Refactoring

Roll out C++20 features. Update headers with include-what-you-use.
Remove a few static variables. Avoid uses of non-qualified size_t.
Use east const and pragma once more often. Cleanup Doxygen blocks.
Remove utility functions when the STL provides alternatives.

Author: jngrad

maintainer/CI/build_cmake.sh

@@ -386,7 +386,6 @@ if [ "${with_coverage}" = true ] || [ "${with_coverage_python}" = true ]; then
         echo "Running lcov and gcov..."
         codecov_opts="${codecov_opts} --gcov"
         "${srcdir}/maintainer/CI/run_lcov.sh" coverage.info
-        rm coverage.info
     fi
     if [ "${with_coverage_python}" = true ]; then
         echo "Running python3-coverage..."

src/core/BoxGeometry.hpp

@@ -23,7 +23,6 @@
 #include "lees_edwards/LeesEdwardsBC.hpp"
 
 #include <utils/Vector.hpp>
-#include <utils/math/sgn.hpp>
 
 #include <bitset>
 #include <cassert>
@@ -176,6 +175,7 @@ class BoxGeometry {
    * @param box_l Length that should be set.
    */
   void set_length(Utils::Vector3d const &box_l) {
+    assert(box_l > Utils::Vector3d::broadcast(0.));
     m_length = box_l;
     m_length_inv = {1. / box_l[0], 1. / box_l[1], 1. / box_l[2]};
     m_length_half = 0.5 * box_l;
@@ -213,9 +213,8 @@ class BoxGeometry {
    *         periodic images, i.e. <tt>a - b</tt>.
    */
   template <typename T>
-  ESPRESSO_ATTR_ALWAYS_INLINE inline Utils::Vector<T, 3>
-  get_mi_vector(const Utils::Vector<T, 3> &a,
-                const Utils::Vector<T, 3> &b) const {
+  ESPRESSO_ATTR_ALWAYS_INLINE inline Utils::Vector3<T>
+  get_mi_vector(Utils::Vector3<T> const &a, Utils::Vector3<T> const &b) const {
     if (type() == BoxType::LEES_EDWARDS) {
       auto const shear_plane_normal = lees_edwards_bc().shear_plane_normal;
       auto a_tmp = a;
@@ -228,8 +227,8 @@ class BoxGeometry {
                                         m_length_inv, m_periodic);
     }
     assert(type() == BoxType::CUBOID);
-    return {get_mi_coord(a[0], b[0], 0), get_mi_coord(a[1], b[1], 1),
-            get_mi_coord(a[2], b[2], 2)};
+    return {get_mi_coord(a[0], b[0], 0u), get_mi_coord(a[1], b[1], 1u),
+            get_mi_coord(a[2], b[2], 2u)};
   }
 
   /**
@@ -247,13 +246,13 @@ class BoxGeometry {
    *         periodic images, i.e. <tt>a - b</tt>.
    */
   template <typename T>
-  ESPRESSO_ATTR_ALWAYS_INLINE inline Utils::Vector<T, 3>
+  ESPRESSO_ATTR_ALWAYS_INLINE inline Utils::Vector3<T>
   get_mi_vector(T const &a0, T const &a1, T const &a2, T const &b0, T const &b1,
                 T const &b2) const {
     if (type() == BoxType::LEES_EDWARDS) {
       auto const shear_plane_normal = lees_edwards_bc().shear_plane_normal;
-      auto a_tmp = Utils::Vector<T, 3>{a0, a1, a2};
-      auto b_tmp = Utils::Vector<T, 3>{b0, b1, b2};
+      auto a_tmp = Utils::Vector3<T>{a0, a1, a2};
+      auto b_tmp = Utils::Vector3<T>{b0, b1, b2};
       a_tmp[shear_plane_normal] = Algorithm::periodic_fold(
           a_tmp[shear_plane_normal], m_length[shear_plane_normal]);
       b_tmp[shear_plane_normal] = Algorithm::periodic_fold(
@@ -262,8 +261,8 @@ class BoxGeometry {
                                         m_length_inv, m_periodic);
     }
     assert(type() == BoxType::CUBOID);
-    return {get_mi_coord(a0, b0, 0), get_mi_coord(a1, b1, 1),
-            get_mi_coord(a2, b2, 2)};
+    return {get_mi_coord(a0, b0, 0u), get_mi_coord(a1, b1, 1u),
+            get_mi_coord(a2, b2, 2u)};
   }
 
