Enable clang-tidy checks

.clang-tidy

@@ -34,6 +34,7 @@ Checks: "*,
         -misc-unused-parameters,
         -hicpp-multiway-paths-covered,
         -cert-err58-cpp,
+        -cppcoreguidelines-pro-bounds-constant-array-index,
 
         google-readability-avoid-underscore-in-googletest-name,
         google-upgrade-googletest-case,
@@ -71,7 +72,6 @@ Checks: "*,
         -cppcoreguidelines-owning-memory,
         -cppcoreguidelines-prefer-member-initializer,
         -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
-        -cppcoreguidelines-pro-bounds-constant-array-index,
         -cppcoreguidelines-pro-bounds-pointer-arithmetic,
         -cppcoreguidelines-pro-type-cstyle-cast,
         -cppcoreguidelines-pro-type-member-init,
@@ -91,7 +91,6 @@ Checks: "*,
         -hicpp-member-init,
         -hicpp-no-array-decay,
         -hicpp-no-malloc,
-        -hicpp-signed-bitwise,
         -hicpp-special-member-functions,
         -hicpp-use-equals-default,
         -hicpp-use-noexcept,
@@ -102,7 +101,6 @@ Checks: "*,
         -llvm-header-guard,
         -llvm-include-order,
         -llvm-namespace-comment,
-        -misc-confusable-identifiers,
         -misc-const-correctness,
         -misc-non-private-member-variables-in-classes,
         -modernize-avoid-c-arrays,
@@ -122,7 +120,6 @@ Checks: "*,
         -readability-else-after-return,
         -readability-function-cognitive-complexity,
         -readability-identifier-length,
-        -readability-identifier-naming,
         -readability-implicit-bool-conversion,
         -readability-inconsistent-declaration-parameter-name,
         -readability-isolate-declaration,
@@ -148,25 +145,24 @@ CheckOptions:
   # - camel_Snake_Back
   # - Camel_Snake_Case
   # - aNy_CasE
-  #
-  # Entries that are commented out probably aren't needed but it should be verified
-  readability-identifier-naming.VariableCase: 'lower_case'
-  readability-identifier-naming.FunctionCase: 'Camel_Snake_Case'
+
+  # readability-identifier-naming.VariableCase: 'lower_case'
+  # readability-identifier-naming.FunctionCase: 'Camel_Snake_Case'
   readability-identifier-naming.NamespaceCase: 'lower_case'
   readability-identifier-naming.MacroDefinitionCase: 'UPPER_CASE'
   readability-identifier-naming.TypedefCase: 'CamelCase'
   readability-identifier-naming.TypeAliasCase: 'CamelCase'
   readability-identifier-naming.EnumCase: 'CamelCase'
-  readability-identifier-naming.ConstantCase: 'lower_case'
+  # readability-identifier-naming.ConstantCase: 'lower_case'
 
-  readability-identifier-naming.ConstantPrefix: 'k_'
-  readability-identifier-naming.GlobalVariablePrefix: 'g_'
+  # readability-identifier-naming.ConstantPrefix: 'k_'
+  # readability-identifier-naming.GlobalVariablePrefix: 'g_'
 
   readability-identifier-naming.ClassCase: 'CamelCase'
-  # readability-identifier-naming.MemberCase: 'lower_case'
-  # readability-identifier-naming.MethodCase: 'CamelCase'
-  readability-identifier-naming.PrivateMemberSuffix: '_'
-  readability-identifier-naming.PrivateMethodSuffix: '_'
+  # readability-identifier-naming.MemberCase: 'lower_case' # This entry might not be needed
+  # readability-identifier-naming.MethodCase: 'CamelCase' # This entry might not be needed
+  # readability-identifier-naming.PrivateMemberSuffix: '_'
+  # readability-identifier-naming.PrivateMethodSuffix: '_'
 
-  # readability-identifier-naming.StructCase: 'CamelCase'
+  hicpp-signed-bitwise.IgnorePositiveIntegerLiterals: 'true'
 ...

