Refactoring

CMakeLists.txt

@@ -1,12 +1,13 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 project(MySources)
 
 file(GLOB MySourcesFiles ${CMAKE_CURRENT_LIST_DIR}/*.hpp ${CMAKE_CURRENT_LIST_DIR}/*.cpp)
-add_library(${PROJECT_NAME} ${MySourcesFiles} )
+add_library(${PROJECT_NAME} STATIC ${MySourcesFiles} )
 target_compile_features(${PROJECT_NAME} PUBLIC cxx_std_20)
 
 #Download external dependencies NOTE: If the user has one of these libs it shouldn't be downloaded again.
 include(${CMAKE_CURRENT_LIST_DIR}/cmake/DownloadProject.cmake)
+include(FetchContent)
 if (CMAKE_VERSION VERSION_LESS 3.2)
     set(UPDATE_DISCONNECTED_IF_AVAILABLE "")
 else()
@@ -18,108 +19,236 @@ if(NOT EXISTS ${EXTERNAL_DEPS_DIR})
 endif()
 ##Create directory for the external libraries
 file(MAKE_DIRECTORY ${EXTERNAL_DEPS_DIR})
-if(${USE_POLYSCOPE})
-        set(POLYSCOPE_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/polyscope)
-        download_project(PROJ               POLYSCOPE
-                         GIT_REPOSITORY     https://github.com/nmwsharp/polyscope.git
+
+set(DRMSimulationModelDir "/home/iason/Coding/Libraries/DRMSimulationModel")
+set(DRMSimulationModelBuildDir ${CMAKE_BINARY_DIR}/_deps)
+add_subdirectory(${DRMSimulationModelDir} ${DRMSimulationModelBuildDir})
+target_link_libraries(${PROJECT_NAME} PUBLIC DRMSimulationModel_lib)
+#target_include_directories(${PROJECT_NAME} PUBLIC DRMSimulationModel_)
+
+#target_sources(${PROJECT_NAME} PUBLIC ${DRMSimulationModelDir}/simulationmodel.hpp)
+if(${USE_DLIB})
+        FetchContent_Declare(dlib
+                         GIT_REPOSITORY     https://github.com/davisking/dlib.git
                          GIT_TAG	    master
-                         PREFIX             ${EXTERNAL_DEPS_DIR}
-                         BINARY_DIR		${POLYSCOPE_BINARY_DIR}
-                         ${UPDATE_DISCONNECTED_IF_AVAILABLE}
-        )
-        add_subdirectory(${POLYSCOPE_SOURCE_DIR} ${POLYSCOPE_BINARY_DIR})
-        add_compile_definitions(POLYSCOPE_DEFINED)
-        target_sources(${PROJECT_NAME} PUBLIC ${POLYSCOPE_SOURCE_DIR}/deps/imgui/imgui/misc/cpp/imgui_stdlib.cpp)
+          )
+        FetchContent_MakeAvailable(dlib)
+        #add_subdirectory(${DLIB_SOURCE_DIR} ${DLIB_BIN_DIR})
+        if(${MYSOURCES_STATIC_LINK})
+                target_link_libraries(${PROJECT_NAME} PUBLIC -static dlib::dlib)
+        else()
+                target_link_libraries(${PROJECT_NAME} PUBLIC dlib::dlib)
+        endif()
+        add_compile_definitions(DLIB_DEFINED)
 endif()
 
+## polyscope
+if(#[[NOT TARGET polyscope AND]] ${USE_POLYSCOPE})
+message("Using polyscope")
+        FetchContent_Declare(polyscope
+                                 GIT_REPOSITORY     https://github.com/nmwsharp/polyscope.git
+                                 GIT_TAG      master
+          )
+        FetchContent_MakeAvailable(polyscope)
+        target_include_directories(${PROJECT_NAME} PUBLIC ${polyscope_SOURCE_DIR}/include)
+#        target_include_directories(${PROJECT_NAME} PUBLIC ${polyscope_SOURCE_DIR}/deps/imgui)
+        target_sources(${PROJECT_NAME} PUBLIC ${polyscope_SOURCE_DIR}/deps/imgui/imgui/misc/cpp/imgui_stdlib.h ${polyscope_SOURCE_DIR}/deps/imgui/imgui/misc/cpp/imgui_stdlib.cpp)
+        target_link_libraries(${PROJECT_NAME} PUBLIC polyscope)
+endif()
+#if(NOT TARGET polyscope AND ${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} ${POLYSCOPE_BINARY_DIR})
+#        add_compile_definitions(POLYSCOPE_DEFINED)
+
+#        message("Using polyscope..")
+#        target_include_directories(${PROJECT_NAME} PUBLIC ${POLYSCOPE_SOURCE_DIR}/include)
+#        target_link_libraries(${PROJECT_NAME} PUBLIC polyscope)
+#endif()
+
 ##vcglib devel branch
-download_project(PROJ		    vcglib_devel
+FetchContent_Declare(vcglib
                  GIT_REPOSITORY     https://gitea-s2i2s.isti.cnr.it/manolas/vcglib.git
                  GIT_TAG	    devel
-                 PREFIX             ${EXTERNAL_DEPS_DIR}
-                 ${UPDATE_DISCONNECTED_IF_AVAILABLE}
-)
-add_subdirectory(${vcglib_devel_SOURCE_DIR} ${vcglib_devel_BINARY_DIR})
-target_sources(${PROJECT_NAME} PUBLIC ${vcglib_devel_SOURCE_DIR}/wrap/ply/plylib.cpp)
+  )
+FetchContent_MakeAvailable(vcglib)
+target_include_directories(${PROJECT_NAME} PUBLIC ${vcglib_SOURCE_DIR})
+target_sources(${PROJECT_NAME} PUBLIC ${vcglib_SOURCE_DIR}/wrap/ply/plylib.cpp)
 
-##matplot++ lib
-set(MATPLOTPLUSPLUS_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/matplot)
-download_project(PROJ               MATPLOTPLUSPLUS
+###matplot++ lib
+FetchContent_Declare(matplot
                  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})
+                 GIT_TAG		master
+  )
+FetchContent_MakeAvailable(matplot)
 
 ##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
+if(NOT TARGET ThreedBeamFEA)
+FetchContent_Declare(threed-beam-fea
                  GIT_REPOSITORY      https://gitea-s2i2s.isti.cnr.it/manolas/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} ${threed-beam-fea_BINARY_DIR})
+                 GIT_TAG		master
+  )
+FetchContent_MakeAvailable(threed-beam-fea)
+endif()
+target_link_libraries(${PROJECT_NAME} PUBLIC ThreedBeamFEA)
+target_include_directories(${PROJECT_NAME} PUBLIC ${threed-beam-fea_SOURCE_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}
-                 ${UPDATE_DISCONNECTED_IF_AVAILABLE}
-)
-option(TBB_BUILD_TESTS           "Build TBB tests and enable testing infrastructure" OFF)
-add_subdirectory(${TBB_SOURCE_DIR} ${TBB_BINARY_DIR})
-link_directories(${TBB_BINARY_DIR})
-###Eigen 3 NOTE: Eigen is required on the system the code is ran
-find_package(Eigen3 3.3 REQUIRED)
+#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} ${threed-beam-fea_BINARY_DIR})
+
+find_package(Eigen3 3.4 REQUIRED)
 if(MSVC)
         add_compile_definitions(_HAS_STD_BYTE=0)
 endif(MSVC)
-#link_directories(${CMAKE_CURRENT_LIST_DIR}/boost_graph/libs)
 
 if(${MYSOURCES_STATIC_LINK})
-        message("Linking statically")
-        target_link_libraries(${PROJECT_NAME} PUBLIC -static Eigen3::Eigen matplot ThreedBeamFEA ${TBB_BINARY_DIR}/libtbb_static.a #[[tbb_static]] pthread gfortran quadmath)
-else()
-#    set_target_properties(${PROJECT_NAME} PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
-        target_link_libraries(${PROJECT_NAME} PUBLIC Eigen3::Eigen matplot ThreedBeamFEA tbb pthread)
-        if(${USE_POLYSCOPE})
-        message("Using polyscope")
-                target_link_libraries(${PROJECT_NAME} PUBLIC polyscope)
-        endif()
+        message("STATIC LINK MY SOURCES:" ${MYSOURCES_STATIC_LINK})
 endif()
+if(${MYSOURCES_STATIC_LINK})
+        message("Linking statically here")
+        target_link_libraries(${PROJECT_NAME} PUBLIC #[[-static]] Eigen3::Eigen pthread gfortran quadmath matplot)
+else()
+        target_link_libraries(${PROJECT_NAME} PUBLIC Eigen3::Eigen tbb pthread matplot)
+endif()
+
 target_link_directories(MySources PUBLIC ${CMAKE_CURRENT_LIST_DIR}/boost_graph/libs)
 target_include_directories(${PROJECT_NAME}
     PUBLIC ${CMAKE_CURRENT_LIST_DIR}/boost_graph
     PUBLIC ${vcglib_devel_SOURCE_DIR}
-    PUBLIC ${threed-beam-fea_SOURCE_DIR}
-        PUBLIC matplot
+#    PUBLIC ${threed-beam-fea_SOURCE_DIR}
     )
 
-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}
-                         ${UPDATE_DISCONNECTED_IF_AVAILABLE}
-        )
-        add_subdirectory(${ENSMALLEN_SOURCE_DIR} ${ENSMALLEN_BINARY_DIR})
-        set(ARMADILLO_SOURCE_DIR "/home/iason/Coding/Libraries/armadillo")
-        add_subdirectory(${ARMADILLO_SOURCE_DIR} ${EXTERNAL_DEPS_DIR}/armadillo_build)
-        if(${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  armadillo ensmallen)
-        endif()
-        target_include_directories(${PROJECT_NAME} PUBLIC ${ARMADILLO_SOURCE_DIR}/include ${ENSMALLEN_SOURCE_DIR})
+
+#if(USE_ENSMALLEN)
+set(ARMADILLO_SOURCE_DIR "/home/iason/Coding/Libraries/armadillo")
+set(ARMADILLO_BIN_DIR "/home/iason/Coding/Libraries/armadillo/build")
+add_subdirectory(${ARMADILLO_SOURCE_DIR} ${ARMADILLO_BIN_DIR})
+target_include_directories(${PROJECT_NAME} PUBLIC ${ARMADILLO_SOURCE_DIR}/include)
+add_compile_definitions(ARMA_DONT_USE_WRAPPER)
+target_link_libraries(${PROJECT_NAME} PUBLIC "/home/iason/Coding/Libraries/armadillo/build/libarmadillo.a" #[[blas lapack]])
+#find_package(Armadillo REQUIRED)
+#target_link_libraries(${PROJECT_NAME} PUBLIC ${ARMADILLO_LIBRARIES})
+
+#if(NOT TARGET ThreedBeamFEA)
+#FetchContent_Declare(armadillo
+#                 GIT_REPOSITORY   https://gitlab.com/conradsnicta/armadillo-code.git
+#                 GIT_TAG	"11.2.x"
+#  )
+#FetchContent_MakeAvailable(armadillo)
+#find_package(Armadillo REQUIRED)
+#endif()
+#target_link_libraries(${PROJECT_NAME} PUBLIC "/home/iason/Coding/build/FormFInder/Debug/_deps/armadillo-build/libarmadillo.a")
+
+
+if(${USE_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}
+                 ${UPDATE_DISCONNECTED_IF_AVAILABLE}
+)
+target_include_directories(${PROJECT_NAME}
+PUBLIC ${ENSMALLEN_SOURCE_DIR}/include)
+add_compile_definitions(USE_ENSMALLEN)
+###ENSMALLEN
+#FetchContent_Declare(ensmallen
+#                 GIT_REPOSITORY  https://github.com/mlpack/ensmallen.git
+#                 GIT_TAG	master
+#  )
+#FetchContent_MakeAvailable(ensmallen)
+#target_link_libraries(${PROJECT_NAME} PRIVATE ensmallen)
+#target_include_directories(${PROJECT_NAME}
+#PUBLIC ${ensmallen_SOURCE_DIR}/include)
+#add_compile_definitions(USE_ENSMALLEN)
 endif()
+
+##Chrono
+##add_subdirectory("/home/iason/Coding/build/external dependencies/CHRONO-src" "/home/iason/Coding/build/external dependencies/CHRONO-src/build")
+##set(Chrono_DIR "/home/iason/Coding/Libraries/chrono-7.0.3/build/Release/cmake")
+#set(Chrono_DIR "/home/iason/Coding/Libraries/chrono-7.0.3/build/Release/cmake")
+##LIST(APPEND CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}/../Chrono/lib")
+#find_package(Chrono CONFIG
+#                 )
+#if (NOT Chrono_FOUND)
+#        message("Could not find Chrono or one of its required modules")
+#        return()
+#endif()
+#set_target_properties(${PROJECT_NAME} PROPERTIES
+#            COMPILE_FLAGS "${CHRONO_CXX_FLAGS} ${EXTRA_COMPILE_FLAGS}"
+#            COMPILE_DEFINITIONS "CHRONO_DATA_DIR=\"${CHRONO_DATA_DIR}\""
+#            LINK_FLAGS "${CHRONO_LINKER_FLAGS}")
+#include_directories(${CHRONO_INCLUDE_DIRS})
+#target_link_libraries(${PROJECT_NAME} PUBLIC ${CHRONO_LIBRARIES})
+target_include_directories(${PROJECT_NAME} PUBLIC "/home/iason/Coding/Libraries/chrono-7.0.3/src" #[[${CHRONO_INCLUDE_DIRS}]] #[["/home/iason/Coding/Libraries/chrono-7.0.3/src"]] 	#[["/usr/include/irrlicht"]] )
+#target_link_directories(${PROJECT_NAME} PRIVATE "/home/iason/Coding/build/external dependencies/CHRONO-src/build/RelWithDebInfo/lib")
+#target_link_libraries(${PROJECT_NAME} PUBLIC "/home/iason/Coding/build/external dependencies/CHRONO-src/build/RelWithDebInfo/lib/libChronoEngine.a")
+target_link_libraries(${PROJECT_NAME} PUBLIC "/home/iason/Coding/Libraries/chrono-7.0.3/build/Release/lib/libChronoEngine.a")
+
+
+#add_subdirectory("/home/iason/Coding/Projects/Approximating shapes with flat patterns/Elastic rods/ElasticRods")
+#set(MESHFEM_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/meshfem)
+#download_project(PROJ			MESHFEM
+#                 GIT_REPOSITORY		https://github.com/MeshFEM/MeshFEM.git
+#                 GIT_TAG		3847ffaeb6e9c4bbe15f0f81f5c773c7c481c059
+#                 BINARY_DIR		${MESHFEM_BINARY_DIR}
+#                 PREFIX             	${EXTERNAL_DEPS_DIR}
+#                 ${UPDATE_DISCONNECTED_IF_AVAILABLE}
+#)
+#add_subdirectory(${MESHFEM_SOURCE_DIR} ${MESHFEM_BINARY_DIR})
+#target_link_libraries(${PROJECT_NAME} PUBLIC MeshFEM)
+##target_include_directories(${PROJECT_NAME}
+##PUBLIC ${MESHFEM_SOURCE_DIR}/include)
+##add_compile_definitions(USE_ENSMALLEN)
+
+##DER by panetta fork
+##set(FETCHCONTENT_SOURCE_DIR_LIBIGL "/home/iason/Coding/Libraries/libigl/cmake" CACHE PATH "not set")
+#set(LIBIGL_INCLUDE_DIR "/home/iason/Coding/Projects/Approximating shapes with flat patterns/Elastic rods/ElasticRods/3rdparty/libigl/include")
+##list(PREPEND CMAKE_MODULE_PATH "/home/iason/Coding/Libraries/libigl/cmake")
+##include(libigl)
+##add_subdirectory("/home/iason/Coding/Projects/Approximating shapes with flat patterns/Elastic rods/ElasticRods/3rdparty/MeshFEM/" ${EXTERNAL_DEPS_DIR}/MeshFEM)
+#set(DER_Panetta_dir "/home/iason/Coding/Projects/Approximating shapes with flat patterns/Elastic rods/DER_panneta_fork")
+#set(DER_Panetta_bin_dir "/home/iason/Coding/build/external dependencies/DER_panetta_fork")
+#add_subdirectory(${DER_Panetta_dir} ${DER_Panetta_bin_dir})
+##add_subdirectory("/home/iason/Coding/Projects/Approximating shapes with flat patterns/Elastic rods/ElasticRods/3rdparty/MeshFEM" "/home/iason/Coding/build/external dependencies/MeshFEM")
+##add_subdirectory("/home/iason/Coding/Projects/Approximating shapes with flat patterns/Elastic rods/ElasticRods/3rdparty/RotationOptimization" "/home/iason/Coding/build/external dependencies/RotationOptimization" )
+#target_link_directories(${PROJECT_NAME} PUBLIC "/home/iason/Coding/build/Elastic rods/DER_panneta_fork/Debug")
+#target_link_libraries(${PROJECT_NAME} PUBLIC RigidRodLinkages ElasticRods rotation_optimization MeshFEM "/home/iason/Coding/build/Elastic rods/DER_panneta_fork/Debug/3rdparty/visvalingam_simplify/src/libVisvalingamSimplify.a")
+#target_include_directories(${PROJECT_NAME} PUBLIC ${DER_Panetta_dir} )
+
+##TBB
+if(NOT TARGET tbb_static AND NOT TARGET 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}
+#                         ${UPDATE_DISCONNECTED_IF_AVAILABLE}
+#        )
+#	option(TBB_BUILD_TESTS           "Build TBB tests and enable testing infrastructure" OFF)
+#        add_subdirectory(${TBB_SOURCE_DIR} ${TBB_BINARY_DIR})
+#link_directories(${TBB_BINARY_DIR})
+message("Using tbb")
+        FetchContent_Declare(tbb
+                                 GIT_REPOSITORY      https://github.com/wjakob/tbb.git
+                                 GIT_TAG             master
+          )
+        FetchContent_MakeAvailable(tbb)
+#        target_link_libraries(${PROJECT_NAME} PRIVATE tbb_static)
+endif()
+target_link_libraries(${PROJECT_NAME} PRIVATE tbb_static)

CMakeLists.txt.user

@@ -1,355 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 4.14.2, 2021-07-15T10:27:01. -->
-<qtcreator>
- <data>
-  <variable>EnvironmentId</variable>
-  <value type="QByteArray">{4ab9621f-3cb4-4d5c-a5a5-8f7ea53a6f0f}</value>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.ActiveTarget</variable>
-  <value type="int">0</value>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.EditorSettings</variable>
-  <valuemap type="QVariantMap">
-   <value type="bool" key="EditorConfiguration.AutoIndent">false</value>
-   <value type="bool" key="EditorConfiguration.AutoSpacesForTabs">false</value>
-   <value type="bool" key="EditorConfiguration.CamelCaseNavigation">true</value>
-   <valuemap type="QVariantMap" key="EditorConfiguration.CodeStyle.0">
-    <value type="QString" key="language">Cpp</value>
-    <valuemap type="QVariantMap" key="value">
-     <value type="QByteArray" key="CurrentPreferences">CppGlobal</value>
-    </valuemap>
-   </valuemap>
-   <valuemap type="QVariantMap" key="EditorConfiguration.CodeStyle.1">
-    <value type="QString" key="language">QmlJS</value>
-    <valuemap type="QVariantMap" key="value">
-     <value type="QByteArray" key="CurrentPreferences">QmlJSGlobal</value>
-    </valuemap>
-   </valuemap>
-   <value type="int" key="EditorConfiguration.CodeStyle.Count">2</value>
-   <value type="QByteArray" key="EditorConfiguration.Codec">UTF-8</value>
-   <value type="bool" key="EditorConfiguration.ConstrainTooltips">false</value>
-   <value type="int" key="EditorConfiguration.IndentSize">4</value>
-   <value type="bool" key="EditorConfiguration.KeyboardTooltips">false</value>
-   <value type="int" key="EditorConfiguration.MarginColumn">80</value>
-   <value type="bool" key="EditorConfiguration.MouseHiding">true</value>
-   <value type="bool" key="EditorConfiguration.MouseNavigation">true</value>
-   <value type="int" key="EditorConfiguration.PaddingMode">1</value>
-   <value type="bool" key="EditorConfiguration.ScrollWheelZooming">true</value>
-   <value type="bool" key="EditorConfiguration.ShowMargin">false</value>
-   <value type="int" key="EditorConfiguration.SmartBackspaceBehavior">0</value>
-   <value type="bool" key="EditorConfiguration.SmartSelectionChanging">true</value>
-   <value type="bool" key="EditorConfiguration.SpacesForTabs">true</value>
-   <value type="int" key="EditorConfiguration.TabKeyBehavior">0</value>
-   <value type="int" key="EditorConfiguration.TabSize">8</value>
-   <value type="bool" key="EditorConfiguration.UseGlobal">true</value>
-   <value type="int" key="EditorConfiguration.Utf8BomBehavior">1</value>
-   <value type="bool" key="EditorConfiguration.addFinalNewLine">true</value>
-   <value type="bool" key="EditorConfiguration.cleanIndentation">true</value>
-   <value type="bool" key="EditorConfiguration.cleanWhitespace">true</value>
-   <value type="QString" key="EditorConfiguration.ignoreFileTypes">*.md, *.MD, Makefile</value>
-   <value type="bool" key="EditorConfiguration.inEntireDocument">false</value>
-   <value type="bool" key="EditorConfiguration.skipTrailingWhitespace">true</value>
-  </valuemap>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.PluginSettings</variable>
-  <valuemap type="QVariantMap">
-   <valuemap type="QVariantMap" key="AutoTest.ActiveFrameworks">
-    <value type="bool" key="AutoTest.Framework.Boost">true</value>
-    <value type="bool" key="AutoTest.Framework.Catch">true</value>
-    <value type="bool" key="AutoTest.Framework.GTest">true</value>
-    <value type="bool" key="AutoTest.Framework.QtQuickTest">true</value>
-    <value type="bool" key="AutoTest.Framework.QtTest">true</value>
-   </valuemap>
-   <valuemap type="QVariantMap" key="AutoTest.CheckStates"/>
-   <value type="int" key="AutoTest.RunAfterBuild">0</value>
-   <value type="bool" key="AutoTest.UseGlobal">true</value>
-   <valuemap type="QVariantMap" key="ClangTools">
-    <value type="bool" key="ClangTools.AnalyzeOpenFiles">true</value>
-    <value type="bool" key="ClangTools.BuildBeforeAnalysis">true</value>
-    <value type="QString" key="ClangTools.DiagnosticConfig">Builtin.DefaultTidyAndClazy</value>
-    <value type="int" key="ClangTools.ParallelJobs">6</value>
-    <valuelist type="QVariantList" key="ClangTools.SelectedDirs"/>
-    <valuelist type="QVariantList" key="ClangTools.SelectedFiles"/>
-    <valuelist type="QVariantList" key="ClangTools.SuppressedDiagnostics"/>
-    <value type="bool" key="ClangTools.UseGlobalSettings">true</value>
-   </valuemap>
-  </valuemap>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.Target.0</variable>
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beam.hpp

@@ -1,80 +0,0 @@
-#ifndef BEAM_HPP
-#define BEAM_HPP
-#include <assert.h>
-#include <cmath>
-#include <iostream>
-#include <string>
-
-struct RectangularBeamDimensions {
-  inline static std::string name{"Rectangular"};
-  double b;
-  double h;
-
-  double A{0}; // cross sectional area
-
-  struct MomentsOfInertia
-  {
-      double I2{0}; // second moment of inertia
-      double I3{0}; // third moment of inertia
-      double J{0};  // torsional constant (polar moment of inertia)
-  } inertia;
-
-  RectangularBeamDimensions(const double &width, const double &height) : b(width), h(height)
-  {
-      assert(width > 0 && height > 0);
-      updateProperties();
-  }
-  RectangularBeamDimensions() : b(0.002), h(0.002) { updateProperties(); }
-  std::string toString() const {
-    return std::string("b=") + std::to_string(b) + std::string(" h=") +
-           std::to_string(h);
-  }
-
-  void updateProperties()
-  {
-      A = b * h;
-      inertia.I2 = b * std::pow(h, 3) / 12;
-      inertia.I3 = h * std::pow(b, 3) / 12;
-      inertia.J = inertia.I2 + inertia.I3;
-  }
-  static void computeMomentsOfInertia(const RectangularBeamDimensions &dimensions,
-                                      MomentsOfInertia &inertia);
-};
-
-struct CylindricalBeamDimensions {
-  inline static std::string name{"Cylindrical"};
-  double od; // Cylinder outside diameter
-  double
-      id; // Cylinder inside diameter
-          // https://www.engineeringtoolbox.com/area-moment-inertia-d_1328.html
-  CylindricalBeamDimensions(const double &outsideDiameter,
-                            const double &insideDiameter)
-      : od(outsideDiameter), id(insideDiameter) {
-    assert(outsideDiameter > 0 && insideDiameter > 0 &&
-           outsideDiameter > insideDiameter);
-  }
-  CylindricalBeamDimensions() : od(0.03), id(0.026) {}
-};
-
-struct ElementMaterial
-{
-    double poissonsRatio;
-    double youngsModulus;
-    double G;
-    ElementMaterial(const double &poissonsRatio, const double &youngsModulus)
-        : poissonsRatio(poissonsRatio), youngsModulus(youngsModulus)
-    {
-        assert(poissonsRatio <= 0.5 && poissonsRatio >= -1);
-        updateProperties();
-    }
-    ElementMaterial() : poissonsRatio(0.3), youngsModulus(200 * 1e9) { updateProperties(); }
-    std::string toString() const
-    {
-        return std::string("Material:") + std::string("\nPoisson's ratio=")
-               + std::to_string(poissonsRatio) + std::string("\nYoung's Modulus(GPa)=")
-               + std::to_string(youngsModulus / 1e9);
-    }
-    void updateProperties() { G = youngsModulus / (2 * (1 + poissonsRatio)); }
-};
-
-#endif // BEAM_HPP

chronoseulerlinearsimulationmodel.cpp

@@ -0,0 +1,13 @@
+#include "chronoseulerlinearsimulationmodel.hpp"
+
+ChronosEulerLinearSimulationModel::ChronosEulerLinearSimulationModel() {}
+
+SimulationResults ChronosEulerLinearSimulationModel::executeSimulation(
+    const std::shared_ptr<SimulationJob> &pJob) {
+  ChronosEulerSimulationModel simulationModel;
+  simulationModel.settings.analysisType =
+      ChronosEulerSimulationModel::Settings::AnalysisType::Linear;
+  auto simulationResults = simulationModel.executeSimulation(pJob);
+  simulationResults.simulationModelUsed = label;
+  return simulationResults;
+}

chronoseulerlinearsimulationmodel.hpp

@@ -0,0 +1,15 @@
+#ifndef CHRONOSEULERLINEARSIMULATIONMODEL_HPP
+#define CHRONOSEULERLINEARSIMULATIONMODEL_HPP
+
+#include "chronoseulersimulationmodel.hpp"
+
+class ChronosEulerLinearSimulationModel : public ChronosEulerSimulationModel {
+public:
+  ChronosEulerLinearSimulationModel();
+  SimulationResults
+  executeSimulation(const std::shared_ptr<SimulationJob> &pJob);
+  inline static std::string label{"Linear_" +
+                                  ChronosEulerSimulationModel::label};
+};
+
+#endif // CHRONOSEULERLINEARSIMULATIONMODEL_HPP

chronoseulernonlinearsimulationmodel.cpp

@@ -0,0 +1,13 @@
+#include "chronoseulernonlinearsimulationmodel.hpp"
+
+ChronosEulerNonLinearSimulationModel::ChronosEulerNonLinearSimulationModel() {}
+
+SimulationResults ChronosEulerNonLinearSimulationModel::executeSimulation(
+    const std::shared_ptr<SimulationJob> &pJob) {
+  ChronosEulerSimulationModel simulationModel;
+  simulationModel.settings.analysisType =
+      ChronosEulerSimulationModel::Settings::AnalysisType::NonLinear;
+  auto simulationResults = simulationModel.executeSimulation(pJob);
+  simulationResults.simulationModelUsed = label;
+  return simulationResults;
+}

chronoseulernonlinearsimulationmodel.hpp

@@ -0,0 +1,16 @@
+#ifndef CHRONOSEULERNONLINEARSIMULATIONMODEL_HPP
+#define CHRONOSEULERNONLINEARSIMULATIONMODEL_HPP
+
+#include "chronoseulersimulationmodel.hpp"
+
+class ChronosEulerNonLinearSimulationModel
+    : public ChronosEulerSimulationModel {
+public:
+  ChronosEulerNonLinearSimulationModel();
+  SimulationResults
+  executeSimulation(const std::shared_ptr<SimulationJob> &pJob);
+  inline static std::string label{"NonLinear_" +
+                                  ChronosEulerSimulationModel::label};
+};
+
+#endif // CHRONOSEULERNONLINEARSIMULATIONMODEL_HPP

chronoseulersimulationmodel.cpp

@@ -0,0 +1,307 @@
+#include "chronoseulersimulationmodel.hpp"
+#include <chrono/fea/ChBeamSectionEuler.h>
+#include <chrono/fea/ChBuilderBeam.h>
+#include <chrono/fea/ChLoadsBeam.h>
+#include <chrono/fea/ChMesh.h>
+#include <chrono/fea/ChNodeFEAxyzrot.h>
+#include <chrono/physics/ChBody.h>
+#include <chrono/physics/ChSystemSMC.h>
+#include <chrono/solver/ChIterativeSolverLS.h>
+#include "chrono/physics/ChLoadContainer.h"
+
+#include <chrono/assets/ChVisualization.h>
+#include <chrono/fea/ChElementBeamEuler.h>
+#include <chrono/fea/ChVisualizationFEAmesh.h>
+
+using namespace chrono;
+using namespace chrono::fea;
+std::shared_ptr<ChMesh> ChronosEulerSimulationModel::convertToChronosMesh_Euler(
+    const std::shared_ptr<SimulationEdgeMesh>& pMesh,
+    std::vector<std::shared_ptr<ChNodeFEAxyzrot>>&
+        edgeMeshVertsToChronosNodes) {
+  auto mesh_chronos = chrono_types::make_shared<ChMesh>();
+  edgeMeshVertsToChronosNodes.clear();
+  edgeMeshVertsToChronosNodes.resize(pMesh->VN(), nullptr);
+
+  // add nodes
+  for (int vi = 0; vi < pMesh->VN(); vi++) {
+    const auto& vertex = pMesh->vert[vi];
+    ChVector<> vertexPos(vertex.cP()[0], vertex.cP()[1], vertex.cP()[2]);
+    edgeMeshVertsToChronosNodes[vi] =
+        chrono_types::make_shared<ChNodeFEAxyzrot>(ChFrame<>(vertexPos));
+    mesh_chronos->AddNode(edgeMeshVertsToChronosNodes[vi]);
+  }
+  // add elements
+  ChBuilderBeamEuler builder;
+  for (int ei = 0; ei < pMesh->EN(); ei++) {
+    const SimulationEdgeMesh::EdgeType& edge = pMesh->edge[ei];
+    // define end-points
+    const auto vi0 = pMesh->getIndex(edge.cV(0));
+    const auto vi1 = pMesh->getIndex(edge.cV(1));
+    // define cross section
+    const Element& element = pMesh->elements[ei];
+    const double beam_wz = element.dimensions.getDim1();
+    const double beam_wy = element.dimensions.getDim2();
+    const double E = element.material.youngsModulus;
+    //        const double poisson = element.material.poissonsRatio;
+    const double density = 1e0;
+
+    //        auto msection =
+    //        chrono_types::make_shared<ChBeamSectionEulerAdvanced>();
+    auto msection =
+        chrono_types::make_shared<ChBeamSectionEulerEasyRectangular>(
+            beam_wy, beam_wz, E, element.material.G, density);
+    msection->SetArea(element.dimensions.A);
+    msection->SetIyy(element.dimensions.inertia.I2);
+    msection->SetIzz(element.dimensions.inertia.I3);
+    msection->SetJ(element.dimensions.inertia.J);
+    //        msection->SetDensity(density);
+    //        msection->SetYoungModulus(E);
+    //        msection->SetGwithPoissonRatio(poisson);
+    //        //        msection->SetBeamRaleyghDamping(0.0);
+    //        msection->SetAsRectangularSection(beam_wy, beam_wz);
+    builder.BuildBeam(
+        mesh_chronos,  // the mesh where to put the created nodes and elements
+        msection,  // the ChBeamSectionEuler to use for the ChElementBeamEuler
+                   // elements
+        1,         // the number of ChElementBeamEuler to create
+        edgeMeshVertsToChronosNodes[vi0],  // the 'A' point in space (beginning
+                                           // of beam)
+        edgeMeshVertsToChronosNodes[vi1],  // the 'B' point in space (end of
+                                           // beam)
+        ChVector<>(0, 0, 1)
+        // ChVector<>(0, cos(rot_rad), sin(rot_rad))
+    );  // the 'Y' up direction of the section for the beam
+  }
+
+  return mesh_chronos;
+}
+
+ChronosEulerSimulationModel::ChronosEulerSimulationModel() {}
+
+// SimulationResults ChronosEulerSimulationModel::executeSimulation(
+//    const std::shared_ptr<SimulationJob> &pJob)
+//{}
+
+// chrono::ChSystemSMC convertToChronosSystem(const
+// std::shared_ptr<SimulationJob> &pJob)
+//{
+//    chrono::ChSystemSMC my_system;
+//}
+
+void ChronosEulerSimulationModel::parseForces(
+    const std::shared_ptr<chrono::fea::ChMesh>& mesh_chronos,
+    const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+        edgeMeshVertsToChronoNodes,
+    const std::unordered_map<VertexIndex, Vector6d>& nodalExternalForces) {
+  mesh_chronos->SetAutomaticGravity(false);
+  for (const std::pair<VertexIndex, Vector6d>& externalForce :
+       nodalExternalForces) {
+    const int& forceVi = externalForce.first;
+    const Vector6d& force = externalForce.second;
+    edgeMeshVertsToChronoNodes[forceVi]->SetForce(
+        ChVector<>(force[0], force[1], force[2]));
+    edgeMeshVertsToChronoNodes[forceVi]->SetTorque(
+        ChVector<>(force[3], force[4], force[5]));
+  }
+}
+
+void ChronosEulerSimulationModel::parseForcedDisplacements(
+    const std::shared_ptr<const SimulationJob>& pJob,
+    const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+        edgeMeshVertsToChronoNodes,
+    chrono::ChSystemSMC& my_system) {
+  assert(!edgeMeshVertsToChronoNodes.empty());
+
+  ChState x;
+  ChStateDelta v;
+  double t;
+  for (const std::pair<VertexIndex, Eigen::Vector3d>& forcedDisplacement :
+       pJob->nodalForcedDisplacements) {
+    assert(false);
+    std::cerr << "Forced displacements dont work" << std::endl;
+    //    std::terminate();
+    const int& constrainedVi = forcedDisplacement.first;
+    ChVector<double> displacementVector(
+        pJob->nodalForcedDisplacements.at(constrainedVi));
+    const std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>& constrainedChronoNode =
+        edgeMeshVertsToChronoNodes[constrainedVi];
+    constrainedChronoNode->NodeIntStateGather(0, x, 0, v, t);
+    std::cout << "state rows:" << x.rows() << std::endl;
+    std::cout << "state cols:" << x.cols() << std::endl;
+    //    x = x + displacementVector;
+    constrainedChronoNode->NodeIntStateScatter(0, x, 0, v, t);
+  }
+}
+void ChronosEulerSimulationModel::parseConstrainedVertices(
+    const std::shared_ptr<const SimulationJob>& pJob,
+    const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+        edgeMeshVertsToChronoNodes,
+    chrono::ChSystemSMC& my_system) {
+  assert(!edgeMeshVertsToChronoNodes.empty());
+  for (const std::pair<VertexIndex, std::unordered_set<int>>&
+           constrainedVertex : pJob->constrainedVertices) {
+    const int& constrainedVi = constrainedVertex.first;
+    const std::unordered_set<int>& constrainedDoF = constrainedVertex.second;
+    // Create a truss
+    auto truss = chrono_types::make_shared<ChBody>();
+    truss->SetBodyFixed(true);
+    my_system.Add(truss);
+    const std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>& constrainedChronoNode =
+        edgeMeshVertsToChronoNodes[constrainedVi];
+    auto constraint = chrono_types::make_shared<ChLinkMateGeneric>();
+    constraint->SetConstrainedCoords(
+        constrainedDoF.contains(0), constrainedDoF.contains(1),
+        constrainedDoF.contains(2), constrainedDoF.contains(3),
+        constrainedDoF.contains(4), constrainedDoF.contains(5));
+    constraint->Initialize(constrainedChronoNode, truss, false,
+                           constrainedChronoNode->Frame(),
+                           constrainedChronoNode->Frame());
+    my_system.Add(constraint);
+  }
+}
+
+SimulationResults ChronosEulerSimulationModel::executeSimulation(
+    const std::shared_ptr<SimulationJob>& pJob) {
+  assert(pJob->pMesh->VN() != 0);
+  //  const bool structureInitialized = mesh_chronos != nullptr;
+  //  const bool wasInitializedWithDifferentStructure =
+  //      structureInitialized &&
+  //      (pJob->pMesh->EN() != mesh_chronos->GetNelements() ||
+  //       pJob->pMesh->VN() != mesh_chronos->GetNnodes());
+  //  if (!structureInitialized || wasInitializedWithDifferentStructure) {
+  setStructure(pJob->pMesh);
+  //  }
+  chrono::ChSystemSMC my_system;
+  //    chrono::irrlicht::ChIrrApp application(&my_system,
+  //                                           L"Irrlicht FEM visualization",
+  //                                           irr::core::dimension2d<irr::u32>(800,
+  //                                           600),
+  //                                           chrono::irrlicht::VerticalDir::Z,
+  //                                           false,
+  //                                           true);
+  //    const std::string chronoDataFolderPath =
+  //    "/home/iason/Coding/build/external "
+  //                                             "dependencies/CHRONO-src/data/";
+  //    application.AddTypicalLogo(chronoDataFolderPath +
+  //    "logo_chronoengine_alpha.png");
+  //    application.AddTypicalSky(chronoDataFolderPath + "skybox/");
+  //    application.AddTypicalLights();
+  //    application.AddTypicalCamera(irr::core::vector3df(0, (irr::f32) 0.6,
+  //    -1));
+  //    my_system.SetTimestepperType(chrono::ChTimestepper::Type::EULER_IMPLICIT_LINEARIZED);
+  // parse forces
+  parseForcedDisplacements(pJob, edgeMeshVertsToChronoNodes, my_system);
+  parseForces(mesh_chronos, edgeMeshVertsToChronoNodes,
+              pJob->nodalExternalForces);
+  // parse constrained vertices
+  parseConstrainedVertices(pJob, edgeMeshVertsToChronoNodes, my_system);
+  //    std::dynamic_pointer_cast<std::shared_ptr<ChNodeFEAxyzrot>>(mesh_chronos->GetNode(1))
+  //        ->SetFixed(true);
+  // and load containers must be added to your system
+  //    auto mvisualizemesh =
+  //    chrono_types::make_shared<ChVisualizationFEAmesh>(*(mesh_chronos.get()));
+  //    mvisualizemesh->SetFEMdataType(ChVisualizationFEAmesh::E_PLOT_NODE_DISP_NORM);
+  //    mvisualizemesh->SetColorscaleMinMax(0.0, 5.50);
+  //    mvisualizemesh->SetShrinkElements(false, 0.85);
+  //    mvisualizemesh->SetSmoothFaces(false);
+  //    mesh_chronos->AddAsset(mvisualizemesh);
+
+  //    application.AssetBindAll();
+  //    application.AssetUpdateAll();
+  my_system.Add(mesh_chronos);
+
+  auto solver = chrono_types::make_shared<ChSolverMINRES>();
+  my_system.SetSolver(solver);
+  solver->SetMaxIterations(1e5);
+  solver->EnableWarmStart(
+      true);  // IMPORTANT for convergence when using EULER_IMPLICIT_LINEARIZED
+  solver->EnableDiagonalPreconditioner(true);
+  //  solver->SetTolerance(1e-15);
+  my_system.SetSolverForceTolerance(1e-15);
+
+  SimulationResults simulationResults;
+  //#ifdef POLYSCOPE_DEFINED
+  //  solver->SetVerbose(true);
+  //  //  edgeMeshVertsToChronoNodes[10]->Frame().Move({0, 0, 1e-1});
+  //  simulationResults.converged = my_system.DoEntireKinematics(5e2);
+  ////  edgeMeshVertsToChronoNodes[10]->SetForce({0, 0, 1e6});
+  //#else
+  solver->SetVerbose(false);
+  if (settings.analysisType == Settings::AnalysisType::Linear) {
+    simulationResults.converged = my_system.DoStaticLinear();
+    //    simulationResults.converged = my_system.DoStaticRelaxing();
+  } else {
+    simulationResults.converged = my_system.DoStaticNonlinear();
+    //    simulationResults.converged = my_system.DoStaticRelaxing();
+  }
+  //#endif
+  if (!simulationResults.converged) {
+    std::cerr << "Simulation failed" << std::endl;
+    assert(false);
+    return simulationResults;
+  }
+
+  //    my_system.SetTimestepperType(ChTimestepper::Type::EULER_IMPLICIT_LINEARIZED);
+  //    application.SetTimestep(0.001);
+
+  //    while (application.GetDevice()->run()) {
+  //        application.BeginScene();
+  //        application.DrawAll();
+  //        application.EndScene();
+  //    }
+  simulationResults.pJob = pJob;
+  simulationResults.displacements.resize(pJob->pMesh->VN());
+  simulationResults.rotationalDisplacementQuaternion.resize(pJob->pMesh->VN());
+  for (size_t vi = 0; vi < pJob->pMesh->VN(); vi++) {
+    const auto node_chronos = edgeMeshVertsToChronoNodes[vi];
+    const auto posDisplacement =
+        node_chronos->Frame().GetPos() - node_chronos->GetX0().GetPos();
+    //        std::cout << "Node " << vi << " coordinate x= " <<
+    //        node_chronos->Frame().GetPos().x()
+    //                  << "    y=" << node_chronos->Frame().GetPos().y()
+    //                  << "    z=" << node_chronos->Frame().GetPos().z() <<
+    //                  "\n";
+    // Translations
+    simulationResults.displacements[vi][0] = posDisplacement[0];
+    simulationResults.displacements[vi][1] = posDisplacement[1];
+    simulationResults.displacements[vi][2] = posDisplacement[2];
+    // Rotations
+    chrono::ChQuaternion<double> rotQuat = node_chronos->GetRot();
+    simulationResults.rotationalDisplacementQuaternion[vi] =
+        Eigen::Quaternion<double>(rotQuat.e0(), rotQuat.e1(), rotQuat.e2(),
+                                  rotQuat.e3());
+    const Eigen::Vector3d eulerAngles =
+        simulationResults.rotationalDisplacementQuaternion[vi]
+            .toRotationMatrix()
+            .eulerAngles(0, 1, 2);
+    //        std::cout << "Euler angles:" << eulerAngles << std::endl;
+    simulationResults.displacements[vi][3] = eulerAngles[0];
+    simulationResults.displacements[vi][4] = eulerAngles[1];
+    simulationResults.displacements[vi][5] = eulerAngles[2];
+  }
+
+  simulationResults.simulationModelUsed = label;
+  return simulationResults;
+
+  //    VCGEdgeMesh deformedMesh;
+  //    deformedMesh.copy(*(pJob->pMesh));
+  //    for (size_t vi = 0; vi < pJob->pMesh->VN(); vi++) {
+  //        const std::shared_ptr<ChNodeFEAxyzrot> node_chronos =
+  //        edgeMeshVertsToChronosNodes[vi]; deformedMesh.vert[vi].P() =
+  //        CoordType(node_chronos->GetPos()[0],
+  //                                              node_chronos->GetPos()[1],
+  //                                              node_chronos->GetPos()[2]);
+  //    }
+
+  //    deformedMesh.updateEigenEdgeAndVertices();
+  //    deformedMesh.setLabel("deformed");
+  //    deformedMesh.registerForDrawing();
+  //    polyscope::show();
+  //    return simulationResults;
+}
+
+void ChronosEulerSimulationModel::setStructure(
+    const std::shared_ptr<SimulationEdgeMesh>& pMesh) {
+  mesh_chronos = convertToChronosMesh_Euler(pMesh, edgeMeshVertsToChronoNodes);
+}

