folder, test_folder, fields, n_proc, t_max=1) + +def test_tensile_adventitia_Potential_viscosity(n_proc): + test_folder = "tensile_adventitia_Potential_viscosity" + run_with_reference(base_folder, test_folder, fields, n_proc, t_max=1) From 0d1dc5a2053174c1009ad94caaeed771f8bb2934 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Mon, 16 Sep 2024 11:30:32 -0700 Subject: [PATCH 12/16] Adding note about likely error in Newtonian tangent --- Code/Source/svFSI/mat_models_carray.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Code/Source/svFSI/mat_models_carray.h b/Code/Source/svFSI/mat_models_carray.h index 13b0c835..85f80d31 100644 --- a/Code/Source/svFSI/mat_models_carray.h +++ b/Code/Source/svFSI/mat_models_carray.h @@ -1234,6 +1234,8 @@ void get_visc_stress_pot(const double mu, const int eNoN, const Array& N * The viscous 2nd Piola-Kirchhoff stress is given by a pull-back operation * Svis = 2 * mu * J * F^-1 * d_dev * F^-T * + * Note, there is likely an error/bug in the tangent contributions that leads to suboptimal nonlinear convergence + * * @tparam nsd Number of spatial dimensions * @param mu Solid viscosity parameter * @param eNoN Number of nodes in an element From e6bc6110077a7900d226a7a357e9b81c39a6a5c3 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Mon, 16 Sep 2024 11:56:51 -0700 Subject: [PATCH 13/16] Add ustruct viscosity tests, update load profile description in READMEs --- .../README.md | 2 +- .../README.md | 2 +- .../README.md | 32 ++++ .../generate_load.py | 34 ++++ .../load.dat | 3 + .../load.png | 3 + .../mesh/mesh-complete.mesh.vtu | 3 + .../mesh/mesh-surfaces/X0.vtp | 3 + .../mesh/mesh-surfaces/X1.vtp | 3 + .../mesh/mesh-surfaces/Y0.vtp | 3 + .../mesh/mesh-surfaces/Y1.vtp | 3 + .../mesh/mesh-surfaces/Z0.vtp | 3 + .../mesh/mesh-surfaces/Z1.vtp | 3 + .../movie.avi | 3 + .../movie.gif | 3 + .../plot_z1_face_displacement.py | 145 ++++++++++++++++++ .../result_001.vtu | 3 + .../svFSIplus.xml | 127 +++++++++++++++ .../z1_face_displacement.dat | 3 + .../z1_face_displacement.png | 3 + .../z1_face_displacement_no_viscosity.dat | 3 + .../README.md | 27 ++++ .../generate_load.py | 34 ++++ .../load.dat | 3 + .../load.png | 3 + .../mesh/mesh-complete.mesh.vtu | 3 + .../mesh/mesh-surfaces/X0.vtp | 3 + .../mesh/mesh-surfaces/X1.vtp | 3 + .../mesh/mesh-surfaces/Y0.vtp | 3 + .../mesh/mesh-surfaces/Y1.vtp | 3 + .../mesh/mesh-surfaces/Z0.vtp | 3 + .../mesh/mesh-surfaces/Z1.vtp | 3 + .../movie.avi | 3 + .../movie.gif | 3 + .../plot_z1_face_displacement.py | 145 ++++++++++++++++++ .../result_001.vtu | 3 + .../svFSIplus.xml | 127 +++++++++++++++ .../z1_face_displacement.dat | 3 + .../z1_face_displacement.png | 3 + .../z1_face_displacement_no_viscosity.dat | 3 + tests/test_ustruct.py | 8 + 41 files changed, 771 insertions(+), 2 deletions(-) create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/README.md create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/generate_load.py create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/load.dat create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/load.png create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-complete.mesh.vtu create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X0.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/X1.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y0.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Y1.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z0.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.avi create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.gif create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/result_001.vtu create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png create mode 100644 tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/README.md create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/generate_load.py create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.dat create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.png create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.avi create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.gif create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/result_001.vtu create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png create mode 100644 tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md index 9ff7b10c..89e11caa 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/README.md @@ -16,7 +16,7 @@ $$ \mathbf{S}_{vis} = 2 \mu J \mathbf{F}^{-1} \mathbf{d}^{dev} \mathbf{F}^{-T} $$ -The load profile is a 0.5s ramp to 1e5 dynes/cm^2, then held for another 0.5s. +The load profile is a 0.25s ramp to the max value, then held for 0.25s, then a 0.25s ramp down to 0, then held for 0.25s. The load is applied on the Z1 face in the z-direction. ![Load Profile](load.png) diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md b/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md index 43273587..b7701399 100644 --- a/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/README.md @@ -12,7 +12,7 @@ $$ -The load profile is a 0.5s ramp to 1e5 dynes/cm^2, then held for another 0.5s. +The load profile is a 0.25s ramp to the max value, then held for 0.25s, then a 0.25s ramp down to 0, then held for 0.25s. The load is applied on the Z1 face in the z-direction. ![Load Profile](load.png) diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/README.md b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/README.md new file mode 100644 index 00000000..89e11caa --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/README.md @@ -0,0 +1,32 @@ +This test case simulates pulling and releasing a slab of material +described by the Guccione material model and a Newtonian solid viscosity model. +In this viscosity model, the viscous deviatoric Cauchy stress is identical to that +for a Newtonian fluid: + +$$ +\sigma^{dev}_{vis} = 2 \mu \mathbf{d}^{dev} +$$ +where +$$ +\mathbf{d}^{dev} = \frac{1}{2} (\nabla_x \mathbf{v} + (\nabla_x \mathbf{v})^T) - \frac{1}{3} (\nabla_x \cdot \mathbf{v}) \mathbf{I} +$$ + +The viscous part of the 2nd Piola-Kirchhoff stress is then given by a pull-back operation +$$ +\mathbf{S}_{vis} = 2 \mu J \mathbf{F}^{-1} \mathbf{d}^{dev} \mathbf{F}^{-T} +$$ + +The load profile is a 0.25s ramp to the max value, then held for 0.25s, then a 0.25s ramp down to 0, then held for 0.25s. +The load is applied on the Z1 face in the z-direction. + +![Load Profile](load.png) + +The load data is defined in `load.dat`, which can be generated with +`load.py` + +The resulting deformation is shown in the video below: +![Deformation](movie.gif) + +The z-displacement of the Z1 face is plotted below: +![Z1 Displacement](z1_face_displacement.png) + diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/generate_load.py b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/generate_load.py new file mode 100644 index 00000000..88e2ac57 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/generate_load.py @@ -0,0 +1,34 @@ +import numpy as np +import os + +# Go to directory of this script +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Number of timesteps and number of Fourier modes +n_timesteps = 1001 +n_modes = 256 + +# Generate time