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Refactoring

This commit is contained in:
iasonmanolas 2021-12-23 15:51:23 +02:00
parent 56e5e043f6
commit c9fc6ccd08
6 changed files with 417 additions and 313 deletions
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32
CMakeLists.txt
View File

@ -15,28 +15,19 @@ if(NOT EXISTS ${EXTERNAL_DEPS_DIR})
endif()
##Create directory for the external libraries
file(MAKE_DIRECTORY ${EXTERNAL_DEPS_DIR})
#message(${POLYSCOPE_ALREADY_COMPILED})
if(${USE_POLYSCOPE})
set(POLYSCOPE_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/polyscope)
download_project(PROJ POLYSCOPE
GIT_REPOSITORY https://github.com/nmwsharp/polyscope.git
GIT_TAG master
PREFIX ${EXTERNAL_DEPS_DIR}
BINARY_DIR ${POLYSCOPE_BINARY_DIR}
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
add_subdirectory(${POLYSCOPE_SOURCE_DIR} ${POLYSCOPE_BINARY_DIR})
add_compile_definitions(POLYSCOPE_DEFINED)
endif()
#dlib
set(DLIB_BIN_DIR ${CMAKE_CURRENT_BINARY_DIR}/dlib_bin)
file(MAKE_DIRECTORY ${DLIB_BIN_DIR})
download_project(PROJ DLIB
GIT_REPOSITORY https://github.com/davisking/dlib.git
GIT_TAG master
BINARY_DIR ${DLIB_BIN_DIR}
PREFIX ${EXTERNAL_DEPS_DIR}
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
add_subdirectory(${DLIB_SOURCE_DIR} ${DLIB_BINARY_DIR})
##vcglib devel branch
download_project(PROJ vcglib_devel
GIT_REPOSITORY https://github.com/IasonManolas/vcglib.git
@ -45,27 +36,36 @@ download_project(PROJ vcglib_devel
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
add_subdirectory(${vcglib_devel_SOURCE_DIR} ${vcglib_devel_BINARY_DIR})
##matplot++ lib
set(MATPLOTPLUSPLUS_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/matplot)
download_project(PROJ MATPLOTPLUSPLUS
GIT_REPOSITORY https://github.com/alandefreitas/matplotplusplus
GIT_TAG master
BINARY_DIR ${MATPLOTPLUSPLUS_BINARY_DIR}
PREFIX ${EXTERNAL_DEPS_DIR}
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
add_subdirectory(${MATPLOTPLUSPLUS_SOURCE_DIR} ${MATPLOTPLUSPLUS_BINARY_DIR})
##threed-beam-fea
set(threed-beam-fea_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/threed-beam-fea)
download_project(PROJ threed-beam-fea
GIT_REPOSITORY https://github.com/IasonManolas/threed-beam-fea.git
GIT_TAG master
BINARY_DIR ${threed-beam-fea_BINARY_DIR}
PREFIX ${EXTERNAL_DEPS_DIR}
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
add_subdirectory(${threed-beam-fea_SOURCE_DIR} ${threed-beam-fea_BINARY_DIR})
##TBB
set(TBB_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/tbb)
download_project(PROJ TBB
GIT_REPOSITORY https://github.com/wjakob/tbb.git
GIT_TAG master
PREFIX ${EXTERNAL_DEPS_DIR}
BINARY_DIR ${TBB_BINARY_DIR}
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
option(TBB_BUILD_TESTS "Build TBB tests and enable testing infrastructure" OFF)
@ -83,13 +83,12 @@ target_include_directories(${PROJECT_NAME}
PUBLIC ${CMAKE_CURRENT_LIST_DIR}/boost_graph
PUBLIC ${vcglib_devel_SOURCE_DIR}
PUBLIC ${threed-beam-fea_SOURCE_DIR}
# PUBLIC ${MySourcesFiles}
)
if(${MYSOURCES_STATIC_LINK})
message("Linking statically")
target_link_libraries(${PROJECT_NAME} -static Eigen3::Eigen matplot dlib::dlib ThreedBeamFEA ${TBB_BINARY_DIR}/libtbb_static.a pthread gfortran quadmath)
target_link_libraries(${PROJECT_NAME} -static Eigen3::Eigen matplot ThreedBeamFEA ${TBB_BINARY_DIR}/libtbb_static.a pthread gfortran quadmath)
else()
target_link_libraries(${PROJECT_NAME} Eigen3::Eigen matplot dlib::dlib ThreedBeamFEA tbb pthread)
target_link_libraries(${PROJECT_NAME} Eigen3::Eigen matplot ThreedBeamFEA tbb pthread)
if(${USE_POLYSCOPE})
target_link_libraries(${PROJECT_NAME} polyscope)
endif()
@ -98,9 +97,11 @@ target_link_directories(MySources PUBLIC ${CMAKE_CURRENT_LIST_DIR}/boost_graph/l
if(USE_ENSMALLEN)
##ENSMALLEN
set(ENSMALLEN_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/ensmallen)
download_project(PROJ ENSMALLEN
GIT_REPOSITORY https://github.com/mlpack/ensmallen.git
GIT_TAG master
BINARY_DIR ${ENSMALLEN_BINARY_DIR}
PREFIX ${EXTERNAL_DEPS_DIR}
${UPDATE_DISCONNECTED_IF_AVAILABLE}
)
@ -110,7 +111,6 @@ if(USE_ENSMALLEN)
if(${MYSOURCES_STATIC_LINK})
target_link_libraries(${PROJECT_NAME} PUBLIC "-static" ensmallen ${EXTERNAL_DEPS_DIR}/armadillo_build/libarmadillo.a)
else()
target_link_libraries(${PROJECT_NAME} PUBLIC)
target_link_libraries(${PROJECT_NAME} PUBLIC armadillo ensmallen)
endif()
target_include_directories(${PROJECT_NAME} PUBLIC ${ARMADILLO_SOURCE_DIR}/include)

