Format files and fix --std=c++17 problem

Author: Ruochun

src/DEM/API.h

@@ -355,7 +355,8 @@ class DEMSolver {
     void SetCDFutureDriftEffDriftSafetyFactor(float factor) {
         future_drift_eff_drift_safety_factor = clampBetween(factor, 1.0f, 10.0f);
     }
-    /// @brief Set bounds (as a fraction of max drift) that clamp dT's waiting behavior before sending a new kT work order.
+    /// @brief Set bounds (as a fraction of max drift) that clamp dT's waiting behavior before sending a new kT work
+    /// order.
     /// @details Default is lower=0, upper=1 (send as late as safely possible). `upper=0` makes dT send immediately
     /// (close to the old behavior, but still with the safety factor). Values must satisfy 0 <= lower <= upper <= 1.
     void SetCDFutureDriftSendBounds(float lower_ratio, float upper_ratio) {

src/DEM/APIPrivate.cpp

@@ -295,7 +295,7 @@ void DEMSolver::jitifyKernels() {
     equipIntegrationScheme(m_subs);
     equipKernelIncludes(m_subs);
 
-        // Jitify may require a defined device to derive the arch
+    // Jitify may require a defined device to derive the arch
     std::thread kT_build([&]() {
         DEME_GPU_CALL(cudaSetDevice(kT->streamInfo.device));
         kT->jitifyKernels(m_subs, m_jitify_options);
@@ -326,7 +326,6 @@ void DEMSolver::jitifyKernels() {
             }
         }
     }
-
 }
 
 void DEMSolver::getContacts_impl(std::vector<bodyID_t>& idA,
@@ -1196,29 +1195,32 @@ void DEMSolver::setSimParams() {
         // Silently bring down m_approx_max_vel
         m_approx_max_vel = threshold_error_out_vel;
     }
-    { // Adaptive Timestep -- currently only Hertz const. 
+    {  // Adaptive Timestep -- currently only Hertz const.
         if (adapt_ts_type == ADAPT_TS_TYPE::HERTZ_CONST) {
             auto sqr = [](double x) { return x * x; };
             auto effective_E = [&](double E1, double nu1, double E2, double nu2) -> double {
-                if (E1 <= 0.0 || E2 <= 0.0) return 0.0;
-                return 1.0 / ( ((1.0 - sqr(nu1)) / E1) + ((1.0 - sqr(nu2)) / E2) );
+                if (E1 <= 0.0 || E2 <= 0.0)
+                    return 0.0;
+                return 1.0 / (((1.0 - sqr(nu1)) / E1) + ((1.0 - sqr(nu2)) / E2));
             };  // max effektive E* over all material contacts
             double Eeff_max = 0.0;
             for (size_t i = 0; i < m_loaded_materials.size(); ++i) {
                 const auto& A = m_loaded_materials[i]->mat_prop;
-                const double E1  = (A.count("E")  ? (double)A.at("E")  : 0.0);
+                const double E1 = (A.count("E") ? (double)A.at("E") : 0.0);
                 const double nu1 = (A.count("nu") ? (double)A.at("nu") : 0.3);
                 for (size_t j = i; j < m_loaded_materials.size(); ++j) {
                     const auto& B = m_loaded_materials[j]->mat_prop;
-                    const double E2  = (B.count("E")  ? (double)B.at("E")  : 0.0);
+                    const double E2 = (B.count("E") ? (double)B.at("E") : 0.0);
                     const double nu2 = (B.count("nu") ? (double)B.at("nu") : 0.3);
                     const double Ee = effective_E(E1, nu1, E2, nu2);
-                    if (Ee > Eeff_max) Eeff_max = Ee;
+                    if (Ee > Eeff_max)
+                        Eeff_max = Ee;
                 }
-            } // lowest mass
+            }  // lowest mass
             double min_mass = std::numeric_limits<double>::infinity();
             for (double m : m_template_clump_mass)
-                if (m > 0.0 && m < min_mass) min_mass = m;
+                if (m > 0.0 && m < min_mass)
+                    min_mass = m;
             const double r_min = (double)m_smallest_radius;
             if (std::isfinite(min_mass) && r_min > 0.0 && Eeff_max > 0.0) {
                 const double R_eff = 0.5 * r_min;
@@ -1227,14 +1229,15 @@ void DEMSolver::setSimParams() {
                 const double dt_hertz = (PI / (2.0 * N_DT)) * std::sqrt(m_eff / KH);
                 if (dt_hertz > 0.0 && std::isfinite(dt_hertz)) {
                     m_ts_size = dt_hertz;  // <- set const. timestep
-                    DEME_INFO("Adaptive time step 'hertz_const': dt = %.9g  (m_min=%.6g, r_min=%.6g, E*=%.6g, N_DT=%.1f)",
-                            m_ts_size, min_mass, r_min, Eeff_max, N_DT);
+                    DEME_INFO(
+                        "Adaptive time step 'hertz_const': dt = %.9g  (m_min=%.6g, r_min=%.6g, E*=%.6g, N_DT=%.1f)",
+                        m_ts_size, min_mass, r_min, Eeff_max, N_DT);
                 } else {
                     DEME_WARNING("hertz_const erzeugte ungueltigen dt; behalte bisherigen Wert %.7g.", m_ts_size);
                 }
             } else {
                 DEME_WARNING("hertz_const: fehlende/ungueltige Daten (m_min=%g, r_min=%g, E*=%g); dt bleibt %.7g.",
-                            min_mass, r_min, Eeff_max, m_ts_size);
+                             min_mass, r_min, Eeff_max, m_ts_size);
             }
         }
     }