values from 0 to 1 +time = np.linspace(0, 1, n_timesteps) + +# Generate 0.25s ramp to max load, then hold for 0.25s, then 0.25s ramp down to 0, then hold for 0.25s +load = np.zeros(n_timesteps) +max_load= -1e2 +load[time < 0.25] = max_load * time[time < 0.25] / 0.25 +load[(time >= 0.25) & (time < 0.5)] = max_load +load[(time >= 0.5) & (time < 0.75)] = max_load * (1 - (time[(time >= 0.5) & (time < 0.75)] - 0.5) / 0.25) +load[time >= 0.75] = 0 + +# Write the time and load values to a text file +with open("load.dat", "w") as file: + file.write(f"{n_timesteps} {n_modes}\n") + for t, s in zip(time, load): + file.write(f"{t:.3f} {s:.3f}\n") + +# Plot the load values +import matplotlib.pyplot as plt +plt.plot(time, load) +plt.xlabel("Time (s)") +plt.ylabel("load (dynes/cm^2)") +plt.title("Active load") +plt.savefig("load.png") \ No newline at end of file diff --git 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b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp new file mode 100644 index 00000000..22122b6f --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/mesh/mesh-surfaces/Z1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2bdc7813853e641c5a71c20f1cea215c9c0215523f51272c5650077614dcb29 +size 3245 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.avi b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.avi new file mode 100644 index 00000000..7aa01e56 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.avi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6d3b3aeaa3f7ed69a0380f2ef521b469845948d0c73a40ddbfe2c525cc7d6796 +size 6696188 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.gif b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.gif new file mode 100644 index 00000000..abf13afb --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/movie.gif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:70ec054e059b6f00ab53239a4230f9c77934aa25583144aeb017d9644993265e +size 938216 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py new file mode 100644 index 00000000..609cb008 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/plot_z1_face_displacement.py @@ -0,0 +1,145 @@ +''' +Plots the displacement of the z1 face of the mesh over time +''' + +import matplotlib.pyplot as plt +import numpy as np +import pyvista as pv +import os +import glob +import xml.etree.ElementTree as ET + +def get_timestep(result_file): + ''' + Extracts the timestep of a results_###.vtu file + ''' + # If file path is provided, get the file name + file_name = os.path.basename(result_file) + + # Get the ###.vtu part + s = file_name.split('_')[-1] + + # Get the ### part + s = s.split('.')[0] + + # Return as integer + return int(s) + +def get_start_end_step(results_folder): + """ + Automatically determine the start timestep, end timestep, and step size based on all + svFSI results file in results_folder. + + Args: + results_folder: A string of absolute file path of folder containing results of + svFSIplus simulation. This usually ends with 16-procs/ or other + number. + + Returns: + (start_timestep, end_timestep, step): A tuple of 3 integers, giving the first + timestep of results to process, the last timestep, and the step size. + + """ + + # Get list of all .vtu files in results_folder sorted by time step + list_of_files = sorted( filter( os.path.isfile, + glob.glob(os.path.join(results_folder, '*.vtu')) ), key = get_timestep) + + # Get start time from the first result file (list_of_files[0]) + start_file_name = os.path.basename(list_of_files[0]) + start_timestep = int("".join([i for i in start_file_name if i.isdigit()])) + print('Start timestep:', start_timestep) + + # Get end time from the last result file (list_of_files[-1]) + end_file_name = os.path.basename(list_of_files[-1]) + end_timestep = int("".join([i for i in end_file_name if i.isdigit()])) + print('End timestep:', end_timestep) + + # Get step size by looking at second time step + start_plus_one_file_name = os.path.basename(list_of_files[1]) + start_time_plus_one = int("".join([i for i in start_plus_one_file_name if i.isdigit()])) + step = start_time_plus_one - start_timestep + print('Step:', step) + + return (start_timestep, end_timestep, step) + +def get_timestep_size(svfsiplus_xml_file): + ''' + Reads the timestep size from an svFSIplus XML file. + + Args: + svfsiplus_xml_file: The file path to the svFSIplus XML input file + + Returns: + timestep_size: The size of the timestep in the input file + ''' + # Parse the XML file + tree = ET.parse(svfsiplus_xml_file) + root = tree.getroot() + + # Find the element containing the Time_step_size + timestep_size = None + for elem in root.iter(): + if elem.tag == 'Time_step_size': + timestep_size = float(elem.text) + break + + return timestep_size + + +# Move to this script's directory +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Load the z1 face +mesh = pv.read("mesh/mesh-surfaces/Z1.vtp") + +# Get the start timestep, end timestep, and step size +start_timestep, end_timestep, step = get_start_end_step("4-procs/") + +# Get the timestep size +timestep_size = get_timestep_size("svFSIPlus.xml") + +# Get the time values +time = np.arange(start_timestep, end_timestep + 1, step) * timestep_size + +# Loop over the results files +displacements = [] +for n in range(start_timestep, end_timestep + 1, step): + # Load the results file + result_file = f"4-procs/result_{n:03d}.vtu" + result = pv.read(result_file) + + # Sample displacement at the z1 face + displacement = mesh.sample(result).point_data['Displacement'][:, 2].mean() + + # Append to the list + displacements.append(displacement) + +# Save the displacements to a text file +with open("z1_face_displacement.dat", "w") as file: + file.write(f"{len(time)}\n") + for t, s in zip(time, displacements): + file.write(f"{t:.3f} {s:.3f}\n") + + +# Plot the displacement +plt.plot(time, displacements, label="With viscosity") +plt.xlabel("Time (s)") +plt.ylabel("z Displacement (cm)") +plt.title("Z1 face displacement") + +# Plot the displacement with no viscosity +if os.path.exists("z1_face_displacement_no_viscosity.dat"): + with open("z1_face_displacement_no_viscosity.dat", "r") as file: + lines = file.readlines() + n = int(lines[0]) + time_no_viscosity = np.zeros(n) + displacements_no_viscosity = np.zeros(n) + for i, line in enumerate(lines[1:]): + time_no_viscosity[i], displacements_no_viscosity[i] = map(float, line.split()) + + plt.plot(time_no_viscosity, displacements_no_viscosity, label="Without viscosity") + + +plt.legend() +plt.savefig("z1_face_displacement.png") \ No newline at end of file diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/result_001.vtu b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/result_001.vtu new file mode 100644 index 00000000..13b5d36f --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/result_001.