5
drmsimulationmodel.cpp
View File

@ -1833,10 +1833,13 @@ SimulationResults DRMSimulationModel::computeResults(const std::shared_ptr<Simul
results.debug_q_normal[vi] = q_normal;
results.debug_q_nr[vi] = q_nr_nInit;
results.rotationalDisplacementQuaternion[vi]
//Eigen::Quaterniond R
= (q_normal
* (q_f1_nInit * q_nr_nInit)); //q_f1_nDeformed * q_nr_nDeformed * q_normal;
//Update the displacement vector to contain the euler angles
const Eigen::Vector3d eulerAngles = results.rotationalDisplacementQuaternion[vi]
const Eigen::Vector3d eulerAngles = results
.rotationalDisplacementQuaternion[vi]
// R
.toRotationMatrix()
.eulerAngles(0, 1, 2);
results.displacements[vi][3] = eulerAngles[0];

25
reducedmodeloptimizer_structs.hpp
View File

@ -62,8 +62,12 @@ struct xRange
}
};
enum OptimizationParameterIndex { E, A, I2, I3, J, R, Theta, NumberOfOptimizationParameters };
struct Settings
{
std::filesystem::path intermediateResultsDirectoryPath;
std::vector<std::vector<OptimizationParameterIndex>> optimizationVariables;
enum NormalizationStrategy { NonNormalized, Epsilon };
std::vector<xRange> parameterRanges;
inline static vector<std::string> normalizationStrategyStrings{"NonNormalized", "Epsilon"};
@ -72,7 +76,6 @@ struct xRange
NormalizationStrategy normalizationStrategy{Epsilon};
double translationNormalizationParameter{0.003};
double rotationNormalizationParameter{3};
bool splitGeometryMaterialOptimization{false};
struct ObjectiveWeights
{
double translational{1};
@ -86,6 +89,7 @@ struct xRange
inline static std::string NumberOfFunctionCalls{"NumberOfFunctionCalls"};
inline static std::string SolverAccuracy{"SolverAccuracy"};
inline static std::string TranslationalObjectiveWeight{"TransObjWeight"};
inline static std::string OptimizationParameters{"OptimizationParameters"};
};
void save(const std::filesystem::path &saveToPath)
@ -103,6 +107,7 @@ struct xRange
json[JsonKeys::NumberOfFunctionCalls] = numberOfFunctionCalls;
json[JsonKeys::SolverAccuracy] = solverAccuracy;
json[JsonKeys::TranslationalObjectiveWeight] = objectiveWeights.translational;
json[JsonKeys::OptimizationParameters] = optimizationVariables;
std::filesystem::path jsonFilePath(
std::filesystem::path(saveToPath).append(JsonKeys::filename));
@ -137,6 +142,9 @@ struct xRange
xRangeIndex++;
}
optimizationVariables
= std::vector<std::vector<ReducedPatternOptimization::OptimizationParameterIndex>>(
(json.at(JsonKeys::OptimizationParameters)));
numberOfFunctionCalls = json.at(JsonKeys::NumberOfFunctionCalls);
solverAccuracy = json.at(JsonKeys::SolverAccuracy);
objectiveWeights.translational = json.at(JsonKeys::TranslationalObjectiveWeight);
@ -175,7 +183,7 @@ struct xRange
os << "Normalization strategy";
os << "Trans weight";
os << "Rot weight";
os << "Splitted geo from mat opt";
os << "Optimization parameters";
// os << std::endl;
}
@ -193,7 +201,18 @@ struct xRange
+ std::to_string(translationNormalizationParameter);
os << objectiveWeights.translational;
os << objectiveWeights.rotational;
os << (splitGeometryMaterialOptimization == true ? "true" : "false");
//export optimization parameters
std::vector<std::vector<int>> vv;
for (const std::vector<OptimizationParameterIndex> &v : optimizationVariables) {
std::vector<int> vi;
vi.reserve(v.size());
for (const OptimizationParameterIndex &parameter : v) {
vi.emplace_back(parameter);
}
vv.push_back(vi);
}
os << Utilities::toString(vv);
}
};

