main.cpp

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/*
 * -------------------------------------------
 * Copyright (c) 2021 - 2026 Prashant K. Jha
 * -------------------------------------------
 * PeriDEM https://github.com/prashjha/PeriDEM
 *
 * Two-particle regression test: one deck stack for every geometry; only geom name,
 * model dimension (2 vs 3), and particle placement differ.
 *
 * Reference meshes are always defined at the origin (same canonical shape for mesh
 * groups 0 and 1). Particle positions are set only in Particle_Generation — do not
 * bake translation into the second particle's geomParams (that broke the general
 * path vs twop_circ_inbuilt).
 *
 * Layout (run_base defaults to the current working directory):
 *   <run_base>/<geom_name>/inp/   — input.json, meshes
 *   <run_base>/<geom_name>/out/   — VTU, log.txt (Output.Path must end with a separator)
 *
 * -outputDir <path>  optional parent for all runs (each geometry still gets
 *                    its own <geom>/inp and <geom>/out under this path).
 * -inputDir <path>   optional parent for inp trees only (default: same as -outputDir base).
 * -allGeometries     run every geometry in geom::acceptable_geometries (overrides -geometry).
 * -geometry <name>   run a single geometry (must be in acceptable_geometries). If omitted,
 *                    default is circle (unless -allGeometries is set).
 */
 
#include "geom/geomObjectsUtil.h"
#include "inp/deckIncludes.h"
#include "util/io.h"
#include "util/function.h"
#include "material/materialUtil.h"
#include "periDEMModel.h"
#include <cmath>
#include <filesystem>
#include <format>
#include <fstream>
#include <stdexcept>
#include <thread>
#include <vector>
 
namespace {
 
std::string directoryPathWithTrailingSep(const std::filesystem::path &dir) {
  namespace fs = std::filesystem;
  fs::path n = fs::absolute(dir).lexically_normal();
  std::string s = n.string();
  if (!s.empty() && s.back() != '/' && s.back() != '\\')
    s += fs::path::preferred_separator;
  return s;
}
 
bool is3DGeometry(const std::string &g) {
  return g == "sphere" || g == "ellipsoid" || g == "cube" || g == "cuboid" || g == "cylinder" ||
         g == "sphere_minus_sphere" || g == "cuboid_minus_cuboid" || g == "open_cuboid_channel_3d";
}
 
bool isAcceptableGeometryName(const std::string &g) {
  for (const std::string &n : geom::getAcceptableGeometries()) {
    if (n == g)
      return true;
  }
  return false;
}
 
json buildInputJson(const std::string &geomName, const std::string &output_path_for_deck,
                    const std::filesystem::path &mesh_file_1,
                    const std::filesystem::path &mesh_file_2) {
 
  const double s = 0.001;
  const double mesh_size = s / 5.0;
  const double horizon = 3.0 * mesh_size;
  const double particle_dist = 0.001;
 
  const double poisson1 = 0.25;
  const double rho1 = 1200.0;
  const double K1 = 2.16e+7;
  const double E1 = material::toE(K1, poisson1);
  const double G1 = material::toGE(E1, poisson1);
  const double Gc1 = 50.0;
 
  const double poisson2 = 0.25;
  const double rho2 = 1200.0;
  const double K2 = 2.16e+7;
  const double E2 = material::toE(K2, poisson2);
  const double G2 = material::toGE(E2, poisson2);
  const double Gc2 = 50.0;
 
  const double R_contact_factor = 0.95;
  const double Kn_11 = 18.0 * util::harmonicMean(K1, K1) / (M_PI * std::pow(horizon, 5));
  const double Kn_22 = 18.0 * util::harmonicMean(K2, K2) / (M_PI * std::pow(horizon, 5));
  const double Kn_12 = 18.0 * util::harmonicMean(K1, K2) / (M_PI * std::pow(horizon, 5));
  const double beta_n_eps = 0.9;
  const double friction_coeff = 0.5;
  const double beta_n_factor = 100.0;
 
  const int model_dim = is3DGeometry(geomName) ? 3 : 2;
 
  /* Reference shapes at origin for both mesh groups (same as twop_circ_inbuilt). */
  const util::Point origin(0.0, 0.0, 0.0);
  const std::vector<double> gp_ref = geom::exampleGeomParams(geomName, origin, s);
 
