all_wo_vector

.gitlab-ci.yml

@@ -41,6 +41,40 @@ status_pending:
   stage: prepare
   script: sh maintainer/gh_post_status.sh pending
 
+style:
+  <<: *global_job_definition
+  stage: build
+  dependencies: []
+  before_script:
+    - git config --global --add safe.directory ${CI_PROJECT_DIR}
+    - git submodule deinit .
+  script:
+    - sh maintainer/CI/fix_style.sh
+  tags:
+    - espresso
+    - no-cuda
+  variables:
+    GIT_SUBMODULE_STRATEGY: none
+  artifacts:
+    paths:
+    - style.patch
+    expire_in: 1 week
+    when: on_failure
+
+style_doxygen:
+  <<: *global_job_definition
+  stage: build
+  dependencies: []
+  script:
+    - mkdir build
+    - cd build
+    - cp ../maintainer/configs/maxset.hpp myconfig.hpp
+    - cmake .. -D ESPRESSO_BUILD_WITH_CUDA=ON -D ESPRESSO_BUILD_WITH_GSL=ON -D ESPRESSO_BUILD_WITH_HDF5=ON -D ESPRESSO_BUILD_WITH_SCAFACOS=ON -D ESPRESSO_BUILD_WITH_WALBERLA=ON -D ESPRESSO_BUILD_WITH_WALBERLA_FFT=ON -D ESPRESSO_BUILD_WITH_STOKESIAN_DYNAMICS=ON -D ESPRESSO_BUILD_WITH_CALIPER=ON
+    - sh ../maintainer/CI/dox_warnings.sh
+  tags:
+    - espresso
+    - no-cuda
+
 ### Builds without CUDA
 
 default:
@@ -402,6 +436,29 @@ empty:
     - cuda
     - numa
 
+check_sphinx:
+  <<: *global_job_definition
+  stage: additional_checks
+  needs:
+    - cuda12-maxset
+  when: on_success
+  script:
+    - cd ${CI_PROJECT_DIR}/build
+    - make -t && make sphinx
+    - make -j2 tutorials
+    - make check_utils
+    - bash ${CI_PROJECT_DIR}/maintainer/CI/doc_warnings.sh
+    - python3 ${CI_PROJECT_DIR}/maintainer/CI/jupyter_warnings.py
+  artifacts:
+    paths:
+    - build/doc/sphinx
+    expire_in: 1 week
+  tags:
+    - espresso
+    - cuda
+    - numa
+    - reuse-artifacts-same-arch
+
 run_tutorials:
   <<: *global_job_definition
   stage: additional_checks
@@ -430,6 +487,25 @@ run_tutorials:
   only:
     - schedules
 
+run_doxygen:
+  <<: *global_job_definition
+  stage: additional_checks
+  needs:
+    - cuda12-maxset
+  when: on_success
+  script:
+    - cd ${CI_PROJECT_DIR}/build
+    - make -t && make doxygen
+  artifacts:
+    paths:
+    - build/doc/doxygen
+    expire_in: 1 week
+  tags:
+    - espresso
+    - no-cuda
+    - numa
+    - reuse-artifacts-same-arch
+
 maxset_no_gpu:
   <<: *global_job_definition
   stage: additional_checks

maintainer/walberla_kernels/code_generation_context.py

@@ -26,7 +26,6 @@
 import pystencils_walberla
 
 
-
 def earmark_generated_kernels():
     """
     Add an earmark at the beginning of generated kernels to document the

maintainer/walberla_kernels/generate_lb_kernels.py

@@ -149,7 +149,9 @@ def paramlist(parameters, keys):
             params
         )
 
-    block_offsets = tuple(ps.TypedSymbol(f"block_offset_{i}", np.uint32) for i in range(3))
+    block_offsets = tuple(
+        ps.TypedSymbol(f"block_offset_{i}", np.uint32)
+        for i in range(3))
 