83
simulation_structs.hpp
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@ -539,7 +539,7 @@ struct SimulationResults
const std::filesystem::path outputFolderPath = outputFolder.empty()
? std::filesystem::current_path()
: std::filesystem::path(outputFolder);
std::cout << "Saving results to:" << outputFolderPath << std::endl;
// std::cout << "Saving results to:" << outputFolderPath << std::endl;
std::filesystem::path simulationJobOutputFolderPath
= std::filesystem::path(outputFolderPath).append("SimulationJob");
std::filesystem::create_directories(simulationJobOutputFolderPath);
@ -569,34 +569,19 @@ struct SimulationResults
void load(const std::filesystem::path &loadFromPath, const std::filesystem::path &loadJobFrom)
{
//load job
pJob->load(std::filesystem::path(loadJobFrom).append("SimulationJob.json").string());
//Use the first .eigenBin file for loading the displacements
for (auto const &entry : std::filesystem::recursive_directory_iterator(loadFromPath)) {
if (filesystem::is_regular_file(entry) && entry.path().extension() == ".eigenBin") {
Eigen::MatrixXd displacements_eigen;
Eigen::read_binary(entry.path().string(), displacements_eigen);
displacements = Utilities::fromEigenMatrix(displacements_eigen);
break;
load(loadFromPath);
}
void load(const std::filesystem::path &loadFromPath, const std::shared_ptr<SimulationJob> &pJob)
{
this->pJob = pJob;
load(loadFromPath);
}
rotationalDisplacementQuaternion.resize(pJob->pMesh->VN());
for (int vi = 0; vi < pJob->pMesh->VN(); vi++) {
rotationalDisplacementQuaternion[vi] = Eigen::AngleAxisd(displacements[vi][3],
Eigen::Vector3d::UnitX())
* Eigen::AngleAxisd(displacements[vi][4],
Eigen::Vector3d::UnitY())
* Eigen::AngleAxisd(displacements[vi][5],
Eigen::Vector3d::UnitZ());
}
}
#ifdef POLYSCOPE_DEFINED
void unregister() const {
void unregister() const
{
if (!polyscope::hasCurveNetwork(getLabel())) {
std::cerr << "No curve network registered with a name: " << getLabel()
<< std::endl;
std::cerr << "No curve network registered with a name: " << getLabel() << std::endl;
std::cerr << "Nothing to remove." << std::endl;
return;
}
@ -641,13 +626,17 @@ struct SimulationResults
// std::unordered_set<int> interfaceNodes{1, 3, 5, 7, 9, 11};
// std::unordered_set<int> interfaceNodes{3, 7, 11, 15, 19, 23};
std::unordered_set<int> interfaceNodes{};
// std::unordered_set<int> interfaceNodes{};
for (VertexIndex vi = 0; vi < mesh->VN(); vi++) {
const Vector6d &nodalDisplacement = displacements[vi];
nodalDisplacements.row(vi) = Eigen::Vector3d(nodalDisplacement[0],
nodalDisplacement[1],
nodalDisplacement[2]);
if (interfaceNodes.contains(vi)) {
