bump clang-tidy to 21

.clang-tidy

@@ -27,6 +27,7 @@ performance-*,
 -performance-enum-size,
 
 portability-*,
+-portability-avoid-pragma-once,
 
 readability-*,
 -readability-avoid-const-params-in-decls,
@@ -35,6 +36,8 @@ readability-*,
 -readability-function-cognitive-complexity,
 -readability-identifier-length,
 -readability-magic-numbers,
+-readability-make-member-function-const,
+-readability-math-missing-parentheses,
 -readability-named-parameter,
 -readability-redundant-inline-specifier,
 -readability-redundant-string-init,

.github/workflows/validate.yml

@@ -189,7 +189,7 @@ jobs:
 
   clang-tidy:
     runs-on: ubuntu-latest
-    container: xzzx/devel:clang-18
+    container: xzzx/devel:clang-21
     steps:
       - name: versions
         run: |
@@ -225,7 +225,7 @@ jobs:
 
       - name: run clang-tidy
         working-directory: ./source
-        run: run-clang-tidy-18 -p ../build -header-filter 'source' -j 2 '^(?!.*_deps).*$' 
+        run: run-clang-tidy-21 -p ../build -header-filter 'source' -j 2 '^(?!.*_deps).*$' 
 
   clang-format:
     runs-on: ubuntu-latest

examples/Argon/Argon.cpp

@@ -18,6 +18,7 @@
 #include <CLI/Config.hpp>
 #include <CLI/Formatter.hpp>
 #include <Kokkos_Core.hpp>
+#include <algorithm>
 #include <fstream>
 #include <iomanip>
 #include <iostream>
@@ -227,7 +228,7 @@ void LJ(Config& config)
             if ((config.temperature > 0_r) && (step > 5000))
             {
                 config.temperature -= 7.8e-3_r;
-                if (config.temperature < 0_r) config.temperature = 0_r;
+                config.temperature = std::max(config.temperature, 0_r);
             }
 
             langevinThermostat.set(config.gamma, config.temperature * 0.5_r, config.dt);

examples/Argon/MultiResArgon.cpp

@@ -18,6 +18,7 @@
 #include <CLI/Config.hpp>
 #include <CLI/Formatter.hpp>
 #include <Kokkos_Core.hpp>
+#include <algorithm>
 #include <fstream>
 #include <iomanip>
 #include <iostream>
@@ -243,7 +244,7 @@ void LJ(Config& config)
             if ((config.temperature > 0_r) && (step > 5000))
             {
                 config.temperature -= 7.8e-3_r;
-                if (config.temperature < 0_r) config.temperature = 0_r;
+                config.temperature = std::max(config.temperature, 0_r);
             }
 
             langevinThermostat.set(config.gamma, config.temperature * 0.5_r, config.dt);

examples/BinaryLennardJones/NPT.cpp

@@ -16,6 +16,8 @@
 
 #include <fmt/format.h>
 
+#include <algorithm>
+
 #include "action/BerendsenBarostat.hpp"
 #include "action/BerendsenThermostat.hpp"
 #include "action/LennardJones.hpp"
@@ -34,7 +36,7 @@ void npt(YAML::Node& config, data::Atoms& atoms, data::Subdomain& subdomain)
     constexpr real_t cellRatio = 0.5_r;
     const real_t skin = config["LJ"]["skin"].as<real_t>();
     auto rcVec = config["LJ"]["cutoff"].as<std::vector<real_t>>();
-    const real_t rc = *std::max_element(rcVec.begin(), rcVec.end());
+    const real_t rc = std::ranges::max(rcVec);
     const real_t neighborCutoff = rc + skin;
     auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
 

examples/BinaryLennardJones/NVT.cpp

@@ -16,6 +16,8 @@
 
 #include <fmt/format.h>
 
+#include <algorithm>
+
 #include "action/BerendsenThermostat.hpp"
 #include "action/LennardJones.hpp"
 #include "action/VelocityVerlet.hpp"
@@ -33,7 +35,7 @@ void nvt(YAML::Node& config, data::Atoms& atoms, const data::Subdomain& subdomai
     constexpr real_t cellRatio = 0.5_r;
     const real_t skin = config["LJ"]["skin"].as<real_t>();
     auto rcVec = config["LJ"]["cutoff"].as<std::vector<real_t>>();
-    const real_t rc = *std::max_element(rcVec.begin(), rcVec.end());
+    const real_t rc = std::ranges::max(rcVec);
     const real_t neighborCutoff = rc + skin;
     auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
 