   BoxType type() const { return m_type; }
@@ -293,8 +292,8 @@ class BoxGeometry {
       auto const shear_plane_normal = le.shear_plane_normal;
       auto const shear_direction = le.shear_direction;
       auto const dy = x[shear_plane_normal] - y[shear_plane_normal];
-      if (fabs(dy) > length_half()[shear_plane_normal]) {
-        ret[shear_direction] -= Utils::sgn(dy) * le.shear_velocity;
+      if (std::fabs(dy) > length_half()[shear_plane_normal]) {
+        ret[shear_direction] -= std::copysign(le.shear_velocity, dy);
       }
     }
     return ret;
@@ -329,7 +328,7 @@ class BoxGeometry {
    */
   auto folded_position(Utils::Vector3d const &pos) const {
     auto pos_folded = pos;
-    for (unsigned int i = 0u; i < 3u; i++) {
+    for (auto i = 0u; i < 3u; i++) {
       if (m_periodic[i]) {
         pos_folded[i] = Algorithm::periodic_fold(pos[i], m_length[i]);
       }

src/core/Particle.hpp

@@ -72,7 +72,7 @@ struct ThermalStonerWohlfarthParameters {
   /** angle between the director and dipole moment of a Stoner-Wohlfarth
    * particle */
   double phi0 = 0.;
-  /** saturation magnetisation of a polarisable particle */
+  /** saturation magnetisation of a polarizable particle */
   double sat_mag = 0.;
   /**
    * @brief Inverse anisotropy field in reduced units.

src/core/accumulators/AutoUpdateAccumulators.hpp

@@ -23,6 +23,8 @@
 
 #include "system/Leaf.hpp"
 
+#include <vector>
+
 namespace Accumulators {
 
 class AutoUpdateAccumulators : public System::Leaf<AutoUpdateAccumulators> {

src/core/analysis/statistics.cpp

@@ -30,8 +30,6 @@
 #include "Particle.hpp"
 #include "cell_system/CellStructure.hpp"
 #include "communication.hpp"
-#include "errorhandling.hpp"
-#include "npt.hpp"
 #include "particle_reduction.hpp"
 #include "system/System.hpp"
 
@@ -49,7 +47,6 @@
 #include <functional>
 #include <limits>
 #include <numbers>
-#include <stdexcept>
 #include <tuple>
 #include <utility>
 #include <vector>

src/core/bond_breakage/bond_breakage.cpp

@@ -31,8 +31,10 @@
 #include <boost/mpi.hpp>
 #include <boost/serialization/access.hpp>
 
+#include <algorithm>
 #include <cassert>
 #include <memory>
+#include <span>
 #include <unordered_set>
 #include <utility>
 #include <variant>

src/core/bond_breakage/bond_breakage.hpp

@@ -31,7 +31,7 @@
 
 namespace BondBreakage {
 
-/** Stores one or two bond parnters for pair/angle bonds */
+/** Stores one or two bond partners for pair/angle bonds */
 using BondPartners = std::array<std::optional<int>, 2>;
 
 enum class ActionType {

src/core/bond_error.hpp

@@ -18,8 +18,8 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef ESPRESSO_BOND_ERROR_HPP
-#define ESPRESSO_BOND_ERROR_HPP
+
+#pragma once
 
 #include <exception>
 #include <span>
@@ -47,5 +47,3 @@ struct BondInvalidSizeError : std::exception {
 
   int size;
 };
-
-#endif // ESPRESSO_BOND_ERROR_HPP

src/core/bonded_interactions/bonded_interaction_data.cpp

@@ -19,13 +19,10 @@
 
 #include "bonded_interaction_data.hpp"
 
-#include "BoxGeometry.hpp"
-#include "cell_system/CellStructure.hpp"
 #include "immersed_boundary/ImmersedBoundaries.hpp"
 #include "rigid_bond.hpp"
 #include "system/System.hpp"
 #include "thermalized_bond.hpp"
-#include "thermostat.hpp"
 
 #include <algorithm>
 #include <numeric>

src/core/bonded_interactions/bonded_interaction_data.hpp

@@ -26,7 +26,6 @@
 
 #include <config/config.hpp>
 
-#include "angle_common.hpp"
 #include "angle_cosine.hpp"
 #include "angle_cossquare.hpp"
 #include "angle_harmonic.hpp"
@@ -46,17 +45,16 @@
 #include "thermalized_bond.hpp"
 
 #include "BondList.hpp"
-#include "TabulatedPotential.hpp"
+#include "Particle.hpp"
 #include "system/Leaf.hpp"
 
 #include <algorithm>
 #include <cassert>
 #include <cmath>
+#include <memory>
 #include <optional>
-#include <stdexcept>
 #include <unordered_map>
 #include <variant>
-#include <vector>
 
 /** Interaction type for unused bonded interaction slots */
 struct NoneBond {
@@ -129,7 +127,7 @@ class BondedInteractionsMap : public System::Leaf<BondedInteractionsMap> {
   }
   virtual void activate_bond(mapped_type const &ptr);
   virtual void deactivate_bond(mapped_type const &ptr);
-  mapped_type at(key_type const &key) const { return m_params.at(key); }
+  mapped_type const &at(key_type const &key) const { return m_params.at(key); }
   bool contains(key_type const &key) const { return m_params.contains(key); }
   bool empty() const { return m_params.empty(); }
   auto size() const { return m_params.size(); }