// Eigen::Quaternion<double> Rx(Eigen::AngleAxis(nodalDisplacement[2],Eigen::Vector3d(1, 0, 0)));
// Eigen::Quaternion<double> Ry(Eigen::AngleAxis(nodalDisplacement[4],Eigen::Vector3d(0, 1, 0)));
// Eigen::Quaternion<double> Rz(Eigen::AngleAxis(nodalDisplacement[5],Eigen::Vector3d(0, 0, 1)));
// Eigen::Quaternion<double> R=Rx*Ry*Rz;
// if (interfaceNodes.contains(vi)) {
auto deformedNormal = rotationalDisplacementQuaternion[vi] * Eigen::Vector3d(0, 0, 1);
auto deformedFrameY = rotationalDisplacementQuaternion[vi] * Eigen::Vector3d(0, 1, 0);
auto deformedFrameX = rotationalDisplacementQuaternion[vi] * Eigen::Vector3d(1, 0, 0);
@ -663,14 +652,14 @@ struct SimulationResults
framesX_initial.row(vi) = Eigen::Vector3d(1, 0, 0);
framesY_initial.row(vi) = Eigen::Vector3d(0, 1, 0);
framesZ_initial.row(vi) = Eigen::Vector3d(0, 0, 1);
} else {
framesX.row(vi) = Eigen::Vector3d(0, 0, 0);
framesY.row(vi) = Eigen::Vector3d(0, 0, 0);
framesZ.row(vi) = Eigen::Vector3d(0, 0, 0);
framesX_initial.row(vi) = Eigen::Vector3d(0, 0, 0);
framesY_initial.row(vi) = Eigen::Vector3d(0, 0, 0);
framesZ_initial.row(vi) = Eigen::Vector3d(0, 0, 0);
}
// } else {
// framesX.row(vi) = Eigen::Vector3d(0, 0, 0);
// framesY.row(vi) = Eigen::Vector3d(0, 0, 0);
// framesZ.row(vi) = Eigen::Vector3d(0, 0, 0);
// framesX_initial.row(vi) = Eigen::Vector3d(0, 0, 0);
// framesY_initial.row(vi) = Eigen::Vector3d(0, 0, 0);
// framesZ_initial.row(vi) = Eigen::Vector3d(0, 0, 0);
// }
}
polyscopeHandle_deformedEdmeMesh->updateNodePositions(mesh->getEigenVertices()
+ nodalDisplacements);
@ -741,6 +730,32 @@ struct SimulationResults
return polyscopeHandle_deformedEdmeMesh;
}
#endif
private:
void load(const std::filesystem::path &loadFromPath)
{
converged = true; //assuming it has converged
assert(pJob != nullptr);
//load job
//Use the first .eigenBin file for loading the displacements
for (auto const &entry : std::filesystem::recursive_directory_iterator(loadFromPath)) {
if (filesystem::is_regular_file(entry) && entry.path().extension() == ".eigenBin") {
Eigen::MatrixXd displacements_eigen;
Eigen::read_binary(entry.path().string(), displacements_eigen);
displacements = Utilities::fromEigenMatrix(displacements_eigen);
break;
}
}
rotationalDisplacementQuaternion.resize(pJob->pMesh->VN());
for (int vi = 0; vi < pJob->pMesh->VN(); vi++) {
rotationalDisplacementQuaternion[vi] = Eigen::AngleAxisd(displacements[vi][3],
Eigen::Vector3d::UnitX())
* Eigen::AngleAxisd(displacements[vi][4],
Eigen::Vector3d::UnitY())
* Eigen::AngleAxisd(displacements[vi][5],
Eigen::Vector3d::UnitZ());
}
}
};
#endif // SIMULATIONHISTORY_HPP

