WIP (modular structure). Added new folder in src to keep geometry objects and utilities. JSON file can be used to run the PeriDEM model. Need to convert all yaml file into json format, and test library

Author: prashjha

CMakeLists.txt

@@ -124,9 +124,6 @@ endif()
 # #<<<<<<<<<< Threads >>>>>>>>>>#
 find_package(Threads REQUIRED)
 
-# #<<<<<<<<<< YAML >>>>>>>>>>#
-find_package(YamlCpp REQUIRED)
-
 # #<<<<<<<<<< VTK >>>>>>>>>>#
 #find_package(VTK REQUIRED)
 find_package(VTK COMPONENTS CommonCore CommonDataModel IOXML)
@@ -171,11 +168,12 @@ add_subdirectory(external/)
 
 # PeriDEM sub-directories
 add_subdirectory(src/util)
+add_subdirectory(src/geom)
 add_subdirectory(src/rw)
 add_subdirectory(src/inp)
 add_subdirectory(src/material)
 add_subdirectory(src/loading)
-add_subdirectory(src/geometry)
+add_subdirectory(src/fracture)
 add_subdirectory(src/fe)
 add_subdirectory(src/particle)
 add_subdirectory(src/nsearch)

CMakePresets.json

@@ -0,0 +1,47 @@
+{
+    "version": 3,
+    "cmakeMinimumRequired": {
+        "major": 3,
+        "minor": 10,
+        "patch": 0
+    },
+    "configurePresets": [
+        {
+            "name": "default",
+            "displayName": "Default Config",
+            "description": "Default build using Ninja generator",
+            "generator": "Ninja",
+            "cacheVariables": {
+                "CMAKE_BUILD_TYPE": "Release",
+                "CMAKE_CXX_STANDARD": "23",
+                "Enable_CMAKE_Debug_Build": "TRUE",
+                "Enable_Documentation": "FALSE", 
+                "Enable_Tests": "FALSE",
+                "Enable_High_Load_Tests": "FALSE",
+                "Disable_Docker_MPI_Tests": "TRUE",
+                "Enable_Apps": "TRUE"
+            }
+        },
+        {
+            "name": "debug",
+            "inherits": "default",
+            "displayName": "Debug Config",
+            "description": "Debug build with tests enabled",
+            "cacheVariables": {
+                "CMAKE_BUILD_TYPE": "Debug",
+                "Enable_Tests": "TRUE",
+                "Enable_Apps": "TRUE"
+            }
+        }
+    ],
+    "buildPresets": [
+        {
+            "name": "default",
+            "configurePreset": "default"
+        },
+        {
+            "name": "debug",
+            "configurePreset": "debug"
+        }
+    ]
+}

README.md

@@ -230,16 +230,15 @@ the implementation, interested readers can look at
 Core dependencies are:
   - [cmake](https://cmake.org/) (>= 3.10.2) 
   - [vtk](https://vtk.org/) (>= 7.1.1)
-  - [yaml-cpp](https://github.com/jbeder/yaml-cpp) (>= 0.5.2)
   - [metis](https://github.com/KarypisLab/METIS) (>= 5.1.0)
   - MPI
 
 Following dependencies are included in the `PeriDEM` library in `external` folder (see [external/README.md](./external/README.md) for more details):
   - [fast-cpp-csv-parser](https://github.com/ben-strasser/fast-cpp-csv-parser/tree/master) (version included - master)
-  - [fmt](https://github.com/fmtlib/fmt) (>= 7.1.3, version included - 10.2.1)
   - [nanoflann](https://github.com/jlblancoc/nanoflann) (>= 1.3.2, version included - v1.5.5)
   - [taskflow](https://github.com/taskflow/taskflow) (>= 3.7.0)
   - [doxygen-awesome-css](https://github.com/jothepro/doxygen-awesome-css) (>= v2.3.3) 
+  - [nlohmann_json](https://github.com/nlohmann/json) (>= 3.12.0)
 
 ### Building the code
 If all the dependencies are installed on the global path (e.g., `/usr/local/`), 

apps/example-modular/main.cpp

@@ -10,7 +10,7 @@
 
 #include "inp/deckIncludes.h"
 
-#include <fmt/format.h>
+#include <format>
 #include <fstream>
 #include <iostream>
 #include <random>
@@ -115,7 +115,7 @@ int main(int argc, char *argv[]) {
   auto bcDeckJson = inp::BCDeck::getExampleJson(0, 1, 2, false, util::Point());
 