chronoseulersimulationmodel.hpp

@@ -0,0 +1,55 @@
+#ifndef CHRONOSEULERSIMULATIONMODEL_HPP
+#define CHRONOSEULERSIMULATIONMODEL_HPP
+
+#include "simulationmodel.hpp"
+
+namespace chrono {
+class ChSystemSMC;
+namespace fea {
+class ChMesh;
+class ChNodeFEAxyzrot;
+}  // namespace fea
+}  // namespace chrono
+
+class ChronosEulerSimulationModel : public SimulationModel {
+  std::shared_ptr<chrono::fea::ChMesh> mesh_chronos;
+  std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>
+      edgeMeshVertsToChronoNodes;
+
+  static void parseConstrainedVertices(
+      const std::shared_ptr<const SimulationJob>& pJob,
+      const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+          edgeMeshVertsToChronoNodes,
+      chrono::ChSystemSMC& my_system);
+  static void parseForces(
+      const std::shared_ptr<chrono::fea::ChMesh>& mesh_chronos,
+      const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+          edgeMeshVertsToChronoNodes,
+      const std::unordered_map<VertexIndex, Vector6d>& nodalExternalForces);
+
+  static void parseForcedDisplacements(
+      const std::shared_ptr<const SimulationJob>& pJob,
+      const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+          edgeMeshVertsToChronoNodes,
+      chrono::ChSystemSMC& my_system);
+
+ public:
+  ChronosEulerSimulationModel();
+  SimulationResults executeSimulation(
+      const std::shared_ptr<SimulationJob>& pJob) override;
+  void setStructure(const std::shared_ptr<SimulationEdgeMesh>& pMesh) override;
+  static std::shared_ptr<chrono::fea::ChMesh> convertToChronosMesh_Euler(
+      const std::shared_ptr<SimulationEdgeMesh>& pMesh,
+      std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>>&
+          edgeMeshVertsToChronosNodes);
+
+  inline const static std::string label{"Chronos_Euler"};
+
+  struct Settings {
+    enum AnalysisType { Linear = 0, NonLinear };
+    AnalysisType analysisType{NonLinear};
+  };
+  Settings settings;
+};
+
+#endif  // CHRONOSEULERSIMULATIONMODEL_HPP

chronosigasimulationmodel.cpp

@@ -0,0 +1,300 @@
+#include "chronosigasimulationmodel.hpp"
+#include "chrono/physics/ChLoadContainer.h"
+#include <chrono/fea/ChBeamSectionEuler.h>
+#include <chrono/fea/ChBuilderBeam.h>
+#include <chrono/fea/ChLoadsBeam.h>
+#include <chrono/fea/ChMesh.h>
+#include <chrono/fea/ChNodeFEAxyzrot.h>
+#include <chrono/physics/ChBody.h>
+#include <chrono/physics/ChSystemSMC.h>
+#include <chrono/solver/ChIterativeSolverLS.h>
+
+#include <chrono/assets/ChVisualization.h>
+#include <chrono/fea/ChElementBeamEuler.h>
+#include <chrono/fea/ChVisualizationFEAmesh.h>
+
+using namespace chrono;
+using namespace chrono::fea;
+std::shared_ptr<ChMesh> ChronosIGASimulationModel::convertToChronosMesh_IGA(
+    const std::shared_ptr<SimulationEdgeMesh> &pMesh,
+    std::vector<std::shared_ptr<ChNodeFEAxyzrot>> &edgeMeshVertsToChronosNodes)
+{
+    auto mesh_chronos = chrono_types::make_shared<ChMesh>();
+    edgeMeshVertsToChronosNodes.clear();
+    edgeMeshVertsToChronosNodes.resize(pMesh->VN(), nullptr);
+
+    //add nodes
+    for (int vi = 0; vi < pMesh->VN(); vi++) {
+        const auto &vertex = pMesh->vert[vi];
+        ChVector<> vertexPos(vertex.cP()[0], vertex.cP()[1], vertex.cP()[2]);
+        edgeMeshVertsToChronosNodes[vi] = chrono_types::make_shared<ChNodeFEAxyzrot>(
+            ChFrame<>(vertexPos));
+        mesh_chronos->AddNode(edgeMeshVertsToChronosNodes[vi]);
+    }
+    //add elements
+    ChBuilderBeamIGA builder;
+    for (int ei = 0; ei < pMesh->EN(); ei++) {
+        const SimulationEdgeMesh::EdgeType &edge = pMesh->edge[ei];
+        //define end-points
+        const auto vi0 = pMesh->getIndex(edge.cV(0));
+        const auto vi1 = pMesh->getIndex(edge.cV(1));
+        //define cross section
+        const Element &element = pMesh->elements[ei];
+        const double beam_wz = element.dimensions.getDim1();
+        const double beam_wy = element.dimensions.getDim2();
+        const double E = element.material.youngsModulus;
+        //        const double poisson = element.material.poissonsRatio;
+        const double density = 1e0;
+
+        //        auto msection = chrono_types::make_shared<ChBeamSectionEulerAdvanced>();
+        auto msection = chrono_types::make_shared<ChBeamSectionCosseratEasyRectangular>(
+            beam_wy, beam_wz, E, element.material.G, density);
+        //        msection->SetDensity(density);
+        //        msection->SetYoungModulus(E);
+        //        msection->SetGwithPoissonRatio(poisson);
+        //        //        msection->SetBeamRaleyghDamping(0.0);
+        //        msection->SetAsRectangularSection(beam_wy, beam_wz);
+        builder
+            .BuildBeam(mesh_chronos, // the mesh where to put the created nodes and elements
+                       msection, // the ChBeamSectionEuler to use for the ChElementBeamEuler elements
+                       1,        // the number of ChElementBeamEuler to create
+                       edgeMeshVertsToChronosNodes[vi0], // the 'A' point in space (beginning of beam)
+                       edgeMeshVertsToChronosNodes[vi1], // the 'B' point in space (end of beam)
+                       ChVector<>(0, 0, 1),
+                       3
+                       // ChVector<>(0, cos(rot_rad), sin(rot_rad))
+            ); // the 'Y' up direction of the section for the beam
+        const auto lastBeamNodesVector = builder.GetLastBeamNodes();
+        //        assert(lastBeamNodesVector.size() == 4);
+        edgeMeshVertsToChronosNodes[vi0] = std::dynamic_pointer_cast<ChNodeFEAxyzrot>(
+            mesh_chronos->GetNode(mesh_chronos->GetNnodes() - lastBeamNodesVector.size()));
+        edgeMeshVertsToChronosNodes[vi1] = std::dynamic_pointer_cast<ChNodeFEAxyzrot>(
+            mesh_chronos->GetNode(mesh_chronos->GetNnodes() - 1));
+        //        std::cout << edgeMeshVertsToChronosNodes[vi1]->GetCoord().pos[0] << " "
+        //                  << edgeMeshVertsToChronosNodes[vi1]->GetCoord().pos[1] << " "
+        //                  << edgeMeshVertsToChronosNodes[vi1]->GetCoord().pos[2] << std::endl;
+        //        std::cout << lastBeamNodesVector.back()->GetCoord().pos[0] << " "
+        //                  << lastBeamNodesVector.back()->GetCoord().pos[1] << " "
+        //                  << lastBeamNodesVector.back()->GetCoord().pos[2] << std::endl;
+        //        int i = 0;
+        //        i++;
+    }
+
+    return mesh_chronos;
+}
+
+//SimulationResults ChronosEulerSimulationModel::executeSimulation(
+//    const std::shared_ptr<SimulationJob> &pJob)
+//{}
+
+//chrono::ChSystemSMC convertToChronosSystem(const std::shared_ptr<SimulationJob> &pJob)
+//{
+//    chrono::ChSystemSMC my_system;
+//}
+
+void ChronosIGASimulationModel::parseForces(
+    const std::shared_ptr<chrono::fea::ChMesh> &mesh_chronos,
+    const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>> &edgeMeshVertsToChronoNodes,
+    const std::unordered_map<VertexIndex, Vector6d> &nodalExternalForces)
+{
+    mesh_chronos->SetAutomaticGravity(false);
+    for (const std::pair<VertexIndex, Vector6d> &externalForce : nodalExternalForces) {
+        const int &forceVi = externalForce.first;
+        const Vector6d &force = externalForce.second;
+        edgeMeshVertsToChronoNodes[forceVi]->SetForce(ChVector<>(force[0], force[1], force[2]));
+        edgeMeshVertsToChronoNodes[forceVi]->SetTorque(ChVector<>(force[3], force[4], force[5]));
+        std::cout << "Force on vertex:" << std::endl;
+        std::cout << edgeMeshVertsToChronoNodes[forceVi]->GetCoord().pos[0] << " "
+                  << edgeMeshVertsToChronoNodes[forceVi]->GetCoord().pos[1] << " "
+                  << edgeMeshVertsToChronoNodes[forceVi]->GetCoord().pos[2] << std::endl;
+    }
+}
+
+void ChronosIGASimulationModel::parseConstrainedVertices(
+    const std::shared_ptr<const SimulationJob> &pJob,
+    const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>> &edgeMeshVertsToChronoNodes,
+    chrono::ChSystemSMC &my_system)
+{
+    assert(!edgeMeshVertsToChronoNodes.empty());
+    for (const std::pair<VertexIndex, std::unordered_set<int>> &constrainedVertex :
+         pJob->constrainedVertices) {
+        const int &constrainedVi = constrainedVertex.first;
+        const std::unordered_set<int> &constrainedDoF = constrainedVertex.second;
+        // Create a truss
+        auto truss = chrono_types::make_shared<ChBody>();
+        truss->SetBodyFixed(true);
+        my_system.Add(truss);
+        const auto &constrainedChronoNode = edgeMeshVertsToChronoNodes[constrainedVi];
+        std::cout << "Constrained vertex:" << std::endl;
+        std::cout << edgeMeshVertsToChronoNodes[constrainedVi]->GetCoord().pos[0] << " "
+                  << edgeMeshVertsToChronoNodes[constrainedVi]->GetCoord().pos[1] << " "
+                  << edgeMeshVertsToChronoNodes[constrainedVi]->GetCoord().pos[2] << std::endl;
+        // Create a constraint at the end of the beam
+        auto constr_a = chrono_types::make_shared<ChLinkMateGeneric>();
+        constr_a->SetConstrainedCoords(constrainedDoF.contains(0),
+                                       constrainedDoF.contains(1),
+                                       constrainedDoF.contains(2),
+                                       constrainedDoF.contains(3),
+                                       constrainedDoF.contains(4),
+                                       constrainedDoF.contains(5));
+        constr_a->Initialize(constrainedChronoNode,
+                             truss,
+                             false,
+                             constrainedChronoNode->Frame(),
+                             constrainedChronoNode->Frame());
+        //        const auto frameNode = constrainedChronoNode->Frame();
+        my_system.Add(constr_a);
+
+        //        edgeMeshVertsToChronoNodes[constrainedVi]->SetFixed(true);
+        //        if (vertexIsFullyConstrained) {
+        //        } else {
+        //            std::cerr << "Currently only rigid vertices are handled." << std::endl;
+        //            //            SimulationResults simulationResults;
+        //            //            simulationResults.converged = false;
+        //            //            assert(false);
+        //            //            return simulationResults;
+        //        }
+    }
+}
+
+SimulationResults ChronosIGASimulationModel::executeSimulation(
+    const std::shared_ptr<SimulationJob> &pJob)
+{
+    //    assert(pJob->pMesh->VN() != 0);
+    //    const bool structureInitialized = mesh_chronos != nullptr;
+    //    const bool wasInitializedWithDifferentStructure = structureInitialized
+    //                                                      && (pJob->pMesh->EN()
+    //                                                              != mesh_chronos->GetNelements()
+    //                                                          || pJob->pMesh->VN()
+    //                                                                 != mesh_chronos->GetNnodes());
+    chrono::ChSystemSMC my_system;
+    //    if (!structureInitialized || wasInitializedWithDifferentStructure) {
+    setStructure(pJob->pMesh);
+    my_system.Add(mesh_chronos);
+    //    }
+    //    chrono::irrlicht::ChIrrApp application(&my_system,
+    //                                           L"Irrlicht FEM visualization",
+    //                                           irr::core::dimension2d<irr::u32>(800, 600),
+    //                                           chrono::irrlicht::VerticalDir::Z,
+    //                                           false,
+    //                                           true);
+    //    const std::string chronoDataFolderPath = "/home/iason/Coding/build/external "
+    //                                             "dependencies/CHRONO-src/data/";
+    //    application.AddTypicalLogo(chronoDataFolderPath + "logo_chronoengine_alpha.png");
+    //    application.AddTypicalSky(chronoDataFolderPath + "skybox/");
+    //    application.AddTypicalLights();
+    //    application.AddTypicalCamera(irr::core::vector3df(0, (irr::f32) 0.6, -1));
+    //    my_system.SetTimestepperType(chrono::ChTimestepper::Type::EULER_IMPLICIT_LINEARIZED);
+    const auto node_0 = std::dynamic_pointer_cast<ChNodeFEAxyzrot>(mesh_chronos->GetNode(0));
+    //parse forces
+    //    std::cout << node_0->GetCoord().pos[0] << " " << node_0->GetCoord().pos[1] << " "
+    //              << node_0->GetCoord().pos[2] << std::endl;
+    parseForces(mesh_chronos, edgeMeshVertsToChronoNodes, pJob->nodalExternalForces);
+    //    std::cout << node_0->GetCoord().pos[0] << " " << node_0->GetCoord().pos[1] << " "
+    //              << node_0->GetCoord().pos[2] << std::endl;
+
+    //parse constrained vertices
+    //    std::cout << node_0->GetCoord().pos[0] << " " << node_0->GetCoord().pos[1] << " "
+    //              << node_0->GetCoord().pos[2] << std::endl;
+    //    parseConstrainedVertices(pJob, edgeMeshVertsToChronoNodes, my_system);
+
+    //    std::cout << node_0->GetCoord().pos[0] << " " << node_0->GetCoord().pos[1] << " "
+    //              << node_0->GetCoord().pos[2] << std::endl;
+    //    std::dynamic_pointer_cast<std::shared_ptr<ChNodeFEAxyzrot>>(mesh_chronos->GetNode(1))
+    //        ->SetFixed(true);
+    // and load containers must be added to your system
+    //    auto mvisualizemesh = chrono_types::make_shared<ChVisualizationFEAmesh>(*(mesh_chronos.get()));
+    //    mvisualizemesh->SetFEMdataType(ChVisualizationFEAmesh::E_PLOT_NODE_DISP_NORM);
+    //    mvisualizemesh->SetColorscaleMinMax(0.0, 5.50);
+    //    mvisualizemesh->SetShrinkElements(false, 0.85);
+    //    mvisualizemesh->SetSmoothFaces(false);
+    //    mesh_chronos->AddAsset(mvisualizemesh);
+
+    //    application.AssetBindAll();
+    //    application.AssetUpdateAll();
+
+    auto solver = chrono_types::make_shared<ChSolverMINRES>();
+    my_system.SetSolver(solver);
+    solver->SetMaxIterations(1e5);
+    //    solver->SetTolerance(1e-12);
+    solver->EnableWarmStart(true); // IMPORTANT for convergence when using EULER_IMPLICIT_LINEARIZED
+    solver->EnableDiagonalPreconditioner(true);
+    //    my_system.SetSolverForceTolerance(1e-9);
+    solver->SetVerbose(true);
+
+    std::cout << node_0->GetCoord().pos[0] << " " << node_0->GetCoord().pos[1] << " "
+              << node_0->GetCoord().pos[2] << std::endl;
+    SimulationResults simulationResults;
+    simulationResults.converged = my_system.DoStaticNonlinear();
+    //    simulationResults.converged = my_system.DoStaticLinear();
+    std::cout << node_0->GetCoord().pos[0] << " " << node_0->GetCoord().pos[1] << " "
+              << node_0->GetCoord().pos[2] << std::endl;
+    if (!simulationResults.converged) {
+        std::cerr << "Simulation failed" << std::endl;
+        assert(false);
+        return simulationResults;
+    }
+
+    //    my_system.SetTimestepperType(ChTimestepper::Type::EULER_IMPLICIT_LINEARIZED);
+    //    application.SetTimestep(0.001);
+
+    //    while (application.GetDevice()->run()) {
+    //        application.BeginScene();
+    //        application.DrawAll();
+    //        application.EndScene();
+    //    }
+    simulationResults.pJob = pJob;
+    simulationResults.displacements.resize(pJob->pMesh->VN());
+    simulationResults.rotationalDisplacementQuaternion.resize(pJob->pMesh->VN());
+    for (size_t vi = 0; vi < pJob->pMesh->VN(); vi++) {
+        const auto node_chronos = edgeMeshVertsToChronoNodes[vi];
+        std::cout << node_chronos->GetCoord().pos[0] << " " << node_chronos->GetCoord().pos[1]
+                  << " " << node_chronos->GetCoord().pos[2] << std::endl;
+        int i = 0;
+        i++;
+        assert(node_chronos != nullptr);
+        const auto posDisplacement = node_chronos->Frame().GetPos()
+                                     - node_chronos->GetX0().GetPos();
+        //        std::cout << "Node " << vi << " coordinate x= " << node_chronos->Frame().GetPos().x()
+        //                  << "    y=" << node_chronos->Frame().GetPos().y()
+        //                  << "    z=" << node_chronos->Frame().GetPos().z() << "\n";
+        //Translations
+        simulationResults.displacements[vi][0] = posDisplacement[0];
+        simulationResults.displacements[vi][1] = posDisplacement[1];
+        simulationResults.displacements[vi][2] = posDisplacement[2];
+        //Rotations
+        chrono::ChQuaternion<double> rotQuat = node_chronos->GetRot();
+        simulationResults.rotationalDisplacementQuaternion[vi]
+            = Eigen::Quaternion<double>(rotQuat.e0(), rotQuat.e1(), rotQuat.e2(), rotQuat.e3());
+        const ChVector<double> eulerAngles = rotQuat.Q_to_Euler123();
+        //        std::cout << "Euler angles:" << eulerAngles << std::endl;
+        simulationResults.displacements[vi][3] = eulerAngles[0];
+        simulationResults.displacements[vi][4] = eulerAngles[1];
+        simulationResults.displacements[vi][5] = eulerAngles[2];
+    }
+
+    simulationResults.simulationModelUsed = label;
+    return simulationResults;
+
+    //    VCGEdgeMesh deformedMesh;
+    //    deformedMesh.copy(*(pJob->pMesh));
+    //    for (size_t vi = 0; vi < pJob->pMesh->VN(); vi++) {
+    //        const std::shared_ptr<ChNodeFEAxyzrot> node_chronos = edgeMeshVertsToChronosNodes[vi];
+    //        deformedMesh.vert[vi].P() = CoordType(node_chronos->GetPos()[0],
+    //                                              node_chronos->GetPos()[1],
+    //                                              node_chronos->GetPos()[2]);
+    //    }
+
+    //    deformedMesh.updateEigenEdgeAndVertices();
+    //    deformedMesh.setLabel("deformed");
+    //    deformedMesh.registerForDrawing();
+    //    polyscope::show();
+    //    return simulationResults;
+}
+
+void ChronosIGASimulationModel::setStructure(const std::shared_ptr<SimulationEdgeMesh> &pMesh)
+{
+    mesh_chronos = convertToChronosMesh_IGA(pMesh, edgeMeshVertsToChronoNodes);
+}
+
+ChronosIGASimulationModel::ChronosIGASimulationModel() {}

chronosigasimulationmodel.hpp

@@ -0,0 +1,39 @@
+#ifndef CHRONOSIGASIMULATIONMODEL_HPP
+#define CHRONOSIGASIMULATIONMODEL_HPP
+
+#include "simulationmodel.hpp"
+
+namespace chrono {
+class ChSystemSMC;
+namespace fea {
+class ChMesh;
+class ChNodeFEAxyzrot;
+} // namespace fea
+} // namespace chrono
+
+class ChronosIGASimulationModel : public SimulationModel
+{
+    std::shared_ptr<chrono::fea::ChMesh> mesh_chronos;
+    std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>> edgeMeshVertsToChronoNodes;
+
+    static void parseConstrainedVertices(
+        const std::shared_ptr<const SimulationJob> &pJob,
+        const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>> &edgeMeshVertsToChronoNodes,
+        chrono::ChSystemSMC &my_system);
+    static void parseForces(
+        const std::shared_ptr<chrono::fea::ChMesh> &mesh_chronos,
+        const std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>> &edgeMeshVertsToChronoNodes,
+        const std::unordered_map<VertexIndex, Vector6d> &nodalExternalForces);
+
+public:
+    ChronosIGASimulationModel();
+    SimulationResults executeSimulation(const std::shared_ptr<SimulationJob> &pJob) override;
+    void setStructure(const std::shared_ptr<SimulationEdgeMesh> &pMesh) override;
+    static std::shared_ptr<chrono::fea::ChMesh> convertToChronosMesh_IGA(
+        const std::shared_ptr<SimulationEdgeMesh> &pMesh,
+        std::vector<std::shared_ptr<chrono::fea::ChNodeFEAxyzrot>> &edgeMeshVertsToChronosNodes);
+
+    inline const static std::string label{"Chronos_linear_IGA"};
+};
+
+#endif // CHRONOSIGASIMULATIONMODEL_HPP

csvfile.hpp

@@ -9,39 +9,43 @@
 #include <string>
 #include <vector>
 
-class csvFile;
+class CSVFile;
 
-inline static csvFile &endrow(csvFile &file);
-inline static csvFile &flush(csvFile &file);
+inline static CSVFile& endrow(CSVFile& file);
+inline static CSVFile& flush(CSVFile& file);
 
-class csvFile {
+class CSVFile {
   std::ofstream fs_;
   bool is_first_;
   const std::string separator_;
   const std::string escape_seq_;
   const std::string special_chars_;
 
-  public:
-  csvFile(const std::filesystem::path &filename,
-          const bool &overwrite,
+ public:
+  CSVFile(const std::filesystem::path& filename,
+          const bool& overwrite,
           const std::string separator = ",")
-      : fs_(), is_first_(true), separator_(separator), escape_seq_("\""), special_chars_("\"")
-  {
-      fs_.exceptions(std::ios::failbit | std::ios::badbit);
-      if (filename.empty()) {
-          fs_.copyfmt(std::cout);
-          fs_.clear(std::cout.rdstate());
-          fs_.basic_ios<char>::rdbuf(std::cout.rdbuf());
-      } else {
-          if (!std::filesystem::exists(filename)) {
-              std::ofstream outfile(filename);
-              outfile.close();
-          }
-          overwrite ? fs_.open(filename, std::ios::trunc) : fs_.open(filename, std::ios::app);
+      : fs_(),
+        is_first_(true),
+        separator_(separator),
+        escape_seq_("\""),
+        special_chars_("\"") {
+    fs_.exceptions(std::ios::failbit | std::ios::badbit);
+    if (filename.empty()) {
+      fs_.copyfmt(std::cout);
+      fs_.clear(std::cout.rdstate());
+      fs_.basic_ios<char>::rdbuf(std::cout.rdbuf());
+    } else {
+      if (!std::filesystem::exists(filename)) {
+        std::ofstream outfile(filename);
+        outfile.close();
       }
+      overwrite ? fs_.open(filename, std::ios::trunc)
+                : fs_.open(filename, std::ios::app);
+    }
   }
 
-  ~csvFile() {
+  ~CSVFile() {
     flush();
     fs_.close();
   }
@@ -53,55 +57,52 @@ class csvFile {
     is_first_ = true;
   }
 
-  csvFile &operator<<(csvFile &(*val)(csvFile &)) { return val(*this); }
+  CSVFile& operator<<(CSVFile& (*val)(CSVFile&)) { return val(*this); }
 
-  csvFile &operator<<(const char *val) { return write(escape(val)); }
+  CSVFile& operator<<(const char* val) { return write(escape(val)); }
 
-  csvFile &operator<<(const std::string &val) { return write(escape(val)); }
+  CSVFile& operator<<(const std::string& val) { return write(escape(val)); }
 
-  template<typename T>
-  csvFile &operator<<(const T &val)
-  {
-      return write(val);
+  template <typename T>
+  CSVFile& operator<<(const T& val) {
+    return write(val);
   }
 
-  template<typename T>
-  static std::vector<std::vector<T>> parse(const std::filesystem::path &csvFilepath)
-  {
-      std::vector<std::vector<T>> resultCSV;
-      if (!std::filesystem::exists(csvFilepath)) {
-          std::cerr << "The file does not exist:" << csvFilepath.string() << std::endl;
-          return resultCSV;
-      }
-
-      std::ifstream inputfile(csvFilepath.string().c_str());
-      if (!inputfile.is_open()) {
-          std::cerr << "Can't open file:" << csvFilepath.string() << std::endl;
-          return resultCSV;
-      }
-      std::vector<T> row;
-      std::string line;
-      using Tokenizer = boost::tokenizer<boost::escaped_list_separator<char>>;
-      while (std::getline(inputfile, line)) {
-          Tokenizer tokenizer(line);
-          row.resize(std::distance(tokenizer.begin(), tokenizer.end()));
-          std::transform(tokenizer.begin(), tokenizer.end(), row.begin(), [](const std::string &el) {
-              return boost::lexical_cast<T>(el);
-          });
-          //          std::cout << std::endl;
-          //          row.assign(tokenizer.begin(), tokenizer.end());
-          //          for (const auto &el : row) {
-          //              std::cout << el << " ";
-          //          }
-          //          std::cout << std::endl;
-          resultCSV.push_back(row);
-      }
-
+  static std::vector<std::vector<std::string>> parse(
+      const std::filesystem::path& csvFilepath) {
+    std::vector<std::vector<std::string>> resultCSV;
+    if (!std::filesystem::exists(csvFilepath)) {
+      std::cerr << "The file does not exist:" << csvFilepath.string()
+                << std::endl;
       return resultCSV;
+    }
+
+    std::ifstream inputfile(csvFilepath.string().c_str());
+    if (!inputfile.is_open()) {
+      std::cerr << "Can't open file:" << csvFilepath.string() << std::endl;
+      return resultCSV;
+    }
+    std::vector<std::string> row;
+    std::string line;
+    using Tokenizer = boost::tokenizer<boost::escaped_list_separator<char>>;
+    while (std::getline(inputfile, line)) {
+      Tokenizer tokenizer(line);
+      const int numOfCols = std::distance(tokenizer.begin(), tokenizer.end());
+      row.resize(numOfCols);
+      std::copy(tokenizer.begin(), tokenizer.end(), row.begin());
+      //          std::transform(tokenizer.begin(), tokenizer.end(),
+      //          row.begin(), [](const std::string &el) {
+      //              return boost::lexical_cast<T>(el);
+      //          });
+      resultCSV.push_back(row);
+    }
+
+    return resultCSV;
   }
 
-private:
-  template <typename T> csvFile &write(const T &val) {
+ private:
+  template <typename T>
+  CSVFile& write(const T& val) {
     if (!is_first_) {
       fs_ << separator_;
     } else {
@@ -111,7 +112,7 @@ private:
     return *this;
   }
 
-  std::string escape(const std::string &val) {
+  std::string escape(const std::string& val) {
     std::ostringstream result;
     result << '"';
     std::string::size_type to, from = 0u, len = val.length();
@@ -125,14 +126,14 @@ private:
   }
 };
 
-inline static csvFile &endrow(csvFile &file) {
+inline static CSVFile& endrow(CSVFile& file) {
   file.endrow();
   return file;
 }
 
-inline static csvFile &flush(csvFile &file) {
+inline static CSVFile& flush(CSVFile& file) {
   file.flush();
   return file;
 }
 