src/dust/dust_cuda_tests.cpp

@@ -37,7 +37,7 @@ TEST(tDUSTTestSputteringTimescale,
 
   bool is_true;
 
-  is_true = testingUtilities::nearlyEqualDbl(k_fiducial_num, test_num, abs_diff, ulps_diff);
+  is_true = testing_utilities::nearlyEqualDbl(k_fiducial_num, test_num, abs_diff, ulps_diff);
 
   EXPECT_TRUE(is_true) << "The fiducial value is:       " << k_fiducial_num << std::endl
                        << "The test value is:           " << test_num << std::endl
@@ -61,7 +61,7 @@ TEST(tDUSTTestSputteringGrowthRate,
 
   bool is_true;
 
-  is_true = testingUtilities::nearlyEqualDbl(k_fiducial_num, test_num, abs_diff, ulps_diff);
+  is_true = testing_utilities::nearlyEqualDbl(k_fiducial_num, test_num, abs_diff, ulps_diff);
 
   EXPECT_TRUE(is_true) << "The fiducial value is:       " << k_fiducial_num << std::endl
                        << "The test value is:           " << test_num << std::endl

src/grid/grid3D.cpp

@@ -265,7 +265,7 @@ void Grid3D::Initialize(struct parameters *P)
 #endif
 
 #ifdef COSMOLOGY
-  H.OUTPUT_SCALE_FACOR = not P->scale_outputs_file[0] == '\0';
+  H.OUTPUT_SCALE_FACOR = not(P->scale_outputs_file[0] == '\0');
 #endif
 
   H.Output_Initial = true;

src/hydro/hydro_cuda_tests.cu

@@ -72,7 +72,7 @@ TEST(tHYDROCalcDt3D, CorrectInputExpectCorrectOutput)
   double absoluteDiff;
   int64_t ulpsDiff;
   bool areEqual;
-  areEqual = testingUtilities::nearlyEqualDbl(fiducialDt, testData, absoluteDiff, ulpsDiff);
+  areEqual = testing_utilities::nearlyEqualDbl(fiducialDt, testData, absoluteDiff, ulpsDiff);
   EXPECT_TRUE(areEqual) << "The fiducial value is:       " << fiducialDt << std::endl
                         << "The test value is:           " << testData << std::endl
                         << "The absolute difference is:  " << absoluteDiff << std::endl
@@ -106,7 +106,7 @@ TEST(tHYDROHydroInverseCrossingTime, CorrectInputExpectCorrectOutput)
                                                             velocityZ, cellSizeX, cellSizeY, cellSizeZ, gamma);
 
   // Check results
-  testingUtilities::checkResults(fiducialInverseCrossingTime, testInverseCrossingTime, "inverse crossing time");
+  testing_utilities::checkResults(fiducialInverseCrossingTime, testInverseCrossingTime, "inverse crossing time");
 }
 // =============================================================================
 // End of tests for the hydroInverseCrossingTime function
@@ -140,7 +140,7 @@ TEST(tMHDMhdInverseCrossingTime, CorrectInputExpectCorrectOutput)
                              magneticZ, cellSizeX, cellSizeY, cellSizeZ, gamma);
 
   // Check results
-  testingUtilities::checkResults(fiducialInverseCrossingTime, testInverseCrossingTime, "inverse crossing time");
+  testing_utilities::checkResults(fiducialInverseCrossingTime, testInverseCrossingTime, "inverse crossing time");
 }
 // =============================================================================
 // End of tests for the mhdInverseCrossingTime function

src/io/io_tests.cpp

@@ -23,14 +23,14 @@ TEST(tHYDROtMHDReadGridHdf5, RestartSlowWaveExpectCorrectOutput)
   int const num_ranks = 4;
 
   // Generate the data to read from
-  systemTest::SystemTestRunner initializer(false, true, false);
+  system_test::SystemTestRunner initializer(false, true, false);
   initializer.numMpiRanks = num_ranks;
   initializer.chollaLaunchParams.append(" tout=0.0 outstep=0.0");
   initializer.launchCholla();
   std::string const read_directory = initializer.getOutputDirectory() + "/";
 