   // create this block from the BCData static function
-  bcDeckJson["Displacement_BC"]["Set_1"] = inp::BCBaseDeck::getExampleJson("Displacement_BC", false, util::geometry::GeomData(),
+  bcDeckJson["Displacement_BC"]["Set_1"] = inp::BCBaseDeck::getExampleJson("Displacement_BC", false, geom::GeomData(),
         {0}, {}, "", {}, "", {},
         {1, 2}, true, "", {});
   // or explicitly, we can do
@@ -127,15 +127,15 @@ int main(int argc, char *argv[]) {
   double v_mag = 0.1; // m/s
   {
     // create this block from the ICData static function
-    bcDeckJson["IC"]["Set_1"] = inp::BCBaseDeck::getExampleJson("IC", false, util::geometry::GeomData(),
+    bcDeckJson["IC"]["Set_1"] = inp::BCBaseDeck::getExampleJson("IC", false, geom::GeomData(),
                                                                    {1}, {}, "", {}, "", {},
                                                                    {}, true, "Constant_Velocity", {v_mag*0.1, v_mag*0.9, 0.});
     // or explicitly, we can do
     // initCondJson.at("Constant_Velocity").at("Particle_List") = std::vector<size_t>({1});
     // initCondJson.at("Constant_Velocity").at("Velocity_Vector") = std::vector<double>{v_mag*0.1, v_mag*0.9, 0.};
   }
   {
-    bcDeckJson["IC"]["Set_2"] = inp::BCBaseDeck::getExampleJson("IC", false, util::geometry::GeomData(),
+    bcDeckJson["IC"]["Set_2"] = inp::BCBaseDeck::getExampleJson("IC", false, geom::GeomData(),
                                                                    {2}, {}, "", {}, "", {},
                                                                    {}, true, "Constant_Velocity", {v_mag*0.5, v_mag*0.5, 0.});
   }
@@ -155,7 +155,7 @@ int main(int argc, char *argv[]) {
   auto pDeckJson = json({});
 
   //// create particle geometry json
-  std::vector<util::geometry::GeomData> pGeomVec(3); // 3 geometry groups
+  std::vector<geom::GeomData> pGeomVec(3); // 3 geometry groups
 
   pGeomVec[0].d_geomName = "rectangle_minus_rectangle";
   // parameters
@@ -198,7 +198,7 @@ int main(int argc, char *argv[]) {
   // contact pair 1 - 1
   pContactJson["Set_1_1"] = inp::ContactPairDeck::getExampleJson(0.95,
       true, false, false,
-      1e+22, 0.95, 0., 1., 1., 1., 0.);
+      1e+22, 0.95, 0., 1., 1., 1., 0., 25000.);
   // copy other pairs
   pContactJson["Set_1_2"] = {{"Copy_Data", std::vector<int>({1, 1})}};
   pContactJson["Set_2_2"] = {{"Copy_Data", std::vector<int>({1, 1})}};
@@ -217,15 +217,15 @@ int main(int argc, char *argv[]) {
 
   // p1
   pGenJson["Data"]["0"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"o", 0.}, {"s", 1.},
-                           {"geom_id", 0}, {"mat_id", 0}, {"mesh_id", 0}, {"contact_id", 0}};
+                           {"geom_id", 0}, {"mat_id", 0}, {"contact_id", 0}};
 
   // p1
   pGenJson["Data"]["1"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"o", 0.}, {"s", 1.},
-                           {"geom_id", 1}, {"mat_id", 1}, {"mesh_id", 1}, {"contact_id", 1}};
+                           {"geom_id", 1}, {"mat_id", 1}, {"contact_id", 1}};
 
   // p1
   pGenJson["Data"]["2"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"o", 0.}, {"s", 1.},
-                           {"geom_id", 2}, {"mat_id", 1}, {"mesh_id", 2}, {"contact_id", 1}};
+                           {"geom_id", 2}, {"mat_id", 1}, {"contact_id", 1}};
 