-#endif // CSVFILE_HPP
+#endif  // CSVFILE_HPP

der_leimer.hpp

@@ -0,0 +1,193 @@
+#ifndef DER_LEIMER_HPP
+#define DER_LEIMER_HPP
+
+//#include "ElasticRod.hh"
+#include "simulationmodel.hpp"
+#include <Eigen/Sparse>
+
+class DER_leimer : public SimulationModel
+{
+public:
+    DER_leimer();
+    virtual SimulationResults executeSimulation(const std::shared_ptr<SimulationJob> &pJob) override;
+    struct RodParams
+    {
+        double thickness;
+        double kstretching; //stretching stiffness
+        double kbending;    //bending stiffness
+        double ktwist;      //twisting stiffness
+        double kanchorpos;  //anchor positional stiffness
+        double kanchordir;  //anchor directional stiffness
+        double rho;         //density
+        double restlength;
+    };
+
+    struct RodState
+    {
+        Eigen::MatrixXd centerlinePositions;
+        Eigen::VectorXi centerlineIndices; //"global" indices of centerline vertices
+        Eigen::MatrixXd
+            directors; //normal vectors to each segment. They are called "directors" here because thats how they call them in the weaving geodesics paper
+        Eigen::MatrixXd matDirNormal;   //Normal vector of each segment
+        Eigen::MatrixXd matDirBinormal; //Binormal vector of each segment
+        Eigen::VectorXd thetas;
+        Eigen::MatrixXd centerlineVelocities;
+        Eigen::VectorXd directorAngVel;
+        Eigen::MatrixXd curvatures;
+    };
+
+    class Rod
+    {
+    public:
+        Rod(const RodState &startState,
+            const Eigen::VectorXd &widths,
+            RodParams &params,
+            bool isClosed);
+
+        enum RodVisibilityState { RS_TRANSLUCENT = 0, RS_VISIBLE, RS_HIDDEN };
+
+        bool isClosed() const { return isClosed_; }
+
+        void setVisibilityState(RodVisibilityState state) { visState_ = state; }
+        RodVisibilityState visibilityState() const { return visState_; }
+
+        Eigen::Vector3d rodColor() const;
+        Eigen::Vector3d rodColor(int seg) const;
+        int rodColorID() const { return colorID_; }
+        void cycleColor();
+        int numVertices() const { return (int) curState.centerlinePositions.rows(); }
+        int numSegments() const { return (int) curState.thetas.size(); }
+        double arclength() const;
+        RodState curState;
+        RodState startState;
+
+        Eigen::VectorXd widths;
+        Eigen::VectorXd restlens;
+        Eigen::VectorXd masses;
+        Eigen::VectorXd momInertia;
+        Eigen::VectorXi segColors;
+        Eigen::MatrixXd vSegParams; // stretch, bend, twist, restlength
+        RodParams params;
+
+        void initializeRestQuantities();
+
+    private:
+        int colorID_;
+        bool isClosed_;
+        RodVisibilityState visState_;
+    };
+
+    struct Anchor
+    {
+        int rod;
+        int seg;
+        double bary; // where along the segment should the anchor be placed?[0,1]. 0 at the beginning , 1 at the end
+        Eigen::Vector3d position;
+        Eigen::Vector3d normal;
+        double ratio; //??
+        double k_pos;
+        double k_dir;
+    };
+
+    struct Intersection
+    {
+        int intersectionIndex;
+        int globalVi;
+        Eigen::MatrixXi rodSegmentIndices;
+        Eigen::Matrix3d rotationMatrix;
+    };
+
+    struct SimParams
+    {
+        bool allowSliding;
+        Eigen::MatrixXd *anchorPoints;
+        Eigen::MatrixXd *anchorNormals;
+        bool gravityEnabled{true};
+        Eigen::Vector3d gravityDir;
+        double floorHeight;
+        double floorWeight;
+    };
+
+    class RodConfig
+    {
+    public:
+        ~RodConfig();
+
+        void addRod(Rod *rod);
+        void addAnchor(Anchor a);
+        void addIntersection(Intersection inter);
+        void initWeave(); // Call after all constraints initialized
+        int numRods() const { return (int) rods.size(); }
+        int numAnchors() const { return (int) anchors.size(); }
+        int numVertices() const { return (int) vertices.rows(); }
+        int numIntersections() const { return (int) intersections.size(); }
+        void reset();
+        void createVisualizationMesh(Eigen::MatrixXd &Q, Eigen::MatrixXi &F);
+        Eigen::Vector3d shadeRodSegment(Eigen::Vector3d light,
+                                        int rod,
+                                        int segment,
+                                        bool showCover) const;
+        void saveRodGeometry(const std::string &prefix);
+
+        std::vector<Rod *> rods;
+        std::vector<Anchor> anchors;
+        std::vector<Intersection> intersections;
+        Eigen::MatrixXd vertices;
+
+        bool showConstraints;
+        bool allowSliding;
+        double decay; //?
+        int getNumDoF() const;
+    };
+
+    void setStructure(const std::shared_ptr<SimulationEdgeMesh> &pMesh) override;
+
+private:
+    bool simulateOneStepGrid(RodConfig *config);
+
+    void rAndJGrid(const RodConfig &config,
+                   Eigen::VectorXd &r,
+                   Eigen::SparseMatrix<double> *Jr,
+                   double &gravityPE,
+                   Eigen::VectorXd &gravityForces,
+                   const SimParams &params,
+                   double &externalForcesPE,
+                   const Eigen::VectorXd &externalForces = Eigen::VectorXd(),
+                   std::vector<Eigen::Triplet<int>> *H_index = NULL,
+                   std::vector<double> *H_value = NULL,
+                   Eigen::SparseMatrix<double> *Ju = NULL,
+                   std::vector<Eigen::Triplet<int>> *Hu_index = NULL,
+                   std::vector<double> *Hu_value = NULL);
+
+    RodConfig *readRodGrid(const std::shared_ptr<SimulationEdgeMesh> &pMesh,
+                           const std::vector<int> &numVertsPerRod,
+                           const std::vector<int> &vInd,
+                           const std::vector<Eigen::Vector3d> &verts,
+                           const std::vector<Eigen::Vector3d> &binorms,
+                           const std::vector<RodParams> &rodparams,
+                           const std::vector<Anchor> &anchors,
+                           const double decay = 1.0,
+                           double *vStiffness = 0,
+                           double *restVerts = 0,
+                           double *restNormals = 0,
+                           const std::vector<double> &thetas = std::vector<double>(),
+                           double *eulers = 0);
+    double lineSearchGrid(RodConfig &config,
+                          const Eigen::VectorXd &update,
+                          const SimParams &params,
+                          const Eigen::VectorXd &externalForces = Eigen::VectorXd());
+    SimulationResults constructSimulationResults(const std::shared_ptr<SimulationJob> &pJob,
+                                                 RodConfig *config) const;
+    Eigen::Vector3d getPerpendicularVector(const Eigen::Vector3d &t) const;
+
+    double energy;
+    Eigen::VectorXd updateVec;
+    double forceResidual;
+    int iter{0};
+    std::shared_ptr<SimulationJob> pJob;
+
+    //    std::unique_ptr<ElasticRod> pRod;
+};
+
+Eigen::Matrix3d eulerRotation(double e0, double e1, double e2, int deriv = -1, int deriv2 = -1);
+#endif // DER_LEIMER_HPP

drmsimulationmodel.hpp

@@ -1,295 +0,0 @@
-#ifndef BEAMFORMFINDER_HPP
-#define BEAMFORMFINDER_HPP
-
-//#ifdef USE_MATPLOT
-//#include "matplot.h"
-#include <matplot/matplot.h>
-//#endif
-#include "simulationmesh.hpp"
-#include "simulationmodel.hpp"
-#include <Eigen/Dense>
-#include <filesystem>
-#include <unordered_set>
-
-#ifdef USE_ENSMALLEN
-#include <armadillo>
-#include <ensmallen.hpp>
-#endif
-
-struct SimulationJob;
-
-enum DoF { Ux = 0, Uy, Uz, Nx, Ny, Nr, NumDoF };
-using DoFType = int;
-using EdgeType = VCGEdgeMesh::EdgeType;
-using VertexType = VCGEdgeMesh::VertexType;
-
-struct DifferentiateWithRespectTo {
-  const VertexType &v;
-  const DoFType &dofi;
-};
-
-class DRMSimulationModel : public SimulationModel
-{
-public:
-    struct Settings
-    {
-        bool shouldDraw{false};
-        bool beVerbose{false};
-        bool shouldCreatePlots{false};
-        //        int drawingStep{0};
-        //        double residualForcesMovingAverageDerivativeNormThreshold{1e-8};
-        //        double residualForcesMovingAverageNormThreshold{1e-8};
-        double Dtini{0.1};
-        double xi{0.9969};
-        std::optional<double> shouldUseTranslationalKineticEnergyThreshold;
-        int gradualForcedDisplacementSteps{50};
-        //        int desiredGradualExternalLoadsSteps{1};
-        double gamma{0.8};
-        double totalResidualForcesNormThreshold{1e-8};
-        double totalExternalForcesNormPercentageTermination{1e-8};
-        std::optional<int> maxDRMIterations;
-        std::optional<int> debugModeStep;
-        std::optional<double> totalTranslationalKineticEnergyThreshold;
-        std::optional<double> averageResidualForcesCriterionThreshold;
-        std::optional<double> linearGuessForceScaleFactor;
-        //        std::optional<int> intermediateResultsSaveStep;
-        std::optional<bool> saveIntermediateBestStates;
-        std::optional<double> viscousDampingFactor;
-        bool useKineticDamping{true};
-        Settings() {}
-        void save(const std::filesystem::path &jsonFilePath) const;
-        bool load(const std::filesystem::path &filePath);
-        struct JsonLabels
-        {
-            const std::string shouldDraw{"shouldDraw"};
-            const std::string beVerbose{"beVerbose"};
-            const std::string shouldCreatePlots{"shouldCreatePlots"};
-            const std::string Dtini{"DtIni"};
-            const std::string xi{"xi"};
-            const std::string gamma{"gamma"};
-            const std::string totalResidualForcesNormThreshold;
-            const std::string maxDRMIterations{"maxIterations"};
-            const std::string debugModeStep{"debugModeStep"};
-            const std::string totalTranslationalKineticEnergyThreshold{
-                "totalTranslationaKineticEnergyThreshold"};
-            const std::string averageResidualForcesCriterionThreshold{
-                "averageResidualForcesThreshold"};
-            const std::string linearGuessForceScaleFactor{"linearGuessForceScaleFactor"};
-            const std::string viscousDampingFactor{"viscousDampingFactor"};
-        };
-        static JsonLabels jsonLabels;
-    };
-
-private:
-    Settings mSettings;
-    double Dt{mSettings.Dtini};
-    bool checkedForMaximumMoment{false};
-    bool shouldTemporarilyDampForces{false};
-    bool shouldTemporarilyAmplifyForces{true};
-    double externalMomentsNorm{0};
-    size_t mCurrentSimulationStep{0};
-    matplot::line_handle plotHandle;
-    std::vector<double> plotYValues;
-    size_t numOfDampings{0};
-    int externalLoadStep{1};
-    std::vector<bool> isVertexConstrained;
-    std::vector<bool> isRigidSupport;
-    double minTotalResidualForcesNorm{std::numeric_limits<double>::max()};
-
-    const std::string meshPolyscopeLabel{"Simulation mesh"};
-    std::unique_ptr<SimulationMesh> pMesh;
-    std::unordered_map<VertexIndex, std::unordered_set<DoFType>> constrainedVertices;
-    SimulationHistory history;
-    //  Eigen::Tensor<double, 4> theta3Derivatives;
-    //  std::unordered_map<MyKeyType, double, key_hash> theta3Derivatives;
-    bool shouldApplyInitialDistortion = false;
-    //#ifdef USE_ENSMALLEN
-    //    std::shared_ptr<SimulationJob> pJob;
-    //#endif
-    void reset(const std::shared_ptr<SimulationJob> &pJob, const Settings &settings);
-    void updateNodalInternalForces(
-        const std::unordered_map<VertexIndex, std::unordered_set<DoFType>> &fixedVertices);
-    void updateNodalExternalForces(
-        const std::unordered_map<VertexIndex, Vector6d> &nodalForces,
-        const std::unordered_map<VertexIndex, std::unordered_set<DoFType>> &fixedVertices);
-    void updateResidualForces();
-    void updateRotationalDisplacements();
-    void updateElementalLengths();
-
-    void updateNodalMasses();
-
-    void updateNodalAccelerations();
-
-    void updateNodalVelocities();
-
-    void updateNodalDisplacements();
-
-    void applyForcedDisplacements(
-        const std::unordered_map<VertexIndex, Eigen::Vector3d> &nodalForcedDisplacements);
-
-    Vector6d computeElementTorsionalForce(const Element &element,
-                                          const Vector6d &displacementDifference,
-                                          const std::unordered_set<DoFType> &constrainedDof);
-
-    //  BeamFormFinder::Vector6d computeElementFirstBendingForce(
-    //      const Element &element, const Vector6d &displacementDifference,
-    //      const std::unordered_set<gsl::index> &constrainedDof);
-
-    //  BeamFormFinder::Vector6d computeElementSecondBendingForce(
-    //      const Element &element, const Vector6d &displacementDifference,
-    //      const std::unordered_set<gsl::index> &constrainedDof);
-
-    void updateKineticEnergy();
-
-    void resetVelocities();
-
-    SimulationResults computeResults(const std::shared_ptr<SimulationJob> &pJob);
-
-    void updateNodePosition(
-        VertexType &v,
-        const std::unordered_map<VertexIndex, std::unordered_set<DoFType>> &fixedVertices);
-
-    void applyDisplacements(
-        const std::unordered_map<VertexIndex, std::unordered_set<DoFType>> &fixedVertices);
-
-#ifdef POLYSCOPE_DEFINED
-    void draw(const std::string &screenshotsFolder = {});
-#endif
-  void
-  updateNodalInternalForce(Vector6d &nodalInternalForce,
-                           const Vector6d &elementInternalForce,
-                           const std::unordered_set<DoFType> &nodalFixedDof);
-
-  Vector6d computeElementInternalForce(
-      const Element &elem, const Node &n0, const Node &n1,
-      const std::unordered_set<DoFType> &n0ConstrainedDof,
-      const std::unordered_set<DoFType> &n1ConstrainedDof);
-
-  Vector6d computeElementAxialForce(const ::EdgeType &e) const;
-  VectorType computeDisplacementDifferenceDerivative(
-      const EdgeType &e, const DifferentiateWithRespectTo &dui) const;
-  double
-  computeDerivativeElementLength(const EdgeType &e,
-                                 const DifferentiateWithRespectTo &dui) const;
-
-  VectorType computeDerivativeT1(const EdgeType &e,
-                                 const DifferentiateWithRespectTo &dui) const;
-
-  VectorType
-  computeDerivativeOfNormal(const VertexType &v,
-                            const DifferentiateWithRespectTo &dui) const;
-
-  VectorType computeDerivativeT3(const EdgeType &e,
-                                 const DifferentiateWithRespectTo &dui) const;
-
-  VectorType computeDerivativeT2(const EdgeType &e,
-                                 const DifferentiateWithRespectTo &dui) const;
-
-  double computeDerivativeTheta2(const EdgeType &e, const VertexIndex &evi,
-                                 const VertexIndex &dwrt_evi,
-                                 const DoFType &dwrt_dofi) const;
-
-  void updateElementalFrames();
-
-  VectorType computeDerivativeOfR(const EdgeType &e,
-                                  const DifferentiateWithRespectTo &dui) const;
-
-
-  static double computeDerivativeOfNorm(const VectorType &x,
-                                        const VectorType &derivativeOfX);
-  static VectorType computeDerivativeOfCrossProduct(
-      const VectorType &a, const VectorType &derivativeOfA, const VectorType &b,
-      const VectorType &derivativeOfB);
-
-  double computeTheta3(const EdgeType &e, const VertexType &v);
-  double computeDerivativeTheta3(const EdgeType &e, const VertexType &v,
-                                 const DifferentiateWithRespectTo &dui) const;
-  double computeTotalPotentialEnergy();
-  void computeRigidSupports();
-  void updateNormalDerivatives();
-  void updateT1Derivatives();
-  void updateT2Derivatives();
-  void updateT3Derivatives();
-  void updateRDerivatives();
-
-  double computeDerivativeTheta1(const EdgeType &e, const VertexIndex &evi,
-                                 const VertexIndex &dwrt_evi,
-                                 const DoFType &dwrt_dofi) const;
-
-  //  void updatePositionsOnTheFly(
-  //      const std::unordered_map<VertexIndex,
-  //      std::unordered_set<gsl::index>>
-  //          &fixedVertices);
-
-  void updateResidualForcesOnTheFly(
-      const std::unordered_map<VertexIndex, std::unordered_set<DoFType>>
-          &fixedVertices);
-
-  void updatePositionsOnTheFly(
-      const std::unordered_map<VertexIndex, std::unordered_set<DoFType>>
-          &fixedVertices);
-
-  void updateNodeNormal(
-      VertexType &v,
-      const std::unordered_map<VertexIndex, std::unordered_set<DoFType>>
-          &fixedVertices);
-
-  void applyForcedNormals(
-      const std::unordered_map<VertexIndex, VectorType> nodalForcedRotations);
-
-  void printCurrentState() const;
-
-  void printDebugInfo() const;
-
-  double computeTotalInternalPotentialEnergy();
-
-  void applySolutionGuess(const SimulationResults &solutionGuess,
-                          const std::shared_ptr<SimulationJob> &pJob);
-
-  void updateNodeNr(VertexType &v);
-
-  void applyKineticDamping(const std::shared_ptr<SimulationJob> &pJob);
-
-  virtual SimulationResults executeSimulation(const std::shared_ptr<SimulationJob> &pJob);
-
-  void reset(const std::shared_ptr<SimulationJob> &pJob);
-
-  public:
-  DRMSimulationModel();
-  SimulationResults executeSimulation(const std::shared_ptr<SimulationJob> &pJob,
-                                      const Settings &settings,
-                                      const SimulationResults &solutionGuess = SimulationResults());
-#ifdef USE_ENSMALLEN
-  double EvaluateWithGradient(const arma::mat &x, arma::mat &g);
-  void setJob(const std::shared_ptr<SimulationJob> &pJob);
-  SimulationMesh *getDeformedMesh(const arma::mat &x);
-
-#endif
-
-  static void runUnitTests();
-};
-
-inline DRMSimulationModel::Settings::JsonLabels DRMSimulationModel::Settings::jsonLabels;
-
-template <typename PointType> PointType Cross(PointType p1, PointType p2) {
-  return p1 ^ p2;
-}
-
-inline size_t currentStep{0};
-inline bool TriggerBreakpoint(const VertexIndex &vi, const EdgeIndex &ei,
-                              const DoFType &dofi) {
-  const size_t numberOfVertices = 10;
-  const VertexIndex middleNodeIndex = numberOfVertices / 2;
-  //  return vi == middleNodeIndex && dofi == 1;
-  return dofi == 1 && ((vi == 1 && ei == 0) || (vi == 9 && ei == 9));
-}
-
-inline bool TriggerBreakpoint(const VertexIndex &vi, const EdgeIndex &ei) {
-  const size_t numberOfVertices = 10;
-  const VertexIndex middleNodeIndex = numberOfVertices / 2;
-  return (vi == middleNodeIndex);
-  //  return (vi == 0 || vi == numberOfVertices - 1) && currentStep == 1;
-  return (vi == 1 && ei == 0) || (vi == 9 && ei == 9);
-}
-
-#endif // BEAMFORMFINDER_HPP

edgemesh.cpp

@@ -1,495 +0,0 @@
-#include "edgemesh.hpp"
-#include "vcg/simplex/face/topology.h"
-//#include <wrap/nanoply/include/nanoplyWrapper.hpp>
-#include <wrap/io_trimesh/export.h>
-#include <wrap/io_trimesh/import.h>
-
-Eigen::MatrixX2i VCGEdgeMesh::getEigenEdges() const { return eigenEdges; }
-
-std::vector<vcg::Point2i> VCGEdgeMesh::getEdges()
-{
-    getEdges(eigenEdges);
-    std::vector<vcg::Point2i> edges(eigenEdges.rows());
-    for (int ei = 0; ei < eigenEdges.rows(); ei++) {
-        edges[ei] = vcg::Point2i(eigenEdges(ei, 0), eigenEdges(ei, 1));
-    }
-    return edges;
-}
-
-Eigen::MatrixX3d VCGEdgeMesh::getEigenVertices() {
-    getVertices(eigenVertices);
-  return eigenVertices;
-}
-
-Eigen::MatrixX3d VCGEdgeMesh::getEigenEdgeNormals() const {
-  return eigenEdgeNormals;
-}
-
-bool VCGEdgeMesh::save(const std::filesystem::__cxx11::path &meshFilePath)
-{
-    std::string filename = meshFilePath;
-    if (filename.empty()) {
-        filename = std::filesystem::current_path().append(getLabel() + ".ply").string();
-    } else if (std::filesystem::is_directory(std::filesystem::path(meshFilePath))) {
-        filename = std::filesystem::path(meshFilePath).append(getLabel() + ".ply").string();
-    }
-    assert(std::filesystem::path(filename).extension().string() == ".ply");
-    unsigned int mask = 0;
-    mask |= vcg::tri::io::Mask::IOM_VERTCOORD;
-    mask |= vcg::tri::io::Mask::IOM_EDGEINDEX;
-    mask |= vcg::tri::io::Mask::IOM_VERTNORMAL;
-    mask |= vcg::tri::io::Mask::IOM_VERTCOLOR;
-    //    if (nanoply::NanoPlyWrapper<VCGEdgeMesh>::SaveModel(filename.c_str(), *this, mask, false) != 0) {
-    if (vcg::tri::io::Exporter<VCGEdgeMesh>::Save(*this, filename.c_str(), mask) != 0) {
-        return false;
-    }
-    return true;
-}
-
-void VCGEdgeMesh::GeneratedRegularSquaredPattern(
-    const double angleDeg, std::vector<std::vector<vcg::Point2d>> &pattern,
-    const size_t &desiredNumberOfSamples) {
-  static const size_t piSamples = 10;
-
-  // generate a pattern in a 1x1 quad
-  const vcg::Point2d offset(0, 0);
-
-  const size_t samplesNo = desiredNumberOfSamples;
-  //      std::max(desiredNumberOfSamples, size_t(piSamples * (angleDeg /
-  //      180)));
-  const double angle = vcg::math::ToRad(angleDeg);
-
-  pattern.clear();
-
-  // first arm
-  std::vector<vcg::Point2d> arm;
-  {
-    for (int k = 0; k <= samplesNo; k++) {
-      const double t = double(k) / samplesNo;
-      const double a = (1 - t) * angle;
-      // const double r = vcg::math::Sin(t*M_PI_2) /*(1-((1-t)*(1-t)))*/ *
-      // 0.5;
-      const double r = t * 0.5; // linear
-
-      vcg::Point2d p(vcg::math::Cos(a), vcg::math::Sin(a));
-
-      arm.push_back((p * r));
-    }
-    pattern.push_back(arm);
-  }
-
-  // other arms
-  for (int i = 0; i < 3; i++) {
-    for (vcg::Point2d &p : arm) {
-      p = vcg::Point2d(-p.Y(), p.X());
-    }
-    pattern.push_back(arm);
-  }
-
-  assert(pattern.size() == 4);
-
-  // offset all
-  for (auto &arm : pattern) {
-    for (vcg::Point2d &p : arm) {
-      p += offset;
-    }
-  }
-}
-
-void VCGEdgeMesh::createSpiral(const float &degreesOfArm,
-                               const size_t &numberOfSamples) {
-  std::vector<std::vector<vcg::Point2d>> spiralPoints;
-  GeneratedRegularSquaredPattern(degreesOfArm, spiralPoints, numberOfSamples);
-
-  for (size_t armIndex = 0; armIndex < spiralPoints.size(); armIndex++) {
-    for (size_t pointIndex = 0; pointIndex < spiralPoints[armIndex].size() - 1;
-         pointIndex++) {
-      const vcg::Point2d p0 = spiralPoints[armIndex][pointIndex];
-      const vcg::Point2d p1 = spiralPoints[armIndex][pointIndex + 1];
-      CoordType n(0, 0, 1);
-      auto ei = vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(
-          *this, VCGEdgeMesh::CoordType(p0.X(), p0.Y(), 0),
-          VCGEdgeMesh::CoordType(p1.X(), p1.Y(), 0));
-      ei->cV(0)->N() = n;
-      ei->cV(1)->N() = n;
-    }
-  }
-
-  //  setDefaultAttributes();
-}
-
-bool VCGEdgeMesh::createSpanGrid(const size_t squareGridDimension) {
-  return createSpanGrid(squareGridDimension, squareGridDimension);
-}
-
-bool VCGEdgeMesh::createSpanGrid(const size_t desiredWidth,
-                                 const size_t desiredHeight) {
-  std::cout << "Grid of dimensions:" << desiredWidth << "," << desiredHeight
-            << std::endl;
-  const VCGEdgeMesh::CoordType n(0, 0, 1);
-  int x = 0;
-  int y = 0;
-  //  for (size_t vi = 0; vi < numberOfVertices; vi++) {
-  while (y <= desiredHeight) {
-    //    std::cout << x << " " << y << std::endl;
-    auto p = VCGEdgeMesh::CoordType(x, y, 0);
-    vcg::tri::Allocator<VCGEdgeMesh>::AddVertex(*this, p, n);
-    x++;
-    if (x > desiredWidth) {
-      x = 0;
-      y++;
-    }
-  }
-
-  for (size_t vi = 0; vi < VN(); vi++) {
-    int x = vi % (desiredWidth + 1);
-    int y = vi / (desiredWidth + 1);
-    const bool isCornerNode = (y == 0 && x == 0) ||
-                              (y == 0 && x == desiredWidth) ||
-                              (y == desiredHeight && x == 0) ||
-                              (y == desiredHeight && x == desiredWidth);
-    if (isCornerNode) {
-      continue;
-    }
-    if (y == 0) { // row 0.Connect with node above
-      vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi,
-                                                vi + desiredWidth + 1);
-      continue;
-    } else if (x == 0) { // col 0.Connect with node to the right
-      vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi, vi + 1);
-      continue;
-    } else if (y == desiredHeight) { // row 0.Connect with node below
-      //      vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi,
-      //                                                vi - (desiredWidth +
-      //                                                1));
-      continue;
-    } else if (x == desiredWidth) { // row 0.Connect with node to the left
-      //      vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi, vi - 1);
-      continue;
-    }
-
-    vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi, vi + desiredWidth + 1);
-    vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi, vi + 1);
-    //    vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi,
-    //                                              vi - (desiredWidth + 1));
-    //    vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, vi, vi - 1);
-  }
-
-  vcg::tri::Allocator<VCGEdgeMesh>::DeleteVertex(*this, vert[0]);
-  vcg::tri::Allocator<VCGEdgeMesh>::DeleteVertex(*this, vert[desiredWidth]);
-  vcg::tri::Allocator<VCGEdgeMesh>::DeleteVertex(
-      *this, vert[desiredHeight * (desiredWidth + 1)]);
-  vcg::tri::Allocator<VCGEdgeMesh>::DeleteVertex(
-      *this, vert[(desiredHeight + 1) * (desiredWidth + 1) - 1]);
-  vcg::tri::Allocator<VCGEdgeMesh>::CompactVertexVector(*this);
-  getEdges(eigenEdges);
-  getVertices(eigenVertices);
-  //  vcg::tri::Allocator<VCGEdgeMesh>::CompactEdgeVector(*this);
-
-  //  const size_t numberOfEdges =
-  //      desiredHeight * (desiredWidth - 1) + desiredWidth * (desiredHeight -
-  //      1);
-  //  handleBeamDimensions._handle->data.resize(
-  //      numberOfEdges, CylindricalElementDimensions(0.03, 0.026));
-  //  handleBeamMaterial._handle->data.resize(numberOfEdges,
-  //                                          ElementMaterial(0.3, 200));
-
-  return true;
-}
-
-bool VCGEdgeMesh::load(const std::filesystem::__cxx11::path &meshFilePath)
-{
-    std::string usedPath = meshFilePath;
-    if (std::filesystem::path(meshFilePath).is_relative()) {
-        usedPath = std::filesystem::absolute(meshFilePath).string();
-    }
-    assert(std::filesystem::exists(usedPath));
-    Clear();
-    //  if (!loadUsingNanoply(usedPath)) {
-    //    std::cerr << "Error: Unable to open " + usedPath << std::endl;
-    //    return false;
-    //  }
-    if (!loadUsingDefaultLoader(usedPath)) {
-        std::cerr << "Error: Unable to open " + usedPath << std::endl;
-        return false;
-    }
-
-    getEdges(eigenEdges);
-    getVertices(eigenVertices);
-    vcg::tri::UpdateTopology<VCGEdgeMesh>::VertexEdge(*this);
-    label = std::filesystem::path(meshFilePath).stem().string();
-
-    const bool printDebugInfo = false;
-    if (printDebugInfo) {
-        std::cout << meshFilePath << " was loaded successfuly." << std::endl;
-        std::cout << "Mesh has " << EN() << " edges." << std::endl;
-    }
-
-    label = std::filesystem::path(meshFilePath).stem().string();
-    return true;
-}
-
-//bool VCGEdgeMesh::loadUsingNanoply(const std::string &plyFilename) {
-
-//  this->Clear();
-//  //  assert(plyFileHasAllRequiredFields(plyFilename));
-//  // Load the ply file
-//  unsigned int mask = 0;
-//  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTCOORD;
-//  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTNORMAL;
-//  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTCOLOR;
-//  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_EDGEINDEX;
-//  if (nanoply::NanoPlyWrapper<VCGEdgeMesh>::LoadModel(plyFilename.c_str(),
-//                                                      *this, mask) != 0) {
-//    return false;
-//  }
-//  return true;
-//}
-
-bool VCGEdgeMesh::loadUsingDefaultLoader(const std::string &plyFilename)
-{
-    Clear();
-    //  assert(plyFileHasAllRequiredFields(plyFilename));
-    // Load the ply file
-    int mask = 0;
-    mask |= vcg::tri::io::Mask::IOM_VERTCOORD;
-    mask |= vcg::tri::io::Mask::IOM_VERTNORMAL;
-    mask |= vcg::tri::io::Mask::IOM_VERTCOLOR;
-    mask |= vcg::tri::io::Mask::IOM_EDGEINDEX;
-    //  if (nanoply::NanoPlyWrapper<VCGEdgeMesh>::LoadModel(plyFilename.c_str(),
-    //                                                      *this, mask) != 0) {
-    if (vcg::tri::io::Importer<VCGEdgeMesh>::Open(*this, plyFilename.c_str(), mask) != 0) {
-        return false;
-    }
-    return true;
-}
-
-// bool VCGEdgeMesh::plyFileHasAllRequiredFields(const std::string
-// &plyFilename)
-// {
-//  const nanoply::Info info(plyFilename);
-//  const std::vector<nanoply::PlyElement>::const_iterator edgeElemIt =
-//      std::find_if(info.elemVec.begin(), info.elemVec.end(),
-//                   [&](const nanoply::PlyElement &plyElem) {
-//                     return plyElem.plyElem == nanoply::NNP_EDGE_ELEM;
-//                   });
-//  if (edgeElemIt == info.elemVec.end()) {
-//    std::cerr << "Ply file is missing edge elements." << std::endl;
-//    return false;
-//  }
-
-//  const std::vector<nanoply::PlyProperty> &edgePropertyVector =
-//      edgeElemIt->propVec;
-//  return hasPlyEdgeProperty(plyFilename, edgePropertyVector,
-//                            plyPropertyBeamDimensionsID) &&
-//         hasPlyEdgeProperty(plyFilename, edgePropertyVector,
-//                            plyPropertyBeamMaterialID);
-//}
-
-Eigen::MatrixX3d VCGEdgeMesh::getNormals() const {
-  Eigen::MatrixX3d vertexNormals;
-  vertexNormals.resize(VN(), 3);
-
-  for (int vertexIndex = 0; vertexIndex < VN(); vertexIndex++) {
-    VCGEdgeMesh::CoordType vertexNormal =
-        vert[static_cast<size_t>(vertexIndex)].cN();
-    vertexNormals.row(vertexIndex) =
-        vertexNormal.ToEigenVector<Eigen::Vector3d>();
-  }
-
-  return vertexNormals;
-}
-void VCGEdgeMesh::getEdges(Eigen::MatrixX3d &edgeStartingPoints,
-                           Eigen::MatrixX3d &edgeEndingPoints) const {
-  edgeStartingPoints.resize(EN(), 3);
-  edgeEndingPoints.resize(EN(), 3);
-  for (int edgeIndex = 0; edgeIndex < EN(); edgeIndex++) {
-    const VCGEdgeMesh::EdgeType &edge = this->edge[edgeIndex];
-    edgeStartingPoints.row(edgeIndex) =
-        edge.cP(0).ToEigenVector<Eigen::Vector3d>();
-    edgeEndingPoints.row(edgeIndex) =
-        edge.cP(1).ToEigenVector<Eigen::Vector3d>();
-  }
-}
-
-VCGEdgeMesh::VCGEdgeMesh() {}
-
-void VCGEdgeMesh::updateEigenEdgeAndVertices() {
-#ifdef POLYSCOPE_DEFINED
-  getEdges(eigenEdges);
-  getVertices(eigenVertices);
-#endif
-}
-
-bool VCGEdgeMesh::copy(VCGEdgeMesh &mesh) {
-  vcg::tri::Append<VCGEdgeMesh, VCGEdgeMesh>::MeshCopy(*this, mesh);
-  label = mesh.getLabel();
-  eigenEdges = mesh.getEigenEdges();
-  if (eigenEdges.rows() == 0) {
-    getEdges(eigenEdges);
-  }
-  eigenVertices = mesh.getEigenVertices();
-  if (eigenVertices.rows() == 0) {
-    getVertices(eigenVertices);
-  }
-  vcg::tri::UpdateTopology<VCGEdgeMesh>::VertexEdge(*this);
-
-  return true;
-}
-
-void VCGEdgeMesh::set(const std::vector<double> &vertexPositions, const std::vector<int> &edges)
-{
-    Clear();
-    for (int ei = 0; ei < edges.size(); ei += 2) {
-        const int vi0 = edges[ei];
-        const int vi1 = edges[ei + 1];
-        const int vi0_offset = 3 * vi0;
-        const int vi1_offset = 3 * vi1;
-        const CoordType p0(vertexPositions[vi0_offset],
-                           vertexPositions[vi0_offset + 1],
-                           vertexPositions[vi0_offset + 2]);
-        const CoordType p1(vertexPositions[vi1_offset],
-                           vertexPositions[vi1_offset + 1],
-                           vertexPositions[vi1_offset + 2]);
-        auto eIt = vcg::tri::Allocator<VCGEdgeMesh>::AddEdge(*this, p0, p1);
-        CoordType n(0, 0, 1);
-        eIt->cV(0)->N() = n;
-        eIt->cV(1)->N() = n;
-    }
-    removeDuplicateVertices();
-
-    updateEigenEdgeAndVertices();
-}
-
-void VCGEdgeMesh::removeDuplicateVertices()
-{
-    vcg::tri::Clean<VCGEdgeMesh>::MergeCloseVertex(*this, 0.000061524);
-    vcg::tri::Allocator<VCGEdgeMesh>::CompactVertexVector(*this);
-    vcg::tri::Allocator<VCGEdgeMesh>::CompactEdgeVector(*this);
-    vcg::tri::UpdateTopology<VCGEdgeMesh>::VertexEdge(*this);
-}
-
-void VCGEdgeMesh::removeDuplicateVertices(
-    vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<VertexPointer> &pu_vertices,
-    vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<EdgePointer> &pu_edges)
-{
-    vcg::tri::Clean<VCGEdgeMesh>::MergeCloseVertex(*this, 0.000061524);
-    vcg::tri::Allocator<VCGEdgeMesh>::CompactVertexVector(*this, pu_vertices);
-    vcg::tri::Allocator<VCGEdgeMesh>::CompactEdgeVector(*this, pu_edges);
-    vcg::tri::UpdateTopology<VCGEdgeMesh>::VertexEdge(*this);
-}
-
-void VCGEdgeMesh::deleteDanglingVertices() {
-    vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<VertexPointer> pu;
-    deleteDanglingVertices(pu);
-}
-
-void VCGEdgeMesh::deleteDanglingVertices(vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<TriMesh::VertexPointer> &pu) {
-    for (VertexType &v : vert) {
-        std::vector<VCGEdgeMesh::EdgePointer> incidentElements;
-        vcg::edge::VEStarVE(&v, incidentElements);
-        if (incidentElements.size() == 0 && !v.IsD()) {
-            vcg::tri::Allocator<VCGEdgeMesh>::DeleteVertex(*this, v);
-        }
-    }
-
-    vcg::tri::Allocator<VCGEdgeMesh>::CompactVertexVector(*this, pu);
-    vcg::tri::Allocator<VCGEdgeMesh>::CompactEdgeVector(*this);
-
-    updateEigenEdgeAndVertices();
-}
-
-void VCGEdgeMesh::getVertices(Eigen::MatrixX3d &vertices) {
-    vertices = Eigen::MatrixX3d();
-    vertices.resize(VN(), 3);
-    for (int vi = 0; vi < VN(); vi++) {
-        if (vert[vi].IsD()) {
-            continue;
-        }
-        VCGEdgeMesh::CoordType vertexCoordinates =
-            vert[static_cast<size_t>(vi)].cP();
-        vertices.row(vi) = vertexCoordinates.ToEigenVector<Eigen::Vector3d>();
-    }
-}
-
-void VCGEdgeMesh::getEdges(Eigen::MatrixX2i &edges) {
-  edges = Eigen::MatrixX2i();
-  edges.resize(EN(), 2);
-  for (int edgeIndex = 0; edgeIndex < EN(); edgeIndex++) {
-    const VCGEdgeMesh::EdgeType &edge = this->edge[edgeIndex];
-    assert(!edge.IsD());
-    auto vp0 = edge.cV(0);
-    auto vp1 = edge.cV(1);
-    assert(vcg::tri::IsValidPointer(*this, vp0) &&
-           vcg::tri::IsValidPointer(*this, vp1));
-    const size_t vi0 = vcg::tri::Index<VCGEdgeMesh>(*this, vp0);
-    const size_t vi1 = vcg::tri::Index<VCGEdgeMesh>(*this, vp1);
-    assert(vi0 != -1 && vi1 != -1);
-    edges.row(edgeIndex) = Eigen::Vector2i(vi0, vi1);
-  }
-}
-
-void VCGEdgeMesh::printVertexCoordinates(const size_t &vi) const {
-  std::cout << "vi:" << vi << " " << vert[vi].cP()[0] << " " << vert[vi].cP()[1]
-            << " " << vert[vi].cP()[2] << std::endl;
-}
-
-#ifdef POLYSCOPE_DEFINED
-//TODO: make const getEigenVertices is not
-polyscope::CurveNetwork *VCGEdgeMesh::registerForDrawing(
-    const std::optional<std::array<double, 3>> &desiredColor,
-    const double &desiredRadius,
-    const bool &shouldEnable)
-{
-    PolyscopeInterface::init();
-    const double drawingRadius = desiredRadius;
-    updateEigenEdgeAndVertices();
-    polyscope::CurveNetwork *polyscopeHandle_edgeMesh
-        = polyscope::registerCurveNetwork(label, getEigenVertices(), getEigenEdges());
-    //    std::cout << "EDGES:" << polyscopeHandle_edgeMesh->nEdges() << std::endl;
-    assert(polyscopeHandle_edgeMesh->nEdges() == getEigenEdges().rows()
-           && polyscopeHandle_edgeMesh->nNodes() == getEigenVertices().rows());
-
-    polyscopeHandle_edgeMesh->setEnabled(shouldEnable);
-    polyscopeHandle_edgeMesh->setRadius(drawingRadius, true);
-    if (desiredColor.has_value()) {
-        const glm::vec3 desiredColor_glm(desiredColor.value()[0],
-                                         desiredColor.value()[1],
-                                         desiredColor.value()[2]);
-        polyscopeHandle_edgeMesh->setColor(desiredColor_glm);
-    }
-
-    return polyscopeHandle_edgeMesh;
-}
-
-void VCGEdgeMesh::unregister() const {
-  if (!polyscope::hasCurveNetwork(label)) {
-    std::cerr << "No curve network registered with a name: " << getLabel()
-              << std::endl;
-    std::cerr << "Nothing to remove." << std::endl;
-    return;
-  }
-  polyscope::removeCurveNetwork(label);
-}
-
-void VCGEdgeMesh::drawInitialFrames(polyscope::CurveNetwork *polyscopeHandle_initialMesh) const
-{
-    Eigen::MatrixX3d frameInitialX(VN(), 3);
-    Eigen::MatrixX3d frameInitialY(VN(), 3);
-    Eigen::MatrixX3d frameInitialZ(VN(), 3);
-    for (int vi = 0; vi < VN(); vi++) {
-        frameInitialX.row(vi) = Eigen::Vector3d(1, 0, 0);
-        frameInitialY.row(vi) = Eigen::Vector3d(0, 1, 0);
-        frameInitialZ.row(vi) = Eigen::Vector3d(0, 0, 1);
-    }
-    polyscopeHandle_initialMesh->addNodeVectorQuantity("FrameX", frameInitialX)
-        ->setVectorColor(glm::vec3(1, 0, 0))
-        ->setEnabled(true);
-    polyscopeHandle_initialMesh->addNodeVectorQuantity("FrameY", frameInitialY)
-        ->setVectorColor(glm::vec3(0, 1, 0))
-        ->setEnabled(true);
-    polyscopeHandle_initialMesh->addNodeVectorQuantity("FrameZ", frameInitialZ)
-        ->setVectorColor(glm::vec3(0, 0, 1))
-        ->setEnabled(true);
-}
-#endif