  /* Same integration window and IC gap as twop_circ_inbuilt (stable dt). */
  const double final_time = 0.0001; // 0.012;
  const size_t num_steps = 1000; //36000;
  const size_t dt_out_n = num_steps / 4; // 10;
 
  auto modelDeckJson = inp::ModelDeck::getExampleJson(static_cast<size_t>(model_dim), final_time, num_steps,
                                                      "finite_difference", "central_difference",
                                                      true, 2, "Multi_Particle", 0);
 
  auto outputDeckJson = inp::OutputDeck::getExampleJson("vtu", output_path_for_deck,
      std::vector<std::string>({"Displacement", "Velocity", "Force", "Damage_Z", "Damage", "Particle_ID"}),
      dt_out_n, 2, true, "zlib", true, 1, "", true);
 
  auto bcDeckJson = inp::BCDeck::getExampleJson(0, 1, 1, true, util::Point(0, -10, 0));
 
  bcDeckJson["Displacement_BC"]["Set_1"] = inp::BCBaseDeck::getExampleJson("Displacement_BC", false, geom::GeomData(),
      {0}, {}, "", {}, "", {},
      {1, 2}, true, "", {});
 
  const double free_fall_dist = particle_dist - horizon;
  const double free_fall_vel = -std::sqrt(2.0 * std::abs(-10.0) * std::max(1e-30, free_fall_dist));
  bcDeckJson["IC"]["Set_1"] = inp::BCBaseDeck::getExampleJson("IC", false, geom::GeomData(),
      {1}, {}, "", {}, "", {},
      {}, false, "Constant_Velocity", {0.0, free_fall_vel, 0.0});
 
  auto pDeckJson = json({});
 
  std::vector<geom::GeomData> pGeomVec(2);
  pGeomVec[0].d_geomName = geomName;
  pGeomVec[0].d_geomParams = gp_ref;
  pGeomVec[1].d_geomName = geomName;
  pGeomVec[1].d_geomParams = gp_ref;
 
  pDeckJson["Particle"] = inp::ParticleDeck::getParticleGeomExampleJson(pGeomVec);
 
  const std::string f1 = mesh_file_1.string();
  const std::string f2 = mesh_file_2.string();
  auto meshSet1 = json({{"File", f1},
                        {"CreateMesh",
                         {{"Flag", true},
                          {"Info", "gmsh_builtin_mesh"},
                          {"Mesh_Size", mesh_size},
                          {"Write_Mesh_File", true}}}});
  auto meshSet2 = json({{"File", f2},
                        {"CreateMesh",
                         {{"Flag", true},
                          {"Info", "gmsh_builtin_mesh"},
                          {"Mesh_Size", mesh_size},
                          {"Write_Mesh_File", true}}}});
  pDeckJson["Mesh"] = json({{"Sets", 2}, {"Set_1", meshSet1}, {"Set_2", meshSet2}});
 
  auto pMatJson = inp::ParticleDeck::getParticleMaterialExampleJson(2);
  pMatJson["Set_1"] = inp::MaterialDeck::getExampleJson("PDState", false, horizon,
      0, rho1, K1, G1, Gc1, true, 1);
  pMatJson["Set_2"] = inp::MaterialDeck::getExampleJson("PDState", false, horizon,
      0, rho2, K2, G2, Gc2, true, 1);
  pDeckJson["Material"] = pMatJson;
 
  auto pContactJson = inp::ParticleDeck::getParticleContactExampleJson(2);
  json contact_base = inp::ContactPairDeck::getExampleJson(R_contact_factor,
      true, false, false,
      Kn_11, beta_n_eps, friction_coeff, 1.0, beta_n_factor, 1.0, 0.0, 0.0);
 
  pContactJson["Set_1_1"] = contact_base;
  pContactJson["Set_1_1"]["Kn"] = Kn_11;
  pContactJson["Set_1_2"] = contact_base;
  pContactJson["Set_1_2"]["Kn"] = Kn_12;
  pContactJson["Set_2_2"] = contact_base;
  pContactJson["Set_2_2"]["Kn"] = Kn_22;
  pDeckJson["Contact"] = pContactJson;
 
  pDeckJson["Neighbor"] = inp::PNeighborDeck::getExampleJson("simple_all", 10.0, 40, 0.5);
 
  auto pGenJson = inp::PGenDeck::getExampleJson("From_File");
  pGenJson["Data"]["N"] = 2;
 
  /*
   * Placement matches twop_circ: lower particle corner at (s,s[,s]); upper at
   * (s, 2*s + particle_dist + s, [s]) so vertical gap is particle_dist between
   * outer extents (same as R1=R2=s in twop_circ).
   */
  if (model_dim == 2) {
    pGenJson["Data"]["0"] = {
        {"x", s}, {"y", s}, {"z", 0.0},
        {"theta", 0.0}, {"s", 1.0},
        {"ax", 0.0}, {"ay", 0.0}, {"az", 1.0},
        {"geom_id", 0}, {"mat_id", 0}, {"contact_id", 0}
    };
    pGenJson["Data"]["1"] = {
        {"x", s}, {"y", 2.0 * s + particle_dist + s}, {"z", 0.0},
        {"theta", M_PI}, {"s", 1.0},
        {"ax", 0.0}, {"ay", 0.0}, {"az", 1.0},
        {"geom_id", 1}, {"mat_id", 1}, {"contact_id", 1}
    };
  } else {
    pGenJson["Data"]["0"] = {
        {"x", s}, {"y", s}, {"z", s},
        {"theta", 0.0}, {"s", 1.0},
        {"ax", 0.0}, {"ay", 0.0}, {"az", 1.0},
        {"geom_id", 0}, {"mat_id", 0}, {"contact_id", 0}
    };
    pGenJson["Data"]["1"] = {
        {"x", s}, {"y", 2.0 * s + particle_dist + s}, {"z", s},
        {"theta", M_PI}, {"s", 1.0},
        {"ax", 0.0}, {"ay", 0.0}, {"az", 1.0},
        {"geom_id", 1}, {"mat_id", 1}, {"contact_id", 1}
    };
  }
  pDeckJson["Particle_Generation"] = pGenJson;
 