   // add to json
   pDeckJson["Particle_Generation"] = pGenJson;

apps/peridynamics/main.cpp

@@ -14,14 +14,14 @@
 #include "material/materialUtil.h"
 #include "particle/baseParticle.h"
 #include "util/function.h"
-#include "util/geomObjects.h"
+#include "geom/geomObjects.h"
 #include "util/matrix.h"
 #include "util/methods.h"
 #include "util/point.h"
 #include "inp/pdecks/contactDeck.h"
 #include "rw/reader.h"
 #include "util/function.h"
-#include "util/geom.h"
+#include "geom/geom.h"
 #include "util/methods.h"
 #include "util/randomDist.h"
 #include "util/parallelUtil.h"
@@ -34,7 +34,8 @@
 #include "fe/elemIncludes.h"
 #include "fe/meshUtil.h"
 
-#include <fmt/format.h>
+#include <format>
+#include <print>
 #include <fstream>
 #include <iostream>
 #include <random>
@@ -101,7 +102,7 @@ class Model : public model::DEMModel {
 
     // output avg time info
     if (dbg_condition) {
-      log(fmt::format("    Avg time (ms): \n"
+      log(std::format("    Avg time (ms): \n"
                       "      {:48s} = {:8d}\n"
                       "      {:48s} = {:8d}\n",
                       "peridynamics force", size_t(getKeyData("avg_peridynamics_force_time")),
@@ -112,19 +113,19 @@ class Model : public model::DEMModel {
       appendKeyData("avg_extf_compute_time", 0.);
     }
 
-    log(fmt::format("    {:50s} = {:8d} \n",
+    log(std::format("    {:50s} = {:8d} \n",
                     "Force reset time (ms)",
                     size_t(force_reset_time)
         ),
         2, dbg_condition, 3);
 
-    log(fmt::format("    {:50s} = {:8d} \n",
+    log(std::format("    {:50s} = {:8d} \n",
                     "External force time (ms)",
                     size_t(extf_time)
         ),
         2, dbg_condition, 3);
 
-    log(fmt::format("    {:50s} = {:8d} \n",
+    log(std::format("    {:50s} = {:8d} \n",
                     "Peridynamics force time (ms)",
                     size_t(pd_time)
         ),
@@ -154,18 +155,18 @@ int main(int argc, char *argv[]) {
   if (input.cmdOptionExists("-nThreads")) nThreads = std::stoi(input.getCmdOption("-nThreads"));
   else {
     nThreads = 2;
-    util::io::print(fmt::format("Running Peridynamics with number of threads = {}\n", nThreads));
+    std::print("Running Peridynamics with number of threads = {}\n", nThreads);
   }
   // set number of threads
   util::parallel::initNThreads(nThreads);
-  util::io::print(fmt::format("Number of threads = {}\n", util::parallel::getNThreads()));
+  std::print("Number of threads = {}\n", util::parallel::getNThreads());
 
   std::string filename;
   if (input.cmdOptionExists("-i"))
     filename = input.getCmdOption("-i");
   else {
     filename = "./example/input_1.yaml";
-    util::io::print(fmt::format("Running Peridynamics with example input file = {}\n", filename));
+    std::print("Running Peridynamics with example input file = {}\n", filename);
   }
 
   // current time

apps/twoparticle_demo/main.cpp

@@ -10,31 +10,27 @@
 
 #include <PeriDEMConfig.h>
 
+#include "inp/input.h"
 #include "model/dem/demModel.h"
 #include "material/materialUtil.h"
 #include "particle/baseParticle.h"
 #include "util/function.h"
-#include "util/geomObjects.h"
+#include "geom/geomObjects.h"
 #include "util/matrix.h"
-#include "util/methods.h"
+#include "util/vecMethods.h"
 #include "util/point.h"
-#include "inp/pdecks/contactDeck.h"
 #include "rw/reader.h"
 #include "util/function.h"
-#include "util/geom.h"
-#include "util/methods.h"
+#include "geom/geomUtilFunctions.h"
+#include "util/vecMethods.h"
 #include "util/randomDist.h"
 #include "util/parallelUtil.h"
-#include "inp/decks/materialDeck.h"
-#include "inp/decks/modelDeck.h"
-#include "inp/decks/outputDeck.h"
-#include "inp/decks/restartDeck.h"
 #include "rw/vtkParticleWriter.h"
 #include "rw/vtkParticleReader.h"
 #include "fe/elemIncludes.h"
 #include "fe/meshUtil.h"
 