edgemesh.hpp

@@ -1,127 +0,0 @@
-#ifndef EDGEMESH_HPP
-#define EDGEMESH_HPP
-#include "beam.hpp"
-#include "mesh.hpp"
-#include "utilities.hpp"
-#include <vcg/complex/complex.h>
-#include <vector>
-#include <wrap/io_trimesh/import.h>
-#include <optional>
-#include <array>
-
-#ifdef POLYSCOPE_DEFINED
-#include <polyscope/curve_network.h>
-#endif
-
-using EdgeIndex = size_t;
-
-class VCGEdgeMeshEdgeType;
-class VCGEdgeMeshVertexType;
-
-struct VCGEdgeMeshUsedTypes
-: public vcg::UsedTypes<vcg::Use<VCGEdgeMeshVertexType>::AsVertexType,
-	vcg::Use<VCGEdgeMeshEdgeType>::AsEdgeType> {};
-
-class VCGEdgeMeshVertexType
-: public vcg::Vertex<VCGEdgeMeshUsedTypes, vcg::vertex::Coord3d,
-	vcg::vertex::Normal3d, vcg::vertex::BitFlags,
-	vcg::vertex::Color4b, vcg::vertex::VEAdj> {};
-class VCGEdgeMeshEdgeType
-: public vcg::Edge<VCGEdgeMeshUsedTypes, vcg::edge::VertexRef,
-	vcg::edge::BitFlags, vcg::edge::EEAdj,
-	vcg::edge::VEAdj> {};
-
-class VCGEdgeMesh
-    : public vcg::tri::TriMesh<std::vector<VCGEdgeMeshVertexType>, std::vector<VCGEdgeMeshEdgeType>>,
-      public Mesh
-{
-protected:
-    Eigen::MatrixX2i eigenEdges;
-    Eigen::MatrixX3d eigenVertices;
-    Eigen::MatrixX3d eigenEdgeNormals;
-
-    void getEdges(Eigen::MatrixX2i &edges);
-    void getVertices(Eigen::MatrixX3d &vertices);
-
-public:
-    VCGEdgeMesh();
-    template<typename MeshElement>
-    size_t getIndex(const MeshElement &meshElement)
-    {
-        return vcg::tri::Index<VCGEdgeMesh>(*this, meshElement);
-    }
-    void updateEigenEdgeAndVertices();
-    /*
-             * The copy function shold be a virtual function of the base interface Mesh class.
-             * https://stackoverflow.com/questions/2354210/can-a-class-member-function-template-be-virtual
-             * use type erasure (?)
-             * */
-    bool copy(VCGEdgeMesh &mesh);
-
-    void set(const std::vector<double> &vertexPositions, const std::vector<int> &edges);
-
-    void removeDuplicateVertices();
-    virtual void deleteDanglingVertices();
-    virtual void deleteDanglingVertices(
-        vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<VertexPointer> &pu);
-
-    void getEdges(Eigen::MatrixX3d &edgeStartingPoints, Eigen::MatrixX3d &edgeEndingPoints) const;
-
-    Eigen::MatrixX3d getNormals() const;
-
-    bool plyFileHasAllRequiredFields(const std::string &plyFilename);
-
-    //    bool loadUsingNanoply(const std::string &plyFilename);
-
-    bool load(const std::filesystem::path &meshFilePath) override;
-    bool save(const std::filesystem::path &meshFilePath = std::filesystem::path()) override;
-
-    bool createSpanGrid(const size_t squareGridDimension);
-    bool createSpanGrid(const size_t desiredWidth, const size_t desiredHeight);
-    void createSpiral(const float &degreesOfArm, const size_t &numberOfSamples);
-
-    Eigen::MatrixX2i getEigenEdges() const;
-    std::vector<vcg::Point2i> getEdges();
-
-    Eigen::MatrixX3d getEigenVertices();
-    Eigen::MatrixX3d getEigenEdgeNormals() const;
-    void printVertexCoordinates(const size_t &vi) const;
-#ifdef POLYSCOPE_DEFINED
-    polyscope::CurveNetwork *registerForDrawing(
-        const std::optional<std::array<double, 3>> &desiredColor = std::nullopt,
-        const double &desiredRadius = 0.001,
-        const bool &shouldEnable = true);
-    void unregister() const;
-    void drawInitialFrames(polyscope::CurveNetwork *polyscopeHandle_initialMesh) const;
-#endif
-    void removeDuplicateVertices(
-        vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<VertexPointer> &pu_vertices,
-        vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<EdgePointer> &pu_edges);
-
-    void centerMesh()
-    {
-        CoordType centerOfMass(0, 0, 0);
-
-        for (const auto &v : vert) {
-            centerOfMass = centerOfMass + v.cP();
-        }
-        centerOfMass = centerOfMass / VN();
-        for (auto &v : vert) {
-            v.P() = v.cP() - centerOfMass;
-        }
-    }
-
-private:
-    void GeneratedRegularSquaredPattern(const double angleDeg,
-                                        std::vector<std::vector<vcg::Point2d>> &pattern,
-                                        const size_t &desiredNumberOfSamples);
-    bool loadUsingDefaultLoader(const std::string &plyFilename);
-};
-
-using VectorType = VCGEdgeMesh::CoordType;
-using CoordType = VCGEdgeMesh::CoordType;
-using VertexPointer = VCGEdgeMesh::VertexPointer;
-using EdgePointer = VCGEdgeMesh::EdgePointer;
-using ConstVCGEdgeMesh = VCGEdgeMesh;
-
-#endif // EDGEMESH_HPP

formFinder_unitTestFiles/Cylindrical/simpleBeam.ply

@@ -7,7 +7,6 @@ property float z           { z coordinate, too }
 property float nx
 property float ny
 property float nz
-
 element edge 4            { there are 6 "face" elements in the file }
 property int vertex1
 property int vertex2
@@ -24,4 +23,4 @@ end_header
 0 1 2 0.03 0.026 2 0.3 200
 1 2 2 0.03 0.026 2 0.3 200
 2 3 2 0.03 0.026 2 0.3 200
-3 4 2 0.03 0.026 2 0.3 200
+3 4 2 0.03 0.026 2 0.3 200

formFinder_unitTestFiles/rectangularCrossSection/longSpanGridshell.ply

@@ -0,0 +1,374 @@
+ply
+format ascii 1.0
+comment nanoply generated
+element vertex 140
+property double x
+property double y
+property double z
+property double nx
+property double ny
+property double nz
+element edge 220
+property int vertex1
+property int vertex2
+end_header
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formFinder_unitTestFiles/rectangularCrossSection/shortSpanGridshell.ply

@@ -0,0 +1,69 @@
+ply
+format ascii 1.0
+element vertex 21           { define "vertex" element, 8 of them in file }
+property float x           { vertex contains float "x" coordinate }
+property float y           { y coordinate is also a vertex property }
+property float z           { z coordinate, too }
+property float nx
+property float ny
+property float nz
+element edge 24            { there are 6 "face" elements in the file }
+property int vertex1
+property int vertex2
+property list uchar float beam_dimensions
+property list uchar float beam_material {poissons ratio , young's modulus in GPascal}
+end_header
+
+0 0 0 0 0 1
+1 0 0 0 0 1
+2 0 0 0 0 1
+3 0 0 0 0 1
+4 0 0 0 0 1
+0 1 0 0 0 1
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+1 4 0 0 0 1
+2 4 0 0 0 1
+3 4 0 0 0 1
+4 4 0 0 0 1
+
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+1 2 2 0.03 0.026 2 0.3 200
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+19 20 2 0.03 0.026 2 0.3 200

formFinder_unitTestFiles/rectangularCrossSection/simpleBeam.ply

@@ -0,0 +1,26 @@
+ply
+format ascii 1.0
+element vertex 5           { define "vertex" element, 8 of them in file }
+property float x           { vertex contains float "x" coordinate }
+property float y           { y coordinate is also a vertex property }
+property float z           { z coordinate, too }
+property float nx
+property float ny
+property float nz
+element edge 4            { there are 6 "face" elements in the file }
+property int vertex1
+property int vertex2
+property list uchar float beam_dimensions
+property list uchar float beam_material {poissons ratio , young's modulus in GPascal}
+end_header
+
+0 0 0 0 0 1
+1 0 0 0 0 1
+2 0 0 0 0 1
+3 0 0 0 0 1
+4 0 0 0 0 1
+
+0 1 2 0.03 0.026 2 0.3 200
+1 2 2 0.03 0.026 2 0.3 200
+2 3 2 0.03 0.026 2 0.3 200
+3 4 2 0.03 0.026 2 0.3 200

linearsimulationmodel.cpp

@@ -1,274 +0,0 @@
-#include "linearsimulationmodel.hpp"
-//#include "gsl/gsl"
-
-std::vector<fea::Elem> LinearSimulationModel::getFeaElements(
-    const std::shared_ptr<SimulationMesh> &pMesh)
-{
-    const int numberOfEdges = pMesh->EN();
-    std::vector<fea::Elem> elements(numberOfEdges);
-    for (int edgeIndex = 0; edgeIndex < numberOfEdges; edgeIndex++) {
-        const SimulationMesh::CoordType &evn0 = pMesh->edge[edgeIndex].cV(0)->cN();
-        const SimulationMesh::CoordType &evn1 = pMesh->edge[edgeIndex].cV(1)->cN();
-        const std::vector<double> nAverageVector{(evn0[0] + evn1[0]) / 2,
-                                                 (evn0[1] + evn1[1]) / 2,
-                                                 (evn0[2] + evn1[2]) / 2};
-        const Element &element = pMesh->elements[edgeIndex];
-        const double E = element.material.youngsModulus;
-        fea::Props feaProperties(E * element.dimensions.A,
-                                 E * element.dimensions.inertia.I3,
-                                 E * element.dimensions.inertia.I2,
-                                 element.material.G * element.dimensions.inertia.J,
-                                 nAverageVector);
-        const int vi0 = pMesh->getIndex(pMesh->edge[edgeIndex].cV(0));
-        const int vi1 = pMesh->getIndex(pMesh->edge[edgeIndex].cV(1));
-        elements[edgeIndex] = fea::Elem(vi0, vi1, feaProperties);
-    }
-
-    return elements;
-}
-
-std::vector<fea::Node> LinearSimulationModel::getFeaNodes(
-    const std::shared_ptr<SimulationMesh> &pMesh)
-{
-    const int numberOfNodes = pMesh->VN();
-    std::vector<fea::Node> feaNodes(numberOfNodes);
-    for (int vi = 0; vi < numberOfNodes; vi++) {
-        const CoordType &p = pMesh->vert[vi].cP();
-        feaNodes[vi] = fea::Node(p[0], p[1], p[2]);
-    }
-
-    return feaNodes;
-}
-
-std::vector<fea::BC> LinearSimulationModel::getFeaFixedNodes(
-    const std::shared_ptr<SimulationJob> &job)
-{
-    std::vector<fea::BC> boundaryConditions;
-    //        boundaryConditions.reserve(job->constrainedVertices.size() * 6
-    //                                   + job->nodalForcedDisplacements.size() * 3);
-    for (auto fixedVertex : job->constrainedVertices) {
-        const int vertexIndex = fixedVertex.first;
-        for (int dofIndex : fixedVertex.second) {
-            boundaryConditions.emplace_back(
-                fea::BC(vertexIndex, static_cast<fea::DOF>(dofIndex), 0));
-        }
-    }
-
-    for (auto forcedDisplacement : job->nodalForcedDisplacements) {
-        const int vi = forcedDisplacement.first;
-        for (int dofIndex = 0; dofIndex < 3; dofIndex++) {
-            boundaryConditions.emplace_back(
-                fea::BC(vi, static_cast<fea::DOF>(dofIndex), forcedDisplacement.second[dofIndex]));
-        }
-    }
-
-    return boundaryConditions;
-}
-
-std::vector<fea::Force> LinearSimulationModel::getFeaNodalForces(
-    const std::shared_ptr<SimulationJob> &job)
-{
-    std::vector<fea::Force> nodalForces;
-    nodalForces.reserve(job->nodalExternalForces.size() * 6);
-
-    for (auto nodalForce : job->nodalExternalForces) {
-        for (int dofIndex = 0; dofIndex < 6; dofIndex++) {
-            if (nodalForce.second[dofIndex] == 0) {
-                continue;
-            }
-            fea::Force f(nodalForce.first, dofIndex, nodalForce.second[dofIndex]);
-            nodalForces.emplace_back(f);
-        }
-    }
-
-    return nodalForces;
-}
-
-SimulationResults LinearSimulationModel::getResults(
-    const fea::Summary &feaSummary, const std::shared_ptr<SimulationJob> &simulationJob)
-{
-    SimulationResults results;
-    results.converged = feaSummary.converged;
-    if (!results.converged) {
-        return results;
-    }
-
-    results.executionTime = feaSummary.total_time_in_ms * 1000;
-    // displacements
-    results.displacements.resize(feaSummary.num_nodes);
-    results.rotationalDisplacementQuaternion.resize(feaSummary.num_nodes);
-    for (int vi = 0; vi < feaSummary.num_nodes; vi++) {
-        results.displacements[vi] = Vector6d(feaSummary.nodal_displacements[vi]);
-
-        const Vector6d &nodalDisplacement = results.displacements[vi];
-        Eigen::Quaternion<double> q_nx;
-        q_nx = Eigen::AngleAxis<double>(nodalDisplacement[3], Eigen::Vector3d(1, 0, 0));
-        Eigen::Quaternion<double> q_ny;
-        q_ny = Eigen::AngleAxis<double>(nodalDisplacement[4], Eigen::Vector3d(0, 1, 0));
-        Eigen::Quaternion<double> q_nz;
-        q_nz = Eigen::AngleAxis<double>(nodalDisplacement[5], Eigen::Vector3d(0, 0, 1));
-        results.rotationalDisplacementQuaternion[vi] = q_nx * q_ny * q_nz;
-    }
-    results.setLabelPrefix("Linear");
-
-    //  // Convert forces
-    //  // Convert to vector of eigen matrices of the form force component-> per
-    //  // Edge
-    //  const int numDof = 6;
-    //  const size_t numberOfEdges = feaSummary.element_forces.size();
-    //  edgeForces =
-    //      std::vector<Eigen::VectorXd>(numDof, Eigen::VectorXd(2 *
-    //      numberOfEdges));
-    //  for (gsl::index edgeIndex = 0; edgeIndex < numberOfEdges; edgeIndex++) {
-    //    for (gsl::index forceComponentIndex = 0; forceComponentIndex < numDof;
-    //         forceComponentIndex++) {
-    //      (edgeForces[forceComponentIndex])(2 * edgeIndex) =
-    //          feaSummary.element_forces[edgeIndex][forceComponentIndex];
-    //      (edgeForces[forceComponentIndex])(2 * edgeIndex + 1) =
-    //          feaSummary.element_forces[edgeIndex][numDof +
-    //          forceComponentIndex];
-    //    }
-    //  }
-
-    for (int ei = 0; ei < feaSummary.num_elems; ei++) {
-        const std::vector<double> &elementForces = feaSummary.element_forces[ei];
-        const Element &element = simulationJob->pMesh->elements[ei];
-        //Axial
-        const double elementPotentialEnergy_axial_v0 = std::pow(elementForces[0], 2)
-                                                       * element.initialLength
-                                                       / (4 * element.material.youngsModulus
-                                                          * element.dimensions.A);
-        const double elementPotentialEnergy_axial_v1 = std::pow(elementForces[6], 2)
-                                                       * element.initialLength
-                                                       / (4 * element.material.youngsModulus
-                                                          * element.dimensions.A);
-        const double elementPotentialEnergy_axial = elementPotentialEnergy_axial_v0
-                                                    + elementPotentialEnergy_axial_v1;
-        //Shear
-        const double elementPotentialEnergy_shearY_v0 = std::pow(elementForces[1], 2)
-                                                        * element.initialLength
-                                                        / (4 * element.dimensions.A
-                                                           * element.material.G);
-        const double elementPotentialEnergy_shearZ_v0 = std::pow(elementForces[2], 2)
-                                                        * element.initialLength
-                                                        / (4 * element.dimensions.A
-                                                           * element.material.G);
-        const double elementPotentialEnergy_shearY_v1 = std::pow(elementForces[7], 2)
-                                                        * element.initialLength
-                                                        / (4 * element.dimensions.A
-                                                           * element.material.G);
-        const double elementPotentialEnergy_shearZ_v1 = std::pow(elementForces[8], 2)
-                                                        * element.initialLength
-                                                        / (4 * element.dimensions.A
-                                                           * element.material.G);
-        const double elementPotentialEnergy_shear = elementPotentialEnergy_shearY_v0
-                                                    + elementPotentialEnergy_shearZ_v0
-                                                    + elementPotentialEnergy_shearY_v1
-                                                    + elementPotentialEnergy_shearZ_v1;
-        //Bending
-        const double elementPotentialEnergy_bendingY_v0 = std::pow(elementForces[4], 2)
-                                                          * element.initialLength
-                                                          / (4 * element.material.youngsModulus
-                                                             * element.dimensions.inertia.I2);
-        const double elementPotentialEnergy_bendingZ_v0 = std::pow(elementForces[5], 2)
-                                                          * element.initialLength
-                                                          / (4 * element.material.youngsModulus
-                                                             * element.dimensions.inertia.I3);
-        const double elementPotentialEnergy_bendingY_v1 = std::pow(elementForces[10], 2)
-                                                          * element.initialLength
-                                                          / (4 * element.material.youngsModulus
-                                                             * element.dimensions.inertia.I2);
-        const double elementPotentialEnergy_bendingZ_v1 = std::pow(elementForces[11], 2)
-                                                          * element.initialLength
-                                                          / (4 * element.material.youngsModulus
-                                                             * element.dimensions.inertia.I3);
-        const double elementPotentialEnergy_bending = elementPotentialEnergy_bendingY_v0
-                                                      + elementPotentialEnergy_bendingZ_v0
-                                                      + elementPotentialEnergy_bendingY_v1
-                                                      + elementPotentialEnergy_bendingZ_v1;
-        //Torsion
-        const double elementPotentialEnergy_torsion_v0 = std::pow(elementForces[3], 2)
-                                                         * element.initialLength
-                                                         / (4 * element.dimensions.inertia.J
-                                                            * element.material.G);
-        const double elementPotentialEnergy_torsion_v1 = std::pow(elementForces[9], 2)
-                                                         * element.initialLength
-                                                         / (4 * element.dimensions.inertia.J
-                                                            * element.material.G);
-        const double elementPotentialEnergy_torsion = elementPotentialEnergy_torsion_v0
-                                                      + elementPotentialEnergy_torsion_v1;
-        const double elementInternalPotentialEnergy = elementPotentialEnergy_axial
-                                                      + elementPotentialEnergy_shear
-                                                      + elementPotentialEnergy_bending
-                                                      + elementPotentialEnergy_torsion;
-        results.internalPotentialEnergy += elementInternalPotentialEnergy;
-    }
-    results.pJob = simulationJob;
-
-    return results;
-}
-
-SimulationResults LinearSimulationModel::executeSimulation(
-    const std::shared_ptr<SimulationJob> &pSimulationJob)
-{
-    assert(pSimulationJob->pMesh->VN() != 0);
-    const bool wasInitializedWithDifferentStructure = pSimulationJob->pMesh->EN()
-                                                          != simulator.structure.elems.size()
-                                                      || pSimulationJob->pMesh->VN()
-                                                             != simulator.structure.nodes.size();
-    if (!simulator.wasInitialized() || wasInitializedWithDifferentStructure) {
-        setStructure(pSimulationJob->pMesh);
-    }
-    //  printInfo(job);
-
-    // create the default options
-    fea::Options opts;
-    opts.save_elemental_forces = false;
-    opts.save_nodal_displacements = false;
-    opts.save_nodal_forces = false;
-    opts.save_report = false;
-    opts.save_tie_forces = false;
-    //  if (!elementalForcesOutputFilepath.empty()) {
-    //    opts.save_elemental_forces = true;
-    //    opts.elemental_forces_filename = elementalForcesOutputFilepath;
-    //  }
-    //  if (!nodalDisplacementsOutputFilepath.empty()) {
-    //    opts.save_nodal_displacements = true;
-    //    opts.nodal_displacements_filename = nodalDisplacementsOutputFilepath;
-    //  }
-
-    // have the program output status updates
-    opts.verbose = false;
-
-    // form an empty vector of ties
-    std::vector<fea::Tie> ties;
-
-    // also create an empty list of equations
-    std::vector<fea::Equation> equations;
-    auto fixedVertices = getFeaFixedNodes(pSimulationJob);
-    auto nodalForces = getFeaNodalForces(pSimulationJob);
-    fea::Summary feaResults = simulator.solve(fixedVertices, nodalForces, ties, equations, opts);
-
-    SimulationResults results = getResults(feaResults, pSimulationJob);
-    results.pJob = pSimulationJob;
-    return results;
-}
-
-void LinearSimulationModel::setStructure(const std::shared_ptr<SimulationMesh> &pMesh)
-{
-    fea::BeamStructure structure(getFeaNodes(pMesh), getFeaElements(pMesh));
-    simulator.initialize(structure);
-}
-
-void LinearSimulationModel::printInfo(const fea::BeamStructure &job)
-{
-    std::cout << "Details regarding the fea::Job:" << std::endl;
-    std::cout << "Nodes:" << std::endl;
-    for (fea::Node n : job.nodes) {
-        std::cout << n << std::endl;
-    }
-    std::cout << "Elements:" << std::endl;
-    for (Eigen::Vector2i e : job.elems) {
-        std::cout << e << std::endl;
-    }
-}

linearsimulationmodel.hpp

@@ -1,32 +0,0 @@
-#ifndef LINEARSIMULATIONMODEL_HPP
-#define LINEARSIMULATIONMODEL_HPP
-
-#include "simulationmodel.hpp"
-#include "threed_beam_fea.h"
-#include <filesystem>
-#include <vector>
-
-class LinearSimulationModel : public SimulationModel
-{
-public:
-    LinearSimulationModel(){
-
-    }
-    static std::vector<fea::Elem> getFeaElements(const std::shared_ptr<SimulationMesh> &pMesh);
-
-    static std::vector<fea::Node> getFeaNodes(const std::shared_ptr<SimulationMesh> &pMesh);
-    static std::vector<fea::BC> getFeaFixedNodes(const std::shared_ptr<SimulationJob> &job);
-
-    static std::vector<fea::Force> getFeaNodalForces(const std::shared_ptr<SimulationJob> &job);
-    static SimulationResults getResults(const fea::Summary &feaSummary,
-                                        const std::shared_ptr<SimulationJob> &simulationJob);
-
-    SimulationResults executeSimulation(const std::shared_ptr<SimulationJob> &simulationJob);
-    void setStructure(const std::shared_ptr<SimulationMesh> &pMesh);
-
-private:
-    fea::ThreedBeamFEA simulator;
-    static void printInfo(const fea::BeamStructure &job);
-};
-
-#endif // LINEARSIMULATIONMODEL_HPP

mesh.hpp

@@ -1,31 +0,0 @@
-#ifndef MESH_HPP
-#define MESH_HPP
-
-#include <filesystem>
-#include <string>
-
-class Mesh
-{
-protected:
-    std::string label{"empty_label"};
-
-public:
-  virtual ~Mesh() = default;
-  virtual bool load(const std::filesystem::path &meshFilePath) { return false; }
-  virtual bool save(const std::filesystem::path &meshFilePath) { return false; }
-
-  std::string getLabel() const;
-  void setLabel(const std::string &newLabel);
-  void prependToLabel(const std::string &text);
-};
-
-inline std::string Mesh::getLabel() const { return label; }
-
-inline void Mesh::setLabel(const std::string &newLabel) { label = newLabel; }
-
-inline void Mesh::prependToLabel(const std::string &text)
-{
-    label = text + label;
-}
-
-#endif // MESH_HPP

nlohmann/json_fwd.hpp

@@ -0,0 +1,175 @@
+//     __ _____ _____ _____
+//  __|  |   __|     |   | |  JSON for Modern C++
+// |  |  |__   |  |  | | | |  version 3.11.2
+// |_____|_____|_____|_|___|  https://github.com/nlohmann/json
+//
+// SPDX-FileCopyrightText: 2013-2022 Niels Lohmann <https://nlohmann.me>
+// SPDX-License-Identifier: MIT
+
+#ifndef INCLUDE_NLOHMANN_JSON_FWD_HPP_
+#define INCLUDE_NLOHMANN_JSON_FWD_HPP_
+
+#include <cstdint> // int64_t, uint64_t
+#include <map> // map
+#include <memory> // allocator
+#include <string> // string
+#include <vector> // vector
+
+// #include <nlohmann/detail/abi_macros.hpp>
+//     __ _____ _____ _____
+//  __|  |   __|     |   | |  JSON for Modern C++
+// |  |  |__   |  |  | | | |  version 3.11.2
+// |_____|_____|_____|_|___|  https://github.com/nlohmann/json
+//
+// SPDX-FileCopyrightText: 2013-2022 Niels Lohmann <https://nlohmann.me>
+// SPDX-License-Identifier: MIT
+
+
+
+// This file contains all macro definitions affecting or depending on the ABI
+
+#ifndef JSON_SKIP_LIBRARY_VERSION_CHECK
+    #if defined(NLOHMANN_JSON_VERSION_MAJOR) && defined(NLOHMANN_JSON_VERSION_MINOR) && defined(NLOHMANN_JSON_VERSION_PATCH)
+        #if NLOHMANN_JSON_VERSION_MAJOR != 3 || NLOHMANN_JSON_VERSION_MINOR != 11 || NLOHMANN_JSON_VERSION_PATCH != 2
+            #warning "Already included a different version of the library!"
+        #endif
+    #endif
+#endif
+
+#define NLOHMANN_JSON_VERSION_MAJOR 3   // NOLINT(modernize-macro-to-enum)
+#define NLOHMANN_JSON_VERSION_MINOR 11  // NOLINT(modernize-macro-to-enum)
+#define NLOHMANN_JSON_VERSION_PATCH 2   // NOLINT(modernize-macro-to-enum)
+
+#ifndef JSON_DIAGNOSTICS
+    #define JSON_DIAGNOSTICS 0
+#endif
+
+#ifndef JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON
+    #define JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON 0
+#endif
+
+#if JSON_DIAGNOSTICS
+    #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS _diag
+#else
+    #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS
+#endif
+
+#if JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON
+    #define NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON _ldvcmp
+#else
+    #define NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON
+#endif
+
+#ifndef NLOHMANN_JSON_NAMESPACE_NO_VERSION
+    #define NLOHMANN_JSON_NAMESPACE_NO_VERSION 0
+#endif
+
+// Construct the namespace ABI tags component
+#define NLOHMANN_JSON_ABI_TAGS_CONCAT_EX(a, b) json_abi ## a ## b
+#define NLOHMANN_JSON_ABI_TAGS_CONCAT(a, b) \
+    NLOHMANN_JSON_ABI_TAGS_CONCAT_EX(a, b)
+
+#define NLOHMANN_JSON_ABI_TAGS                                       \
+    NLOHMANN_JSON_ABI_TAGS_CONCAT(                                   \
+            NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS,                       \
+            NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON)
+
+// Construct the namespace version component
+#define NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT_EX(major, minor, patch) \
+    _v ## major ## _ ## minor ## _ ## patch
+#define NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT(major, minor, patch) \
+    NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT_EX(major, minor, patch)
+
+#if NLOHMANN_JSON_NAMESPACE_NO_VERSION
+#define NLOHMANN_JSON_NAMESPACE_VERSION
+#else
+#define NLOHMANN_JSON_NAMESPACE_VERSION                                 \
+    NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT(NLOHMANN_JSON_VERSION_MAJOR, \
+                                           NLOHMANN_JSON_VERSION_MINOR, \
+                                           NLOHMANN_JSON_VERSION_PATCH)
+#endif
+
+// Combine namespace components
+#define NLOHMANN_JSON_NAMESPACE_CONCAT_EX(a, b) a ## b
+#define NLOHMANN_JSON_NAMESPACE_CONCAT(a, b) \
+    NLOHMANN_JSON_NAMESPACE_CONCAT_EX(a, b)
+
+#ifndef NLOHMANN_JSON_NAMESPACE
+#define NLOHMANN_JSON_NAMESPACE               \
+    nlohmann::NLOHMANN_JSON_NAMESPACE_CONCAT( \
+            NLOHMANN_JSON_ABI_TAGS,           \
+            NLOHMANN_JSON_NAMESPACE_VERSION)
+#endif
+
+#ifndef NLOHMANN_JSON_NAMESPACE_BEGIN
+#define NLOHMANN_JSON_NAMESPACE_BEGIN                \
+    namespace nlohmann                               \
+    {                                                \
+    inline namespace NLOHMANN_JSON_NAMESPACE_CONCAT( \
+                NLOHMANN_JSON_ABI_TAGS,              \
+                NLOHMANN_JSON_NAMESPACE_VERSION)     \
+    {
+#endif
+
+#ifndef NLOHMANN_JSON_NAMESPACE_END
+#define NLOHMANN_JSON_NAMESPACE_END                                     \
+    }  /* namespace (inline namespace) NOLINT(readability/namespace) */ \
+    }  // namespace nlohmann
+#endif
+
+
+/*!
+@brief namespace for Niels Lohmann
+@see https://github.com/nlohmann
+@since version 1.0.0
+*/
+NLOHMANN_JSON_NAMESPACE_BEGIN
+
+/*!
+@brief default JSONSerializer template argument
+
+This serializer ignores the template arguments and uses ADL
+([argument-dependent lookup](https://en.cppreference.com/w/cpp/language/adl))
+for serialization.
+*/
+template<typename T = void, typename SFINAE = void>
+struct adl_serializer;
+
+/// a class to store JSON values
+/// @sa https://json.nlohmann.me/api/basic_json/
+template<template<typename U, typename V, typename... Args> class ObjectType =
+         std::map,
+         template<typename U, typename... Args> class ArrayType = std::vector,
+         class StringType = std::string, class BooleanType = bool,
+         class NumberIntegerType = std::int64_t,
+         class NumberUnsignedType = std::uint64_t,
+         class NumberFloatType = double,
+         template<typename U> class AllocatorType = std::allocator,
+         template<typename T, typename SFINAE = void> class JSONSerializer =
+         adl_serializer,
+         class BinaryType = std::vector<std::uint8_t>>
+class basic_json;
+
+/// @brief JSON Pointer defines a string syntax for identifying a specific value within a JSON document
+/// @sa https://json.nlohmann.me/api/json_pointer/
+template<typename RefStringType>
+class json_pointer;
+
+/*!
+@brief default specialization
+@sa https://json.nlohmann.me/api/json/
+*/
+using json = basic_json<>;
+
+/// @brief a minimal map-like container that preserves insertion order
+/// @sa https://json.nlohmann.me/api/ordered_map/
+template<class Key, class T, class IgnoredLess, class Allocator>
+struct ordered_map;
+
+/// @brief specialization that maintains the insertion order of object keys
+/// @sa https://json.nlohmann.me/api/ordered_json/
+using ordered_json = basic_json<nlohmann::ordered_map>;
+
+NLOHMANN_JSON_NAMESPACE_END
+
+#endif  // INCLUDE_NLOHMANN_JSON_FWD_HPP_