   // Reload data and run the test
-  systemTest::SystemTestRunner loadRun(false, true, false);
+  system_test::SystemTestRunner loadRun(false, true, false);
   loadRun.numMpiRanks = num_ranks;
   loadRun.chollaLaunchParams.append(" init=Read_Grid nfile=0 indir=" + read_directory);
 

src/main_tests.cpp

@@ -18,10 +18,10 @@
 #include "utils/testing_utilities.h"
 
 /// This is the global variable to store the path to the root of Cholla
-testingUtilities::GlobalString globalChollaRoot;
-testingUtilities::GlobalString globalChollaBuild;
-testingUtilities::GlobalString globalChollaMachine;
-testingUtilities::GlobalString globalMpiLauncher;
+testing_utilities::GlobalString globalChollaRoot;
+testing_utilities::GlobalString globalChollaBuild;
+testing_utilities::GlobalString globalChollaMachine;
+testing_utilities::GlobalString globalMpiLauncher;
 bool globalRunCholla;
 bool globalCompareSystemTestResults;
 

src/mhd/ct_electric_fields_tests.cu

@@ -31,6 +31,7 @@
  * \brief Test fixture for tMHDCalculateCTElectricFields test suite
  *
  */
+// NOLINTNEXTLINE(readability-identifier-naming)
 class tMHDCalculateCTElectricFields : public ::testing::Test
 {
  public:
@@ -116,9 +117,9 @@ class tMHDCalculateCTElectricFields : public ::testing::Test
     for (size_t i = 0; i < fiducialData.size(); i++) {
       int xid, yid, zid;
       cuda_utilities::compute3DIndices(i, nx, ny, xid, yid, zid);
-      testingUtilities::checkResults(fiducialData.at(i), testCTElectricFields.at(i),
-                                     "value at i = " + std::to_string(i) + ", xid  = " + std::to_string(xid) +
-                                         ", yid  = " + std::to_string(yid) + ", zid  = " + std::to_string(zid));
+      testing_utilities::checkResults(fiducialData.at(i), testCTElectricFields.at(i),
+                                      "value at i = " + std::to_string(i) + ", xid  = " + std::to_string(xid) +
+                                          ", yid  = " + std::to_string(yid) + ", zid  = " + std::to_string(zid));
     }
   }
 };
@@ -267,7 +268,7 @@ TEST(tMHDCTSlope, CorrectInputExpectCorrectOutput)
   ASSERT_EQ(test_data.size(), fiducial_data.size());
 
   for (size_t i = 0; i < test_data.size(); i++) {
-    testingUtilities::checkResults(fiducial_data.at(i), test_data.at(i), "");
+    testing_utilities::checkResults(fiducial_data.at(i), test_data.at(i), "");
   }
 }
 // =============================================================================

src/mhd/magnetic_divergence_tests.cu

@@ -61,7 +61,7 @@ TEST(tMHDGrid3DcheckMagneticDivergence, CorrectInputExpectCorrectOutput)
   MPI_Finalize();
   // Perform Comparison
   Real const fiducialDivergence = 3.6318132783263106 / 1E15;
-  testingUtilities::checkResults(fiducialDivergence, max_magnetic_divergence, "maximum divergence");
+  testing_utilities::checkResults(fiducialDivergence, max_magnetic_divergence, "maximum divergence");
 }
 // =============================================================================
 // End of tests for the magnetic field divergence functions

src/mhd/magnetic_update_tests.cu

@@ -25,6 +25,7 @@
  * \brief Test fixture for tMHDUpdateMagneticField3D test suite
  *
  */
+// NOLINTNEXTLINE(readability-identifier-naming)
 class tMHDUpdateMagneticField3D : public ::testing::Test
 {
  public:
@@ -103,9 +104,9 @@ class tMHDUpdateMagneticField3D : public ::testing::Test
     for (size_t i = 0; i < fiducialData.size(); i++) {
       int xid, yid, zid;
       cuda_utilities::compute3DIndices(i, nx, ny, xid, yid, zid);
-      testingUtilities::checkResults(fiducialData.at(i), destinationGrid.at(i),
-                                     "value at i = " + std::to_string(i) + ", xid  = " + std::to_string(xid) +
-                                         ", yid  = " + std::to_string(yid) + ", zid  = " + std::to_string(zid));
+      testing_utilities::checkResults(fiducialData.at(i), destinationGrid.at(i),
+                                      "value at i = " + std::to_string(i) + ", xid  = " + std::to_string(xid) +
+                                          ", yid  = " + std::to_string(yid) + ", zid  = " + std::to_string(zid));
     }
   }
 };