-#include <fmt/format.h>
+#include <format>
 #include <fstream>
 #include <iostream>
 #include <random>
@@ -102,7 +98,7 @@ class Model : public model::DEMModel {
         else if (particle_mesh_p->getElementType() == util::vtk_type_tetra)
           elem = new fe::TetElem(d_modelDeck_p->d_quadOrder);
         else {
-          std::cerr << fmt::format("Error: Can not compute strain/stress as the element "
+          std::cerr << std::format("Error: Can not compute strain/stress as the element "
                                    "type = {} is not yet supported in this routine.\n", particle_mesh_p->getElementType());
           exit(EXIT_FAILURE);
         }
@@ -132,7 +128,7 @@ class Model : public model::DEMModel {
   void integrate() override {
     // perform output at the beginning
     if (d_n == 0 && d_outputDeck_p->d_performOut) {
-      log(fmt::format("{}: Output step = {}, time = {:.6f} \n", d_name, d_n, d_time),
+      log(std::format("{}: Output step = {}, time = {:.6f} \n", d_name, d_n, d_time),
           2);
       output();
     }
@@ -146,7 +142,7 @@ class Model : public model::DEMModel {
 
     for (size_t i = d_n; i < d_modelDeck_p->d_Nt; i++) {
 
-      log(fmt::format("{}: Time step: {}, time: {:8.6f}, steps completed = {}%\n",
+      log(std::format("{}: Time step: {}, time: {:8.6f}, steps completed = {}%\n",
                       d_name,
                       i,
                       d_time,
@@ -160,7 +156,7 @@ class Model : public model::DEMModel {
       double integrate_time =
               util::methods::timeDiff(t1, steady_clock::now());
 
-      log(fmt::format("  Integration time (ms) = {}\n", integrate_time),
+      log(std::format("  Integration time (ms) = {}\n", integrate_time),
           2, d_n % d_infoN == 0, 3);
 
       if (d_pDeck_p->d_testName == "two_particle") {
@@ -250,7 +246,7 @@ class Model : public model::DEMModel {
     if (util::isLess(d_maxY, max_y_loc))
       d_maxY = max_y_loc;
 
-    log(fmt::format("max y: {} \n", d_maxY), 2, d_n % d_infoN == 0, 3);
+    log(std::format("max y: {} \n", d_maxY), 2, d_n % d_infoN == 0, 3);
 
     // compute ideal values
     static int contact_pp_ideal = -1;
@@ -392,18 +388,18 @@ int main(int argc, char *argv[]) {
   if (input.cmdOptionExists("-nThreads")) nThreads = std::stoi(input.getCmdOption("-nThreads"));
   else {
     nThreads = 2;
-    util::io::print(fmt::format("Running TwoParticle_Demo with number of threads = {}\n", nThreads));
+    std::print("Running TwoParticle_Demo with number of threads = {}\n", nThreads);
   }
   // set number of threads
   util::parallel::initNThreads(nThreads);
-  util::io::print(fmt::format("Number of threads = {}\n", util::parallel::getNThreads()));
+  std::print("Number of threads = {}\n", util::parallel::getNThreads());
 
   std::string filename;
   if (input.cmdOptionExists("-i"))
     filename = input.getCmdOption("-i");
   else {
     filename = "./example/input_0.yaml";
-    util::io::print(fmt::format("Running TwoParticle_Demo with example input file = {}\n", filename));
+    std::print("Running TwoParticle_Demo with example input file = {}\n", filename);
   }
 
   // current time

external/CMakeLists.txt

@@ -7,7 +7,6 @@
 # file LICENSE)
 
 # add_subdirectory(csv)
-add_subdirectory(fmt EXCLUDE_FROM_ALL)
 # add_subdirectory(nanoflann)
 # add_subdirectory(taskflow)
 #add_subdirectory(nlohmann_json)

external/README.md

@@ -10,11 +10,6 @@
 - current version - v2.3.3
 - download link (current version) - [https://github.com/jothepro/doxygen-awesome-css/releases/tag/v2.3.3](https://github.com/jothepro/doxygen-awesome-css/releases/tag/v2.3.3)
 
-## fmt
-- project page - [https://github.com/fmtlib/fmt](https://github.com/fmtlib/fmt)
-- current version - 10.2.1
-- download link (current version) - [https://github.com/fmtlib/fmt/releases/tag/10.2.1](https://github.com/fmtlib/fmt/releases/tag/10.2.1)
-
 ## nanoflann
 - project page - [https://github.com/jlblancoc/nanoflann](https://github.com/jlblancoc/nanoflann)
 - current version - v1.5.5