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:56a59efe0cb8214f54659f34cac97ef0c5028652abea1f434d23037768b9a26f +size 81000 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml new file mode 100644 index 00000000..4ed1b551 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml @@ -0,0 +1,127 @@ + + + + + 0 + 3 + 1 + 0.01 + 0.50 + STOP_SIM + + 1 + result + 1 + 1 + + 100 + 0 + + 1 + 0 + 0 + + + + + + + mesh/mesh-complete.mesh.vtu + + + mesh/mesh-surfaces/X0.vtp + + + + mesh/mesh-surfaces/X1.vtp + + + + mesh/mesh-surfaces/Y0.vtp + + + + mesh/mesh-surfaces/Y1.vtp + + + + mesh/mesh-surfaces/Z0.vtp + + + + mesh/mesh-surfaces/Z1.vtp + + + (0.0, 0.0, 1.0) + (1.0, 0.0, 0.0) + + + + + + + + + + true + 1 + 12 + 1e-9 + + 1.0e-2 + 1.0e5 + 0.48333 + + + 50.0 + + + + 100.0 + 8.0 + 6.0 + 12.0 + + + ST91 + + + true + true + true + true + true + true + true + true + true + true + + + + + fsils + + 1e-10 + 400 + + + + Dir + 0.0 + true + false + + + + Neu + Unsteady + load.dat + false + + + + + + + diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat new file mode 100644 index 00000000..3ce36d1e --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7cdbab100c4083030d6b985dee8de2aea92f8d06947f0c0c28bac88583324383 +size 1204 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png new file mode 100644 index 00000000..c48ff077 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:98693767369223dd9499a8193ed2abaaadd3cf4a4d2639266b2ed2b0d0361047 +size 45457 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat new file mode 100644 index 00000000..c6f60849 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/z1_face_displacement_no_viscosity.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:57946cded688a39112963bea3113a6b62e1f02de972fb4b1b7e988226e9ada87 +size 1217 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/README.md b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/README.md new file mode 100644 index 00000000..fd87ceda --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/README.md @@ -0,0 +1,27 @@ +This test case simulates pulling and releasing a slab of material +described by the Guccione material model and a pseudo-potential solid viscosity model. +In this viscosity model, the so-called viscous pseudo-potential $\Psi_{vis}$ is +given by +$$ +\Psi_{vis} = \frac{\mu}{2} \text{tr}(\dot{\mathbf{E}}) +$$ +The viscous part of the 2nd Piola-Kirchhoff stress is then given by +$$ +S_{vis} = \frac{\partial \Psi_{vis}}{\partial \dot{\mathbf{E}}} = \mu \dot{\mathbf{E}} +$$ + + + +The load profile is a 0.25s ramp to the max value, then held for 0.25s, then a 0.25s ramp down to 0, then held for 0.25s. +The load is applied on the Z1 face in the z-direction. + +![Load Profile](load.png) + +The load data is defined in `load.dat`, which can be generated with +`load.py` + +The resulting deformation is shown in the video below: +![Deformation](movie.gif) + +The z-displacement of the Z1 face is plotted below: +![Z1 Displacement](z1_face_displacement.png) diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/generate_load.py b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/generate_load.py new file mode 100644 index 00000000..88e2ac57 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/generate_load.py @@ -0,0 +1,34 @@ +import numpy as np +import os + +# Go to directory of this script +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Number of timesteps and number of Fourier modes +n_timesteps = 1001 +n_modes = 256 + +# Generate time values from 0 to 1 +time = np.linspace(0, 1, n_timesteps) + +# Generate 0.25s ramp to max load, then hold for 0.25s, then 0.25s ramp down to 0, then hold for 0.25s +load = np.zeros(n_timesteps) +max_load= -1e2 +load[time < 0.25] = max_load * time[time < 0.25] / 0.25 +load[(time >= 0.25) & (time < 0.5)] = max_load +load[(time >= 0.5) & (time < 0.75)] = max_load * (1 - (time[(time >= 0.5) & (time < 0.75)] - 0.5) / 0.25) +load[time >= 0.75] = 0 + +# Write the time and load values to a text file +with open("load.dat", "w") as file: + file.write(f"{n_timesteps} {n_modes}\n") + for t, s in zip(time, load): + file.write(f"{t:.3f} {s:.3f}\n") + +# Plot the load values +import matplotlib.pyplot as plt +plt.plot(time, load) +plt.xlabel("Time (s)") +plt.ylabel("load (dynes/cm^2)") +plt.title("Active load") +plt.savefig("load.png") \ No newline at end of file diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.dat b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.dat new file mode 100644 index 00000000..0e638709 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1baa9ed6cf748d42b962453326733347bb3f82c1bd9c49a653568896e15e1e6c +size 13723 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.png b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.png new file mode 100644 index 00000000..5b70832a --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/load.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c58557b9830a4b793a2bb89cf130bdc4540104d8190db0c64dc59e0da1cf8d9b +size 22901 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu new file mode 100644 index 00000000..f09242eb --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-complete.mesh.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d74418f571657908b5c4e73f7cc5ce040fd300ac444b1c893ab23001bb6e09ae +size 7499 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp new file mode 100644 index 00000000..904401ad --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3f71480fecee6f177719ab68b14bb2b61bbbce8fc745c87576fd51f3fb0b3ef8 +size 3655 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp new file mode 100644 index 00000000..20b2d0e5 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/X1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bd46bcf90705c0e062aa658846aacb9091334a56fffac81715631628cd1f097f +size 3669 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp new file mode 100644 index 00000000..19c7f008 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1ef44a9a441563692f58baccf576b3c10e6df4277046d1054db5ab821d498bf0 +size 4795 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp new file mode 100644 index 00000000..7ac40cb0 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Y1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4d2ad3c14f29583d9d2015b0c0ba681b66c0d2380e4b8851ca30a2cb81773183 +size 4629 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp new file mode 100644 index 00000000..49112c41 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z0.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6ee78716770c3ed486e5e81d32f90226e215bc095b5cda4f5c708218b84ee407 +size 3188 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp new file mode 100644 index 00000000..22122b6f --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/mesh/mesh-surfaces/Z1.vtp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2bdc7813853e641c5a71c20f1cea215c9c0215523f51272c5650077614dcb29 +size 3245 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.avi b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.avi new file mode 100644 index 00000000..3a9190a5 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.avi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a0de1f8dcee62c6bc64c602dca56942238273a19a46ac1cb78cb59e2c6c11944 +size 6604474 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.gif b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.gif new file mode 100644 index 00000000..e040c47c --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/movie.gif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0d2dd0b4d57583df9fc1cd0f3b162d642e0c76cf6bb576dd5a5d9e1a2884a4ee +size 899618 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py new file mode 100644 index 00000000..609cb008 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/plot_z1_face_displacement.py @@ -0,0 +1,145 @@ +''' +Plots the displacement of the z1 face of the mesh over time +''' + +import matplotlib.pyplot as plt +import numpy as np +import pyvista as pv +import os +import glob +import xml.etree.ElementTree as ET + +def get_timestep(result_file): + ''' + Extracts the timestep of a results_###.vtu file + ''' + # If file path is provided, get the file name + file_name = os.path.basename(result_file) + + # Get the ###.vtu part + s = file_name.split('_')[-1] + + # Get the ### part + s = s.split('.')