polymesh.hpp

@@ -1,296 +0,0 @@
-#ifndef POLYMESH_HPP
-#define POLYMESH_HPP
-#include "mesh.hpp"
-#include "vcg/complex/complex.h"
-#include <filesystem>
-#include <wrap/io_trimesh/export_obj.h>
-#include <wrap/io_trimesh/export_ply.h>
-#include <wrap/io_trimesh/import.h>
-
-#ifdef POLYSCOPE_DEFINED
-#include <polyscope/surface_mesh.h>
-#endif
-class PFace;
-class PVertex;
-class PEdge;
-
-struct PUsedTypes : public vcg::UsedTypes<vcg::Use<PVertex>::AsVertexType,
-                                          vcg::Use<PFace>::AsFaceType,
-                                          vcg::Use<PEdge>::AsEdgeType>
-{};
-
-class PVertex : public vcg::Vertex<PUsedTypes,
-                                   vcg::vertex::Coord3d,
-                                   vcg::vertex::Normal3d,
-                                   vcg::vertex::Mark,
-                                   vcg::vertex::Qualityf,
-                                   vcg::vertex::BitFlags,
-                                   vcg::vertex::VFAdj,
-                                   vcg::vertex::VEAdj>
-{};
-class PEdge : public vcg::Edge<PUsedTypes,
-                               vcg::edge::VertexRef,
-                               vcg::edge::BitFlags,
-                               vcg::edge::EEAdj,
-                               vcg::edge::EFAdj,
-                               vcg::edge::VEAdj,
-                               vcg::edge::EVAdj>
-{};
-
-class PFace : public vcg::Face<PUsedTypes,
-                               vcg::face::PolyInfo // this is necessary  if you use component in
-                                                   // vcg/simplex/face/component_polygon.h
-                               // It says "this class is a polygon and the memory for its components
-                               // (e.g. pointer to its vertices will be allocated dynamically")
-                               ,
-                               //                               vcg::face::FHAdj,
-                               vcg::face::PVFAdj,
-                               vcg::face::PFEAdj,
-                               vcg::face::PFVAdj,
-                               vcg::face::PVFAdj,
-                               //                               vcg::face::PVFAdj,
-                               vcg::face::PFFAdj // Pointer to edge-adjacent face (just like FFAdj )
-                               ,
-                               vcg::face::BitFlags // bit flags
-                               ,
-                               vcg::face::Qualityf // quality
-                               ,
-                               vcg::face::Normal3f // normal
-                               ,
-                               vcg::face::Color4b>
-{};
-
-class VCGPolyMesh
-    : public vcg::tri::TriMesh<std::vector<PVertex>, std::vector<PFace>, std::vector<PEdge>>,
-      public Mesh
-{
-public:
-    virtual bool load(const std::filesystem::__cxx11::path &meshFilePath) override
-    {
-        int mask;
-        vcg::tri::io::Importer<VCGPolyMesh>::LoadMask(meshFilePath.c_str(), mask);
-        int error = vcg::tri::io::Importer<VCGPolyMesh>::Open(*this, meshFilePath.c_str(), mask);
-        if (error != 0) {
-            std::cerr << "Could not load polygonal mesh:" << meshFilePath << std::endl;
-            return false;
-        }
-
-        vcg::tri::UpdateTopology<VCGPolyMesh>::FaceFace(*this);
-        vcg::tri::UpdateTopology<VCGPolyMesh>::VertexEdge(*this);
-        vcg::tri::UpdateTopology<VCGPolyMesh>::VertexFace(*this);
-        vcg::tri::UpdateNormal<VCGPolyMesh>::PerVertexNormalized(*this);
-        vcg::tri::Clean<VCGPolyMesh>::RemoveUnreferencedVertex(*this);
-        //finally remove valence 1 vertices on the border
-        //        vcg::PolygonalAlgorithm<PolyMeshType>::RemoveValence2Vertices(dual);
-        return true;
-    }
-    //    //    vcg::tri::io::ImporterOBJ<VCGPolyMesh>::Open();
-    //    //    unsigned int mask = 0;
-    //    //    mask |= nanoply::NanoPlyWrapper<VCGPolyMesh>::IO_VERTCOORD;
-    //    //    mask |= nanoply::NanoPlyWrapper<VCGPolyMesh>::IO_VERTNORMAL;
-    //    //    mask |= nanoply::NanoPlyWrapper<VCGPolyMesh>::IO_VERTCOLOR;
-    //    //    mask |= nanoply::NanoPlyWrapper<VCGPolyMesh>::IO_EDGEINDEX;
-    //    //    mask |= nanoply::NanoPlyWrapper<VCGPolyMesh>::IO_FACEINDEX;
-    //    //    if (nanoply::NanoPlyWrapper<VCGPolyMesh>::LoadModel(
-    //    //            std::filesystem::absolute(filename).c_str(), *this, mask) !=
-    //    //            0) {
-    //    //      std::cout << "Could not load tri mesh" << std::endl;
-    //    //    }
-    //  }
-    Eigen::MatrixX3d getVertices() const
-    {
-        Eigen::MatrixX3d vertices(VN(), 3);
-        for (size_t vi = 0; vi < VN(); vi++) {
-            VCGPolyMesh::CoordType vertexCoordinates = vert[vi].cP();
-            vertices.row(vi) = vertexCoordinates.ToEigenVector<Eigen::Vector3d>();
-        }
-        return vertices;
-    }
-  std::vector<std::vector<int>> getFaces() const
-  {
-      std::vector<std::vector<int>> faces(FN());
-      for (const VCGPolyMesh::FaceType &f : this->face) {
-          const int fi = vcg::tri::Index<VCGPolyMesh>(*this, f);
-          for (size_t vi = 0; vi < f.VN(); vi++) {
-              const size_t viGlobal = vcg::tri::Index<VCGPolyMesh>(*this, f.cV(vi));
-              faces[fi].push_back(viGlobal);
-          }
-      }
-
-      return faces;
-  }
-
-  //  bool load(const std::filesystem::__cxx11::path &meshFilePath)
-  //  {
-  //      const std::string extension = ".ply";
-  //      std::filesystem::path filePath = meshFilePath;
-  //      assert(std::filesystem::path(filePath).extension().string() == extension);
-  //      unsigned int mask = 0;
-  //      mask |= vcg::tri::io::Mask::IOM_VERTCOORD;
-  //      mask |= vcg::tri::io::Mask::IOM_VERTNORMAL;
-  //      mask |= vcg::tri::io::Mask::IOM_FACEINDEX;
-  //      mask |= vcg::tri::io::Mask::IOM_FACECOLOR;
-  //      if (vcg::tri::io::Importer<VCGPolyMesh>::Open(*this, filePath.c_str()) != 0) {
-  //          return false;
-  //      }
-  //      label = meshFilePath.filename();
-  //      return true;
-  //  }
-
-  bool save(const std::filesystem::__cxx11::path &meshFilePath = std::filesystem::path())
-  {
-      if (meshFilePath.extension() == ".obj") {
-          return saveOBJ(meshFilePath);
-      } else if (meshFilePath.extension() == ".ply") {
-          return savePLY(meshFilePath);
-      }
-
-      return false;
-  }
-
-  bool saveOBJ(const std::filesystem::path &objFilePath = std::filesystem::path())
-  {
-      const std::string extension = ".obj";
-      std::filesystem::path filePath = objFilePath;
-      if (filePath.empty()) {
-          filePath = std::filesystem::current_path().append(getLabel() + extension).string();
-      } else if (std::filesystem::is_directory(std::filesystem::path(objFilePath))) {
-          filePath = std::filesystem::path(objFilePath).append(getLabel() + extension).string();
-      }
-      assert(std::filesystem::path(filePath).extension().string() == extension);
-      unsigned int mask = 0;
-      mask |= vcg::tri::io::Mask::IOM_VERTCOORD;
-      mask |= vcg::tri::io::Mask::IOM_VERTNORMAL;
-      mask |= vcg::tri::io::Mask::IOM_FACEINDEX;
-      mask |= vcg::tri::io::Mask::IOM_FACECOLOR;
-      if (vcg::tri::io::ExporterOBJ<VCGPolyMesh>::Save(*this, filePath.string().c_str(), mask) != 0) {
-          return false;
-      }
-      return true;
-  }
-
-  bool savePLY(const std::filesystem::path &objFilePath = std::filesystem::path())
-  {
-      const std::string extension = ".ply";
-      std::filesystem::path filePath = objFilePath;
-      if (filePath.empty()) {
-          filePath = std::filesystem::current_path().append(getLabel() + extension).string();
-      } else if (std::filesystem::is_directory(std::filesystem::path(objFilePath))) {
-          filePath = std::filesystem::path(objFilePath).append(getLabel() + extension).string();
-      }
-      assert(std::filesystem::path(filePath).extension().string() == extension);
-      unsigned int mask = 0;
-      mask |= vcg::tri::io::Mask::IOM_VERTCOORD;
-      mask |= vcg::tri::io::Mask::IOM_VERTNORMAL;
-      mask |= vcg::tri::io::Mask::IOM_FACEINDEX;
-      mask |= vcg::tri::io::Mask::IOM_FACECOLOR;
-      if (vcg::tri::io::ExporterPLY<VCGPolyMesh>::Save(*this, filePath.string().c_str(), mask, false) != 0) {
-          return false;
-      }
-      return true;
-  }
-
-#ifdef POLYSCOPE_DEFINED
-  polyscope::SurfaceMesh *registerForDrawing(
-      const std::optional<std::array<double, 3>> &desiredColor = std::nullopt,
-      const bool &shouldEnable = true)
-  {
-      auto vertices = getVertices();
-      auto faces = getFaces();
-      PolyscopeInterface::init();
-
-      polyscope::SurfaceMesh *polyscopeHandle_mesh = polyscope::registerSurfaceMesh(label,
-                                                                                    vertices,
-                                                                                    faces);
-
-      const double drawingRadius = 0.002;
-      polyscopeHandle_mesh->setEnabled(shouldEnable);
-      polyscopeHandle_mesh->setEdgeWidth(drawingRadius);
-
-      if (desiredColor.has_value()) {
-          const glm::vec3 desiredColor_glm(desiredColor.value()[0],
-                                           desiredColor.value()[1],
-                                           desiredColor.value()[2]);
-          polyscopeHandle_mesh->setSurfaceColor(glm::normalize(desiredColor_glm));
-      }
-
-      return polyscopeHandle_mesh;
-  }
-#endif
-  void moveToCenter()
-  {
-      CoordType centerOfMass(0, 0, 0);
-
-      for (int vi = 0; vi < VN(); vi++) {
-          centerOfMass += vert[vi].cP();
-      }
-      centerOfMass /= VN();
-      vcg::tri::UpdatePosition<VCGPolyMesh>::Translate(*this, -centerOfMass);
-  }
-
-  /*
-   * Returns the average distance from the center of each edge to the center of its face over the whole mesh
-   * */
-  double getAverageFaceRadius() const
-  {
-      double averageFaceRadius = 0;
-      for (int fi = 0; fi < FN(); fi++) {
-          const VCGPolyMesh::FaceType &f = face[fi];
-          CoordType centerOfFace(0, 0, 0);
-          for (int vi = 0; vi < f.VN(); vi++) {
-              centerOfFace = centerOfFace + f.cP(vi);
-          }
-          centerOfFace /= f.VN();
-
-          double faceRadius = 0;
-          //                    for (int face_ei = 0; face_ei < f.EN(); face_ei++) {
-          //          std::cout << "fi:" << getIndex(f) << std::endl;
-          //          auto vps = f.FVp(0);
-          //          auto vpe = vps;
-          for (int i = 0; i < f.VN(); i++) {
-              faceRadius += vcg::Distance(centerOfFace, (f.cP0(i) + f.cP1(i)) / 2);
-          }
-
-          //          }
-          const int faceEdges = f.VN(); //NOTE: When does this not hold?
-          faceRadius /= faceEdges;
-          averageFaceRadius += faceRadius;
-      }
-      averageFaceRadius /= FN();
-      return averageFaceRadius;
-  }
-
-  bool copy(VCGPolyMesh &copyFrom)
-  {
-      vcg::tri::Append<VCGPolyMesh, VCGPolyMesh>::MeshCopy(*this, copyFrom);
-      label = copyFrom.getLabel();
-      //  eigenEdges = mesh.getEigenEdges();
-      //  if (eigenEdges.rows() == 0) {
-      //    getEdges(eigenEdges);
-      //  }
-      //  eigenVertices = mesh.getEigenVertices();
-      //  if (eigenVertices.rows() == 0) {
-      //    getVertices();
-      //  }
-      vcg::tri::UpdateTopology<VCGPolyMesh>::VertexEdge(*this);
-      vcg::tri::UpdateTopology<VCGPolyMesh>::VertexFace(*this);
-      vcg::tri::UpdateTopology<VCGPolyMesh>::FaceFace(*this);
-      vcg::tri::UpdateTopology<VCGPolyMesh>::AllocateEdge(*this);
-      vcg::tri::UpdateTopology<VCGPolyMesh>::EdgeEdge(*this);
-      //      vcg::tri::UpdateTopology<VCGPolyMesh>::VertexFace(*this);
-
-      return true;
-  }
-
-  VCGPolyMesh(VCGPolyMesh &copyFrom) { copy(copyFrom); }
-  VCGPolyMesh() {}
-  template<typename MeshElement>
-  size_t getIndex(const MeshElement &meshElement) const
-  {
-      return vcg::tri::Index<VCGPolyMesh>(*this, meshElement);
-  }
-};
-
-using ConstVCGPolyMesh = VCGPolyMesh;
-
-#endif // POLYMESH_HPP

reducedmodel.cpp

@@ -0,0 +1,94 @@
+#include "reducedmodel.hpp"
+
+ReducedModel::ReducedModel() : PatternGeometry({1, 0, 0, 2, 1, 2, 1}, {{0, 3}})
+
+{
+    interfaceNodeIndex = 3;
+    label = "ReducedModel";
+    //    constexpr double initialHexSize = 0.3;
+    //    CoordType movableVertex_barycentric(1 - initialHexSize, initialHexSize / 2, initialHexSize / 2);
+    //    const vcg::Triangle3<double> &baseTriangle = getBaseTriangle();
+    //    vert[0].P() = baseTriangle.cP(0) * movableVertex_barycentric[0]
+    //                  + baseTriangle.cP(1) * movableVertex_barycentric[1]
+    //                  + baseTriangle.cP(2) * movableVertex_barycentric[2];
+}
+
+void ReducedModel::updateBaseTriangleGeometry_theta(const double &newTheta_deg)
+{
+    const CoordType baseTriangleHexagonVertexPosition = vert[0].cP();
+
+    const CoordType thetaRotatedHexagonBaseTriangleVertexPosition
+        = vcg::RotationMatrix(PatternGeometry::DefaultNormal, vcg::math::ToRad(newTheta_deg))
+          * baseTriangleHexagonVertexPosition;
+    vert[0].P() = thetaRotatedHexagonBaseTriangleVertexPosition;
+
+    //    constexpr int fanSize = 6;
+    //    for (int rotationCounter = 0; rotationCounter < /*ReducedModelOptimizer::*/ fanSize;
+    //         rotationCounter++) {
+    //        vert[2 * rotationCounter].P() = vcg::RotationMatrix(PatternGeometry::DefaultNormal,
+    //                                                            vcg::math::ToRad(60.0 * rotationCounter))
+    //                                        * thetaRotatedHexagonBaseTriangleVertexPosition;
+    //    }
+    updateEigenEdgeAndVertices();
+}
+
+void ReducedModel::updateBaseTriangleGeometry_R(const double &newR)
+{
+    const CoordType barycentricCoordinates_hexagonBaseTriangleVertex(1 - newR, newR / 2, newR / 2);
+    const vcg::Triangle3<double> &baseTriangle = getBaseTriangle();
+    const CoordType hexagonBaseTriangleVertexPosition
+        = baseTriangle.cP(0) * barycentricCoordinates_hexagonBaseTriangleVertex[0]
+          + baseTriangle.cP(1) * barycentricCoordinates_hexagonBaseTriangleVertex[1]
+          + baseTriangle.cP(2) * barycentricCoordinates_hexagonBaseTriangleVertex[2];
+    vert[0].P() = hexagonBaseTriangleVertexPosition;
+
+    //    constexpr int fanSize = 6;
+    //    for (int rotationCounter = 0; rotationCounter < /*ReducedModelOptimizer::*/ fanSize;
+    //         rotationCounter++) {
+    //        vert[2 * rotationCounter].P() = vcg::RotationMatrix(PatternGeometry::DefaultNormal,
+    //                                                            vcg::math::ToRad(60.0 * rotationCounter))
+    //                                        * hexagonBaseTriangleVertexPosition;
+    //        //        std::cout << vert[2 * rotationCounter].P()[0] << " " << vert[2 * rotationCounter].P()[1]
+    //        //                  << " " << vert[2 * rotationCounter].P()[2] << std::endl;
+    //    }
+    updateEigenEdgeAndVertices();
+}
+
+void ReducedModel::updateBaseTriangleGeometry_theta(
+    const double &newTheta_deg, std::shared_ptr<VCGEdgeMesh> &pReducedModel_edgeMesh)
+{
+    std::dynamic_pointer_cast<ReducedModel>(pReducedModel_edgeMesh)
+        ->updateBaseTriangleGeometry_theta(newTheta_deg);
+}
+
+void ReducedModel::updateBaseTriangleGeometry_R(const double &newR,
+                                                std::shared_ptr<VCGEdgeMesh> &pReducedModel_edgeMesh)
+{
+    std::dynamic_pointer_cast<ReducedModel>(pReducedModel_edgeMesh)
+        ->updateBaseTriangleGeometry_R(newR);
+}
+
+void ReducedModel::createFan(const size_t &fanSize)
+{
+    deleteDanglingVertices();
+    PatternGeometry rotatedPattern;
+    vcg::tri::Append<PatternGeometry, PatternGeometry>::MeshCopy(rotatedPattern, *this);
+    for (int rotationCounter = 1; rotationCounter < fanSize; rotationCounter++) {
+        vcg::Matrix44d R;
+        auto rotationAxis = PatternGeometry::DefaultNormal;
+        R.SetRotateDeg(360.0 / fanSize, rotationAxis);
+        vcg::tri::UpdatePosition<PatternGeometry>::Matrix(rotatedPattern, R);
+        vcg::tri::Append<PatternGeometry, PatternGeometry>::Mesh(*this, rotatedPattern);
+        //For the reduced model we also need to connect to neighbouring base triangles of the fan
+        if (rotationCounter == fanSize - 1) {
+            vcg::tri::Allocator<PatternGeometry>::AddEdge(*this,
+                                                          0,
+                                                          this->VN() - rotatedPattern.VN());
+        }
+        vcg::tri::Allocator<PatternGeometry>::AddEdge(*this,
+                                                      this->VN() - 2 * rotatedPattern.VN(),
+                                                      this->VN() - rotatedPattern.VN());
+        removeDuplicateVertices();
+        updateEigenEdgeAndVertices();
+    }
+}

reducedmodel.hpp

@@ -0,0 +1,20 @@
+#ifndef REDUCEDMODEL_HPP
+#define REDUCEDMODEL_HPP
+
+#include "trianglepatterngeometry.hpp"
+
+class ReducedModel : public PatternGeometry
+{
+
+public:
+    ReducedModel();
+    void updateBaseTriangleGeometry_theta(const double &newTheta_deg);
+    void updateBaseTriangleGeometry_R(const double &newR);
+    static void updateBaseTriangleGeometry_theta(
+        const double &newTheta_deg, std::shared_ptr<VCGEdgeMesh> &pReducedModel_edgeMesh);
+    static void updateBaseTriangleGeometry_R(const double &newR,
+                                             std::shared_ptr<VCGEdgeMesh> &pReducedModel_edgeMesh);
+    void createFan(const size_t &fanSize = 6) override;
+};
+
+#endif // REDUCEDMODEL_HPP

reducedmodelevaluator.hpp

@@ -2,13 +2,250 @@
 #define REDUCEDMODELEVALUATOR_HPP
 
 #include "reducedmodeloptimizer_structs.hpp"
+#include "utilities.hpp"
 
-class ReducedModelEvaluator
-{
-public:
-    ReducedModelEvaluator();
-    static std::vector<double> evaluateReducedModel(
-        ReducedModelOptimization::Results &optimizationResults);
+class ReducedModelEvaluator {
+ public:
+  enum CSVExportingDirection { Vertical = 0, Horizontal };
+  enum CSVExportingData {
+    raw_drm2Reduced = 0,
+    norm_groundTruth2Reduced,
+    raw_and_norm_drm2Reduced,
+    NumberOfDataTypes
+  };
+  inline static std::array<std::string, NumberOfDataTypes>
+      csvExportingDataStrings{"raw_drm2Reduced", "norm_drm2Reduced",
+                              "raw_and_norm_drm2Reduced"};
+  struct ExportingSettings {
+    // exporting settings
+    CSVExportingDirection direction{Horizontal};
+    CSVExportingData data{norm_groundTruth2Reduced};
+    bool shouldWriteHeader{true};
+    std::string resultsLabel;
+  };
+
+  struct Settings {
+#ifdef POLYSCOPE_DEFINED
+    bool shouldDraw{false};
+#endif
+    bool shouldRecomputeGroundTruthResults{false};
+    bool beVerbose{true};
+    NLOHMANN_DEFINE_TYPE_INTRUSIVE(
+        Settings,
+        shouldRecomputeGroundTruthResults,
+        beVerbose
+        //#ifdef POLYSCOPE_DEFINED
+        //                                   ,
+        //                                   shouldDraw
+
+        //#endif
+    )
+    bool save(const std::filesystem::path& jsonFilePath) const;
+    bool load(const std::filesystem::path& jsonFilePath);
+    std::string toString() const {
+      nlohmann::json json = *this;
+      return std::string("Reduced model evaluation settings:" + json.dump());
+    }
+  };
+
+  inline static constexpr int NumberOfEvaluationScenarios = 17;
+  inline static const std::array<std::string, NumberOfEvaluationScenarios>
+      scenariosTestSetLabels{
+          "22Hex_randomBending0",
+          "22Hex_randomBending1",
+          "22Hex_randomBending2",
+          "22Hex_randomBending4",
+          "22Hex_randomBending5",
+          "22Hex_randomBending8",
+          "22Hex_randomBending9",
+          "22Hex_randomBending11",
+          "22Hex_randomBending12",
+          "22Hex_randomBending16",
+          "22Hex_randomBending17",
+          "22Hex_randomBending18",
+          "22Hex_randomBending19",
+          "22Hex_bending_0.01N",
+          "22Hex_pullOppositeVerts_0.05N",
+          "22Hex_cylinder_0.1N",
+          "22Hex_s_0.05N",
+      };
+  inline static constexpr double forceScalingFactor = 1.5;
+  struct Results {
+    std::array<double, NumberOfEvaluationScenarios> distances_drm2reduced;
+    std::array<double, NumberOfEvaluationScenarios>
+        distances_normalizedGroundTruth2reduced;
+    std::array<std::string, NumberOfEvaluationScenarios>
+        evaluationScenarioLabels;
+    std::array<double, NumberOfEvaluationScenarios> maxDisplacements;
+
+    NLOHMANN_DEFINE_TYPE_INTRUSIVE_WITH_DEFAULT(Results,
+                                                evaluationScenarioLabels,
+                                                maxDisplacements)
+
+    inline static std::string defaultFileName{"evaluationResults.json"};
+    void save(const std::filesystem::path& saveToPath) {
+      assert(std::filesystem::is_directory(saveToPath));
+      nlohmann::json json = *this;
+      std::filesystem::path jsonFilePath(
+          std::filesystem::path(saveToPath).append(defaultFileName));
+      std::ofstream jsonFile(jsonFilePath.string());
+      jsonFile << json;
+      jsonFile.close();
+    }
+  };
+  ReducedModelEvaluator();
+  Results evaluateReducedModel(
+      ReducedModelOptimization::Results& optimizationResult,
+      const std::filesystem::path& scenariosDirectoryPath,
+      //        const std::filesystem::path &reducedPatternFilePath,
+      const std::filesystem::path& fullPatternTessellatedResultsDirectoryPath,
+      const ReducedModelEvaluator::Settings& settings);
+  Results evaluateReducedModel(
+      ReducedModelOptimization::Results& optimizationResult,
+      const Settings& settings);
+  static void printResultsVertically(
+      const ReducedModelEvaluator::Results& evaluationResults,
+      CSVFile& csvOutput);
+  static void printResults(
+      const ReducedModelEvaluator::Results& evaluationResults,
+      const std::string& resultsLabel);
+  static void printResultsHorizontally(const Results& evaluationResults,
+                                       CSVFile& csvOutput);
+  static void printResults(const Results& evaluationResults,
+                           const ExportingSettings& exportingSettings,
+                           CSVFile& csvOutput);
+  static void printHeader(const ExportingSettings& exportingSettings,
+                          CSVFile& csvOutput);
+  //    static double evaluateOptimizationSettings(
+  //        const ReducedModelOptimization::Settings &optimizationSettings,
+  //        const std::vector<std::shared_ptr<PatternGeometry>> &pPatterns,
+  //        std::vector<ReducedModelEvaluator::Results>
+  //        &patternEvaluationResults);
+  std::shared_ptr<VCGPolyMesh> pTileIntoSurface;
+  ReducedModelOptimization::Colors::RGBColor color_tesselatedPatterns{
+      24.0 / 255, 23.0 / 255, 23.0 / 255};
+  ReducedModelOptimization::Colors::RGBColor color_tesselatedReducedModels{
+      67.0 / 255, 160.00 / 255, 232.0 / 255};
+  ReducedModelOptimization::Colors::RGBColor color_tileIntoSurface{
+      //      222 / 255.0, 235 / 255.0, 255 / 255.0};
+      156 / 255.0, 195 / 255.0, 254 / 255.0};
+  ReducedModelOptimization::Colors::RGBColor interfaceNodes_color{
+      63.0 / 255, 85.0 / 255, 42.0 / 255};
+  inline static constexpr char* tileIntoSurfaceFileContent = R"~(OFF
+46 66 0
+-0.0745923 0.03573945 0 
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+-0.1102588 0.09807601 0 
+3 0 1 2 
+3 3 1 0 
+3 4 2 1 
+3 5 0 2 
+3 3 6 1 
+3 3 0 7 
+3 8 2 4 
+3 5 9 0 
+3 10 5 2 
+3 3 11 6 
+3 7 0 9 
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+3 10 2 8 
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+3 10 14 5 
+3 12 11 3 
+3 7 9 15 
+3 12 7 16 
+3 10 8 17 
+3 14 13 5 
+3 18 9 13 
+3 19 14 10 
+3 12 20 11 
+3 18 15 9 
+3 16 7 15 
+3 21 12 16 
+3 22 17 8 
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+3 18 13 24 
+3 19 25 14 
+3 21 20 12 
+3 26 11 20 
+3 18 27 15 
+3 16 15 28 
+3 21 16 29 
+3 23 24 13 
+3 23 14 25 
+3 30 18 24 
+3 30 27 18 
+3 15 27 28 
+3 29 16 28 
+3 23 31 24 
+3 23 25 32 
+3 30 24 33 
+3 30 34 27 
+3 35 28 27 
+3 29 28 36 
+3 23 32 31 
+3 24 31 33 
+3 30 33 37 
+3 30 37 34 
+3 35 27 34 
+3 35 36 28 
+3 32 38 31 
+3 33 31 39 
+3 40 37 33 
+3 34 37 41 
+3 35 34 42 
+3 35 43 36 
+3 38 39 31 
+3 40 33 39 
+3 34 41 42 
+3 35 42 43 
+3 44 39 38 
+3 45 43 42 
+)~";
 };
 
-#endif // REDUCEDMODELEVALUATOR_HPP
+#endif  // REDUCEDMODELEVALUATOR_HPP

reducedmodeloptimizer.hpp

@@ -0,0 +1,417 @@
+#ifndef REDUCEDMODELOPTIMIZER_HPP
+#define REDUCEDMODELOPTIMIZER_HPP
+
+//#include "csvfile.hpp"
+#include "drmsimulationmodel.hpp"
+#include "edgemesh.hpp"
+#include "linearsimulationmodel.hpp"
+#ifdef POLYSCOPE_DEFINED
+#include "matplot/matplot.h"
+#endif
+#include <Eigen/Dense>
+#include "reducedmodel.hpp"
+#include "reducedmodeloptimizer_structs.hpp"
+#include "simulationmesh.hpp"
+#ifdef DLIB_DEFINED
+#include <dlib/global_optimization.h>
+#include <dlib/optimization.h>
+#endif
+
+#ifdef POLYSCOPE_DEFINED
+#include "polyscope/color_management.h"
+#endif  // POLYSCOPE_DEFINED
+using PatternVertexIndex = VertexIndex;
+using ReducedModelVertexIndex = VertexIndex;
+
+class ReducedModelOptimizer {
+ public:
+  struct OptimizationState {
+    std::vector<SimulationResults> fullPatternResults;
+    std::vector<double> translationalDisplacementNormalizationValues;
+    std::vector<double> rotationalDisplacementNormalizationValues;
+    std::vector<std::shared_ptr<SimulationJob>> pSimulationJobs_pattern;
+    std::vector<std::shared_ptr<SimulationJob>> simulationJobs_reducedModel;
+    std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>
+        reducedToFullInterfaceViMap;
+    std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>
+        fullPatternOppositeInterfaceViPairs;
+    matplot::line_handle gPlotHandle;
+    std::vector<size_t> objectiveValueHistory_iteration;
+    std::vector<double> objectiveValueHistory;
+    std::vector<double> plotColors;
+    std::array<double,
+               ReducedModelOptimization::OptimizationParameterIndex::
+                   NumberOfOptimizationVariables>
+        parametersInitialValue;
+    std::array<double,
+               ReducedModelOptimization::OptimizationParameterIndex::
+                   NumberOfOptimizationVariables>
+        optimizationInitialValue;
+    std::vector<int> simulationScenarioIndices;
+    double minY{DBL_MAX};
+    std::vector<double> minX;
+    int numOfSimulationCrashes{false};
+    int numberOfFunctionCalls{0};
+    // Variables for finding the full pattern simulation forces
+    std::shared_ptr<SimulationEdgeMesh> pFullPatternSimulationEdgeMesh;
+    std::array<std::function<void(const double& newValue,
+                                  std::shared_ptr<SimulationEdgeMesh>&
+                                      pReducedPatternSimulationEdgeMesh)>,
+               7>
+        functions_updateReducedPatternParameter;
+    std::vector<double> xMin;
+    std::vector<double> xMax;
+    std::vector<double> scenarioWeights;
+    std::vector<ReducedModelOptimization::Settings::ObjectiveWeights>
+        objectiveWeights;
+    std::string simulationModelLabel_reducedModel;
+  };
+
+ private:
+  OptimizationState optimizationState;
+  vcg::Triangle3<double> baseTriangle;
+  std::function<void(
+      const double&,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&,
+      SimulationJob&)>
+      constructScenarioFunction;
+  std::shared_ptr<SimulationEdgeMesh> m_pReducedModelSimulationEdgeMesh;
+  std::shared_ptr<SimulationEdgeMesh> m_pSimulationEdgeMesh_pattern;
+  std::unordered_map<PatternVertexIndex, ReducedModelVertexIndex>
+      m_fullToReducedInterfaceViMap;
+  std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>
+      m_fullPatternOppositeInterfaceViPairs;
+  std::unordered_map<size_t, size_t> nodeToSlot;
+  std::unordered_map<size_t, std::unordered_set<size_t>> slotToNode;
+  std::string optimizationNotes;
+  std::array<
+      std::function<void(
+          const double&,
+          const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&,
+          SimulationJob&)>,
+      ReducedModelOptimization::NumberOfBaseSimulationScenarios>
+      constructBaseScenarioFunctions;
+  std::vector<bool> scenarioIsSymmetrical;
+  int fullPatternNumberOfEdges;
+  std::string fullPatternLabel;
+  //        ReducedModelOptimization::Settings optimizationSettings;
+
+ public:
+  struct FunctionEvaluation {
+    FunctionEvaluation() = default;
+    FunctionEvaluation(const std::vector<double>& x, double y) : x(x), y(y) {}
+
+    std::vector<double> x;
+    double y = std::numeric_limits<double>::quiet_NaN();
+  };
+
+  //    struct ParameterLabels
+  //    {
+  //        inline const static std::string E = {"E"};
+  //        inline const static std::string A = {"A"};
+  //        inline const static std::string I2 ={"I2"};
+  //        inline const static std::string I3 ={"I3"};
+  //        inline const static std::string J = {"J"};
+  //        inline const static std::string th= {"Theta"};
+  //        inline const static std::string R = {"R"};
+  //    };
+  //    inline constexpr static ParameterLabels parameterLabels();
+
+  inline static std::array<
+      std::string,
+      ReducedModelOptimization::NumberOfOptimizationVariables>
+      parameterLabels = {"E", "A", "I2", "I3", "J", "Theta", "R"};
+  constexpr static std::
+      array<double, ReducedModelOptimization::NumberOfBaseSimulationScenarios>
+          simulationScenariosResolution = {12, 12, 22, 22, 22, 22};
+  //          simulationScenariosResolution = {8, 8, 16, 16, 16, 16};
+  //          simulationScenariosResolution = {4, 4, 8, 8, 8, 8};
+  //          simulationScenariosResolution = {2, 2, 4, 4, 4, 4};
+  //          simulationScenariosResolution = {2, 2, 2, 22, 22, 22};
+  //          simulationScenariosResolution = {1, 1, 1, 1, 1, 1};
+  constexpr static std::
+      array<double, ReducedModelOptimization::NumberOfBaseSimulationScenarios>
+          baseScenarioWeights = {1, 1, 2, 2, 2};
+  inline static int totalNumberOfSimulationScenarios =
+      std::accumulate(simulationScenariosResolution.begin(),
+                      simulationScenariosResolution.end(),
+                      0);
+  inline static int fanCardinality{6};
+  inline static double initialValue_R{0.5};
+  inline static double initialValue_theta{0};
+  int interfaceNodeIndex;
+  double operator()(const Eigen::VectorXd& x, Eigen::VectorXd&) const;
+
+  ReducedModelOptimizer();
+  static void computeReducedModelSimulationJob(
+      const SimulationJob& simulationJobOfFullModel,
+      const std::unordered_map<size_t, size_t>& fullToReducedMap,
+      SimulationJob& simulationJobOfReducedModel);
+
+  SimulationJob getReducedSimulationJob(
+      const SimulationJob& fullModelSimulationJob);
+
+  static void runSimulation(const std::string& filename,
+                            std::vector<double>& x);
+
+  static std::vector<std::shared_ptr<SimulationJob>>
+  createFullPatternSimulationJobs(
+      const std::shared_ptr<SimulationEdgeMesh>& pMesh,
+      const std::unordered_map<size_t, size_t>&
+          fullPatternOppositeInterfaceViMap);
+
+  static void createSimulationEdgeMeshes(
+      PatternGeometry& pattern,
+      PatternGeometry& reducedModel,
+      const ReducedModelOptimization::Settings& optimizationSettings,
+      std::shared_ptr<SimulationEdgeMesh>& pFullPatternSimulationEdgeMesh,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh);
+  void computeMaps(
+      const std::unordered_map<size_t, std::unordered_set<size_t>>& slotToNode,
+      PatternGeometry& fullPattern,
+      ReducedModel& reducedPattern,
+      std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap,
+      std::unordered_map<PatternVertexIndex, ReducedModelVertexIndex>&
+          fullToReducedInterfaceViMap,
+      std::vector<std::pair<PatternVertexIndex, ReducedModelVertexIndex>>&
+          fullPatternOppositeInterfaceViMap);
+  static void visualizeResults(
+      const std::vector<std::shared_ptr<SimulationJob>>&
+          fullPatternSimulationJobs,
+      const std::vector<std::shared_ptr<SimulationJob>>&
+          reducedPatternSimulationJobs,
+      const std::vector<ReducedModelOptimization::BaseSimulationScenario>&
+          simulationScenarios,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap);
+  static void registerResultsForDrawing(
+      const std::shared_ptr<SimulationJob>& pFullPatternSimulationJob,
+      const std::shared_ptr<SimulationJob>& pReducedPatternSimulationJob,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap);
+
+  static double computeRawTranslationalError(
+      const std::vector<Vector6d>& fullPatternDisplacements,
+      const std::vector<Vector6d>& reducedPatternDisplacements,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap);
+
+  static double computeDisplacementError(
+      const std::vector<Vector6d>& fullPatternDisplacements,
+      const std::vector<Vector6d>& reducedPatternDisplacements,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap,
+      const double& normalizationFactor);
+
+  static double computeRawRotationalError(
+      const std::vector<Eigen::Quaterniond>& rotatedQuaternion_fullPattern,
+      const std::vector<Eigen::Quaterniond>& rotatedQuaternion_reducedPattern,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap);
+
+  static double computeRotationalError(
+      const std::vector<Eigen::Quaterniond>& rotatedQuaternion_fullPattern,
+      const std::vector<Eigen::Quaterniond>& rotatedQuaternion_reducedPattern,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap,
+      const double& normalizationFactor);
+  static double computeError(
+      const SimulationResults& simulationResults_fullPattern,
+      const SimulationResults& simulationResults_reducedPattern,
+      const std::unordered_map<ReducedModelVertexIndex, PatternVertexIndex>&
+          reducedToFullInterfaceViMap,
+      const double& normalizationFactor_translationalDisplacement,
+      const double& normalizationFactor_rotationalDisplacement,
+      const double& scenarioWeight,
+      const ReducedModelOptimization::Settings::ObjectiveWeights&
+          objectiveWeights);
+  static void constructAxialSimulationScenario(
+      const double& forceMagnitude,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&
+          oppositeInterfaceViPairs,
+      SimulationJob& job);
+
+  static void constructShearSimulationScenario(
+      const double& forceMagnitude,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&
+          oppositeInterfaceViPairs,
+      SimulationJob& job);
+
+  static void constructBendingSimulationScenario(
+      const double& forceMagnitude,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&
+          oppositeInterfaceViPairs,
+      SimulationJob& job);
+
+  static void constructDomeSimulationScenario(
+      const double& forceMagnitude,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&
+          oppositeInterfaceViPairs,
+      SimulationJob& job);
+
+  static void constructSaddleSimulationScenario(
+      const double& forceMagnitude,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&
+          oppositeInterfaceViPairs,
+      SimulationJob& job);
+  static void constructSSimulationScenario(
+      const double& forceMagnitude,
+      const std::vector<std::pair<PatternVertexIndex, PatternVertexIndex>>&
+          oppositeInterfaceViPairs,
+      SimulationJob& job);
+  static std::function<void(
+      const std::vector<double>& x,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern;
+  static std::function<void(
+      const double& newE,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern_material_E;
+  static std::function<void(
+      const double& newA,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern_material_A;
+  static std::function<void(
+      const double& newI,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern_material_I;
+  static std::function<void(
+      const double& newI2,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern_material_I2;
+  static std::function<void(
+      const double& newI3,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern_material_I3;
+  static std::function<void(
+      const double& newJ,
+      std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+      function_updateReducedPattern_material_J;
+  //  static double objective(const std::vector<double>& x);
+  void initializeUpdateReducedPatternFunctions();
+  //    static double objective(const double &xValue);
+
+  ReducedModelOptimization::Results optimize(
+      ConstPatternGeometry& fullPattern,
+      const ReducedModelOptimization::Settings& optimizationSettings);
+
+  void optimize(ConstPatternGeometry& fullPattern,
+                ReducedModelOptimization::Settings& optimizationSettings,
+                ReducedModelOptimization::Results& optimizationResults);
+  static double objective(
+      const std::vector<double>& x,
+      ReducedModelOptimizer::OptimizationState& optimizationState);
+
+ private:
+  void optimize(
+      ReducedModelOptimization::Settings& optimizationSettings,
+      ReducedModelOptimization::Results& results,
+      const std::vector<ReducedModelOptimization::BaseSimulationScenario>&
+          simulationScenarios =
+              std::vector<ReducedModelOptimization::BaseSimulationScenario>(
+                  {ReducedModelOptimization::Axial,
+                   ReducedModelOptimization::Shear,
+                   ReducedModelOptimization::Bending,
+                   ReducedModelOptimization::Dome,
+                   ReducedModelOptimization::Saddle,
+                   ReducedModelOptimization::S}));
+
+  void initializePatterns(
+      PatternGeometry& fullPattern,
+      ReducedModel& reducedModel,
+      const ReducedModelOptimization::Settings& optimizationSettings);
+  static void computeDesiredReducedModelDisplacements(
+      const SimulationResults& fullModelResults,
+      const std::unordered_map<size_t, size_t>& displacementsReducedToFullMap,
+      Eigen::MatrixX3d& optimalDisplacementsOfReducedModel);
+  void runOptimization(const ReducedModelOptimization::Settings& settings,
+                       ReducedModelOptimization::Results& results);
+  void computeMaps(PatternGeometry& fullModel, ReducedModel& reducedModel);
+  void createSimulationEdgeMeshes(
+      PatternGeometry& fullModel,
+      PatternGeometry& reducedModel,
+      const ReducedModelOptimization::Settings& optimizationSettings);
+  void initializeOptimizationParameters(
+      const std::shared_ptr<SimulationEdgeMesh>& mesh,
+      const std::array<ReducedModelOptimization::xRange,
+                       ReducedModelOptimization::NumberOfOptimizationVariables>&
+          optimizationParamters);
+
+  void computeObjectiveValueNormalizationFactors(
+      const ReducedModelOptimization::Settings& optimizationSettings);
+
+  void getResults(const FunctionEvaluation& optimalObjective,
+                  const ReducedModelOptimization::Settings& settings,
+                  ReducedModelOptimization::Results& results);
+  //  double computeFullPatternMaxSimulationForce(
+  //      const ReducedModelOptimization::BaseSimulationScenario& scenario)
+  //      const;
+
+#ifdef DLIB_DEFINED
+  static double objective(const dlib::matrix<double, 0, 1>& x);
+  static double objective(const double& xValue);
+  ReducedModelOptimizer::FunctionEvaluation optimizeWith_dlib(
+      const std::vector<ReducedModelOptimization::OptimizationParameterIndex>&
+          parameterGroup,
+      const ReducedModelOptimization::Settings& settings,
+      const int& totalNumberOfOptimizationParameters);
+  ReducedModelOptimizer::FunctionEvaluation optimizeWith_bobyqa(
+      const std::vector<ReducedModelOptimization::OptimizationParameterIndex>&
+          parameterGroup,
+      const ReducedModelOptimization::Settings& settings);
+#endif
+  std::array<double, ReducedModelOptimization::NumberOfBaseSimulationScenarios>
+  computeFullPatternMaxSimulationForces(
+      const std::vector<ReducedModelOptimization::BaseSimulationScenario>&
+          desiredBaseSimulationScenario) const;
+  std::vector<std::shared_ptr<SimulationJob>> createFullPatternSimulationJobs(
+      const std::shared_ptr<SimulationEdgeMesh>& pMesh,
+      const std::array<
+          double,
+          ReducedModelOptimization::NumberOfBaseSimulationScenarios>&
+          baseScenarioMaxForceMagnitudes) const;
+  std::array<double, ReducedModelOptimization::NumberOfBaseSimulationScenarios>
+  getFullPatternMaxSimulationForces(
+      const std::vector<ReducedModelOptimization::BaseSimulationScenario>&
+          desiredBaseSimulationScenarioIndices,
+      const std::filesystem::path& intermediateResultsDirectoryPath,
+      const bool& recomputeForceMagnitudes);
+  std::array<double, ReducedModelOptimization::NumberOfBaseSimulationScenarios>
+  getFullPatternMaxSimulationForces();
+  void computeScenarioWeights(
+      const std::vector<ReducedModelOptimization::BaseSimulationScenario>&
+          baseSimulationScenarios,
+      const ReducedModelOptimization::Settings& optimizationSettings);
+};
+inline std::function<void(
+    const double& newE,
+    std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+    ReducedModelOptimizer::function_updateReducedPattern_material_E;
+inline std::function<void(
+    const double& newA,
+    std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+    ReducedModelOptimizer::function_updateReducedPattern_material_A;
+inline std::function<void(
+    const double& newI,
+    std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+    ReducedModelOptimizer::function_updateReducedPattern_material_I;
+inline std::function<void(
+    const double& newI2,
+    std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+    ReducedModelOptimizer::function_updateReducedPattern_material_I2;
+inline std::function<void(
+    const double& newI3,
+    std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+    ReducedModelOptimizer::function_updateReducedPattern_material_I3;
+inline std::function<void(
+    const double& newJ,
+    std::shared_ptr<SimulationEdgeMesh>& pReducedPatternSimulationEdgeMesh)>
+    ReducedModelOptimizer::function_updateReducedPattern_material_J;
+inline std::function<void(const std::vector<double>& x,
+                          std::shared_ptr<SimulationEdgeMesh>& m)>
+    ReducedModelOptimizer::function_updateReducedPattern;
+
+extern ReducedModelOptimizer::OptimizationState global;
+
+#endif  // REDUCEDMODELOPTIMIZER_HPP