examples/BinaryLennardJones/SPARTIAN.cpp

@@ -16,6 +16,7 @@
 
 #include <fmt/format.h>
 
+#include <algorithm>
 #include <fstream>
 
 #include "action/ContributeMoleculeForceToAtoms.hpp"
@@ -44,7 +45,7 @@ void spartian(YAML::Node& config,
     constexpr real_t cellRatio = 0.5_r;
     const real_t skin = config["LJ"]["skin"].as<real_t>();
     auto rcVec = config["LJ"]["cutoff"].as<std::vector<real_t>>();
-    const real_t rc = *std::max_element(rcVec.begin(), rcVec.end());
+    const real_t rc = std::ranges::max(rcVec);
     const real_t neighborCutoff = rc + skin;
     auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
 

mrmd/action/LennardJones.cpp

@@ -14,6 +14,8 @@
 
 #include "LennardJones.hpp"
 
+#include <algorithm>
+
 namespace mrmd::action
 {
 void LennardJones::apply(data::Atoms& atoms, HalfVerletList& verletList)
@@ -46,7 +48,7 @@ LennardJones::LennardJones(const std::vector<real_t>& cappingDistance,
                            const bool isShifted)
     : LJ_(cappingDistance, rc, sigma, epsilon, numTypes, isShifted), numTypes_(1)
 {
-    auto rcMax = *std::max_element(rc.begin(), rc.end());
+    auto rcMax = std::ranges::max(rc);
     rcSqr_ = rcMax * rcMax;
 }
 }  // namespace mrmd::action

mrmd/action/VelocityVerlet.cpp

@@ -14,6 +14,8 @@
 
 #include "VelocityVerlet.hpp"
 
+#include <algorithm>
+
 namespace mrmd
 {
 namespace action
@@ -42,7 +44,7 @@ real_t VelocityVerlet::preForceIntegrate(data::Atoms& atoms, const real_t dt)
         pos(idx, 2) += dz;
 
         auto distSqr = dx * dx + dy * dy + dz * dz;
-        if (distSqr > maxDistSqr) maxDistSqr = distSqr;
+        maxDistSqr = std::max(distSqr, maxDistSqr);
     };
     real_t maxDistSqr = 0_r;
     Kokkos::parallel_reduce(

mrmd/action/VelocityVerletLangevinThermostat.cpp

@@ -14,6 +14,8 @@
 
 #include "VelocityVerletLangevinThermostat.hpp"
 
+#include <algorithm>
+
 #include "util/math.hpp"
 
 namespace mrmd
@@ -72,7 +74,7 @@ real_t VelocityVerletLangevinThermostat::preForceIntegrate(data::Atoms& atoms, c
         dx[2] -= pos(idx, 2);
 
         auto distSqr = util::dot3(dx, dx);
-        if (distSqr > maxDistSqr) maxDistSqr = distSqr;
+        maxDistSqr = std::max(distSqr, maxDistSqr);
     };
     real_t maxDistSqr = 0_r;
     Kokkos::parallel_reduce("VelocityVerletLangevinThermostat::preForceIntegrate",

mrmd/communication/PeriodicMapping.cpp

@@ -14,6 +14,8 @@
 
 #include "PeriodicMapping.hpp"
 
+#include <algorithm>
+
 #include "data/Atoms.hpp"
 #include "data/Subdomain.hpp"
 
@@ -37,10 +39,7 @@ void mapIntoDomain(data::Atoms& atoms, const data::Subdomain& subdomain)
             if (subdomain.maxCorner[dim] <= x)
             {
                 x -= subdomain.diameter[dim];
-                if (x < subdomain.minCorner[dim])
-                {
-                    x = subdomain.minCorner[dim];
-                }
+                x = std::max(x, subdomain.minCorner[dim]);
             }
             if (x < subdomain.minCorner[dim])
             {

mrmd/datatypes.hpp

@@ -97,12 +97,12 @@ using real_t = double;
 using Point3D = Kokkos::Array<real_t, 3>;
 using Vector3D = Kokkos::Array<real_t, 3>;
 