[0] + + # Return as integer + return int(s) + +def get_start_end_step(results_folder): + """ + Automatically determine the start timestep, end timestep, and step size based on all + svFSI results file in results_folder. + + Args: + results_folder: A string of absolute file path of folder containing results of + svFSIplus simulation. This usually ends with 16-procs/ or other + number. + + Returns: + (start_timestep, end_timestep, step): A tuple of 3 integers, giving the first + timestep of results to process, the last timestep, and the step size. + + """ + + # Get list of all .vtu files in results_folder sorted by time step + list_of_files = sorted( filter( os.path.isfile, + glob.glob(os.path.join(results_folder, '*.vtu')) ), key = get_timestep) + + # Get start time from the first result file (list_of_files[0]) + start_file_name = os.path.basename(list_of_files[0]) + start_timestep = int("".join([i for i in start_file_name if i.isdigit()])) + print('Start timestep:', start_timestep) + + # Get end time from the last result file (list_of_files[-1]) + end_file_name = os.path.basename(list_of_files[-1]) + end_timestep = int("".join([i for i in end_file_name if i.isdigit()])) + print('End timestep:', end_timestep) + + # Get step size by looking at second time step + start_plus_one_file_name = os.path.basename(list_of_files[1]) + start_time_plus_one = int("".join([i for i in start_plus_one_file_name if i.isdigit()])) + step = start_time_plus_one - start_timestep + print('Step:', step) + + return (start_timestep, end_timestep, step) + +def get_timestep_size(svfsiplus_xml_file): + ''' + Reads the timestep size from an svFSIplus XML file. + + Args: + svfsiplus_xml_file: The file path to the svFSIplus XML input file + + Returns: + timestep_size: The size of the timestep in the input file + ''' + # Parse the XML file + tree = ET.parse(svfsiplus_xml_file) + root = tree.getroot() + + # Find the element containing the Time_step_size + timestep_size = None + for elem in root.iter(): + if elem.tag == 'Time_step_size': + timestep_size = float(elem.text) + break + + return timestep_size + + +# Move to this script's directory +os.chdir(os.path.dirname(os.path.realpath(__file__))) + +# Load the z1 face +mesh = pv.read("mesh/mesh-surfaces/Z1.vtp") + +# Get the start timestep, end timestep, and step size +start_timestep, end_timestep, step = get_start_end_step("4-procs/") + +# Get the timestep size +timestep_size = get_timestep_size("svFSIPlus.xml") + +# Get the time values +time = np.arange(start_timestep, end_timestep + 1, step) * timestep_size + +# Loop over the results files +displacements = [] +for n in range(start_timestep, end_timestep + 1, step): + # Load the results file + result_file = f"4-procs/result_{n:03d}.vtu" + result = pv.read(result_file) + + # Sample displacement at the z1 face + displacement = mesh.sample(result).point_data['Displacement'][:, 2].mean() + + # Append to the list + displacements.append(displacement) + +# Save the displacements to a text file +with open("z1_face_displacement.dat", "w") as file: + file.write(f"{len(time)}\n") + for t, s in zip(time, displacements): + file.write(f"{t:.3f} {s:.3f}\n") + + +# Plot the displacement +plt.plot(time, displacements, label="With viscosity") +plt.xlabel("Time (s)") +plt.ylabel("z Displacement (cm)") +plt.title("Z1 face displacement") + +# Plot the displacement with no viscosity +if os.path.exists("z1_face_displacement_no_viscosity.dat"): + with open("z1_face_displacement_no_viscosity.dat", "r") as file: + lines = file.readlines() + n = int(lines[0]) + time_no_viscosity = np.zeros(n) + displacements_no_viscosity = np.zeros(n) + for i, line in enumerate(lines[1:]): + time_no_viscosity[i], displacements_no_viscosity[i] = map(float, line.split()) + + plt.plot(time_no_viscosity, displacements_no_viscosity, label="Without viscosity") + + +plt.legend() +plt.savefig("z1_face_displacement.png") \ No newline at end of file diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/result_001.vtu b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/result_001.vtu new file mode 100644 index 00000000..d0a09cf3 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/result_001.vtu @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:dafbffac82bd8ed8f5945656a75ee05bf61c73b7adaed04c49c730bf75223687 +size 81248 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml new file mode 100644 index 00000000..7ad66cb6 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml @@ -0,0 +1,127 @@ + + + + + 0 + 3 + 1 + 0.01 + 0.50 + STOP_SIM + + 1 + result + 1 + 1 + + 100 + 0 + + 1 + 0 + 0 + + + + + + + mesh/mesh-complete.mesh.vtu + + + mesh/mesh-surfaces/X0.vtp + + + + mesh/mesh-surfaces/X1.vtp + + + + mesh/mesh-surfaces/Y0.vtp + + + + mesh/mesh-surfaces/Y1.vtp + + + + mesh/mesh-surfaces/Z0.vtp + + + + mesh/mesh-surfaces/Z1.vtp + + + (0.0, 0.0, 1.0) + (1.0, 0.0, 0.0) + + + + + + + + + + true + 1 + 12 + 1e-9 + + 1.0e-2 + 1.0e5 + 0.48333 + + + 50.0 + + + + 100.0 + 8.0 + 6.0 + 12.0 + + + ST91 + + + true + true + true + true + true + true + true + true + true + true + + + + + fsils + + 1e-10 + 400 + + + + Dir + 0.0 + true + false + + + + Neu + Unsteady + load.dat + false + + + + + + + diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat new file mode 100644 index 00000000..52145635 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:900e23f9b4d800bf654699775bf1d91ce31b4d7e5807c79702bbd65de967463a +size 1204 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png new file mode 100644 index 00000000..ccd3b05b --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ab9c4afaa95073f614ee06d3523caa606ad422d79b0e1a6c61567c4b975f289e +size 44709 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat new file mode 100644 index 00000000..c6f60849 --- /dev/null +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/z1_face_displacement_no_viscosity.