src/model/disk_ICs.cpp

@@ -748,7 +748,7 @@ void Grid3D::Disk_3D(parameters p)
   Real r_cool;
 
   // MW model
-  DiskGalaxy galaxy = Galaxies::MW;
+  DiskGalaxy galaxy = Galaxies::MW;  // NOLINT(cppcoreguidelines-slicing)
   // M82 model Galaxies::M82;
 
   M_vir = galaxy.getM_vir();    // viral mass in M_sun

src/mpi/mpi_routines.cpp

@@ -542,23 +542,25 @@ void DomainDecompositionBLOCK(struct parameters *P, struct Header *H, int nx_gin
 
 void Allocate_MPI_DeviceBuffers(struct Header *H)
 {
-  int xbsize = 0, ybsize = 0, zbsize = 0;
+  int xbsize, ybsize, zbsize;
   if (H->ny == 1 && H->nz == 1) {
     xbsize = H->n_fields * H->n_ghost;
     ybsize = 1;
     zbsize = 1;
   }
   // 2D
-  if (H->ny > 1 && H->nz == 1) {
+  else if (H->ny > 1 && H->nz == 1) {
     xbsize = H->n_fields * H->n_ghost * (H->ny - 2 * H->n_ghost);
     ybsize = H->n_fields * H->n_ghost * (H->nx);
     zbsize = 1;
   }
   // 3D
-  if (H->ny > 1 && H->nz > 1) {
+  else if (H->ny > 1 && H->nz > 1) {
     xbsize = H->n_fields * H->n_ghost * (H->ny - 2 * H->n_ghost) * (H->nz - 2 * H->n_ghost);
     ybsize = H->n_fields * H->n_ghost * (H->nx) * (H->nz - 2 * H->n_ghost);
     zbsize = H->n_fields * H->n_ghost * (H->nx) * (H->ny);
+  } else {
+    throw std::runtime_error("MPI buffer size failed to set.");
   }
 
   x_buffer_length = xbsize;

src/particles/feedback_CIC_gpu.cu

@@ -18,18 +18,18 @@
 
   #define TPB_FEEDBACK   128
   #define FEED_INFO_N    6
-  #define i_RES          1
-  #define i_UNRES        2
-  #define i_ENERGY       3
-  #define i_MOMENTUM     4
-  #define i_UNRES_ENERGY 5
+  #define I_RES          1  // unused
+  #define I_UNRES        2  // unused
+  #define I_ENERGY       3  // unused
+  #define I_MOMENTUM     4  // unused
+  #define I_UNRES_ENERGY 5  // used
 
-typedef curandStateMRG32k3a_t feedback_prng_t;
-// typedef curandStatePhilox4_32_10_t feedback_prng_t;
+typedef curandStateMRG32k3a_t FeedbackPrng;
+// typedef curandStatePhilox4_32_10_t FeedbackPrng;
 
 namespace supernova
 {
-feedback_prng_t* randStates;
+FeedbackPrng* randStates;
 part_int_t n_states;
 Real *dev_snr, snr_dt, time_sn_start, time_sn_end;
 int snr_n;
@@ -48,7 +48,7 @@ __device__ double atomicMax(double* address, double val)
 }
   #endif  // O_HIP
 
-__global__ void initState_kernel(unsigned int seed, feedback_prng_t* states)
+__global__ void initState_kernel(unsigned int seed, FeedbackPrng* states)
 {
   int id = blockIdx.x * blockDim.x + threadIdx.x;
   curand_init(seed, id, 0, &states[id]);
@@ -131,7 +131,7 @@ void supernova::initState(struct parameters* P, part_int_t n_local, Real allocat
 