-KOKKOS_INLINE_FUNCTION constexpr real_t operator"" _r(const long double val)
+KOKKOS_INLINE_FUNCTION constexpr real_t operator""_r(const long double val)
 {
     return static_cast<real_t>(val);
 }
 
-KOKKOS_INLINE_FUNCTION constexpr real_t operator"" _r(const unsigned long long val)
+KOKKOS_INLINE_FUNCTION constexpr real_t operator""_r(const unsigned long long val)
 {
     return static_cast<real_t>(val);
 }

pyMRMD/data.cpp

@@ -29,7 +29,7 @@
 namespace py = pybind11;
 
 template <class SLICE_T>
-py::array_t<typename SLICE_T::value_type> getNPArray(const SLICE_T slice)
+py::array_t<typename SLICE_T::value_type> getNPArray(const SLICE_T& slice)
 {
     static_assert(slice.viewRank() == 2 || slice.viewRank() == 3, "Invalid view rank dimension");
 

tests/NPT/NPT.cpp

@@ -117,24 +117,17 @@ class NPT : public ::testing::TestWithParam<Input>
     // void SetUp() override {}
     // void TearDown() override {}
 
-    data::Subdomain subdomain;
-    real_t volume;
-    data::Atoms atoms = data::Atoms(0);
-    real_t rho;
+    data::Subdomain subdomain = {{0_r, 0_r, 0_r}, {Config::Lx, Config::Lx, Config::Lx}, Config::neighborCutoff};
+    real_t volume = {subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2]};
+    data::Atoms atoms = {fillDomainWithAtomsSC(subdomain, idx_c(Config::rho * volume), 1_r)};
+    real_t rho = {real_c(atoms.numLocalAtoms) / volume};
     communication::GhostLayer ghostLayer;
-    action::LennardJones LJ = action::LennardJones(0_r, 0_r, 0_r, 0_r);
+    action::LennardJones LJ = {Config::rc, Config::sigma, Config::epsilon, 0.7_r * Config::sigma};
 
     HalfVerletList verletList;
 
 public:
-    NPT()
-        : subdomain({0_r, 0_r, 0_r}, {Config::Lx, Config::Lx, Config::Lx}, Config::neighborCutoff),
-          volume(subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2]),
-          atoms(fillDomainWithAtomsSC(subdomain, idx_c(Config::rho * volume), 1_r)),
-          rho(real_c(atoms.numLocalAtoms) / volume),
-          LJ(Config::rc, Config::sigma, Config::epsilon, 0.7_r * Config::sigma)
-    {
-    }
+    NPT() = default;
 };
 
 TEST_P(NPT, pressure)

tests/NVT/NVT.cpp

@@ -102,24 +102,17 @@ class NVT : public ::testing::TestWithParam<real_t>
     // void SetUp() override {}
     // void TearDown() override {}
 
-    data::Subdomain subdomain;
-    real_t volume;
-    data::Atoms atoms;
-    real_t rho;
+    data::Subdomain subdomain = { {0_r, 0_r, 0_r}, {Config::Lx, Config::Lx, Config::Lx}, Config::neighborCutoff };
+    real_t volume = { subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2] };
+    data::Atoms atoms = { fillDomainWithAtomsSC(subdomain, idx_c(Config::rho * volume), 1_r) };
+    real_t rho = { real_c(atoms.numLocalAtoms) / volume };
     communication::GhostLayer ghostLayer;
-    action::LennardJones LJ;
+    action::LennardJones LJ = { Config::rc, Config::sigma, Config::epsilon, 0.7_r * Config::sigma };
 
     HalfVerletList verletList;
 
 public:
-    NVT()
-        : subdomain({0_r, 0_r, 0_r}, {Config::Lx, Config::Lx, Config::Lx}, Config::neighborCutoff),
-          volume(subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2]),
-          atoms(fillDomainWithAtomsSC(subdomain, idx_c(Config::rho * volume), 1_r)),
-          rho(real_c(atoms.numLocalAtoms) / volume),
-          LJ(Config::rc, Config::sigma, Config::epsilon, 0.7_r * Config::sigma)
-    {
-    }
+    NVT() = default;
 };
 
 TEST_P(NVT, pressure)