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:57946cded688a39112963bea3113a6b62e1f02de972fb4b1b7e988226e9ada87 +size 1217 diff --git a/tests/test_ustruct.py b/tests/test_ustruct.py index f56a5fab..f3fb9112 100644 --- a/tests/test_ustruct.py +++ b/tests/test_ustruct.py @@ -57,3 +57,11 @@ def test_LV_NeoHookean_passive_sv0D(n_proc): test_folder = "LV_NeoHookean_passive_sv0D" run_with_reference(base_folder, test_folder, fields, n_proc, t_max=3) + +def test_tensile_adventitia_Newtonian_viscosity(n_proc): + test_folder = "tensile_adventitia_Newtonian_viscosity" + run_with_reference(base_folder, test_folder, fields, n_proc, t_max=1) + +def test_tensile_adventitia_Potential_viscosity(n_proc): + test_folder = "tensile_adventitia_Potential_viscosity" + run_with_reference(base_folder, test_folder, fields, n_proc, t_max=1) \ No newline at end of file From 0f677f5ef921b1b0309b88269a2c9d8e9a57c4aa Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Thu, 3 Oct 2024 10:15:13 -0700 Subject: [PATCH 14/16] Change input file to take only "Viscosity". Code determines if Solid_viscosity or Fluid_viscosity from context --- Code/Source/svFSI/Parameters.cpp | 46 +++++++++++-------- Code/Source/svFSI/Parameters.h | 5 +- .../1-rigid-solution/svFSIplus.xml | 4 +- .../3-inflate-cmm/svFSIplus.xml | 4 +- .../pipe_3d/1-rigid-solution/svFSIplus.xml | 4 +- .../cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml | 4 +- .../pipe_3d/3b-prestress-cmm/svFSIplus.xml | 4 +- tests/cases/fluid/carreau_yasuda/README.md | 4 +- .../cases/fluid/carreau_yasuda/svFSIplus.xml | 4 +- tests/cases/fluid/casson/README.md | 4 +- tests/cases/fluid/casson/svFSIplus.xml | 4 +- .../fluid/driven_cavity_2d/svFSIplus.xml | 4 +- tests/cases/fluid/dye_AD/svFSIplus.xml | 4 +- tests/cases/fluid/iliac_artery/svFSIplus.xml | 4 +- tests/cases/fluid/newtonian/README.md | 4 +- tests/cases/fluid/newtonian/svFSIplus.xml | 4 +- tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml | 4 +- .../fluid/pipe_RCR_3d_petsc/svFSIplus.xml | 4 +- .../pipe_RCR_3d_trilinos_bj/svFSIplus.xml | 4 +- .../pipe_RCR_3d_trilinos_ilut/svFSIplus.xml | 4 +- .../cases/fluid/pipe_RCR_genBC/svFSIplus.xml | 4 +- tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml | 4 +- .../cases/fluid/quadratic_tet10/svFSIplus.xml | 4 +- tests/cases/fsi/pipe_3d/svFSIplus.xml | 4 +- tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml | 4 +- .../fsi/pipe_3d_trilinos_bj/svFSIplus.xml | 4 +- .../fsi/pipe_3d_trilinos_ml/svFSIplus.xml | 4 +- .../P1P1/N004/svFSIplus.xml | 4 +- .../P1P1/N008/svFSIplus.xml | 4 +- .../P1P1/N016/svFSIplus.xml | 4 +- .../P1P1/N032/svFSIplus.xml | 4 +- .../P1P1/N064/svFSIplus.xml | 4 +- .../P1P1/N128/svFSIplus.xml | 4 +- .../P1P1/N256/svFSIplus.xml | 4 +- .../P2P1/N004/svFSIplus.xml | 4 +- .../P2P1/N008/svFSIplus.xml | 4 +- .../P2P1/N016/svFSIplus.xml | 4 +- .../P2P1/N032/svFSIplus.xml | 4 +- .../P2P1/N064/svFSIplus.xml | 4 +- .../P2P1/N128/svFSIplus.xml | 4 +- .../svFSIplus.xml | 4 +- .../svFSIplus.xml | 4 +- .../svFSIplus.xml | 4 +- .../svFSIplus.xml | 4 +- 44 files changed, 112 insertions(+), 107 deletions(-) diff --git a/Code/Source/svFSI/Parameters.cpp b/Code/Source/svFSI/Parameters.cpp index afc70e4d..9e3946c8 100644 --- a/Code/Source/svFSI/Parameters.cpp +++ b/Code/Source/svFSI/Parameters.cpp @@ -1075,7 +1075,7 @@ void VariableWallPropsParameters::set_values(tinyxml2::XMLElement* xml_elem) /// @brief Process parameters for various fluid viscosity models. /// /// Define the XML element name for viscosiity parameters. -const std::string FluidViscosityParameters::xml_element_name_ = "Fluid_viscosity"; +const std::string FluidViscosityParameters::xml_element_name_ = "Viscosity"; const std::string FluidViscosityParameters::CONSTANT_MODEL = "Constant"; const std::string FluidViscosityParameters::CARREAU_YASUDA_MODEL = "Carreau-Yasuda"; @@ -1198,7 +1198,7 @@ FluidViscosityParameters::FluidViscosityParameters() // A parameter that must be defined. bool required = true; - // Stores model from the XML element + // Stores model from the XML element model = Parameter("model", "", required); } @@ -1222,14 +1222,14 @@ void FluidViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) auto result = xml_elem->QueryStringAttribute("model", &smodel); if (smodel == nullptr) { - throw std::runtime_error("No MODEL given in the XML element."); + throw std::runtime_error("No MODEL given in the XML element."); } model.set(std::string(smodel)); // Check fluid_viscosity model name. if (model_names.count(model.value()) == 0) { throw std::runtime_error("Unknown fluid viscosity model '" + model.value() + - " in '" + xml_elem->Name() + "'."); + "' in '" + xml_elem->Name() + "'."); } // Set parameters for the given fluid_viscosity model. @@ -1243,7 +1243,7 @@ void FluidViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) /// @brief Process parameters for various solid viscosity models. /// /// Define the XML element name for viscosiity parameters. -const std::string SolidViscosityParameters::xml_element_name_ = "Solid_viscosity"; +const std::string SolidViscosityParameters::xml_element_name_ = "Viscosity"; const std::string SolidViscosityParameters::NEWTONIAN_MODEL = "Newtonian"; const std::string SolidViscosityParameters::POTENTIAL_MODEL = "Potential"; @@ -1323,7 +1323,7 @@ SolidViscosityParameters::SolidViscosityParameters() // A parameter that must be defined. bool required = true; - // Stores model from the XML element + // Stores model from the XML element model = Parameter("model", "", required); } @@ -1335,7 +1335,7 @@ void SolidViscosityParameters::print_parameters() std::cout << "--------------------" << std::endl; std::cout << model.name() << ": '" << model.value() << "'" << std::endl; - // Print parameters for the given Solid_viscosity model. + // Print parameters for the given solid_viscosity model. PrintSolidViscosityModelParamsMap[model.value_](this); } @@ -1347,14 +1347,14 @@ void SolidViscosityParameters::set_values(tinyxml2::XMLElement* xml_elem) auto result = xml_elem->QueryStringAttribute("model", &smodel); if (smodel == nullptr) { - throw std::runtime_error("No MODEL given in the XML element."); + throw std::runtime_error("No MODEL given in the XML element."); } model.set(std::string(smodel)); // Check solid viscosity model name. if (model_names.count(model.value()) == 0) { throw std::runtime_error("Unknown solid viscosity model '" + model.value() + - " in '" + xml_elem->Name() + "'."); + "' in '" + xml_elem->Name() + "'."); } // Set parameters for the given solid viscosity model. @@ -1424,7 +1424,6 @@ DomainParameters::DomainParameters() set_parameter("Relative_tolerance", 1e-4, !required, relative_tolerance); set_parameter("Shell_thickness", 0.0, !required, shell_thickness); set_parameter("Solid_density", 0.5, !required, solid_density); - //set_parameter("Solid_viscosity", 0.9, !required, solid_viscosity); set_parameter("Source_term", 0.0, !required, source_term); set_parameter("Time_step_for_integration", 0.0, !required, time_step_for_integration); } @@ -1481,11 +1480,15 @@ void DomainParameters::set_values(tinyxml2::XMLElement* domain_elem) } else if (name == StimulusParameters::xml_element_name_) { stimulus.set_values(item); - } else if (name == FluidViscosityParameters::xml_element_name_) { - fluid_viscosity.set_values(item); - - } else if (name == SolidViscosityParameters::xml_element_name_) { - solid_viscosity.set_values(item); + } else if (name == FluidViscosityParameters::xml_element_name_ || name == SolidViscosityParameters::xml_element_name_) { + if (equation.value() == "fluid") { + fluid_viscosity.set_values(item); + } else if (equation.value() == "struct" || equation.value() == "ustruct") { + solid_viscosity.set_values(item); + } + else { + throw std::runtime_error("Viscosity model not supported for equation '" + equation.value() + "'."); + } } else if (item->GetText() != nullptr) { auto value = item->GetText(); @@ -1898,11 +1901,14 @@ void EquationParameters::set_values(tinyxml2::XMLElement* eq_elem) } else if (name == StimulusParameters::xml_element_name_) { default_domain->stimulus.set_values(item); - } else if (name == FluidViscosityParameters::xml_element_name_) { - default_domain->fluid_viscosity.set_values(item); - - } else if (name == SolidViscosityParameters::xml_element_name_) { - default_domain->solid_viscosity.set_values(item); + } else if (name == FluidViscosityParameters::xml_element_name_ || name == SolidViscosityParameters::xml_element_name_) { + if (type.value() == "fluid") { + default_domain->fluid_viscosity.set_values(item); + } else if (type.value() == "struct" || type.value() == "ustruct") { + default_domain->solid_viscosity.set_values(item); + } else { + throw std::runtime_error("Viscosity model not supported for equation '" + default_domain->equation.value() + "'."); + } } else if (name == ECGLeadsParameters::xml_element_name_) { ecg_leads.set_values(item); diff --git a/Code/Source/svFSI/Parameters.h b/Code/Source/svFSI/Parameters.h index 2781eba8..4e1a7830 100644 --- a/Code/Source/svFSI/Parameters.h +++ b/Code/Source/svFSI/Parameters.h @@ -1037,9 +1037,9 @@ class FiberReinforcementStressParameters : public ParameterLists /// /// fluid /// 1.06 -/// +/// /// 0.04 -/// +/// /// 0.2 /// /// \endcode @@ -1107,7 +1107,6 @@ class DomainParameters : public ParameterLists Parameter shell_thickness; Parameter solid_density; - //Parameter solid_viscosity; Parameter source_term; Parameter time_step_for_integration; }; diff --git a/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml b/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml index bb627f16..ea9dec2c 100755 --- a/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml +++ b/tests/cases/cmm/iliac_artery_variable_wall_props/1-rigid-solution/svFSIplus.xml @@ -48,9 +48,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml b/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml index 87db25da..bb68a5eb 100755 --- a/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml +++ b/tests/cases/cmm/iliac_artery_variable_wall_props/3-inflate-cmm/svFSIplus.xml @@ -57,9 +57,9 @@ 1e-12 1.06 - + 0.04 - + 1.0 0.5 diff --git a/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml b/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml index 6e96ddb3..ac825aa4 100755 --- a/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml +++ b/tests/cases/cmm/pipe_3d/1-rigid-solution/svFSIplus.xml @@ -44,9 +44,9 @@ 1.06 - + 0.04 - + true 3 10 diff --git a/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml b/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml index 9e287d27..d7407b2a 100644 --- a/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml +++ b/tests/cases/cmm/pipe_3d/3a-inflate-cmm/svFSIplus.xml @@ -53,9 +53,9 @@ 1e-12 1.06 - + 0.04 - + 1.0 0.5 0.2 diff --git a/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml b/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml index 4bcaec1f..0ec907cb 100644 --- a/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml +++ b/tests/cases/cmm/pipe_3d/3b-prestress-cmm/svFSIplus.xml @@ -54,9 +54,9 @@ 1.06 - + 0.04 - + 1.0 0.5 0.2 diff --git a/tests/cases/fluid/carreau_yasuda/README.md b/tests/cases/fluid/carreau_yasuda/README.md index 0a348e15..7ef7b6f5 100755 --- a/tests/cases/fluid/carreau_yasuda/README.md +++ b/tests/cases/fluid/carreau_yasuda/README.md @@ -25,13 +25,13 @@ where The model parameters are specified in the `Viscosity` sub-section ``` - + 0.022 0.22 0.11 0.644 0.392 - + ``` diff --git a/tests/cases/fluid/carreau_yasuda/svFSIplus.xml b/tests/cases/fluid/carreau_yasuda/svFSIplus.xml index ad8dc11b..3432fbae 100644 --- a/tests/cases/fluid/carreau_yasuda/svFSIplus.xml +++ b/tests/cases/fluid/carreau_yasuda/svFSIplus.xml @@ -51,13 +51,13 @@ 1.06 - + 0.022 0.22 0.11 0.644 0.392 - + true diff --git a/tests/cases/fluid/casson/README.md b/tests/cases/fluid/casson/README.md index 5528f21f..87e10ca7 100755 --- a/tests/cases/fluid/casson/README.md +++ b/tests/cases/fluid/casson/README.md @@ -11,11 +11,11 @@ where $k_0(c)$ and $k_1(c)$ are functions of the hematocrit $c$. The model parameters are specified in the `Viscosity` sub-section ``` - + 0.3953 0.22803 0.5 - + ``` diff --git a/tests/cases/fluid/casson/svFSIplus.xml b/tests/cases/fluid/casson/svFSIplus.xml index be7ea31c..8856084a 100644 --- a/tests/cases/fluid/casson/svFSIplus.xml +++ b/tests/cases/fluid/casson/svFSIplus.xml @@ -51,11 +51,11 @@ 1.06 - + 0.3953 0.22803 0.5 - + true diff --git a/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml b/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml index 02efbf98..ea01561a 100755 --- a/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml +++ b/tests/cases/fluid/driven_cavity_2d/svFSIplus.xml @@ -53,9 +53,9 @@ 0.0 100 - + 10 - + true diff --git a/tests/cases/fluid/dye_AD/svFSIplus.xml b/tests/cases/fluid/dye_AD/svFSIplus.xml index 896c8aa1..72938238 100644 --- a/tests/cases/fluid/dye_AD/svFSIplus.xml +++ b/tests/cases/fluid/dye_AD/svFSIplus.xml @@ -49,9 +49,9 @@ 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/iliac_artery/svFSIplus.xml b/tests/cases/fluid/iliac_artery/svFSIplus.xml index 3ceb995f..06b1db1a 100644 --- a/tests/cases/fluid/iliac_artery/svFSIplus.xml +++ b/tests/cases/fluid/iliac_artery/svFSIplus.xml @@ -53,9 +53,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/newtonian/README.md b/tests/cases/fluid/newtonian/README.md index 0f98fd1c..06386b07 100755 --- a/tests/cases/fluid/newtonian/README.md +++ b/tests/cases/fluid/newtonian/README.md @@ -6,7 +6,7 @@ Simulation of a 3D pipe flow problem using a Newtonian viscosity model. The model parameters are specified in the `Viscosity` sub-section ``` - + 0.04 - + ``` diff --git a/tests/cases/fluid/newtonian/svFSIplus.xml b/tests/cases/fluid/newtonian/svFSIplus.xml index aa292b00..4cb18417 100644 --- a/tests/cases/fluid/newtonian/svFSIplus.xml +++ b/tests/cases/fluid/newtonian/svFSIplus.xml @@ -51,9 +51,9 @@ 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml index 0c27eebc..9e2f9512 100755 --- a/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml index d8ad9e1a..3d55be4f 100755 --- a/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d_petsc/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml index 8ebcabaa..11c6c7fd 100755 --- a/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d_trilinos_bj/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml index 9a56223b..bf9eea56 100755 --- a/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_3d_trilinos_ilut/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml index ee6a0905..2668aee4 100644 --- a/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_genBC/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml b/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml index 09aa3366..a9e762d6 100644 --- a/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml +++ b/tests/cases/fluid/pipe_RCR_sv0D/svFSIplus.xml @@ -50,9 +50,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fluid/quadratic_tet10/svFSIplus.xml