10
simulationmesh.cpp
View File

@ -499,13 +499,13 @@ double Element::getMass(const double &materialDensity)
}
void Element::updateRigidity() {
assert(initialLength != 0);
// assert(initialLength != 0);
rigidity.axial = material.youngsModulus * dimensions.A / initialLength;
assert(rigidity.axial != 0);
// assert(rigidity.axial != 0);
rigidity.torsional = material.G * dimensions.inertia.J / initialLength;
assert(rigidity.torsional != 0);
// assert(rigidity.torsional != 0);
rigidity.firstBending = 2 * material.youngsModulus * dimensions.inertia.I2 / initialLength;
assert(rigidity.firstBending != 0);
// assert(rigidity.firstBending != 0);
rigidity.secondBending = 2 * material.youngsModulus * dimensions.inertia.I3 / initialLength;
assert(rigidity.secondBending != 0);
// assert(rigidity.secondBending != 0);
}

75
utilities.hpp
View File

@ -140,7 +140,74 @@ struct Vector6d : public std::array<double, 6> {
};
namespace Utilities {
inline void parseIntegers(const std::string &str, std::vector<size_t> &result) {
//inline std::vector<std::string> split(std::string text, char delim)
//{
// std::string line;
// std::vector<std::string> vec;
// std::stringstream ss(text);
// while (std::getline(ss, line, delim)) {
// vec.push_back(line);
// }
// return vec;
//}
inline std::string_view leftTrimSpaces(const std::string_view& str)
{
std::string_view trimmedString=str;
const auto pos(str.find_first_not_of(" \t\n\r\f\v"));
trimmedString.remove_prefix(std::min(pos, trimmedString.length()));
return trimmedString;
}
inline std::string_view rightTrimSpaces(const std::string_view& str)
{
std::string_view trimmedString=str;
const auto pos(trimmedString.find_last_not_of(" \t\n\r\f\v"));
trimmedString.remove_suffix(std::min(trimmedString.length() - pos - 1,trimmedString.length()));
return trimmedString;
}
inline std::string_view trimLeftAndRightSpaces(std::string_view str)
{
std::string_view trimmedString=str;
trimmedString = leftTrimSpaces(trimmedString);
trimmedString = rightTrimSpaces(trimmedString);
return trimmedString;
}
inline std::vector<std::string> split(const std::string& text, std::string delim)
{
std::vector<std::string> vec;
size_t pos = 0, prevPos = 0;
while (1) {
pos = text.find(delim, prevPos);
if (pos == std::string::npos) {
vec.push_back(text.substr(prevPos));
return vec;
}
vec.push_back(text.substr(prevPos, pos - prevPos));
prevPos = pos + delim.length();
}
}
inline std::string toString(const std::vector<std::vector<int>> &vv)
{
std::string s;
s.append("{");
for (const std::vector<int> &v : vv) {
s.append("{");
for (const int &i : v) {
s.append(std::to_string(i) + ",");
}
s.pop_back();
s.append("}");
}
s.append("}");
return s;
}
inline void parseIntegers(const std::string &str, std::vector<size_t> &result)
{
typedef std::regex_iterator<std::string::const_iterator> re_iterator;
typedef re_iterator::value_type re_iterated;
@ -149,8 +216,9 @@ inline void parseIntegers(const std::string &str, std::vector<size_t> &result) {
re_iterator rit(str.begin(), str.end(), re);
re_iterator rend;
std::transform(rit, rend, std::back_inserter(result),
[](const re_iterated &it) { return std::stoi(it[1]); });
std::transform(rit, rend, std::back_inserter(result), [](const re_iterated &it) {
return std::stoi(it[1]);
});
}
inline Eigen::MatrixXd toEigenMatrix(const std::vector<Vector6d> &v) {
@ -179,7 +247,6 @@ inline std::vector<Vector6d> fromEigenMatrix(const Eigen::MatrixXd &m)
return v;
}
// std::string convertToLowercase(const std::string &s) {
// std::string lowercase;
// std::transform(s.begin(), s.end(), lowercase.begin(),