     # generate thermalized LB
     collision_rule_thermalized = lbmpy.creationfunctions.create_lb_collision_rule(

maintainer/walberla_kernels/lbmpy_espresso.py

@@ -46,11 +46,11 @@ def data_initialisation(self, direction):
         cell_args = [f"it.{direction}() + {bb_vec[i]}".replace('+ -', '-')
                      for i, direction in enumerate("xyz")]
         code = [
-          "auto const InitialisationAdditionalData = elementInitialiser(",
-          f"Cell({', '.join(cell_args)}), blocks, *block);",
-          "element.vel_0 = InitialisationAdditionalData[0];",
-          "element.vel_1 = InitialisationAdditionalData[1];",
-          "element.vel_2 = InitialisationAdditionalData[2];",
+            "auto const InitialisationAdditionalData = elementInitialiser(",
+            f"Cell({', '.join(cell_args)}), blocks, *block);",
+            "element.vel_0 = InitialisationAdditionalData[0];",
+            "element.vel_1 = InitialisationAdditionalData[1];",
+            "element.vel_2 = InitialisationAdditionalData[2];",
         ]
         return "\n".join(code)
 

src/core/unit_tests/p3m_test.cpp

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010-2022 The ESPResSo project
+ * Copyright (C) 2020-2022 The ESPResSo project
  *
  * This file is part of ESPResSo.
  *
@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#define BOOST_TEST_MODULE p3m test
+#define BOOST_TEST_MODULE "P3M utility functions"
 #define BOOST_TEST_DYN_LINK
 #include <boost/test/unit_test.hpp>
 

src/shapes/include/shapes/Ellipsoid.hpp

@@ -23,7 +23,7 @@
 #define SHAPES_ELLIPSOID_HPP
 
 #include "Shape.hpp"
-#include <utils/Array.hpp>
+
 #include <utils/Vector.hpp>
 
 namespace Shapes {

src/shapes/src/HollowConicalFrustum.cpp

@@ -20,9 +20,10 @@
 #include <shapes/HollowConicalFrustum.hpp>
 
 #include <utils/Vector.hpp>
-#include <utils/math/abs.hpp>
 #include <utils/math/coordinate_transformation.hpp>
 
+#include <cmath>
+
 namespace Shapes {
 void HollowConicalFrustum::calculate_dist(const Utils::Vector3d &pos,
                                           double &dist,
@@ -70,7 +71,7 @@ void HollowConicalFrustum::calculate_dist(const Utils::Vector3d &pos,
    */
 
   auto endpoint_angle = pos_phi;
-  if (Utils::abs(pos_phi) < m_central_angle / 2.) {
+  if (std::fabs(pos_phi) < m_central_angle / 2.) {
     // Cannot use Utils::sgn because of pos_phi==0 corner case
     endpoint_angle =
         pos_phi > 0. ? m_central_angle / 2. : -m_central_angle / 2.;
@@ -93,7 +94,7 @@ void HollowConicalFrustum::calculate_dist(const Utils::Vector3d &pos,
   /* It can be that the projection onto the (infinite) line is outside the
    * frustum. In that case, the closest point is actually one of the endpoints.
    */
-  if (Utils::abs(pos_closest_hcf_frame[2]) > m_length / 2.) {
+  if (std::fabs(pos_closest_hcf_frame[2]) > m_length / 2.) {
     pos_closest_hcf_frame =
         pos_closest_hcf_frame[2] > 0. ? r1_endpoint : r2_endpoint;
   }

src/utils/include/utils/math/cylindrical_transformation_parameters.hpp

@@ -16,13 +16,14 @@
  * 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_CYLINDER_TRANSFORMATION_PARAMETERS_HPP
-#define ESPRESSO_CYLINDER_TRANSFORMATION_PARAMETERS_HPP
 
+#pragma once
+
+#include <cmath>
+#include <limits>
 #include <stdexcept>
 #include <string>
 