simulation_structs.hpp

@@ -1,813 +0,0 @@
-#ifndef SIMULATIONSTRUCTS_HPP
-#define SIMULATIONSTRUCTS_HPP
-#include <fstream>
-
-namespace Eigen {
-template <class Matrix>
-void write_binary(const std::string &filename, const Matrix &matrix) {
-  std::ofstream out(filename,
-                    std::ios::out | std::ios::binary | std::ios::trunc);
-  typename Matrix::Index rows = matrix.rows(), cols = matrix.cols();
-  out.write((char *)(&rows), sizeof(typename Matrix::Index));
-  out.write((char *)(&cols), sizeof(typename Matrix::Index));
-  out.write((char *)matrix.data(),
-            rows * cols * sizeof(typename Matrix::Scalar));
-  out.close();
-}
-template <class Matrix>
-void read_binary(const std::string &filename, Matrix &matrix) {
-  std::ifstream in(filename, std::ios::in | std::ios::binary);
-  typename Matrix::Index rows = 0, cols = 0;
-  in.read((char *)(&rows), sizeof(typename Matrix::Index));
-  in.read((char *)(&cols), sizeof(typename Matrix::Index));
-  matrix.resize(rows, cols);
-  in.read((char *)matrix.data(), rows * cols * sizeof(typename Matrix::Scalar));
-  in.close();
-}
-//const static IOFormat CSVFormat(StreamPrecision, DontAlignCols, ", ", "\n");
-//template<class Matrix>
-//void writeToCSV(const std::string &filename, Matrix &matrix)
-//{
-//    ofstream file(filename.c_str());
-//    file << matrix.format(CSVFormat);
-//}
-} // namespace Eigen
-
-#include "simulationmesh.hpp"
-#include "nlohmann/json.hpp"
-#include <string>
-#include <vector>
-
-struct SimulationHistory {
-  SimulationHistory() {}
-
-  size_t numberOfSteps{0};
-  std::string label;
-  std::vector<double> logResidualForces;
-  std::vector<double> kineticEnergy;
-  std::vector<double> potentialEnergies;
-  std::vector<size_t> redMarks;
-  std::vector<double> greenMarks;
-  std::vector<double> residualForcesMovingAverage;
-  std::vector<double> sumOfNormalizedDisplacementNorms;
-  //  std::vector<double> residualForcesMovingAverageDerivativesLog;
-
-  void markRed(const size_t &stepNumber) { redMarks.push_back(stepNumber); }
-
-  void markGreen(const size_t &stepNumber) { greenMarks.push_back(stepNumber); }
-
-  void stepPulse(const SimulationMesh &mesh)
-  {
-      kineticEnergy.push_back(std::log10(mesh.currentTotalKineticEnergy));
-      //    potentialEnergy.push_back(mesh.totalPotentialEnergykN);
-      logResidualForces.push_back(std::log10(mesh.totalResidualForcesNorm));
-      residualForcesMovingAverage.push_back(std::log10(mesh.residualForcesMovingAverage));
-      sumOfNormalizedDisplacementNorms.push_back(std::log10(mesh.sumOfNormalizedDisplacementNorms));
-      //    residualForcesMovingAverageDerivativesLog.push_back(
-      //        std::log(mesh.residualForcesMovingAverageDerivativeNorm));
-  }
-
-  void clear()
-  {
-      logResidualForces.clear();
-      kineticEnergy.clear();
-      potentialEnergies.clear();
-      residualForcesMovingAverage.clear();
-      sumOfNormalizedDisplacementNorms.clear();
-      //      residualForcesMovingAverageDerivativesLog.clear();
-  }
-};
-
-
-namespace nlohmann {
-
-template <> struct adl_serializer<std::unordered_map<VertexIndex, Vector6d>> {
-  static void to_json(json &j,
-                      const std::unordered_map<VertexIndex, Vector6d> &value) {
-    // calls the "to_json" method in T's namespace
-  }
-
-  static void from_json(const nlohmann::json &j,
-                        std::unordered_map<VertexIndex, Vector6d> &m) {
-    std::cout << "Entered." << std::endl;
-    for (const auto &p : j) {
-      m.emplace(p.at(0).template get<VertexIndex>(),
-                p.at(1).template get<std::array<double, 6>>());
-    }
-  }
-};
-} // namespace nlohmann
-
-class SimulationJob {
-  //  const std::unordered_map<VertexIndex, VectorType> nodalForcedNormals;
-  // json labels
-  struct JSONLabels {
-    inline static std::string meshFilename{"mesh filename"};
-    inline static std::string forcedDisplacements{"forced displacements"};
-    inline static std::string constrainedVertices{"fixed vertices"};
-    inline static std::string nodalForces{"forces"};
-    inline static std::string label{"label"};
-    inline static std::string meshLabel{
-        "meshLabel"}; // TODO: should be in the savePly function of the
-                      // simulation mesh class
-  } jsonLabels;
-
-public:
-    inline static std::string jsonDefaultFileName = "SimulationJob.json";
-    std::shared_ptr<SimulationMesh> pMesh;
-    std::string label{"empty_job"};
-    std::unordered_map<VertexIndex, std::unordered_set<int>> constrainedVertices;
-    std::unordered_map<VertexIndex, Vector6d> nodalExternalForces;
-    std::unordered_map<VertexIndex, Eigen::Vector3d> nodalForcedDisplacements;
-    SimulationJob(const std::shared_ptr<SimulationMesh> &m,
-                  const std::string &label,
-                  const std::unordered_map<VertexIndex, std::unordered_set<int>> &cv,
-                  const std::unordered_map<VertexIndex, Vector6d> &ef = {},
-                  const std::unordered_map<VertexIndex, Eigen::Vector3d> &fd = {})
-        : pMesh(m), label(label), constrainedVertices(cv), nodalExternalForces(ef),
-          nodalForcedDisplacements(fd)
-    {}
-    SimulationJob() {}
-    SimulationJob(const std::string &jsonFilename) { load(jsonFilename); }
-
-    bool isEmpty()
-    {
-        return constrainedVertices.empty() && nodalExternalForces.empty()
-               && nodalForcedDisplacements.empty() && pMesh == nullptr;
-  }
-  void remap(const std::unordered_map<size_t, size_t> &sourceToDestinationViMap,
-             SimulationJob &destination_simulationJob) const
-  {
-      std::unordered_map<VertexIndex, std::unordered_set<int>> destination_fixedVertices;
-      for (const auto &source_fixedVertex : this->constrainedVertices) {
-          destination_fixedVertices[sourceToDestinationViMap.at(source_fixedVertex.first)]
-              = source_fixedVertex.second;
-      }
-
-      std::unordered_map<VertexIndex, Vector6d> destination_nodalForces;
-      for (const auto &source_nodalForces : this->nodalExternalForces) {
-          destination_nodalForces[sourceToDestinationViMap.at(source_nodalForces.first)]
-              = source_nodalForces.second;
-      }
-
-      std::unordered_map<VertexIndex, Eigen::Vector3d> destination_forcedDisplacements;
-      for (const auto &source_forcedDisplacements : this->nodalForcedDisplacements) {
-          destination_forcedDisplacements[sourceToDestinationViMap.at(
-              source_forcedDisplacements.first)]
-              = source_forcedDisplacements.second;
-      }
-
-      destination_simulationJob.constrainedVertices = destination_fixedVertices;
-      destination_simulationJob.nodalExternalForces = destination_nodalForces;
-      destination_simulationJob.label = this->getLabel();
-      destination_simulationJob.nodalForcedDisplacements = destination_forcedDisplacements;
-  }
-  SimulationJob getCopy() const {
-    SimulationJob jobCopy;
-    jobCopy.pMesh = std::make_shared<SimulationMesh>();
-    jobCopy.pMesh->copy(*pMesh);
-    jobCopy.label = label;
-    jobCopy.constrainedVertices = constrainedVertices;
-    jobCopy.nodalExternalForces = nodalExternalForces;
-    jobCopy.nodalForcedDisplacements = nodalForcedDisplacements;
-
-    return jobCopy;
-  }
-  std::string getLabel() const { return label; }
-
-  std::string toString() const {
-    nlohmann::json json;
-    if (!constrainedVertices.empty()) {
-      json[jsonLabels.constrainedVertices] = constrainedVertices;
-    }
-    if (!nodalExternalForces.empty()) {
-      std::unordered_map<VertexIndex, std::array<double, 6>> arrForces;
-      for (const auto &f : nodalExternalForces) {
-        arrForces[f.first] = f.second;
-      }
-      json[jsonLabels.nodalForces] = arrForces;
-    }
-
-    return json.dump();
-  }
-
-  void clear()
-  {
-      label = "empty_job";
-      constrainedVertices.clear();
-      nodalExternalForces.clear();
-      nodalForcedDisplacements.clear();
-      if (pMesh.use_count() == 1) {
-          std::cout << "Job mesh is deleted" << std::endl;
-      }
-      pMesh.reset();
-  }
-
-  bool load(const std::string &jsonFilename, const bool &shouldLoadMesh = true)
-  {
-      label = "empty_job";
-      constrainedVertices.clear();
-      nodalExternalForces.clear();
-      nodalForcedDisplacements.clear();
-      const bool beVerbose = false;
-      if (std::filesystem::path(jsonFilename).extension() != ".json") {
-          std::cerr << "A json file is expected as input. The given file has the "
-                       "following extension:"
-                    << std::filesystem::path(jsonFilename).extension() << std::endl;
-          assert(false);
-          return false;
-      }
-
-      if (!std::filesystem::exists(std::filesystem::path(jsonFilename))) {
-          std::cerr << "The json file does not exist. Json file provided:" << jsonFilename
-                    << std::endl;
-          assert(false);
-          return false;
-      }
-
-      if (beVerbose) {
-          std::cout << "Loading json file:" << jsonFilename << std::endl;
-      }
-      nlohmann::json json;
-      std::ifstream ifs(jsonFilename);
-      ifs >> json;
-
-      if (shouldLoadMesh) {
-          pMesh.reset();
-          pMesh = std::make_shared<SimulationMesh>();
-          if (json.contains(jsonLabels.meshFilename)) {
-              const std::string relativeFilepath = json[jsonLabels.meshFilename];
-              const auto meshFilepath = std::filesystem::path(
-                                            std::filesystem::path(jsonFilename).parent_path())
-                                            .append(relativeFilepath);
-              pMesh->load(meshFilepath.string());
-              pMesh->setLabel(json[jsonLabels.meshLabel]); // FIXME: This should be exported using
-                                                           // nanoply but nanoply might not be able
-                                                           // to write a string(??)
-          }
-
-          if (json.contains(jsonLabels.meshLabel)) {
-              pMesh->setLabel(json[jsonLabels.meshLabel]);
-          }
-      }
-
-      if (json.contains(jsonLabels.constrainedVertices)) {
-          constrainedVertices =
-              //      auto conV =
-              json[jsonLabels.constrainedVertices]
-                  .get<std::unordered_map<VertexIndex, std::unordered_set<int>>>();
-          if (beVerbose) {
-              std::cout << "Loaded constrained vertices. Number of constrained "
-                           "vertices found:"
-                        << constrainedVertices.size() << std::endl;
-          }
-      }
-
-      if (json.contains(jsonLabels.nodalForces)) {
-          auto f = 
-              json[jsonLabels.nodalForces].get<std::unordered_map<VertexIndex, std::array<double, 6>>>();
-          for (const auto &force : f) {
-              nodalExternalForces[force.first] = Vector6d(force.second);
-          }
-          if (beVerbose) {
-              std::cout << "Loaded forces. Number of forces found:" << nodalExternalForces.size()
-                        << std::endl;
-          }
-      }
-
-      if (json.contains(jsonLabels.forcedDisplacements)) {
-          //      auto conV =
-          std::unordered_map<VertexIndex, std::array<double, 3>> forcedDisp
-              = json[jsonLabels.forcedDisplacements]
-                    .get<std::unordered_map<VertexIndex, std::array<double, 3>>>();
-
-          for (const auto &fd : forcedDisp) {
-              nodalForcedDisplacements[fd.first] = Eigen::Vector3d(fd.second[0],
-                                                                   fd.second[1],
-                                                                   fd.second[2]);
-          }
-          if (beVerbose) {
-              std::cout << "Loaded forced displacements. Number of forced displaced"
-                           "vertices found:"
-                        << nodalForcedDisplacements.size() << std::endl;
-          }
-      }
-
-      if (json.contains(jsonLabels.label)) {
-          label = json[jsonLabels.label];
-      }
-
-      return true;
-  }
-
-  bool save(const std::string &folderDirectory) const
-  {
-      const std::filesystem::path pathFolderDirectory(folderDirectory);
-      if (!std::filesystem::is_directory(pathFolderDirectory)) {
-          std::cerr << "A folder directory is expected for saving the simulation "
-                       "job. Exiting.."
-                    << std::endl;
-          return false;
-      }
-
-      bool returnValue = true;
-      std::string jsonFilename(
-          std::filesystem::path(pathFolderDirectory)
-              //            .append(label + "_" + pMesh->getLabel() + "_simulationJob.json")
-              .append("SimulationJob.json")
-              .string());
-
-      const std::string meshFilename = std::filesystem::absolute(
-                                           std::filesystem::canonical(
-                                               std::filesystem::path(pathFolderDirectory)))
-                                           .append(pMesh->getLabel() + ".ply")
-                                           .string();
-      returnValue = pMesh->save(meshFilename);
-      nlohmann::json json;
-json[jsonLabels.meshFilename]= std::filesystem::relative(std::filesystem::path(meshFilename),std::filesystem::path(jsonFilename).parent_path()).string();
-      json[jsonLabels.meshLabel]
-          = pMesh->getLabel(); // FIXME: This should be exported using nanoply but
-                               // nanoply might not be able to write a string(??)
-      if (!constrainedVertices.empty()) {
-          json[jsonLabels.constrainedVertices] = constrainedVertices;
-      }
-      if (!nodalExternalForces.empty()) {
-          std::unordered_map<VertexIndex, std::array<double, 6>> arrForces;
-          for (const auto &f : nodalExternalForces) {
-              arrForces[f.first] = f.second;
-          }
-          json[jsonLabels.nodalForces] = arrForces;
-      }
-      if (!nodalForcedDisplacements.empty()) {
-          std::unordered_map<VertexIndex, std::array<double, 3>> forcedDisp;
-          for (const auto &fd : nodalForcedDisplacements) {
-              forcedDisp[fd.first] = {fd.second[0], fd.second[1], fd.second[2]};
-          }
-
-          json[jsonLabels.forcedDisplacements] = forcedDisp;
-      }
-
-      if (!label.empty()) {
-          json[jsonLabels.label] = label;
-      }
-      if (!pMesh->getLabel().empty()) {
-          json[jsonLabels.meshLabel] = pMesh->getLabel();
-      }
-      std::ofstream jsonFile(jsonFilename);
-      jsonFile << json;
-      jsonFile.close();
-      //    std::cout << "Saved simulation job as:" << jsonFilename << std::endl;
-
-      return returnValue;
-  }
-#ifdef POLYSCOPE_DEFINED
-  void registerForDrawing(const std::string &meshLabel, const bool &shouldEnable = false) const
-  {
-      PolyscopeInterface::init();
-      if (meshLabel.empty()) {
-          assert(false);
-          std::cerr << "Expects a mesh label on which to draw the simulation job." << std::endl;
-          return;
-      }
-
-      if (!polyscope::hasCurveNetwork(meshLabel)) {
-          assert(false);
-          std::cerr << "Expects mesh already being registered to draw the "
-                       "simulation job. No struct named "
-                           + meshLabel
-                    << std::endl;
-          return;
-      }
-      std::vector<std::array<double, 3>> nodeColors(pMesh->VN());
-      for (const auto &fixedVertex : constrainedVertices) {
-          const bool hasRotationalDoFConstrained = fixedVertex.second.contains(3)
-                                                   || fixedVertex.second.contains(4)
-                                                   || fixedVertex.second.contains(5);
-          const bool hasTranslationalDoFConstrained = fixedVertex.second.contains(0)
-                                                      || fixedVertex.second.contains(1)
-                                                      || fixedVertex.second.contains(2);
-          if (hasTranslationalDoFConstrained && !hasRotationalDoFConstrained) {
-              nodeColors[fixedVertex.first] = {0, 0, 1};
-          } else if (!hasTranslationalDoFConstrained && hasRotationalDoFConstrained) {
-              nodeColors[fixedVertex.first] = {0, 1, 0};
-          } else {
-              nodeColors[fixedVertex.first] = {0, 1, 1};
-          }
-      }
-      if (!nodalForcedDisplacements.empty()) {
-          for (const std::pair<VertexIndex, Eigen::Vector3d> &viDisplPair :
-               nodalForcedDisplacements) {
-              const VertexIndex vi = viDisplPair.first;
-              nodeColors[vi][0] += 1;
-              nodeColors[vi][0] /= 2;
-              nodeColors[vi][1] += 0;
-              nodeColors[vi][1] /= 2;
-              nodeColors[vi][2] += 0;
-              nodeColors[vi][2] /= 2;
-          }
-      }
-      std::for_each(nodeColors.begin(), nodeColors.end(), [](std::array<double, 3> &color) {
-          const double norm = sqrt(std::pow(color[0], 2) + std::pow(color[1], 2)
-                                   + std::pow(color[2], 2));
-          if (norm > std::pow(10, -7)) {
-              color[0] /= norm;
-              color[1] /= norm;
-              color[2] /= norm;
-          }
-      });
-
-      //      if (!nodeColors.empty()) {
-      //          polyscope::getCurveNetwork(meshLabel)
-      //              ->addNodeColorQuantity("Boundary conditions_" + label, nodeColors)
-      //              ->setEnabled(shouldEnable);
-      //      }
-
-      // per node external forces
-      std::vector<std::array<double, 3>> externalForces(pMesh->VN());
-      for (const auto &forcePair : nodalExternalForces) {
-          auto index = forcePair.first;
-          auto force = forcePair.second;
-          externalForces[index] = {force[0], force[1], force[2]};
-      }
-
-      if (!externalForces.empty()) {
-          polyscope::CurveNetworkNodeVectorQuantity *externalForcesVectors
-              = polyscope::getCurveNetwork(meshLabel)->addNodeVectorQuantity("External force_"
-                                                                                 + label,
-                                                                             externalForces);
-
-          const std::array<double, 3> color_loads{1.0, 0, 0};
-          externalForcesVectors->setVectorColor(
-              glm::vec3(color_loads[0], color_loads[1], color_loads[2]));
-          externalForcesVectors->setEnabled(shouldEnable);
-      }
-      // per node external moments
-      bool hasExternalMoments = false;
-      std::vector<std::array<double, 3>> externalMoments(pMesh->VN());
-      for (const auto &forcePair : nodalExternalForces) {
-          auto index = forcePair.first;
-          const Vector6d &load = forcePair.second;
-          if (load.getRotation().norm() != 0) {
-              hasExternalMoments = true;
-          }
-          externalMoments[index] = {load[3], load[4], load[5]};
-      }
-
-      if (hasExternalMoments) {
-          polyscope::getCurveNetwork(meshLabel)
-              ->addNodeVectorQuantity("External moment_" + label, externalMoments)
-              ->setEnabled(shouldEnable);
-      }
-  }
-  void unregister(const std::string &meshLabel)
-  {
-      if (polyscope::getCurveNetwork(meshLabel) == nullptr) {
-          return;
-      }
-      if (!nodalExternalForces.empty()) {
-          polyscope::getCurveNetwork(meshLabel)->removeQuantity("External force_" + label);
-      }
-      if (!constrainedVertices.empty()) {
-          polyscope::getCurveNetwork(meshLabel)->removeQuantity("Boundary conditions_" + label);
-      }
-
-      // per node external moments
-      bool hasExternalMoments = false;
-      for (const auto &forcePair : nodalExternalForces) {
-          const Vector6d &load = forcePair.second;
-          if (load.getRotation().norm() != 0) {
-              hasExternalMoments = true;
-              break;
-          }
-      }
-      if (hasExternalMoments) {
-          polyscope::getCurveNetwork(meshLabel)->removeQuantity("External moment_" + label);
-      }
-  }
-#endif // POLYSCOPE_DEFINED
-};
-struct SimulationResults
-{
-    /*TODO: remove rotationalDisplacementQuaternion since the last three components of the displacments
- * vector contains the same info using euler angles
-*/
-    inline const static std::string defaultJsonFilename{"SimulationResults.json"};
-    bool converged{false};
-    std::shared_ptr<SimulationJob> pJob;
-    SimulationHistory history;
-    std::vector<Vector6d> debug_drmDisplacements;
-    std::vector<Eigen::Quaternion<double>> debug_q_f1;     //per vertex
-    std::vector<Eigen::Quaternion<double>> debug_q_normal; //per vertex
-    std::vector<Eigen::Quaternion<double>> debug_q_nr;     //per vertex
-    std::vector<Vector6d> displacements;
-    std::vector<Eigen::Quaternion<double>> rotationalDisplacementQuaternion; //per vertex
-    double internalPotentialEnergy{0};
-    double executionTime{0};
-    std::string labelPrefix{"deformed"};
-    inline static char deliminator{' '};
-    SimulationResults() { pJob = std::make_shared<SimulationJob>(); }
-
-    std::vector<VectorType> getTranslationalDisplacements() const
-    {
-        std::vector<VectorType> translationalDisplacements(displacements.size());
-        std::transform(displacements.begin(),
-                       displacements.end(),
-                       translationalDisplacements.begin(),
-                       [&](const Vector6d &d) { return VectorType(d[0], d[1], d[2]); });
-
-        return translationalDisplacements;
-    }
-
-    void setLabelPrefix(const std::string &lp) { labelPrefix += deliminator + lp; }
-    std::string getLabel() const
-    {
-        return labelPrefix + deliminator + pJob->pMesh->getLabel() + deliminator + pJob->getLabel();
-    }
-
-    bool saveDeformedModel(const std::string &outputFolder = std::string())
-    {
-        VCGEdgeMesh m;
-        vcg::tri::Append<VCGEdgeMesh, SimulationMesh>::MeshCopy(m, *pJob->pMesh);
-
-        for (int vi = 0; vi < m.VN(); vi++) {
-            m.vert[vi].P() = m.vert[vi].P()
-                             + CoordType(displacements[vi][0],
-                                         displacements[vi][1],
-                                         displacements[vi][2]);
-        }
-        return m.save(std::filesystem::path(outputFolder).append(getLabel() + ".ply").string());
-    }
-
-    void save(const std::string &outputFolder = std::string())
-    {
-        const std::filesystem::path outputFolderPath = outputFolder.empty()
-                                                           ? std::filesystem::current_path()
-                                                           : std::filesystem::path(outputFolder);
-        //        std::cout << "Saving results to:" << outputFolderPath << std::endl;
-        std::filesystem::path simulationJobOutputFolderPath
-            = std::filesystem::path(outputFolderPath).append("SimulationJob");
-        std::filesystem::create_directories(simulationJobOutputFolderPath);
-        pJob->save(simulationJobOutputFolderPath.string());
-        const std::string filename(getLabel() + "_displacements.eigenBin");
-
-        Eigen::MatrixXd m = Utilities::toEigenMatrix(displacements);
-        const std::filesystem::path resultsFolderPath(
-            std::filesystem::path(outputFolder).append("Results"));
-        std::filesystem::create_directories(resultsFolderPath);
-        Eigen::write_binary(std::filesystem::path(resultsFolderPath).append(filename).string(), m);
-
-        nlohmann::json json;
-
-        json[GET_VARIABLE_NAME(internalPotentialEnergy)] = internalPotentialEnergy;
-
-        std::filesystem::path jsonFilePath(
-            std::filesystem::path(resultsFolderPath).append(defaultJsonFilename));
-        std::ofstream jsonFile(jsonFilePath.string());
-        jsonFile << json;
-        jsonFile.close();
-
-        saveDeformedModel(resultsFolderPath.string());
-    }
-
-    // The comparison of the results happens comparing the 6-dof nodal
-    // displacements
-    bool isEqual(const Eigen::MatrixXd &nodalDisplacements, double &error)
-    {
-        assert(nodalDisplacements.cols() == 6);
-        Eigen::MatrixXd eigenDisplacements = Utilities::toEigenMatrix(this->displacements);
-        const double errorNorm = (eigenDisplacements - nodalDisplacements).norm();
-        error = errorNorm;
-        return errorNorm < 1e-10;
-        //    return eigenDisplacements.isApprox(nodalDisplacements);
-    }
-
-    void load(const std::filesystem::path &loadFromPath, const std::filesystem::path &loadJobFrom)
-    {
-        pJob->load(std::filesystem::path(loadJobFrom).append("SimulationJob.json").string());
-        load(loadFromPath);
-    }
-    void load(const std::filesystem::path &loadFromPath, const std::shared_ptr<SimulationJob> &pJob)
-    {
-        this->pJob = pJob;
-        load(loadFromPath);
-    }
-    static double computeDistance(
-        const SimulationResults &resultsA,
-        const SimulationResults &resultsB,
-        const std::unordered_map<VertexIndex, VertexIndex> &resultsAToResultsBViMap)
-    {
-        double distance = 0;
-        for (std::pair<int, int> resultsAToResultsBViPair : resultsAToResultsBViMap) {
-            const double vertexToVertexDistance
-                = (resultsA.displacements[resultsAToResultsBViPair.first].getTranslation()
-                   - resultsB.displacements[resultsAToResultsBViPair.second].getTranslation())
-                      .norm();
-            distance += vertexToVertexDistance;
-        }
-        return distance;
-    }
-
-    double computeDistance(const SimulationResults &other,
-                           const std::unordered_map<VertexIndex, VertexIndex> &thisToOtherViMap) const
-    {
-        return computeDistance(*this, other, thisToOtherViMap);
-    }
-
-#ifdef POLYSCOPE_DEFINED
-    void unregister() const
-    {
-        if (!polyscope::hasCurveNetwork(getLabel())) {
-            std::cerr << "No curve network registered with a name: " << getLabel() << std::endl;
-            std::cerr << "Nothing to remove." << std::endl;
-            return;
-        }
-        pJob->unregister(getLabel());
-        polyscope::removeCurveNetwork(getLabel());
-    }
-    polyscope::CurveNetwork *registerForDrawing(
-        const std::optional<std::array<double, 3>> &desiredColor = std::nullopt,
-        const bool &shouldEnable = true,
-        const double &desiredRadius = 0.001,
-        //      const double &desiredRadius = 0.0001,
-        const bool &shouldShowFrames = false) const
-    {
-        PolyscopeInterface::init();
-        const std::shared_ptr<SimulationMesh> &mesh = pJob->pMesh;
-        polyscope::CurveNetwork *polyscopeHandle_deformedEdmeMesh;
-        if (!polyscope::hasStructure(getLabel())) {
-            const auto verts = mesh->getEigenVertices();
-            const auto edges = mesh->getEigenEdges();
-            polyscopeHandle_deformedEdmeMesh = polyscope::registerCurveNetwork(getLabel(),
-                                                                               verts,
-                                                                               edges);
-        } else {
-            polyscopeHandle_deformedEdmeMesh = polyscope::getCurveNetwork(getLabel());
-        }
-        polyscopeHandle_deformedEdmeMesh->setEnabled(shouldEnable);
-        polyscopeHandle_deformedEdmeMesh->setRadius(desiredRadius, true);
-        if (desiredColor.has_value()) {
-            const glm::vec3 desiredColor_glm(desiredColor.value()[0],
-                                             desiredColor.value()[1],
-                                             desiredColor.value()[2]);
-            polyscopeHandle_deformedEdmeMesh->setColor(desiredColor_glm);
-        }
-        Eigen::MatrixX3d nodalDisplacements(mesh->VN(), 3);
-        Eigen::MatrixX3d framesX(mesh->VN(), 3);
-        Eigen::MatrixX3d framesY(mesh->VN(), 3);
-        Eigen::MatrixX3d framesZ(mesh->VN(), 3);
-
-        Eigen::MatrixX3d framesX_initial(mesh->VN(), 3);
-        Eigen::MatrixX3d framesY_initial(mesh->VN(), 3);
-        Eigen::MatrixX3d framesZ_initial(mesh->VN(), 3);
-
-        //      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{};
-        for (VertexIndex vi = 0; vi < mesh->VN(); vi++) {
-            const Vector6d &nodalDisplacement = displacements[vi];
-            nodalDisplacements.row(vi) = Eigen::Vector3d(nodalDisplacement[0],
-                                                         nodalDisplacement[1],
-                                                         nodalDisplacement[2]);
-            //           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);
-            framesX.row(vi) = Eigen::Vector3d(deformedFrameX[0],
-                                              deformedFrameX[1],
-                                              deformedFrameX[2]);
-            framesY.row(vi) = Eigen::Vector3d(deformedFrameY[0],
-                                              deformedFrameY[1],
-                                              deformedFrameY[2]);
-            framesZ.row(vi) = Eigen::Vector3d(deformedNormal[0],
-                                              deformedNormal[1],
-                                              deformedNormal[2]);
-            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);
-            //          }
-        }
-        polyscopeHandle_deformedEdmeMesh->updateNodePositions(mesh->getEigenVertices()
-                                                              + nodalDisplacements);
-
-        const double frameRadius_default = 0.035;
-        const double frameLength_default = 0.035;
-        const bool shouldEnable_default = true;
-        //if(showFramesOn.contains(vi)){
-        auto polyscopeHandle_frameX = polyscopeHandle_deformedEdmeMesh
-                                          ->addNodeVectorQuantity("FrameX", framesX);
-        polyscopeHandle_frameX->setVectorLengthScale(frameLength_default);
-        polyscopeHandle_frameX->setVectorRadius(frameRadius_default);
-        polyscopeHandle_frameX->setVectorColor(
-            /*polyscope::getNextUniqueColor()*/ glm::vec3(1, 0, 0));
-        auto polyscopeHandle_frameY = polyscopeHandle_deformedEdmeMesh
-                                          ->addNodeVectorQuantity("FrameY", framesY);
-        polyscopeHandle_frameY->setVectorLengthScale(frameLength_default);
-        polyscopeHandle_frameY->setVectorRadius(frameRadius_default);
-        polyscopeHandle_frameY->setVectorColor(
-            /*polyscope::getNextUniqueColor()*/ glm::vec3(0, 1, 0));
-        auto polyscopeHandle_frameZ = polyscopeHandle_deformedEdmeMesh
-                                          ->addNodeVectorQuantity("FrameZ", framesZ);
-        polyscopeHandle_frameZ->setVectorLengthScale(frameLength_default);
-        polyscopeHandle_frameZ->setVectorRadius(frameRadius_default);
-        polyscopeHandle_frameZ->setVectorColor(
-            /*polyscope::getNextUniqueColor()*/ glm::vec3(0, 0, 1));
-
-        auto polyscopeHandle_initialMesh = polyscope::getCurveNetwork(mesh->getLabel());
-        if (!polyscopeHandle_initialMesh) {
-            polyscopeHandle_initialMesh = mesh->registerForDrawing();
-        }
-
-        //      auto polyscopeHandle_frameX_initial = polyscopeHandle_initialMesh
-        //                                                ->addNodeVectorQuantity("FrameX", framesX_initial);
-        //      polyscopeHandle_frameX_initial->setVectorLengthScale(frameLength_default);
-        //      polyscopeHandle_frameX_initial->setVectorRadius(frameRadius_default);
-        //      polyscopeHandle_frameX_initial->setVectorColor(
-        //          /*polyscope::getNextUniqueColor()*/ glm::vec3(1, 0, 0));
-        //      auto polyscopeHandle_frameY_initial = polyscopeHandle_initialMesh
-        //                                                ->addNodeVectorQuantity("FrameY", framesY_initial);
-        //      polyscopeHandle_frameY_initial->setVectorLengthScale(frameLength_default);
-        //      polyscopeHandle_frameY_initial->setVectorRadius(frameRadius_default);
-        //      polyscopeHandle_frameY_initial->setVectorColor(
-        //          /*polyscope::getNextUniqueColor()*/ glm::vec3(0, 1, 0));
-        //      auto polyscopeHandle_frameZ_initial = polyscopeHandle_initialMesh
-        //                                                ->addNodeVectorQuantity("FrameZ", framesZ_initial);
-        //      polyscopeHandle_frameZ_initial->setVectorLengthScale(frameLength_default);
-        //      polyscopeHandle_frameZ_initial->setVectorRadius(frameRadius_default);
-        //      polyscopeHandle_frameZ_initial->setVectorColor(
-        //          /*polyscope::getNextUniqueColor()*/ glm::vec3(0, 0, 1));
-        //      //}
-        pJob->registerForDrawing(getLabel());
-        //        static bool wasExecuted =false;
-        //        if (!wasExecuted) {
-        //            std::function<void()> callback = [&]() {
-        //                static bool showFrames = shouldShowFrames;
-
-        //                if (ImGui::Checkbox("Show Frames", &showFrames) && showFrames) {
-        //                    polyscopeHandle_frameX->setEnabled(showFrames);
-        //                    polyscopeHandle_frameY->setEnabled(showFrames);
-        //                    polyscopeHandle_frameZ->setEnabled(showFrames);
-        //                }
-        //            };
-
-        //            PolyscopeInterface::addUserCallback(callback);
-        //            wasExecuted = true;
-        //        }
-        return polyscopeHandle_deformedEdmeMesh;
-    }
-#endif
-private:
-    bool 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 (std::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());
-        }
-
-        const std::filesystem::path jsonFilepath = std::filesystem::path(loadFromPath)
-                                                       .append(defaultJsonFilename);
-        if (!std::filesystem::exists(jsonFilepath)) {
-            std::cerr << "Simulation results could not be loaded because filepath does "
-                         "not exist:"
-                      << jsonFilepath << std::endl;
-            return false;
-        }
-        std::ifstream ifs(jsonFilepath);
-        nlohmann::json json;
-        ifs >> json;
-        if (json.contains(GET_VARIABLE_NAME(internalPotentialEnergy))) {
-            internalPotentialEnergy = json.at(GET_VARIABLE_NAME(internalPotentialEnergy));
-        }
-        return true;
-    }
-};
-
-#endif // SIMULATIONHISTORY_HPP