b/tests/cases/fluid/quadratic_tet10/svFSIplus.xml index d578ee3f..0be4a7b6 100755 --- a/tests/cases/fluid/quadratic_tet10/svFSIplus.xml +++ b/tests/cases/fluid/quadratic_tet10/svFSIplus.xml @@ -48,9 +48,9 @@ 0.2 1.06 - + 0.04 - + true diff --git a/tests/cases/fsi/pipe_3d/svFSIplus.xml b/tests/cases/fsi/pipe_3d/svFSIplus.xml index 8b96e124..fb8f03c5 100755 --- a/tests/cases/fsi/pipe_3d/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml b/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml index 7a5de1e0..6254cec5 100755 --- a/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + "Constant" > 0.04 - + 0.2 diff --git a/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml b/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml index 58174209..7232e927 100755 --- a/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_trilinos_bj/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml b/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml index 0118c347..83a619a7 100755 --- a/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_trilinos_ml/svFSIplus.xml @@ -64,9 +64,9 @@ fluid 1.0 - + 0.04 - + 0.2 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml index 53568c1a..6c841099 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N004/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml index 330eafd0..4f0e2837 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N008/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + "Constant" > 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml index be1c9150..a2337808 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N016/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml index 09af1117..77e5a9ee 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N032/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-12 false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml index 3f05e908..601115cb 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N064/svFSIplus.xml @@ -53,9 +53,9 @@ false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml index 84ef7e11..ff3cd9cc 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N128/svFSIplus.xml @@ -53,9 +53,9 @@ false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml index be491440..48712fbf 100644 --- a/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P1P1/N256/svFSIplus.xml @@ -53,9 +53,9 @@ false - + 1.0 - + 10.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml index c617c204..815e63f3 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N004/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml index 71400ef3..0238139f 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N008/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml index f1e18a41..bbc80b4b 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N016/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + "Constant" > 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml index 988ce0c3..f2fbdd7b 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N032/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml index 23f98e0a..60fac398 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N064/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml b/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml index 517a754a..ff2a7758 100644 --- a/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml +++ b/tests/cases/stokes/manufactured_solution/P2P1/N128/svFSIplus.xml @@ -47,9 +47,9 @@ 1e-9 true - + 1.0 - + 0.0 diff --git a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml index 007fb6b3..8784bd6d 100644 --- a/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml +++ b/tests/cases/struct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml @@ -72,9 +72,9 @@ 1.0e5 0.48333 - + 50.0 - + 100.0 diff --git a/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml b/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml index e50e128f..9b1eeeaa 100644 --- a/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml +++ b/tests/cases/struct/tensile_adventitia_Potential_viscosity/svFSIplus.xml @@ -72,9 +72,9 @@ 1.0e5 0.48333 - + 50.0 - + 100.0 diff --git a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml index 4ed1b551..33b8c509 100644 --- a/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml +++ b/tests/cases/ustruct/tensile_adventitia_Newtonian_viscosity/svFSIplus.xml @@ -72,9 +72,9 @@ 1.0e5 0.48333 - + 50.0 - + 100.0 diff --git a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml index 7ad66cb6..28a7309d 100644 --- a/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml +++ b/tests/cases/ustruct/tensile_adventitia_Potential_viscosity/svFSIplus.xml @@ -72,9 +72,9 @@ 1.0e5 0.48333 - + 50.0 - + 100.0 From 4557b07fe4dbc60e117fae98efe406bc8678b878 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Thu, 3 Oct 2024 11:39:52 -0700 Subject: [PATCH 15/16] Replace raw strings with EquationType physics types. Add CMM and stokes to supported physics for fluid viscosity (integration tests now pass). Fixed small typo in pipe_3d_petsc input file viscosity definition --- Code/Source/svFSI/Parameters.cpp | 12 +++++++----- tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/Code/Source/svFSI/Parameters.cpp b/Code/Source/svFSI/Parameters.cpp index 9e3946c8..bcea3dde 100644 --- a/Code/Source/svFSI/Parameters.cpp +++ b/Code/Source/svFSI/Parameters.cpp @@ -1481,9 +1481,10 @@ void DomainParameters::set_values(tinyxml2::XMLElement* domain_elem) stimulus.set_values(item); } else if (name == FluidViscosityParameters::xml_element_name_ || name == SolidViscosityParameters::xml_element_name_) { - if (equation.value() == "fluid") { + auto eq_type = consts::equation_name_to_type.at(equation.value()); + if (eq_type == consts::EquationType::phys_fluid || eq_type == consts::EquationType::phys_CMM || eq_type == consts::EquationType::phys_stokes) { fluid_viscosity.set_values(item); - } else if (equation.value() == "struct" || equation.value() == "ustruct") { + } else if (eq_type == consts::EquationType::phys_struct || eq_type == consts::EquationType::phys_ustruct) { solid_viscosity.set_values(item); } else { @@ -1902,12 +1903,13 @@ void EquationParameters::set_values(tinyxml2::XMLElement* eq_elem) default_domain->stimulus.set_values(item); } else if (name == FluidViscosityParameters::xml_element_name_ || name == SolidViscosityParameters::xml_element_name_) { - if (type.value() == "fluid") { + auto eq_type = consts::equation_name_to_type.at(type.value()); + if (eq_type == consts::EquationType::phys_fluid || eq_type == consts::EquationType::phys_CMM || eq_type == consts::EquationType::phys_stokes) { default_domain->fluid_viscosity.set_values(item); - } else if (type.value() == "struct" || type.value() == "ustruct") { + } else if (eq_type == consts::EquationType::phys_struct || eq_type == consts::EquationType::phys_ustruct) { default_domain->solid_viscosity.set_values(item); } else { - throw std::runtime_error("Viscosity model not supported for equation '" + default_domain->equation.value() + "'."); + throw std::runtime_error("Viscosity model not supported for equation '" + type.value() + "'."); } } else if (name == ECGLeadsParameters::xml_element_name_) { diff --git a/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml b/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml index 6254cec5..30ed00bb 100755 --- a/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml +++ b/tests/cases/fsi/pipe_3d_petsc/svFSIplus.xml @@ -64,7 +64,7 @@ fluid 1.0 - "Constant" > + 0.04 0.2 From 1e5894836ae5dbe41dc56adbe55bc8fec1b42461 Mon Sep 17 00:00:00 2001 From: aabrown100-git Date: Fri, 4 Oct 2024 20:22:23 -0700 Subject: [PATCH 16/16] Removing references to old solid_viscosity --- Code/Source/svFSI/consts.h | 25 +++++++++--------- Code/Source/svFSI/read_files.cpp | 4 --- Code/Source/svFSI/set_equation_props.h | 36 ++++++++++++-------------- Code/Source/svFSI/sv_struct.cpp | 7 +---- 4 files changed, 29 insertions(+), 43 deletions(-) diff --git a/Code/Source/svFSI/consts.h b/Code/Source/svFSI/consts.h index 0d8964c5..f2790ba3 100644 --- a/Code/Source/svFSI/consts.h +++ b/Code/Source/svFSI/consts.h @@ -398,19 +398,18 @@ enum class PhysicalProperyType NA = 0, fluid_density = 1, solid_density = 2, - //solid_viscosity = 3, - elasticity_modulus = 4, - poisson_ratio = 5, - conductivity = 6, - f_x = 7, // internal force x - f_y = 8, // internal force y - f_z = 9, // internal force z - backflow_stab = 10, // stabilization coeff. for backflow divergence - source_term = 11, // external source - damping = 12, - shell_thickness = 13, - ctau_M = 14, // stabilization coeffs. for USTRUCT (momentum, continuity) - ctau_C = 15 + elasticity_modulus = 3, + poisson_ratio = 4, + conductivity = 5, + f_x = 6, // internal force x + f_y = 7, // internal force y + f_z = 8, // internal force z + backflow_stab = 9, // stabilization coeff. for backflow divergence + source_term = 10, // external source + damping = 11, + shell_thickness = 12, + ctau_M = 13, // stabilization coeffs. for USTRUCT (momentum, continuity) + ctau_C = 14 }; enum class PreconditionerType diff --git a/Code/Source/svFSI/read_files.cpp b/Code/Source/svFSI/read_files.cpp index 473e61e7..52ae6809 100644 --- a/Code/Source/svFSI/read_files.cpp +++ b/Code/Source/svFSI/read_files.cpp @@ -1299,10 +1299,6 @@ void read_domain(Simulation* simulation, EquationParameters* eq_params, eqType& } break; - // case PhysicalProperyType::solid_viscosity: - // rtmp = domain_params->solid_viscosity.value(); - // break; - case PhysicalProperyType::source_term: rtmp = domain_params->source_term.value(); break; diff --git a/Code/Source/svFSI/set_equation_props.h b/Code/Source/svFSI/set_equation_props.h index f20b2627..1fb5214d 100644 --- a/Code/Source/svFSI/set_equation_props.h +++ b/Code/Source/svFSI/set_equation_props.h @@ -330,11 +330,10 @@ SetEquationPropertiesMapType set_equation_props = { propL[1][n] = PhysicalProperyType::elasticity_modulus; propL[2][n] = PhysicalProperyType::poisson_ratio; propL[3][n] = PhysicalProperyType::damping; - //propL[4][n] = PhysicalProperyType::solid_viscosity; - propL[5][n] = PhysicalProperyType::f_x; - propL[6][n] = PhysicalProperyType::f_y; + propL[4][n] = PhysicalProperyType::f_x; + propL[5][n] = PhysicalProperyType::f_y; if (simulation->com_mod.nsd == 3) { - propL[7][n] = PhysicalProperyType::f_z; + propL[6][n] = PhysicalProperyType::f_z; } // Set ustruct properties. @@ -342,13 +341,12 @@ SetEquationPropertiesMapType set_equation_props = { propL[0][n] = PhysicalProperyType::solid_density; propL[1][n] = PhysicalProperyType::elasticity_modulus; propL[2][n] = PhysicalProperyType::poisson_ratio; - //propL[3][n] = PhysicalProperyType::solid_viscosity; - propL[4][n] = PhysicalProperyType::ctau_M; - propL[5][n] = PhysicalProperyType::ctau_C; - propL[6][n] = PhysicalProperyType::f_x; - propL[7][n] = PhysicalProperyType::f_y; + propL[3][n] = PhysicalProperyType::ctau_M; + propL[4][n] = PhysicalProperyType::ctau_C; + propL[5][n] = PhysicalProperyType::f_x; + propL[6][n] = PhysicalProperyType::f_y; if (simulation->com_mod.nsd == 3) { - propL[8][n] = PhysicalProperyType::f_z; + propL[7][n] = PhysicalProperyType::f_z; } // Set lElas properties. @@ -570,11 +568,10 @@ SetEquationPropertiesMapType set_equation_props = { propL[1][0] = PhysicalProperyType::damping; propL[2][0] = PhysicalProperyType::elasticity_modulus; propL[3][0] = PhysicalProperyType::poisson_ratio; - //propL[4][0] = PhysicalProperyType::solid_viscosity; - propL[5][0] = PhysicalProperyType::f_x; - propL[6][0] = PhysicalProperyType::f_y; + propL[4][0] = PhysicalProperyType::f_x; + propL[5][0] = PhysicalProperyType::f_y; if (simulation->com_mod.nsd == 3) { - propL[7][0] = PhysicalProperyType::f_z; + propL[6][0] = PhysicalProperyType::f_z; } read_domain(simulation, eq_params, lEq, propL); @@ -614,13 +611,12 @@ SetEquationPropertiesMapType set_equation_props = { propL[0][0] = PhysicalProperyType::solid_density; propL[1][0] = PhysicalProperyType::elasticity_modulus; propL[2][0] = PhysicalProperyType::poisson_ratio; - //propL[3][0] = PhysicalProperyType::solid_viscosity; - propL[4][0] = PhysicalProperyType::ctau_M; - propL[5][0] = PhysicalProperyType::ctau_C; - propL[6][0] = PhysicalProperyType::f_x; - propL[7][0] = PhysicalProperyType::f_y; + propL[3][0] = PhysicalProperyType::ctau_M; + propL[4][0] = PhysicalProperyType::ctau_C; + propL[5][0] = PhysicalProperyType::f_x; + propL[6][0] = PhysicalProperyType::f_y; if (simulation->com_mod.nsd == 3) { - propL[8][0] = PhysicalProperyType::f_z; + propL[7][0] = PhysicalProperyType::f_z; } read_domain(simulation, eq_params, lEq, propL); diff --git a/Code/Source/svFSI/sv_struct.cpp b/Code/Source/svFSI/sv_struct.cpp index 085007e6..224861f1 100644 --- a/Code/Source/svFSI/sv_struct.cpp +++ b/Code/Source/svFSI/sv_struct.cpp @@ -387,7 +387,6 @@ void struct_2d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, // Set parameters // double rho = dmn.prop.at(PhysicalProperyType::solid_density); - //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); double dmp = dmn.prop.at(PhysicalProperyType::damping); Vector fb({dmn.prop.at(PhysicalProperyType::f_x), dmn.prop.at(PhysicalProperyType::f_y)}); double afu = eq.af * eq.beta*dt*dt; @@ -576,7 +575,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in // Set parameters // double rho = dmn.prop.at(PhysicalProperyType::solid_density); - //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); double dmp = dmn.prop.at(PhysicalProperyType::damping); double fb[3]{dmn.prop.at(PhysicalProperyType::f_x), dmn.prop.at(PhysicalProperyType::f_y), @@ -588,7 +586,6 @@ void struct_3d_carray(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const in #ifdef debug_struct_3d dmsg << "rho: " << rho; - dmsg << "mu: " << mu; dmsg << "dmp: " << dmp; dmsg << "afu: " << afu; dmsg << "afv: " << afv; @@ -878,8 +875,7 @@ void struct_3d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, // Set parameters // double rho = dmn.prop.at(PhysicalProperyType::solid_density); - //double mu = dmn.prop.at(PhysicalProperyType::solid_viscosity); - double mu = 0; + double mu = 0.0; double dmp = dmn.prop.at(PhysicalProperyType::damping); Vector fb({dmn.prop.at(PhysicalProperyType::f_x), dmn.prop.at(PhysicalProperyType::f_y), @@ -891,7 +887,6 @@ void struct_3d(ComMod& com_mod, CepMod& cep_mod, const int eNoN, const int nFn, #ifdef debug_struct_3d dmsg << "rho: " << rho; - dmsg << "mu: " << mu; dmsg << "dmp: " << dmp; dmsg << "afu: " << afu; dmsg << "afv: " << afv;