   // Now initialize the poisson random number generator state.
   n_states = n_local * allocation_factor;
-  cudaMalloc((void**)&randStates, n_states * sizeof(feedback_prng_t));
+  cudaMalloc((void**)&randStates, n_states * sizeof(FeedbackPrng));
 
   int ngrid = (n_states - 1) / TPB_FEEDBACK + 1;
   dim3 grid(ngrid);
@@ -233,7 +233,7 @@ __global__ void Cluster_Feedback_Kernel(part_int_t n_local, part_int_t* id, Real
                                         Real xMax, Real yMax, Real zMax, Real dx, Real dy, Real dz, int nx_g, int ny_g,
                                         int nz_g, int n_ghost, Real t, Real dt, Real* dti, Real* info, Real* density,
                                         Real* gasEnergy, Real* energy, Real* momentum_x, Real* momentum_y,
-                                        Real* momentum_z, Real gamma, feedback_prng_t* states, Real* prev_dens,
+                                        Real* momentum_z, Real gamma, FeedbackPrng* states, Real* prev_dens,
                                         int* prev_N, short direction, Real* dev_snr, Real snr_dt, Real time_sn_start,
                                         Real time_sn_end, int n_step)
 {
@@ -308,7 +308,7 @@ __global__ void Cluster_Feedback_Kernel(part_int_t n_local, part_int_t* id, Real
 
           // N = (int) (average_num_sn + 0.5);
 
-          feedback_prng_t state;  // = states[0]; // load initial state
+          FeedbackPrng state;  // = states[0]; // load initial state
 
           curand_init(42, 0, 0, &state);
           unsigned long long skip = n_step * 10000 + id[gtid];
@@ -543,7 +543,7 @@ __global__ void Cluster_Feedback_Kernel(part_int_t n_local, part_int_t* id, Real
                   // atomicAdd(    &energy[indx], e );
                   // atomicAdd(   &density[indx], d );
 
-                  s_info[FEED_INFO_N * tid + i_UNRES_ENERGY] +=
+                  s_info[FEED_INFO_N * tid + I_UNRES_ENERGY] +=
                       direction * (px * px + py * py + pz * pz) / 2 / density[indx] * dV;
 
                   if (abs(momentum_x[indx] / density[indx]) >= C_L) {

src/reconstruction/plmc_cuda_tests.cu

@@ -151,7 +151,7 @@ TEST(tHYDROPlmcReconstructor, CorrectInputExpectCorrectOutput)
               ? 0.0
               : fiducial_interface_left.at(direction)[i];
 
-      testingUtilities::checkResults(
+      testing_utilities::checkResults(
           fiducial_val, test_val,
           "left interface at i=" + std::to_string(i) + ", in direction " + std::to_string(direction));
 
@@ -161,7 +161,7 @@ TEST(tHYDROPlmcReconstructor, CorrectInputExpectCorrectOutput)
                          ? 0.0
                          : fiducial_interface_right.at(direction)[i];
 
-      testingUtilities::checkResults(
+      testing_utilities::checkResults(
           fiducial_val, test_val,
           "right interface at i=" + std::to_string(i) + ", in direction " + std::to_string(direction));
     }
@@ -262,7 +262,7 @@ TEST(tMHDPlmcReconstructor, CorrectInputExpectCorrectOutput)
               ? 0.0
               : fiducial_interface_left.at(direction)[i];
 
-      testingUtilities::checkResults(
+      testing_utilities::checkResults(
           fiducial_val, test_val,
           "left interface at i=" + std::to_string(i) + ", in direction " + std::to_string(direction));
 
@@ -272,7 +272,7 @@ TEST(tMHDPlmcReconstructor, CorrectInputExpectCorrectOutput)
                          ? 0.0
                          : fiducial_interface_right.at(direction)[i];
 
-      testingUtilities::checkResults(
+      testing_utilities::checkResults(
           fiducial_val, test_val,
           "right interface at i=" + std::to_string(i) + ", in direction " + std::to_string(direction));
     }