  return json({{"Model", modelDeckJson},
               {"Output", outputDeckJson},
               {"Force_BC", bcDeckJson["Force_BC"]},
               {"Displacement_BC", bcDeckJson["Displacement_BC"]},
               {"IC", bcDeckJson["IC"]},
               {"Particle", pDeckJson["Particle"]},
               {"Mesh", pDeckJson["Mesh"]},
               {"Material", pDeckJson["Material"]},
               {"Contact", pDeckJson["Contact"]},
               {"Neighbor", pDeckJson["Neighbor"]},
               {"Particle_Generation", pDeckJson["Particle_Generation"]}});
}
 
} // namespace
 
int main(int argc, char *argv[]) {
 
  util::parallel::initMpi(argc, argv);
  int mpiSize = util::parallel::mpiSize(), mpiRank = util::parallel::mpiRank();
  util::io::print(std::format("Initialized MPI. MPI size = {}, MPI rank = {}\n", mpiSize, mpiRank));
  util::io::print(util::parallel::getMpiStatus()->printStr());
 
  util::io::InputParser input(argc, argv);
 
  unsigned int nThreads;
  if (input.cmdOptionExists("-nThreads"))
    nThreads = std::stoi(input.getCmdOption("-nThreads"));
  else {
    nThreads = std::thread::hardware_concurrency();
    util::io::print(std::format("Running test with default number of threads = {}\n", nThreads));
  }
  util::parallel::initNThreads(nThreads);
  util::io::print(std::format("Number of threads = {}\n", util::parallel::getNThreads()));
 
  namespace fs = std::filesystem;
  const fs::path cwd = fs::current_path();
 
  fs::path run_base = cwd;
  if (input.cmdOptionExists("-outputDir")) {
    fs::path p = input.getCmdOption("-outputDir");
    run_base = p.is_absolute() ? std::move(p) : cwd / p;
  }
 
  fs::path inp_base = run_base;
  if (input.cmdOptionExists("-inputDir")) {
    fs::path p = input.getCmdOption("-inputDir");
    inp_base = p.is_absolute() ? std::move(p) : cwd / p;
  }
 
  std::vector<std::string> geometriesToRun;
  if (input.cmdOptionExists("-allGeometries")) {
    geometriesToRun = geom::getAcceptableGeometries();
    util::io::print("twop_general_inbuilt: -allGeometries — running full geometry list.\n");
  } else if (input.cmdOptionExists("-geometry")) {
    const std::string g = input.getCmdOption("-geometry");
    if (!isAcceptableGeometryName(g))
      throw std::runtime_error(
          "twop_general_inbuilt: -geometry \"" + g +
          "\" is not in geom::acceptable_geometries.");
    geometriesToRun = {g};
    util::io::print(std::format("twop_general_inbuilt: single geometry = {}.\n", g));
  } else {
    geometriesToRun = {"circle"};
    util::io::print("twop_general_inbuilt: default geometry = circle (use -geometry <name> or -allGeometries).\n");
  }
 
  for (const std::string &geomName : geometriesToRun) {
    util::io::print(std::format("--- twop_general_inbuilt: geometry = {} ---\n", geomName));
 
    const fs::path out_dir = run_base / geomName / "out";
    const fs::path inp_dir = inp_base / geomName / "inp";
    fs::create_directories(out_dir);
    fs::create_directories(inp_dir);
 
    const std::string output_path_for_deck = directoryPathWithTrailingSep(out_dir);
 
    const fs::path mesh1 = inp_dir / (std::string("mesh_gen_1_") + geomName + ".msh");
    const fs::path mesh2 = inp_dir / (std::string("mesh_gen_2_") + geomName + ".msh");
 
    auto inputJson = buildInputJson(geomName, output_path_for_deck, mesh1, mesh2);
 
    const fs::path input_json_path = inp_dir / (std::string("input_") + geomName + ".json");
    {
      std::ofstream os(input_json_path);
      if (!os)
        throw std::runtime_error("Failed to open " + input_json_path.string() + " for writing.");
      os << inputJson.dump(2);
    }
    util::io::print(std::format("Output directory (VTU, log.txt): {}\n", fs::absolute(out_dir).string()));
    util::io::print(std::format("Input directory (input.json, meshes): {}\n", fs::absolute(inp_dir).string()));
    util::io::print(std::format("Wrote deck to {}\n", fs::absolute(input_json_path).string()));
 
    auto deck = std::make_shared<inp::Input>(inputJson);
 
    PeriDEMModel dem(deck);
    dem.run(deck);
  }
 
  return EXIT_SUCCESS;
}