simulationhistoryplotter.hpp

@@ -1,193 +0,0 @@
-#ifndef SIMULATIONHISTORYPLOTTER_HPP
-#define SIMULATIONHISTORYPLOTTER_HPP
-
-#include "simulation_structs.hpp"
-#include "simulationmesh.hpp"
-#include "utilities.hpp"
-#include <algorithm>
-#include <matplot/matplot.h>
-
-struct SimulationResultsReporter {
-  using VertexType = VCGEdgeMesh::VertexType;
-  using CoordType = VCGEdgeMesh::CoordType;
-
-  SimulationResultsReporter() {}
-
-  void writeStatistics(const SimulationResults &results,
-                       const std::string &reportFolderPath) {
-      std::ofstream file;
-      file.open(std::filesystem::path(reportFolderPath).append("results.txt").string());
-
-      const size_t numberOfSteps = results.history.numberOfSteps;
-      file << "Number of steps " << numberOfSteps << "\n";
-
-      //    file << "Force threshold used " << 1000 << "\n";
-
-      //    assert(numberOfSteps == results.history.potentialEnergy.size() &&
-      //           numberOfSteps == results.history.residualForces.size());
-      // Write kinetic energies
-      const SimulationHistory &history = results.history;
-      if (!history.kineticEnergy.empty()) {
-          file << "Kinetic energies"
-               << "\n";
-          for (size_t step = 0; step < numberOfSteps; step++) {
-              file << history.kineticEnergy[step] << "\n";
-          }
-          file << "\n";
-    }
-
-    if (!history.logResidualForces.empty()) {
-        file << "Residual forces"
-             << "\n";
-        for (size_t step = 0; step < numberOfSteps; step++) {
-            file << history.logResidualForces[step] << "\n";
-        }
-        file << "\n";
-    }
-
-    if (!history.potentialEnergies.empty()) {
-      file << "Potential energies"
-           << "\n";
-      for (size_t step = 0; step < numberOfSteps; step++) {
-        file << history.potentialEnergies[step] << "\n";
-      }
-      file << "\n";
-    }
-    file.close();
-  }
-
-  void reportHistory(const SimulationHistory &history,
-                     const std::string &reportFolderPath,
-                     const std::string &graphSuffix = std::string())
-  {
-      const auto simulationResultPath = std::filesystem::path(reportFolderPath).append(history.label);
-      std::filesystem::create_directories(simulationResultPath);
-      createPlots(history, simulationResultPath.string(), graphSuffix);
-  }
-
-  void reportResults(const std::vector<SimulationResults> &results,
-                     const std::string &reportFolderPath,
-                     const std::string &graphSuffix = std::string()) {
-    if (results.empty()) {
-      return;
-    }
-
-    //    std::filesystem::remove_all(debuggerFolder);
-    std::filesystem::create_directory(reportFolderPath);
-    for (const SimulationResults &simulationResult : results) {
-      const auto simulationResultPath =
-          std::filesystem::path(reportFolderPath)
-              .append(simulationResult.getLabel());
-      std::filesystem::create_directory(simulationResultPath.string());
-
-      createPlots(simulationResult.history, simulationResultPath.string(),
-                  graphSuffix);
-      writeStatistics(simulationResult, simulationResultPath.string());
-    }
-  }
-  static void createPlot(const std::string &xLabel,
-                         const std::string &yLabel,
-                         const std::vector<double> &x,
-                         const std::vector<double> &y,
-                         const std::vector<double> &markerSizes,
-                         const std::vector<double> &c,
-                         const std::string &saveTo = {})
-  {
-      //    matplot::figure(true);
-      matplot::xlabel(xLabel);
-      matplot::ylabel(yLabel);
-      matplot::grid(matplot::on);
-      matplot::scatter(x, y, markerSizes, c)->marker_face(true);
-      if (!saveTo.empty()) {
-          matplot::save(saveTo);
-      }
-  }
-
-  static void createPlot(const std::string &xLabel,
-                         const std::string &yLabel,
-                         const std::vector<double> &YvaluesToPlot,
-                         const std::string &saveTo = {},
-                         const std::vector<size_t> &markPoints = {})
-  {
-      if (YvaluesToPlot.size() < 2) {
-          return;
-      }
-      std::vector<double> colors(YvaluesToPlot.size(), 0.5);
-      std::vector<double> markerSizes(YvaluesToPlot.size(), 5);
-      if (!markPoints.empty()) {
-          for (const auto pointIndex : markPoints) {
-              colors[pointIndex] = 0.9;
-              markerSizes[pointIndex] = 14;
-          }
-      }
-      std::vector<double> x = matplot::linspace(0, YvaluesToPlot.size() - 1, YvaluesToPlot.size());
-      createPlot(xLabel, yLabel, x, YvaluesToPlot, markerSizes, colors, saveTo);
-  }
-
-  void createPlots(const SimulationHistory &history,
-                   const std::string &reportFolderPath,
-                   const std::string &graphSuffix)
-  {
-      const auto graphsFolder = std::filesystem::path(reportFolderPath).append("Graphs");
-      std::filesystem::remove_all(graphsFolder);
-      std::filesystem::create_directory(graphsFolder.string());
-
-      if (!history.kineticEnergy.empty()) {
-          createPlot("Number of Iterations",
-                     "Log of Kinetic Energy log",
-                     history.kineticEnergy,
-                     std::filesystem::path(graphsFolder)
-                         .append("KineticEnergyLog_" + graphSuffix + ".png")
-                         .string(),
-                     history.redMarks);
-      }
-
-      if (!history.logResidualForces.empty()) {
-          createPlot("Number of Iterations",
-                     "Residual Forces norm log",
-                     history.logResidualForces,
-                     std::filesystem::path(graphsFolder)
-                         .append("ResidualForcesLog_" + graphSuffix + ".png")
-                         .string(),
-                     history.redMarks);
-      }
-
-      if (!history.potentialEnergies.empty()) {
-          createPlot("Number of Iterations",
-                     "Potential energy",
-                     history.potentialEnergies,
-                     std::filesystem::path(graphsFolder)
-                         .append("PotentialEnergy_" + graphSuffix + ".png")
-                         .string(),
-                     history.redMarks);
-      }
-      if (!history.residualForcesMovingAverage.empty()) {
-          createPlot("Number of Iterations",
-                     "Residual forces moving average",
-                     history.residualForcesMovingAverage,
-                     std::filesystem::path(graphsFolder)
-                         .append("ResidualForcesMovingAverage_" + graphSuffix + ".png")
-                         .string(),
-                     history.redMarks);
-      }
-      //    if (!history.residualForcesMovingAverageDerivativesLog.empty()) {
-      //        createPlot("Number of Iterations",
-      //                   "Residual forces moving average derivative log",
-      //                   history.residualForcesMovingAverageDerivativesLog,
-      //                   std::filesystem::path(graphsFolder)
-      //                       .append("ResidualForcesMovingAverageDerivativesLog_" + graphSuffix + ".png")
-      //                       .string());
-      //    }
-      if (!history.sumOfNormalizedDisplacementNorms.empty()) {
-          createPlot("Number of Iterations",
-                     "Sum of normalized displacement norms",
-                     history.sumOfNormalizedDisplacementNorms,
-                     std::filesystem::path(graphsFolder)
-                         .append("SumOfNormalizedDisplacementNorms_" + graphSuffix + ".png")
-                         .string(),
-                     history.redMarks);
-      }
-  }
-};
-
-#endif // SIMULATIONHISTORYPLOTTER_HPP

simulationmesh.cpp

@@ -1,511 +0,0 @@
-#include "simulationmesh.hpp"
-//#include <wrap/nanoply/include/nanoplyWrapper.hpp>
-
-SimulationMesh::SimulationMesh() {
-  elements = vcg::tri::Allocator<SimulationMesh>::GetPerEdgeAttribute<Element>(
-      *this, std::string("Elements"));
-  nodes = vcg::tri::Allocator<SimulationMesh>::GetPerVertexAttribute<Node>(
-      *this, std::string("Nodes"));
-}
-
-SimulationMesh::SimulationMesh(VCGEdgeMesh &mesh) {
-  vcg::tri::MeshAssert<VCGEdgeMesh>::VertexNormalNormalized(mesh);
-
-  VCGEdgeMesh::copy(mesh);
-
-  elements = vcg::tri::Allocator<SimulationMesh>::GetPerEdgeAttribute<Element>(
-      *this, std::string("Elements"));
-  nodes = vcg::tri::Allocator<SimulationMesh>::GetPerVertexAttribute<Node>(*this,
-                                                                           std::string("Nodes"));
-  initializeNodes();
-  initializeElements();
-}
-
-SimulationMesh::~SimulationMesh() {
-  vcg::tri::Allocator<SimulationMesh>::DeletePerEdgeAttribute<Element>(*this,
-                                                                    elements);
-  vcg::tri::Allocator<SimulationMesh>::DeletePerVertexAttribute<Node>(*this,
-                                                                   nodes);
-}
-
-SimulationMesh::SimulationMesh(PatternGeometry &pattern) {
-  vcg::tri::MeshAssert<PatternGeometry>::VertexNormalNormalized(pattern);
-  VCGEdgeMesh::copy(pattern);
-
-  elements = vcg::tri::Allocator<SimulationMesh>::GetPerEdgeAttribute<Element>(
-      *this, std::string("Elements"));
-  nodes = vcg::tri::Allocator<SimulationMesh>::GetPerVertexAttribute<Node>(
-      *this, std::string("Nodes"));
-  initializeNodes();
-  initializeElements();
-}
-
-SimulationMesh::SimulationMesh(SimulationMesh &m)
-{
-    vcg::tri::MeshAssert<SimulationMesh>::VertexNormalNormalized(m);
-    VCGEdgeMesh::copy(m);
-
-    elements = vcg::tri::Allocator<SimulationMesh>::GetPerEdgeAttribute<Element>(*this,
-                                                                                 std::string(
-                                                                                     "Elements"));
-    nodes = vcg::tri::Allocator<SimulationMesh>::GetPerVertexAttribute<Node>(*this,
-                                                                             std::string("Nodes"));
-    initializeNodes();
-
-    for (size_t ei = 0; ei < EN(); ei++) {
-        elements[ei] = m.elements[ei];
-    }
-    reset();
-}
-
-SimulationMesh::SimulationMesh(VCGTriMesh &triMesh)
-{
-    vcg::tri::Append<VCGEdgeMesh, VCGTriMesh>::MeshCopy(*this, triMesh);
-    label = triMesh.getLabel();
-    //    eigenEdges = triMesh.getEigenEdges();
-    //    if (eigenEdges.rows() == 0) {
-    getEdges(eigenEdges);
-    //    }
-    //    eigenVertices = triMesh.getEigenVertices();
-    //    if (eigenVertices.rows() == 0) {
-    getVertices(eigenVertices);
-    //    }
-    vcg::tri::UpdateTopology<VCGEdgeMesh>::VertexEdge(*this);
-
-    elements = vcg::tri::Allocator<SimulationMesh>::GetPerEdgeAttribute<Element>(*this,
-                                                                                 std::string(
-                                                                                     "Elements"));
-    nodes = vcg::tri::Allocator<SimulationMesh>::GetPerVertexAttribute<Node>(*this,
-                                                                             std::string("Nodes"));
-    initializeNodes();
-    initializeElements();
-    reset();
-}
-
-void SimulationMesh::computeElementalProperties() {
-  const std::vector<CrossSectionType> elementalDimensions = getBeamDimensions();
-  const std::vector<ElementMaterial> elementalMaterials = getBeamMaterial();
-  assert(EN() == elementalDimensions.size() &&
-         elementalDimensions.size() == elementalMaterials.size());
-
-  for (const EdgeType &e : edge) {
-    const EdgeIndex ei = getIndex(e);
-    elements[e].setDimensions(elementalDimensions[ei]);
-    elements[e].setMaterial(elementalMaterials[ei]);
-  }
-}
-
-void SimulationMesh::initializeNodes() {
-  // set initial and previous locations,
-  for (const VertexType &v : vert) {
-    const VertexIndex vi = getIndex(v);
-    Node &node = nodes[v];
-    node.vi = vi;
-    node.initialLocation = v.cP();
-    node.initialNormal = v.cN();
-    node.derivativeOfNormal.resize(6, VectorType(0, 0, 0));
-
-    node.displacements[3] =
-        v.cN()[0]; // initialize nx diplacement with vertex normal x
-                   //        component
-    node.displacements[4] = v.cN()[1]; // initialize ny(in the paper) diplacement with vertex
-    //        normal
-    // y component.
-
-    // Initialize incident elements
-    std::vector<VCGEdgeMesh::EdgePointer> incidentElements;
-    vcg::edge::VEStarVE(&v, incidentElements);
-    //    assert(
-    //        vcg::tri::IsValidPointer<SimulationMesh>(*this, incidentElements[0]) &&
-    //        incidentElements.size() > 0);
-    if (incidentElements.size() != 0) {
-        nodes[v].incidentElements = incidentElements;
-        node.referenceElement = getReferenceElement(v);
-        //        std::vector<int> incidentElementsIndices(node.incidentElements.size());
-        //        if (drawGlobal && vi == 5) {
-        //            std::vector<glm::vec3> edgeColors(EN(), glm::vec3(0, 1, 0));
-        //            std::vector<glm::vec3> vertexColors(VN(), glm::vec3(0, 1, 0));
-        //            vertexColors[vi] = glm::vec3(0, 0, 1);
-        //            for (int iei = 0; iei < incidentElementsIndices.size(); iei++) {
-        //                incidentElementsIndices[iei] = this->getIndex(node.incidentElements[iei]);
-        //                edgeColors[incidentElementsIndices[iei]] = glm::vec3(1, 0, 0);
-        //            }
-        //            polyHandle->addEdgeColorQuantity("chosenE", edgeColors)->setEnabled(true);
-        //            polyHandle->addNodeColorQuantity("chosenV", vertexColors)->setEnabled(true);
-        //            draw();
-        //        }
-        //        const int referenceElementIndex = getIndex(node.referenceElement);
-        // Initialze alpha angles
-
-        const EdgeType &referenceElement = *node.referenceElement;
-        const VectorType t01 = computeT1Vector(referenceElement.cP(0), referenceElement.cP(1));
-        const VectorType f01 = (t01 - (v.cN() * (t01.dot(v.cN())))).Normalize();
-        node.alphaAngles.reserve(incidentElements.size());
-
-        for (const VCGEdgeMesh::EdgePointer &ep : nodes[v].incidentElements) {
-            assert(referenceElement.cV(0) == ep->cV(0) || referenceElement.cV(0) == ep->cV(1)
-                   || referenceElement.cV(1) == ep->cV(0) || referenceElement.cV(1) == ep->cV(1));
-            const VectorType t1 = computeT1Vector(*ep);
-            const VectorType f1 = t1 - (v.cN() * (t1.dot(v.cN()))).Normalize();
-            const EdgeIndex ei = getIndex(ep);
-            const double alphaAngle = computeAngle(f01, f1, v.cN());
-            node.alphaAngles.emplace_back(std::make_pair(ei, alphaAngle));
-        }
-    }
-  }
-}
-
-void SimulationMesh::reset() {
-  for (const EdgeType &e : edge) {
-    Element &element = elements[e];
-    element.ei = getIndex(e);
-    const VCGEdgeMesh::CoordType p0 = e.cP(0);
-    const VCGEdgeMesh::CoordType p1 = e.cP(1);
-    const vcg::Segment3<double> s(p0, p1);
-    element.initialLength = s.Length();
-    element.length = element.initialLength;
-    element.updateRigidity();
-  }
-
-  for (const VertexType &v : vert) {
-    Node &node = nodes[v];
-    node.vi = getIndex(v);
-    node.initialLocation = v.cP();
-    node.initialNormal = v.cN();
-    node.derivativeOfNormal.resize(6, VectorType(0, 0, 0));
-
-    node.displacements[3] = v.cN()[0]; // initialize nx diplacement with vertex normal x
-                                       //        component
-    node.displacements[4] = v.cN()[1]; // initialize ny(in the paper) diplacement with vertex
-    //        normal
-    // y component.
-
-    const EdgeType &referenceElement = *getReferenceElement(v);
-    const VectorType t01 = computeT1Vector(referenceElement.cP(0), referenceElement.cP(1));
-    const VectorType f01 = (t01 - (v.cN() * (t01.dot(v.cN())))).Normalize();
-    node.alphaAngles.clear();
-    node.alphaAngles.reserve(node.incidentElements.size());
-    for (const VCGEdgeMesh::EdgePointer &ep : nodes[v].incidentElements) {
-        assert(referenceElement.cV(0) == ep->cV(0) || referenceElement.cV(0) == ep->cV(1)
-               || referenceElement.cV(1) == ep->cV(0) || referenceElement.cV(1) == ep->cV(1));
-        const VectorType t1 = computeT1Vector(*ep);
-        const VectorType f1 = t1 - (v.cN() * (t1.dot(v.cN()))).Normalize();
-        const EdgeIndex ei = getIndex(ep);
-        const double alphaAngle = computeAngle(f01, f1, v.cN());
-        node.alphaAngles.emplace_back(std::make_pair(ei, alphaAngle));
-    }
-  }
-}
-
-void SimulationMesh::initializeElements() {
-  for (const EdgeType &e : edge) {
-    Element &element = elements[e];
-    element.ei = getIndex(e);
-    // Initialize dimensions
-    element.dimensions = CrossSectionType();
-    // Initialize material
-    element.material = ElementMaterial();
-    // Initialize lengths
-    const VCGEdgeMesh::CoordType p0 = e.cP(0);
-    const VCGEdgeMesh::CoordType p1 = e.cP(1);
-    const vcg::Segment3<double> s(p0, p1);
-    element.initialLength = s.Length();
-    element.length = element.initialLength;
-    // Initialize const factors
-    element.updateRigidity();
-    element.derivativeT1.resize(
-        2, std::vector<VectorType>(6, VectorType(0, 0, 0)));
-    element.derivativeT2.resize(
-        2, std::vector<VectorType>(6, VectorType(0, 0, 0)));
-    element.derivativeT3.resize(
-        2, std::vector<VectorType>(6, VectorType(0, 0, 0)));
-    element.derivativeT1_jplus1.resize(6, VectorType(0, 0, 0));
-    element.derivativeT1_j.resize(6, VectorType(0, 0, 0));
-    element.derivativeT1_jplus1.resize(6, VectorType(0, 0, 0));
-    element.derivativeT2_j.resize(6, VectorType(0, 0, 0));
-    element.derivativeT2_jplus1.resize(6, VectorType(0, 0, 0));
-    element.derivativeT3_j.resize(6, VectorType(0, 0, 0));
-    element.derivativeT3_jplus1.resize(6, VectorType(0, 0, 0));
-    element.derivativeR_j.resize(6, VectorType(0, 0, 0));
-    element.derivativeR_jplus1.resize(6, VectorType(0, 0, 0));
-  }
-  updateElementalFrames();
-}
-
-void SimulationMesh::updateElementalLengths() {
-  for (const EdgeType &e : edge) {
-    const EdgeIndex ei = getIndex(e);
-    const VertexIndex vi0 = getIndex(e.cV(0));
-    const VCGEdgeMesh::CoordType p0 = e.cP(0);
-    const VertexIndex vi1 = getIndex(e.cV(1));
-    const VCGEdgeMesh::CoordType p1 = e.cP(1);
-    const vcg::Segment3<double> s(p0, p1);
-    const double elementLength = s.Length();
-    elements[e].length = elementLength;
-  }
-}
-
-void SimulationMesh::updateElementalFrames() {
-  for (const EdgeType &e : edge) {
-    const VectorType elementNormal =
-        (e.cV(0)->cN() + e.cV(1)->cN()).Normalize();
-    elements[e].frame = computeElementFrame(e.cP(0), e.cP(1), elementNormal);
-  }
-}
-
-void SimulationMesh::setBeamCrossSection(
-    const CrossSectionType &beamDimensions) {
-  for (size_t ei = 0; ei < EN(); ei++) {
-    elements[ei].dimensions = beamDimensions;
-    elements[ei].updateRigidity();
-  }
-}
-
-void SimulationMesh::setBeamMaterial(const double &pr, const double &ym) {
-  for (size_t ei = 0; ei < EN(); ei++) {
-    elements[ei].setMaterial(ElementMaterial{pr, ym});
-    elements[ei].updateRigidity();
-  }
-}
-
-std::vector<CrossSectionType> SimulationMesh::getBeamDimensions() {
-  std::vector<CrossSectionType> beamDimensions(EN());
-  for (size_t ei = 0; ei < EN(); ei++) {
-    beamDimensions[ei] = elements[ei].dimensions;
-  }
-  return beamDimensions;
-}
-
-std::vector<ElementMaterial> SimulationMesh::getBeamMaterial() {
-  std::vector<ElementMaterial> beamMaterial(EN());
-  for (size_t ei = 0; ei < EN(); ei++) {
-    beamMaterial[ei] = elements[ei].material;
-  }
-  return beamMaterial;
-}
-
-bool SimulationMesh::load(const std::string &plyFilename)
-{
-    this->Clear();
-    //  assert(plyFileHasAllRequiredFields(plyFilename));
-    // Load the ply file
-    //  VCGEdgeMesh::PerEdgeAttributeHandle<CrossSectionType> handleBeamDimensions =
-    //      vcg::tri::Allocator<SimulationMesh>::AddPerEdgeAttribute<
-    //          CrossSectionType>(*this, plyPropertyBeamDimensionsID);
-    //  VCGEdgeMesh::PerEdgeAttributeHandle<ElementMaterial> handleBeamMaterial =
-    //      vcg::tri::Allocator<SimulationMesh>::AddPerEdgeAttribute<ElementMaterial>(
-    //          *this, plyPropertyBeamMaterialID);
-    //  nanoply::NanoPlyWrapper<SimulationMesh>::CustomAttributeDescriptor
-    //      customAttrib;
-    //  customAttrib.GetMeshAttrib(plyFilename);
-    //  customAttrib.AddEdgeAttribDescriptor<CrossSectionType, double, 2>(
-    //      plyPropertyBeamDimensionsID, nanoply::NNP_LIST_INT8_FLOAT64, nullptr);
-    //  /*FIXME: Since I allow CrossSectionType to take two types I should export the
-    //   * type as well such that that when loaded the correct type of cross section
-    //   * is used.
-    //   */
-    //  customAttrib.AddEdgeAttribDescriptor<vcg::Point2d, double, 2>(
-    //      plyPropertyBeamMaterialID, nanoply::NNP_LIST_INT8_FLOAT64, nullptr);
-
-    //  VCGEdgeMesh::PerEdgeAttributeHandle<std::array<double, 6>>
-    //      handleBeamProperties =
-    //          vcg::tri::Allocator<SimulationMesh>::AddPerEdgeAttribute<
-    //              std::array<double, 6>>(*this, plyPropertyBeamProperties);
-    //  customAttrib.AddEdgeAttribDescriptor<std::array<double, 6>, double, 6>(
-    //      plyPropertyBeamProperties, nanoply::NNP_LIST_INT8_FLOAT64, nullptr);
-
-    //  VCGEdgeMesh::PerEdgeAttributeHandle<ElementMaterial>
-    //  handleBeamRigidityContants;
-    //  customAttrib.AddEdgeAttribDescriptor<vcg::Point4f, float, 4>(
-    //      plyPropertyBeamRigidityConstantsID, nanoply::NNP_LIST_INT8_FLOAT32,
-    //      nullptr);
-    //  unsigned int mask = 0;
-    //  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTCOORD;
-    //  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTNORMAL;
-    //  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_EDGEINDEX;
-    //  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_EDGEATTRIB;
-    //  mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_MESHATTRIB;
-    if (!VCGEdgeMesh::load(plyFilename)) {
-        return false;
-    }
-
-    //  elements = vcg::tri::Allocator<SimulationMesh>::GetPerEdgeAttribute<Element>(
-    //      *this, std::string("Elements"));
-    //  nodes = vcg::tri::Allocator<SimulationMesh>::GetPerVertexAttribute<Node>(
-    //      *this, std::string("Nodes"));
-    vcg::tri::UpdateTopology<SimulationMesh>::VertexEdge(*this);
-    initializeNodes();
-    initializeElements();
-    setBeamMaterial(0.3, 1 * 1e9);
-    updateEigenEdgeAndVertices();
-
-    //  if (!handleBeamProperties._handle->data.empty()) {
-    //    for (size_t ei = 0; ei < EN(); ei++) {
-    //      elements[ei] =
-    //      Element::Properties(handleBeamProperties[ei]);
-    //      elements[ei].updateRigidity();
-    //    }
-    //  }
-    //  for (size_t ei = 0; ei < EN(); ei++) {
-    //    elements[ei].setDimensions(handleBeamDimensions[ei]);
-    //    elements[ei].setMaterial(handleBeamMaterial[ei]);
-    //    elements[ei].updateRigidity();
-    //  }
-
-    bool normalsAreAbsent = vert[0].cN().Norm() < 0.000001;
-    if (normalsAreAbsent) {
-        CoordType normalVector(0, 0, 1);
-        std::cout << "Warning: Normals are missing from " << plyFilename
-                  << ". Added normal vector:" << toString(normalVector) << std::endl;
-        for (auto &v : vert) {
-            v.N() = normalVector;
-        }
-    }
-
-    return true;
-}
-
-bool SimulationMesh::save(const std::string &plyFilename)
-{
-    std::string filename = plyFilename;
-    if (filename.empty()) {
-        filename = std::filesystem::current_path().append(getLabel() + ".ply").string();
-    }
-    //    nanoply::NanoPlyWrapper<VCGEdgeMesh>::CustomAttributeDescriptor customAttrib;
-    //    customAttrib.GetMeshAttrib(filename);
-
-    //    std::vector<CrossSectionType> dimensions = getBeamDimensions();
-    //    customAttrib.AddEdgeAttribDescriptor<CrossSectionType, double, 2>(plyPropertyBeamDimensionsID,
-    //                                                                      nanoply::NNP_LIST_INT8_FLOAT64,
-    //                                                                      dimensions.data());
-    //    std::vector<ElementMaterial> material = getBeamMaterial();
-    //    customAttrib.AddEdgeAttribDescriptor<vcg::Point2d, double, 2>(plyPropertyBeamMaterialID,
-    //                                                                  nanoply::NNP_LIST_INT8_FLOAT64,
-    //                                                                  material.data());
-    //    unsigned int mask = 0;
-    //    mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTCOORD;
-    //    mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_EDGEINDEX;
-    //    mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_EDGEATTRIB;
-    //    mask |= nanoply::NanoPlyWrapper<VCGEdgeMesh>::IO_VERTNORMAL;
-    //    if (nanoply::NanoPlyWrapper<VCGEdgeMesh>::SaveModel(filename.c_str(),
-    //                                                        *this,
-    //                                                        mask,
-    //                                                        customAttrib,
-    //                                                        false)
-    //        != 1) {
-    //        return false;
-    //    }
-    if (!VCGEdgeMesh::save(plyFilename)) {
-        return false;
-    }
-    return true;
-}
-
-SimulationMesh::EdgePointer
-SimulationMesh::getReferenceElement(const VCGEdgeMesh::VertexType &v) {
-    const VertexIndex vi = getIndex(v);
-    return nodes[v].incidentElements[0];
-}
-
-VectorType computeT1Vector(const SimulationMesh::EdgeType &e)
-{
-    return computeT1Vector(e.cP(0), e.cP(1));
-}
-
-VectorType computeT1Vector(const CoordType &p0, const CoordType &p1) {
-  const VectorType t1 = (p1 - p0).Normalize();
-  return t1;
-}
-
-Element::LocalFrame computeElementFrame(const CoordType &p0,
-                                        const CoordType &p1,
-                                        const VectorType &elementNormal) {
-  const VectorType t1 = computeT1Vector(p0, p1);
-  const VectorType t2 = (elementNormal ^ t1).Normalize();
-  const VectorType t3 = (t1 ^ t2).Normalize();
-
-  return Element::LocalFrame{t1, t2, t3};
-}
-
-double computeAngle(const VectorType &vector0, const VectorType &vector1,
-                    const VectorType &normalVector) {
-  double cosAngle = vector0.dot(vector1);
-  const double epsilon = std::pow(10, -6);
-  if (abs(cosAngle) > 1 && abs(cosAngle) < 1 + epsilon) {
-    if (cosAngle > 0) {
-      cosAngle = 1;
-
-    } else {
-      cosAngle = -1;
-    }
-  }
-  assert(abs(cosAngle) <= 1);
-  const double angle =
-      acos(cosAngle); // NOTE: I compute the alpha angle not between
-                      // two consecutive elements but rather between
-                      // the first and the ith. Is this correct?
-  assert(!std::isnan(angle));
-
-  const VectorType cp = vector0 ^ vector1;
-  if (cp.dot(normalVector) < 0) {
-      return -angle;
-  }
-  return angle;
-}
-
-//void Element::computeMaterialProperties(const ElementMaterial &material) {
-//    G = material.youngsModulus / (2 * (1 + material.poissonsRatio));
-//}
-
-//void Element::computeCrossSectionArea(const RectangularBeamDimensions &dimensions, double &A)
-//{
-//    A = dimensions.b * dimensions.h;
-//}
-
-//void Element::computeDimensionsProperties(
-//    const RectangularBeamDimensions &dimensions) {
-//  assert(typeid(CrossSectionType) == typeid(RectangularBeamDimensions));
-//  computeCrossSectionArea(dimensions, A);
-//  computeMomentsOfInertia(dimensions, dimensions.inertia);
-//}
-
-//void Element::computeDimensionsProperties(
-//    const CylindricalBeamDimensions &dimensions) {
-//  assert(typeid(CrossSectionType) == typeid(CylindricalBeamDimensions));
-//  A = M_PI * (std::pow(dimensions.od / 2, 2) - std::pow(dimensions.id / 2, 2));
-//  dimensions.inertia.I2 = M_PI * (std::pow(dimensions.od, 4) - std::pow(dimensions.id, 4)) / 64;
-//  dimensions.inertia.I3 = dimensions.inertia.I2;
-//  dimensions.inertia.J = dimensions.inertia.I2 + dimensions.inertia.I3;
-//}
-
-void Element::setDimensions(const CrossSectionType &dimensions) {
-  this->dimensions = dimensions;
-  assert(this->dimensions.A == dimensions.A);
-  //  computeDimensionsProperties(dimensions);
-  updateRigidity();
-}
-
-void Element::setMaterial(const ElementMaterial &material)
-{
-    this->material = material;
-    //  computeMaterialProperties(material);
-    updateRigidity();
-}
-
-double Element::getMass(const double &materialDensity)
-{
-    const double beamVolume = dimensions.A * length;
-    return beamVolume * materialDensity;
-}
-
-void Element::updateRigidity() {
-    //    assert(initialLength != 0);
-    rigidity.axial = material.youngsModulus * dimensions.A / initialLength;
-    //    assert(rigidity.axial != 0);
-    rigidity.torsional = material.G * dimensions.inertia.J / initialLength;
-    //    assert(rigidity.torsional != 0);
-    rigidity.firstBending = 2 * material.youngsModulus * dimensions.inertia.I2 / initialLength;
-    //    assert(rigidity.firstBending != 0);
-    rigidity.secondBending = 2 * material.youngsModulus * dimensions.inertia.I3 / initialLength;
-    //    assert(rigidity.secondBending != 0);
-}