src/DEM/APIPublic.cpp

@@ -739,7 +739,8 @@ void DEMSolver::SetIntegrator(const std::string& intg) {
 
 void DEMSolver::SetAdaptiveTimeStepType(const std::string& type) {
     DEME_WARNING(
-        "SetAdaptiveTimeStepType is a beta feature, currently hertz_const calculates a fixed timestep based on particle size, mass and contact E-modulus.");
+        std::string("SetAdaptiveTimeStepType is a beta feature, currently hertz_const calculates a fixed timestep "
+                    "based on particle size, mass and contact E-modulus."));
     switch (hash_charr(type.c_str())) {
         case ("none"_):
             adapt_ts_type = ADAPT_TS_TYPE::NONE;
@@ -748,10 +749,10 @@ void DEMSolver::SetAdaptiveTimeStepType(const std::string& type) {
             adapt_ts_type = ADAPT_TS_TYPE::HERTZ_CONST;
             break;
         case ("max_vel"_):
-            adapt_ts_type = ADAPT_TS_TYPE::MAX_VEL; // Not implemented yet
+            adapt_ts_type = ADAPT_TS_TYPE::MAX_VEL;  // Not implemented yet
             break;
         case ("int_diff"_):
-            adapt_ts_type = ADAPT_TS_TYPE::INT_DIFF; // Not implemented yet
+            adapt_ts_type = ADAPT_TS_TYPE::INT_DIFF;  // Not implemented yet
             break;
         default:
             DEME_ERROR("Adaptive time step type %s is unknown. Please select another via SetAdaptiveTimeStepType.",
@@ -2206,8 +2207,6 @@ void DEMSolver::Initialize(bool dry_run) {
     // Always clear cache after init
     ClearCache();
 
-
-
     //// TODO: Give a warning if sys_initialized is true and the system is re-initialized: in that case, the user should
     /// know what they are doing
     sys_initialized = true;
@@ -2257,7 +2256,8 @@ void DEMSolver::ShowTimingStats() {
 void DEMSolver::SetGPUTimersEnabled(bool enabled) {
     m_gpu_timers_enabled = enabled;
 
-    // Note: SolverTimers uses cudaEventCreate/Destroy, which are device-scoped. Ensure we operate on the correct device.
+    // Note: SolverTimers uses cudaEventCreate/Destroy, which are device-scoped. Ensure we operate on the correct
+    // device.
     if (enabled) {
         DEME_GPU_CALL(cudaSetDevice(dT->streamInfo.device));
         dT->timers.EnableGpuTimers();

src/DEM/Defines.h

@@ -36,14 +36,15 @@ namespace deme {
 #define DEME_BIN_ENLARGE_RATIO_FOR_FACETS 0.001
 
 // A few pre-computed constants
-constexpr double ONE_OVER_THREE = 1. / 3.; // double for accurancy, all other consts here are used for FP32 or less critical calculations
+constexpr double ONE_OVER_THREE =
+    1. / 3.;  // double for accurancy, all other consts here are used for FP32 or less critical calculations
 constexpr float TWO_OVER_THREE = 2. / 3.;
 constexpr float FOUR_OVER_THREE = 4. / 3.;
 constexpr float FIVE_OVER_THREE = 5. / 3.;
 constexpr float PI = 3.1415926535897932385f;
 constexpr float PI_SQUARED = 9.869604401089358f;
 constexpr float TWO_TIMES_SQRT_FIVE_OVER_THREE = 2.58198889747161f;  // 2. * std::sqrt(5. / 3.)
-constexpr float TWO_TIMES_SQRT_FIVE_OVER_SIX = 1.825741858350554f; // 2. * std::sqrt(5. / 6.)
+constexpr float TWO_TIMES_SQRT_FIVE_OVER_SIX = 1.825741858350554f;   // 2. * std::sqrt(5. / 6.)
 
 constexpr uint8_t VOXEL_RES_POWER2 = sizeof(subVoxelPos_t) * DEME_BITS_PER_BYTE;
 constexpr uint8_t VOXEL_COUNT_POWER2 = sizeof(voxelID_t) * DEME_BITS_PER_BYTE;
@@ -536,7 +537,9 @@ const float DEFAULT_BOX_DOMAIN_ENLARGE_RATIO = 0.2;
 // Initial contact array size; does not matter that much as they can be resized anytime in simulation
 const contactPairs_t INITIAL_CONTACT_ARRAY_SIZE = 1024;
 // For the bin collecting
-struct AxisBounds { int imin, imax; };
+struct AxisBounds {
+    int imin, imax;
+};
 
 // #ifndef CUB_IGNORE_DEPRECATED_API
 // #define CUB_IGNORE_DEPRECATED_API