simulationmesh.hpp

@@ -1,180 +0,0 @@
-#ifndef SIMULATIONMESH_HPP
-#define SIMULATIONMESH_HPP
-
-#include "edgemesh.hpp"
-#include "trianglepatterngeometry.hpp"
-#include <Eigen/Dense>
-
-//extern bool drawGlobal;
-struct Element;
-struct Node;
-using CrossSectionType = RectangularBeamDimensions;
-//using CrossSectionType = CylindricalBeamDimensions;
-
-class SimulationMesh : public VCGEdgeMesh {
-private:
-  void computeElementalProperties();
-  void initializeElements();
-  void initializeNodes();
-  EdgePointer getReferenceElement(const VertexType &v);
-
-  const std::string plyPropertyBeamDimensionsID{"beam_dimensions"};
-  const std::string plyPropertyBeamMaterialID{"beam_material"};
-
-public:
-  PerEdgeAttributeHandle<Element> elements;
-  PerVertexAttributeHandle<Node> nodes;
-  ~SimulationMesh();
-  SimulationMesh(PatternGeometry &pattern);
-  SimulationMesh(ConstVCGEdgeMesh &edgeMesh);
-  SimulationMesh(SimulationMesh &elementalMesh);
-  SimulationMesh(VCGTriMesh &triMesh);
-  void updateElementalLengths();
-  void updateIncidentElements();
-
-  std::vector<VCGEdgeMesh::EdgePointer>
-  getIncidentElements(const VCGEdgeMesh::VertexType &v);
-  virtual bool load(const std::string &plyFilename);
-  std::vector<CrossSectionType> getBeamDimensions();
-  std::vector<ElementMaterial> getBeamMaterial();
-
-  double previousTotalKineticEnergy{0};
-  double previousTotalResidualForcesNorm{0};
-  double currentTotalKineticEnergy{0};
-  double currentTotalTranslationalKineticEnergy{0};
-  double totalResidualForcesNorm{0};
-  double totalExternalForcesNorm{0};
-  double averageResidualForcesNorm{0};
-  double currentTotalPotentialEnergykN{0};
-  double previousTotalPotentialEnergykN{0};
-  double residualForcesMovingAverageDerivativeNorm{0};
-  double residualForcesMovingAverage{0};
-  double sumOfNormalizedDisplacementNorms{0};
-  bool save(const std::string &plyFilename = std::string());
-  void setBeamCrossSection(const CrossSectionType &beamDimensions);
-  void setBeamMaterial(const double &pr, const double &ym);
-  void reset();
-  SimulationMesh();
-  void updateElementalFrames();
-};
-
-struct Element {
-
-  CrossSectionType dimensions;
-  ElementMaterial material;
-
-  void computeMaterialProperties(const ElementMaterial &material);
-  //  void computeDimensionsProperties(const RectangularBeamDimensions &dimensions);
-  //  void computeDimensionsProperties(const CylindricalBeamDimensions &dimensions);
-  void setDimensions(const CrossSectionType &dimensions);
-  void setMaterial(const ElementMaterial &material);
-  double getMass(const double &matrialDensity);
-
-  struct LocalFrame {
-    VectorType t1;
-    VectorType t2;
-    VectorType t3;
-  };
-
-  EdgeIndex ei;
-  double length{0};
-  double initialLength;
-  LocalFrame frame;
-
-  struct Rigidity {
-    double axial;
-    double torsional;
-    double firstBending;
-    double secondBending;
-    std::string toString() const {
-      return std::string("Rigidity:") + std::string("\nAxial=") +
-             std::to_string(axial) + std::string("\nTorsional=") +
-             std::to_string(torsional) + std::string("\nFirstBending=") +
-             std::to_string(firstBending) + std::string("\nSecondBending=") +
-             std::to_string(secondBending);
-    }
-  };
-  Rigidity rigidity;
-  void updateRigidity();
-
-  VectorType f1_j;
-  VectorType f1_jplus1;
-  VectorType f2_j;
-  VectorType f2_jplus1;
-  VectorType f3_j;
-  VectorType f3_jplus1;
-  double cosRotationAngle_j;
-  double cosRotationAngle_jplus1;
-  double sinRotationAngle_j;
-  double sinRotationAngle_jplus1;
-  std::vector<std::vector<VectorType>> derivativeT1;
-  std::vector<std::vector<VectorType>> derivativeT2;
-  std::vector<std::vector<VectorType>> derivativeT3;
-  std::vector<VectorType> derivativeT1_j;
-  std::vector<VectorType> derivativeT1_jplus1;
-  std::vector<VectorType> derivativeT2_j;
-  std::vector<VectorType> derivativeT2_jplus1;
-  std::vector<VectorType> derivativeT3_j;
-  std::vector<VectorType> derivativeT3_jplus1;
-  std::vector<VectorType> derivativeR_j;
-  std::vector<VectorType> derivativeR_jplus1;
-  struct RotationalDisplacements {
-    double theta1{0}, theta2{0}, theta3{0};
-  };
-  RotationalDisplacements rotationalDisplacements_j;
-  RotationalDisplacements rotationalDisplacements_jplus1;
-
-  static void computeCrossSectionArea(const RectangularBeamDimensions &dimensions, double &A);
-};
-
-struct Node {
-  struct Forces {
-    Vector6d external{0};
-    Vector6d internal{0};
-    Vector6d residual{0};
-    Vector6d internalAxial{0};
-    Vector6d internalFirstBending{0};
-    Vector6d internalSecondBending{0};
-    bool hasExternalForce() const { return external.isZero(); }
-  };
-
-  struct Mass {
-    double translational;
-    double rotationalI2;
-    double rotationalI3;
-    double rotationalJ;
-  };
-
-  Mass mass;
-  Vector6d mass_6d;
-  Vector6d damping_6d;
-  VertexIndex vi;
-  CoordType initialLocation;
-  CoordType initialNormal;
-  Vector6d acceleration{0};
-  Forces force;
-  Vector6d velocity{0};
-  double kineticEnergy{0};
-  Vector6d displacements{0};
-  double nR{0};
-  //  std::unordered_map<EdgeIndex, double>
-  //      alphaAngles; // contains the initial angles between the first star element
-  //                   // incident to this node and the other elements of the star
-  //  // has size equal to the valence of the vertex
-  std::vector<std::pair<EdgeIndex, double>> alphaAngles;
-
-  std::vector<VCGEdgeMesh::EdgePointer> incidentElements;
-  std::vector<VectorType> derivativeOfNormal;
-  SimulationMesh::EdgePointer referenceElement;
-};
-
-Element::LocalFrame computeElementFrame(const CoordType &p0,
-                                        const CoordType &p1,
-                                        const VectorType &elementNormal);
-VectorType computeT1Vector(const SimulationMesh::EdgeType &e);
-
-VectorType computeT1Vector(const CoordType &p0, const CoordType &p1);
-double computeAngle(const VectorType &vector0, const VectorType &vector1,
-                    const VectorType &normalVector);
-
-#endif // ELEMENTALMESH_HPP

simulationmodel.hpp

@@ -1,13 +0,0 @@
-#ifndef SIMULATIONMODEL_HPP
-#define SIMULATIONMODEL_HPP
-
-#include "simulation_structs.hpp"
-
-class SimulationModel
-{
-public:
-    virtual SimulationResults executeSimulation(const std::shared_ptr<SimulationJob> &simulationJob)
-        = 0;
-};
-
-#endif // SIMULATIONMODEL_HPP

simulationmodelfactory.cpp

@@ -0,0 +1,25 @@
+#include "simulationmodelfactory.hpp"
+
+SimulationModelFactory::SimulationModelFactory() {}
+
+std::unique_ptr<SimulationModel> SimulationModelFactory::create(
+    const std::string& simulationModelLabel) {
+  if (simulationModelLabel == DRMSimulationModel::label) {
+    return std::make_unique<DRMSimulationModel>();
+  } else if (simulationModelLabel == ChronosEulerSimulationModel::label) {
+    return std::make_unique<ChronosEulerSimulationModel>();
+  } else if (simulationModelLabel == ChronosEulerLinearSimulationModel::label) {
+    return std::make_unique<ChronosEulerLinearSimulationModel>();
+  } else if (simulationModelLabel ==
+             ChronosEulerNonLinearSimulationModel::label) {
+    return std::make_unique<ChronosEulerNonLinearSimulationModel>();
+  } else if (simulationModelLabel == LinearSimulationModel::label) {
+    return std::make_unique<LinearSimulationModel>();
+  }
+  std::cerr
+      << "Simulation model used for computing the optimization results was "
+         "not recognized"
+      << std::endl;
+  assert(false);
+  return nullptr;
+}

simulationmodelfactory.hpp

@@ -0,0 +1,19 @@
+#ifndef SIMULATIONMODELFACTORY_HPP
+#define SIMULATIONMODELFACTORY_HPP
+
+#include "chronoseulerlinearsimulationmodel.hpp"
+#include "chronoseulernonlinearsimulationmodel.hpp"
+#include "chronoseulersimulationmodel.hpp"
+#include "der_leimer.hpp"
+#include "drmsimulationmodel.hpp"
+#include "linearsimulationmodel.hpp"
+#include <string>
+
+class SimulationModelFactory {
+public:
+  SimulationModelFactory();
+  static std::unique_ptr<SimulationModel>
+  create(const std::string &simulationModelLabel);
+};
+
+#endif // SIMULATIONMODELFACTORY_HPP

trianglepatterngeometry.hpp

@@ -1,70 +1,73 @@
 #ifndef FLATPATTERNGEOMETRY_HPP
 #define FLATPATTERNGEOMETRY_HPP
-#include "edgemesh.hpp"
 #include <string>
 #include <unordered_map>
 #include <unordered_set>
-#include "vcgtrimesh.hpp"
+#include "edgemesh.hpp"
 #include "polymesh.hpp"
+#include "vcgtrimesh.hpp"
 
 class PatternGeometry;
 using ConstPatternGeometry = PatternGeometry;
 
-class PatternGeometry : public VCGEdgeMesh
-{
-private:
-  size_t
-  computeTiledValence(const size_t &nodeIndex,
-                      const std::vector<size_t> &numberOfNodesPerSlot) const;
-  size_t getNodeValence(const size_t &nodeIndex) const;
-  size_t getNodeSlot(const size_t &nodeIndex) const;
+class PatternGeometry : public VCGEdgeMesh {
+ private:
+  size_t computeTiledValence(
+      const size_t& nodeIndex,
+      const std::vector<size_t>& numberOfNodesPerSlot) const;
+  size_t getNodeValence(const size_t& nodeIndex) const;
+  size_t getNodeSlot(const size_t& nodeIndex) const;
 
   void addNormals();
   double baseTriangleHeight;
-  double computeBaseTriangleHeight() const;
 
   inline static size_t fanSize{6};
   std::vector<VCGEdgeMesh::CoordType> vertices;
-  const double triangleEdgeSize{1}; // radius edge
+  const double triangleEdgeSize{1};  // radius edge
   std::unordered_map<size_t, size_t> nodeToSlotMap;
   std::unordered_map<size_t, size_t> correspondingNode;
   std::unordered_map<size_t, size_t> nodeTiledValence;
   vcg::Triangle3<double> baseTriangle;
 
-  void
-  constructCorrespondingNodeMap(const std::vector<size_t> &numberOfNodesPerSlot);
+  void constructCorrespondingNodeMap(
+      const std::vector<size_t>& numberOfNodesPerSlot);
 
-  void constructNodeToTiledValenceMap(const std::vector<size_t> &numberOfNodesPerSlot);
+  void constructNodeToTiledValenceMap(
+      const std::vector<size_t>& numberOfNodesPerSlot);
 
-  std::vector<VectorType> getEdgeVectorsWithVertexAsOrigin(std::vector<EdgePointer> &edgePointers,
-                                                           const int &vi);
+  std::vector<VectorType> getEdgeVectorsWithVertexAsOrigin(
+      std::vector<EdgePointer>& edgePointers,
+      const int& vi);
 
-  public:
+ public:
+  inline static VectorType DefaultNormal{0.0, 0.0, 1.0};
   PatternGeometry();
   /*The following function should be a copy constructor with
    * a const argument but this is impossible due to the
    * vcglib interface.
    * */
-  PatternGeometry(PatternGeometry &other);
-  bool load(const std::filesystem::path &meshFilePath) override;
-  void add(const std::vector<vcg::Point3d> &vertices);
-  void add(const std::vector<vcg::Point2i> &edges);
-  void add(const std::vector<vcg::Point3d> &vertices, const std::vector<vcg::Point2i> &edges);
-  void add(const std::vector<size_t> &numberOfNodesPerSlot,
-           const std::vector<vcg::Point2i> &edges);
-  static std::vector<vcg::Point3d>
-  constructVertexVector(const std::vector<size_t> &numberOfNodesPerSlot,
-                        const size_t &fanSize, const double &triangleEdgeSize);
-  bool hasDanglingEdges(const std::vector<size_t> &numberOfNodesPerSlot);
-  bool hasValenceGreaterThan(const std::vector<size_t> &numberOfNodesPerSlot,
-                             const size_t &valenceThreshold);
-  std::vector<vcg::Point3d> getVertices() const;
-  static PatternGeometry createFan(PatternGeometry &pattern);
-  static PatternGeometry createTile(PatternGeometry &pattern);
+  PatternGeometry(PatternGeometry& other);
+  bool load(const std::filesystem::path& meshFilePath) override;
+  void add(const std::vector<vcg::Point3d>& vertices);
+  void add(const std::vector<vcg::Point2i>& edges);
+  void add(const std::vector<vcg::Point3d>& vertices,
+           const std::vector<vcg::Point2i>& edges);
+  void add(const std::vector<size_t>& numberOfNodesPerSlot,
+           const std::vector<vcg::Point2i>& edges);
+  static std::vector<vcg::Point3d> constructVertexVector(
+      const std::vector<size_t>& numberOfNodesPerSlot,
+      const size_t& fanSize,
+      const double& triangleEdgeSize);
+  bool hasDanglingEdges(const std::vector<size_t>& numberOfNodesPerSlot);
+  bool hasValenceGreaterThan(const std::vector<size_t>& numberOfNodesPerSlot,
+                             const size_t& valenceThreshold);
+  std::vector<vcg::Point3d> computeVertices() const;
+  static PatternGeometry createFan(PatternGeometry& pattern);
+  static PatternGeometry createTile(PatternGeometry& pattern);
   double getTriangleEdgeSize() const;
   bool hasUntiledDanglingEdges();
-  std::unordered_map<size_t, std::unordered_set<size_t>>
-  getIntersectingEdges(size_t &numberOfIntersectingEdgePairs) const;
+  std::unordered_map<size_t, std::unordered_set<size_t>> getIntersectingEdges(
+      size_t& numberOfIntersectingEdgePairs) const;
 
   static size_t binomialCoefficient(size_t n, size_t m) {
     assert(n >= m);
@@ -73,60 +76,73 @@ private:
   bool isFullyConnectedWhenFanned();
 
   bool hasIntersectingEdges(
-      const std::string &patternBinaryRepresentation,
-      const std::unordered_map<size_t, std::unordered_set<size_t>>
-          &intersectingEdges);
+      const std::string& patternBinaryRepresentation,
+      const std::unordered_map<size_t, std::unordered_set<size_t>>&
+          intersectingEdges);
   bool isPatternValid();
   size_t getFanSize() const;
-  void add(const std::vector<vcg::Point2d> &vertices,
-           const std::vector<vcg::Point2i> &edges);
+  void add(const std::vector<vcg::Point2d>& vertices,
+           const std::vector<vcg::Point2i>& edges);
 
-  PatternGeometry(const std::vector<size_t> &numberOfNodesPerSlot,
-                  const std::vector<vcg::Point2i> &edges);
-  PatternGeometry(const std::string &filename, bool addNormalsIfAbsent = true);
+  PatternGeometry(const std::vector<size_t>& numberOfNodesPerSlot,
+                  const std::vector<vcg::Point2i>& edges);
+  PatternGeometry(const std::filesystem::path& patternFilePath,
+                  bool addNormalsIfAbsent = true);
 
   bool createHoneycombAtom();
-  void copy(PatternGeometry &copyFrom);
+  void copy(PatternGeometry& copyFrom);
 
-  void tilePattern(VCGEdgeMesh &pattern,
-                   VCGPolyMesh &tileInto,
-                   const int &interfaceNodeIndex,
-                   const bool &shouldDeleteDanglingEdges);
+  void tilePattern(VCGEdgeMesh& pattern,
+                   VCGPolyMesh& tileInto,
+                   const int& interfaceNodeIndex,
+                   const bool& shouldDeleteDanglingEdges);
 
-  void scale(const double &desiredBaseTriangleCentralEdgeSize, const int &interfaceNodeIndex);
+  void scale(const double& desiredBaseTriangleCentralEdgeSize);
 
   double getBaseTriangleHeight() const;
   vcg::Triangle3<double> computeBaseTriangle() const;
+  void updateBaseTriangle();
+  double computeBaseTriangleHeight() const;
+  void updateBaseTriangleHeight();
 
-  PatternGeometry(const std::vector<vcg::Point2d> &vertices, const std::vector<vcg::Point2i> &edges);
-  //  static std::shared_ptr<PatternGeometry> tilePattern(
+  //  PatternGeometry(const std::vector<vcg::Point2d> &vertices, const
+  //  std::vector<vcg::Point2i> &edges); static std::shared_ptr<PatternGeometry>
+  //  tilePattern(
   //      std::vector<PatternGeometry> &pattern,
   //      const std::vector<int> &connectToNeighborsVi,
   //      const VCGPolyMesh &tileInto,
   //      std::vector<int> &tileIntoEdgesToTiledVi,
   //      std::vector<std::vector<size_t>> &perPatternEdges);
-  void createFan(const std::vector<int> &connectToNeighborsVi = std::vector<int>(),
-                 const size_t &fanSize = 6);
-  int interfaceNodeIndex{3}; //TODO: Fix this. This should be automatically computed
-  bool hasAngleSmallerThanThreshold(const std::vector<size_t> &numberOfNodesPerSlot,
-                                    const double &angleThreshold_degrees);
+  virtual void createFan(/*const std::vector<int> &connectToNeighborsVi =
+                            std::vector<int>(),*/
+                         const size_t& fanSize = 6);
+  int interfaceNodeIndex{
+      3};  // TODO: Fix this. This should be automatically computed
+  bool hasAngleSmallerThanThreshold(
+      const std::vector<size_t>& numberOfNodesPerSlot,
+      const double& angleThreshold_degrees,
+      const bool shouldBreak = false);
   vcg::Triangle3<double> getBaseTriangle() const;
-  static std::shared_ptr<PatternGeometry> tilePattern(PatternGeometry &pattern,
-                                                      const std::vector<int> &connectToNeighborsVi,
-                                                      const VCGPolyMesh &tileInto,
-                                                      std::vector<int> &tileIntoEdgesToTiledVi);
   static std::shared_ptr<PatternGeometry> tilePattern(
-      std::vector<ConstPatternGeometry> &patterns,
-      const std::vector<int> &connectToNeighborsVi,
-      const VCGPolyMesh &tileInto,
-      const std::vector<int> &perSurfaceFacePatternIndices,
-      std::vector<size_t> &tileIntoEdgesToTiledVi,
-      std::vector<std::vector<size_t>> &perPatternIndexTiledPatternEdgeIndex);
-  std::unordered_set<VertexIndex> getInterfaceNodes(const std::vector<size_t> &numberOfNodesPerSlot);
-  bool isInterfaceConnected(const std::unordered_set<VertexIndex> &interfaceNodes);
+      PatternGeometry& pattern,
+      const std::vector<int>& connectToNeighborsVi,
+      const VCGPolyMesh& tileInto,
+      std::vector<int>& tileIntoEdgesToTiledVi);
+  static std::shared_ptr<PatternGeometry> tilePattern(
+      std::vector<ConstPatternGeometry>& patterns,
+      const std::vector<int>& connectToNeighborsVi,
+      const VCGPolyMesh& tileInto,
+      const std::vector<int>& perSurfaceFacePatternIndices,
+      std::vector<size_t>& tileIntoEdgesToTiledVi,
+      std::vector<std::vector<size_t>>& perPatternIndexTiledPatternEdgeIndex);
+  std::unordered_set<VertexIndex> getInterfaceNodes(
+      const std::vector<size_t>& numberOfNodesPerSlot);
+  bool isInterfaceConnected(
+      const std::unordered_set<VertexIndex>& interfaceNodes);
   void deleteDanglingVertices() override;
   void deleteDanglingVertices(
-      vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<VertexPointer> &pu) override;
+      vcg::tri::Allocator<VCGEdgeMesh>::PointerUpdater<VertexPointer>& pu)
+      override;
 };
 
-#endif // FLATPATTERNGEOMETRY_HPP
+#endif  // FLATPATTERNGEOMETRY_HPP

utilities.hpp

@@ -1,472 +0,0 @@
-#ifndef UTILITIES_H
-#define UTILITIES_H
-
-#include <Eigen/Dense>
-#include <algorithm>
-#include <array>
-#include <chrono>
-#include <filesystem>
-#include <fstream>
-#include <iterator>
-#include <numeric>
-#include <regex>
-
-#define GET_VARIABLE_NAME(Variable) (#Variable)
-
-struct Vector6d : public std::array<double, 6> {
-  Vector6d() {
-    for (size_t i = 0; i < 6; i++) {
-      this->operator[](i) = 0;
-    }
-  }
-
-  Vector6d(const std::vector<double> &v) {
-    assert(v.size() == 6);
-    std::copy(v.begin(), v.end(), this->begin());
-  }
-
-  Vector6d(const double &d) {
-    for (size_t i = 0; i < 6; i++) {
-      this->operator[](i) = d;
-    }
-  }
-
-  Vector6d(const std::array<double, 6> &arr) : std::array<double, 6>(arr) {}
-
-  Vector6d(const std::initializer_list<double> &initList) {
-    std::copy(initList.begin(), initList.end(), std::begin(*this));
-  }
-
-  Vector6d operator*(const double &d) const {
-    Vector6d result;
-    for (size_t i = 0; i < 6; i++) {
-      result[i] = this->operator[](i) * d;
-    }
-    return result;
-  }
-
-  Vector6d operator*(const Vector6d &v) const {
-    Vector6d result;
-    for (size_t i = 0; i < 6; i++) {
-      result[i] = this->operator[](i) * v[i];
-    }
-    return result;
-  }
-
-  Vector6d operator/(const double &d) const {
-    Vector6d result;
-    for (size_t i = 0; i < 6; i++) {
-      result[i] = this->operator[](i) / d;
-    }
-    return result;
-  }
-
-  Vector6d operator/(const Vector6d &v) const
-  {
-      Vector6d result;
-      for (size_t i = 0; i < 6; i++) {
-          result[i] = this->operator[](i) / v[i];
-      }
-      return result;
-  }
-
-  Vector6d operator+(const Vector6d &v) const {
-    Vector6d result;
-    for (size_t i = 0; i < 6; i++) {
-      result[i] = this->operator[](i) + v[i];
-    }
-    return result;
-  }
-
-  Vector6d operator-(const Vector6d &v) const {
-    Vector6d result;
-    for (size_t i = 0; i < 6; i++) {
-      result[i] = this->operator[](i) - v[i];
-    }
-    return result;
-  }
-
-  Vector6d inverted() const {
-    Vector6d result;
-    for (size_t i = 0; i < 6; i++) {
-      assert(this->operator[](i) != 0);
-      result[i] = 1 / this->operator[](i);
-    }
-    return result;
-  }
-  bool isZero() const {
-    for (size_t i = 0; i < 6; i++) {
-      if (this->operator[](i) != 0)
-        return false;
-    }
-    return true;
-  }
-
-  double squaredNorm() const {
-    double squaredNorm = 0;
-    std::for_each(this->begin(), std::end(*this),
-                  [&](const double &v) { squaredNorm += pow(v, 2); });
-    return squaredNorm;
-  }
-
-  double norm() const { return sqrt(squaredNorm()); }
-
-  bool isFinite() const {
-    return std::any_of(std::begin(*this), std::end(*this), [](const double &v) {
-      if (!std::isfinite(v)) {
-        return false;
-      }
-      return true;
-    });
-  }
-
-  Eigen::Vector3d getTranslation() const {
-    return Eigen::Vector3d(this->operator[](0), this->operator[](1),
-                           this->operator[](2));
-  }
-
-  Eigen::Vector3d getRotation() const
-  {
-      return Eigen::Vector3d(this->operator[](3), this->operator[](4), this->operator[](5));
-  }
-
-  std::string toString() const
-  {
-      std::string s;
-      for (int i = 0; i < 6; i++) {
-          s.append(std::to_string(this->operator[](i)) + ",");
-      }
-      s.pop_back();
-      return s;
-  }
-};
-
-namespace Utilities {
-inline bool compareNat(const std::string &a, const std::string &b)
-{
-    if (a.empty())
-        return true;
-    if (b.empty())
-        return false;
-    if (std::isdigit(a[0]) && !std::isdigit(b[0]))
-        return true;
-    if (!std::isdigit(a[0]) && std::isdigit(b[0]))
-        return false;
-    if (!std::isdigit(a[0]) && !std::isdigit(b[0])) {
-        if (std::toupper(a[0]) == std::toupper(b[0]))
-            return compareNat(a.substr(1), b.substr(1));
-        return (std::toupper(a[0]) < std::toupper(b[0]));
-    }
-
-    // Both strings begin with digit --> parse both numbers
-    std::istringstream issa(a);
-    std::istringstream issb(b);
-    int ia, ib;
-    issa >> ia;
-    issb >> ib;
-    if (ia != ib)
-        return ia < ib;
-
-    // Numbers are the same --> remove numbers and recurse
-    std::string anew, bnew;
-    std::getline(issa, anew);
-    std::getline(issb, bnew);
-    return (compareNat(anew, bnew));
-}
-
-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;
-}
-
-template<typename InputIt>
-inline void normalize(InputIt itBegin, InputIt itEnd)
-{
-    const auto squaredSumOfElements = std::accumulate(itBegin,
-                                                      itEnd,
-                                                      0.0,
-                                                      [](const auto &sum, const auto &el) {
-                                                          return sum + el * el;
-                                                      });
-    assert(squaredSumOfElements != 0);
-    std::transform(itBegin, itEnd, itBegin, [&](auto &element) {
-        return element / std::sqrt(squaredSumOfElements);
-    });
-}
-
-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;
-
-    std::regex re("(\\d+)");
-
-    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]);
-    });
-}
-
-inline Eigen::MatrixXd toEigenMatrix(const std::vector<Vector6d> &v) {
-    Eigen::MatrixXd m(v.size(), 6);
-
-    for (size_t vi = 0; vi < v.size(); vi++) {
-        const Vector6d &vec = v[vi];
-        for (size_t i = 0; i < 6; i++) {
-            m(vi, i) = vec[i];
-        }
-  }
-
-  return m;
-}
-
-inline std::vector<Vector6d> fromEigenMatrix(const Eigen::MatrixXd &m)
-{
-    std::vector<Vector6d> v(m.rows());
-
-    for (size_t vi = 0; vi < m.rows(); vi++) {
-        const Eigen::RowVectorXd &row = m.row(vi);
-        for (size_t i = 0; i < 6; i++) {
-            v[vi][i] = row(i);
-        }
-    }
-
-    return v;
-}
-// std::string convertToLowercase(const std::string &s) {
-//  std::string lowercase;
-//  std::transform(s.begin(), s.end(), lowercase.begin(),
-//                 [](unsigned char c) { return std::tolower(c); });
-//  return lowercase;
-//}
-// bool hasExtension(const std::string &filename, const std::string &extension)
-// {
-//  const std::filesystem::path path(filename);
-//  if (!path.has_extension()) {
-//    std::cerr << "Error: No file extension found in " << filename <<
-//    std::endl; return false;
-//  }
-
-//  const std::string detectedExtension = path.extension().string();
-
-//  if (convertToLowercase(detectedExtension) != convertToLowercase(extension))
-//  {
-//    std::cerr << "Error: detected extension is " + detectedExtension +
-//                     " and not " + extension
-//              << std::endl;
-//    return false;
-//  }
-//  return true;
-//}
-
-inline std::filesystem::path getFilepathWithExtension(const std::filesystem::path &folderPath,
-                                                      const std::string &extension)
-{
-    for (const std::filesystem::directory_entry &dirEntry :
-         std::filesystem::directory_iterator(folderPath)) {
-        if (dirEntry.is_regular_file() && std::filesystem::path(dirEntry).extension() == extension) {
-            return std::filesystem::path(dirEntry);
-        }
-    }
-
-    return "";
-}
-
-} // namespace Utilities
-
-#ifdef POLYSCOPE_DEFINED
-#include "polyscope/curve_network.h"
-#include "polyscope/pick.h"
-#include "polyscope/polyscope.h"
-#include <functional>
-
-namespace PolyscopeInterface {
-inline struct GlobalPolyscopeData
-{
-    std::vector<std::function<void()>> userCallbacks;
-} globalPolyscopeData;
-
-inline void mainCallback()
-{
-    ImGui::PushItemWidth(100); // Make ui elements 100 pixels wide,
-                               // instead of full width. Must have
-                               // matching PopItemWidth() below.
-
-    for (std::function<void()> &userCallback : globalPolyscopeData.userCallbacks) {
-        userCallback();
-    }
-
-    ImGui::PopItemWidth();
-}
-
-inline void addUserCallback(const std::function<void()> &userCallback)
-{
-    globalPolyscopeData.userCallbacks.push_back(userCallback);
-}
-
-inline void deinitPolyscope()
-{
-    if (!polyscope::state::initialized) {
-        return;
-    }
-
-    polyscope::render::engine->shutdownImGui();
-}
-
-inline void init()
-{
-    if (polyscope::state::initialized) {
-        return;
-    }
-    polyscope::init();
-    polyscope::options::groundPlaneEnabled = false;
-    polyscope::view::upDir = polyscope::view::UpDir::ZUp;
-
-    polyscope::state::userCallback = &mainCallback;
-    polyscope::options::autocenterStructures = false;
-    polyscope::options::autoscaleStructures = false;
-}
-using PolyscopeLabel = std::string;
-inline std::pair<PolyscopeLabel, size_t> getSelection()
-{
-    std::pair<polyscope::Structure *, size_t> selection = polyscope::pick::getSelection();
-    if (selection.first == nullptr) {
-        return std::make_pair(std::string(), 0);
-    }
-    return std::make_pair(selection.first->name, selection.second);
-}
-
-inline void registerWorldAxes()
-{
-    PolyscopeInterface::init();
-
-    Eigen::MatrixX3d axesPositions(4, 3);
-    axesPositions.row(0) = Eigen::Vector3d(0, 0, 0);
-    //    axesPositions.row(1) = Eigen::Vector3d(polyscope::state::lengthScale, 0, 0);
-    //    axesPositions.row(2) = Eigen::Vector3d(0, polyscope::state::lengthScale, 0);
-    //    axesPositions.row(3) = Eigen::Vector3d(0, 0, polyscope::state::lengthScale);
-    axesPositions.row(1) = Eigen::Vector3d(1, 0, 0);
-    axesPositions.row(2) = Eigen::Vector3d(0, 1, 0);
-    axesPositions.row(3) = Eigen::Vector3d(0, 0, 1);
-
-    Eigen::MatrixX2i axesEdges(3, 2);
-    axesEdges.row(0) = Eigen::Vector2i(0, 1);
-    axesEdges.row(1) = Eigen::Vector2i(0, 2);
-    axesEdges.row(2) = Eigen::Vector2i(0, 3);
-    Eigen::MatrixX3d axesColors(3, 3);
-    axesColors.row(0) = Eigen::Vector3d(1, 0, 0);
-    axesColors.row(1) = Eigen::Vector3d(0, 1, 0);
-    axesColors.row(2) = Eigen::Vector3d(0, 0, 1);
-
-    const std::string worldAxesName = "World Axes";
-    polyscope::registerCurveNetwork(worldAxesName, axesPositions, axesEdges);
-    polyscope::getCurveNetwork(worldAxesName)->setRadius(0.0001, false);
-    const std::string worldAxesColorName = worldAxesName + " Color";
-    polyscope::getCurveNetwork(worldAxesName)
-        ->addEdgeColorQuantity(worldAxesColorName, axesColors)
-        ->setEnabled(true);
-}
-} // namespace PolyscopeInterface
-
-#endif
-
-// namespace ConfigurationFile {
-
-//}
-//} // namespace ConfigurationFile
-template <typename T1, typename T2>
-void constructInverseMap(const T1 &map, T2 &oppositeMap) {
-  assert(!map.empty());
-  oppositeMap.clear();
-  for (const auto &mapIt : map) {
-    oppositeMap[mapIt.second] = mapIt.first;
-  }
-}
-
-template <typename T> std::string toString(const T &v) {
-  return "(" + std::to_string(v[0]) + "," + std::to_string(v[1]) + "," +
-         std::to_string(v[2]) + ")";
-}
-
-template<typename T>
-std::string to_string_with_precision(const T a_value, const int n = 2)
-{
-    std::ostringstream out;
-    out.precision(n);
-    out << std::fixed << a_value;
-    return out.str();
-}
-
-template<typename T>
-size_t computeHashUnordered(const std::vector<T> &v)
-{
-    size_t hash = 0;
-    for (const auto &el : v) {
-        hash += std::hash<T>{}(el);
-    }
-    return hash;
-}
-
-inline size_t computeHashOrdered(const std::vector<int> &v)
-{
-    std::string elementsString;
-    for (const auto &el : v) {
-        elementsString += std::to_string(el);
-    }
-
-    return std::hash<std::string>{}(elementsString);
-}
-
-#endif // UTILITIES_H

vcgtrimesh.cpp

@@ -6,6 +6,9 @@
 #include <wrap/io_trimesh/export.h>
 #include <wrap/io_trimesh/import.h>
 //#include <wrap/nanoply/include/nanoplyWrapper.hpp>
+#ifdef POLYSCOPE_DEFINED
+#include <polyscope/curve_network.h>
+#endif
 
 bool VCGTriMesh::load(const std::filesystem::__cxx11::path &meshFilePath) {
     assert(std::filesystem::exists(meshFilePath));
@@ -36,6 +39,32 @@ bool VCGTriMesh::load(const std::filesystem::__cxx11::path &meshFilePath) {
     return true;
 }
 
+bool VCGTriMesh::load(std::istringstream &offInputStream)
+{
+    Clear();
+    //  assert(plyFileHasAllRequiredFields(plyFilename));
+    // Load the ply file
+    int mask = 0;
+    mask |= vcg::tri::io::Mask::IOM_VERTCOORD;
+    mask |= vcg::tri::io::Mask::IOM_VERTNORMAL;
+    mask |= vcg::tri::io::Mask::IOM_VERTCOLOR;
+    mask |= vcg::tri::io::Mask::IOM_EDGEINDEX;
+    const bool openingFromStreamErrorCode
+        = vcg::tri::io::ImporterOFF<VCGTriMesh>::OpenStream(*this, offInputStream, mask);
+    if (openingFromStreamErrorCode != 0) {
+        std::cerr << "Error reading from stream:"
+                  << vcg::tri::io::ImporterOFF<VCGTriMesh>::ErrorMsg(openingFromStreamErrorCode)
+                  << std::endl;
+        return false;
+    }
+    vcg::tri::UpdateTopology<VCGTriMesh>::AllocateEdge(*this);
+    vcg::tri::UpdateTopology<VCGTriMesh>::FaceFace(*this);
+    vcg::tri::UpdateTopology<VCGTriMesh>::VertexFace(*this);
+    vcg::tri::UpdateTopology<VCGTriMesh>::VertexEdge(*this);
+    vcg::tri::UpdateNormal<VCGTriMesh>::PerVertexNormalized(*this);
+    return true;
+}
+
 Eigen::MatrixX3d VCGTriMesh::getVertices() const
 {
     //    vcg::tri::Allocator<VCGTriMesh>::CompactVertexVector(m);
@@ -92,8 +121,7 @@ bool VCGTriMesh::save(const std::string plyFilename)
 
 #ifdef POLYSCOPE_DEFINED
 
-polyscope::SurfaceMesh *VCGTriMesh::registerForDrawing(
-    const std::optional<std::array<double, 3>> &desiredColor, const bool &shouldEnable) const
+polyscope::SurfaceMesh *VCGTriMesh::registerForDrawing(const std::optional<std::array<float, 3> > &desiredColor, const bool &shouldEnable) const
 {
     auto vertices = getVertices();
     auto faces = getFaces();
@@ -117,7 +145,7 @@ polyscope::SurfaceMesh *VCGTriMesh::registerForDrawing(
         const glm::vec3 desiredColor_glm(desiredColor.value()[0],
                                          desiredColor.value()[1],
                                          desiredColor.value()[2]);
-        polyscopeHandle_mesh->setSurfaceColor(glm::normalize(desiredColor_glm));
+        polyscopeHandle_mesh->setSurfaceColor(desiredColor_glm);
     }
     return polyscopeHandle_mesh;
 }

vcgtrimesh.hpp

@@ -1,8 +1,8 @@
 #ifndef VCGTRIMESH_HPP
 #define VCGTRIMESH_HPP
-#include "mesh.hpp"
 #include <vcg/complex/complex.h>
 #include <optional>
+#include "mesh.hpp"
 
 #ifdef POLYSCOPE_DEFINED
 #include <polyscope/surface_mesh.h>
@@ -22,39 +22,42 @@ class VCGTriMeshVertex : public vcg::Vertex<VCGTriMeshUsedTypes,
                                             vcg::vertex::Color4b,
                                             vcg::vertex::VFAdj,
                                             vcg::vertex::Qualityd,
-                                            vcg::vertex::VEAdj>
-{};
-class VCGTriMeshFace
-    : public vcg::Face<VCGTriMeshUsedTypes, vcg::face::FFAdj, vcg::face::VFAdj,
-                       vcg::face::VertexRef, vcg::face::BitFlags,
-                       vcg::face::Normal3d> {};
-class VCGTriMeshEdge : public vcg::Edge<VCGTriMeshUsedTypes, vcg::edge::VertexRef, vcg::edge::VEAdj>
-{};
+                                            vcg::vertex::VEAdj> {};
+class VCGTriMeshFace : public vcg::Face<VCGTriMeshUsedTypes,
+                                        vcg::face::FFAdj,
+                                        vcg::face::VFAdj,
+                                        vcg::face::VertexRef,
+                                        vcg::face::BitFlags,
+                                        vcg::face::Normal3d> {};
+class VCGTriMeshEdge : public vcg::Edge<VCGTriMeshUsedTypes,
+                                        vcg::edge::VertexRef,
+                                        vcg::edge::VEAdj> {};
 
 class VCGTriMesh : public vcg::tri::TriMesh<std::vector<VCGTriMeshVertex>,
                                             std::vector<VCGTriMeshFace>,
                                             std::vector<VCGTriMeshEdge>>,
-                   public Mesh
-{
-public:
+                   public Mesh {
+ public:
   VCGTriMesh();
-  VCGTriMesh(const std::string &filename);
-  bool load(const std::filesystem::path &meshFilePath) override;
+  VCGTriMesh(const std::string& filename);
+  bool load(const std::filesystem::path& meshFilePath) override;
+  bool load(std::istringstream& offInputStream);
   Eigen::MatrixX3d getVertices() const;
   Eigen::MatrixX3i getFaces() const;
   bool save(const std::string plyFilename);
-  template <typename MeshElement> size_t getIndex(const MeshElement &element) {
+  template <typename MeshElement>
+  size_t getIndex(const MeshElement& element) {
     return vcg::tri::Index<VCGTriMesh>(*this, element);
   }
 
 #ifdef POLYSCOPE_DEFINED
-  polyscope::SurfaceMesh *registerForDrawing(
-      const std::optional<std::array<double, 3>> &desiredColor = std::nullopt,
-      const bool &shouldEnable = true) const;
+  polyscope::SurfaceMesh* registerForDrawing(
+      const std::optional<std::array<float, 3>>& desiredColor = std::nullopt,
+      const bool& shouldEnable = true) const;
 #endif
   Eigen::MatrixX2i getEdges() const;
   void updateEigenEdgeAndVertices();
   void moveToCenter();
 };
 
-#endif // VCGTRIMESH_HPP
+#endif  // VCGTRIMESH_HPP