-#include <utils/math/abs.hpp>
 #include <utils/math/orthonormal_vec.hpp>
 
 namespace Utils {
@@ -63,30 +64,28 @@ class CylindricalTransformationParameters {
 
 private:
   void validate() const {
-    auto constexpr eps = 10 * std::numeric_limits<double>::epsilon();
-    if (Utils::abs(m_orientation * m_axis) > eps) {
+    auto constexpr eps = 10. * std::numeric_limits<double>::epsilon();
+    if (std::fabs(m_orientation * m_axis) > eps) {
       throw std::runtime_error(
           "CylindricalTransformationParameters: Axis and orientation must be "
           "orthogonal. Scalar product is " +
           std::to_string(m_orientation * m_axis));
     }
-    if (Utils::abs(m_axis.norm() - 1) > eps) {
+    if (std::fabs(m_axis.norm() - 1.) > eps) {
       throw std::runtime_error("CylindricalTransformationParameters: Axis must "
                                "be normalized. Norm is " +
                                std::to_string(m_axis.norm()));
     }
-    if (Utils::abs(m_orientation.norm() - 1) > eps) {
+    if (std::fabs(m_orientation.norm() - 1.) > eps) {
       throw std::runtime_error("CylindricalTransformationParameters: "
                                "orientation must be normalized. Norm is " +
                                std::to_string(m_orientation.norm()));
     }
   }
 
-  const Utils::Vector3d m_center{};
-  const Utils::Vector3d m_axis{0, 0, 1};
-  const Utils::Vector3d m_orientation{1, 0, 0};
+  Utils::Vector3d const m_center{};
+  Utils::Vector3d const m_axis{0., 0., 1.};
+  Utils::Vector3d const m_orientation{1., 0., 0.};
 };
 
 } // namespace Utils
-
-#endif // ESPRESSO_CYLINDER_TRANSFORMATION_PARAMETERS_HPP

src/utils/include/utils/math/sqr.hpp

@@ -1,5 +1,7 @@
 /*
  * Copyright (C) 2010-2022 The ESPResSo project
+ * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
+ *   Max-Planck-Institute for Polymer Research, Theory Group
  *
  * This file is part of ESPResSo.
  *

src/utils/include/utils/quaternion.hpp

@@ -42,6 +42,7 @@
 #include "utils/Array.hpp"
 #include "utils/Vector.hpp"
 #include "utils/matrix.hpp"
+#include "utils/serialization/array.hpp"
 
 #include <cassert>
 #include <cstddef>

src/utils/tests/Vector_test.cpp

@@ -43,7 +43,8 @@
 using Utils::Vector;
 
 /* Number of nontrivial Baxter permutations of length 2n-1. (A001185) */
-#define TEST_NUMBERS {0, 1, 1, 7, 21, 112, 456, 2603, 13203}
+#define TEST_NUMBERS                                                           \
+  { 0, 1, 1, 7, 21, 112, 456, 2603, 13203 }
 
 constexpr int test_numbers[] = TEST_NUMBERS;
 constexpr std::size_t n_test_numbers = sizeof(test_numbers) / sizeof(int);
@@ -62,6 +63,17 @@ BOOST_AUTO_TEST_CASE(initializer_list_constructor) {
   BOOST_CHECK_THROW(Utils::Vector2d({1., 2., 3.}), std::length_error);
 }
 
+BOOST_AUTO_TEST_CASE(span_constructor) {
+  constexpr static std::array<int, n_test_numbers> values(TEST_NUMBERS);
+  constexpr auto view = std::span(values);
+  Vector<int, n_test_numbers> v(view);
+
+  BOOST_CHECK(std::equal(v.begin(), v.end(), test_numbers));
+
+  BOOST_CHECK_THROW(Utils::Vector3i{view}, std::length_error);
+  BOOST_CHECK_THROW(Utils::Vector3i{view.subspan(0u, 2u)}, std::length_error);
+}
+
 BOOST_AUTO_TEST_CASE(iterator_constructor) {
   Vector<int, n_test_numbers> v(std::begin(test_numbers),
                                 std::end(test_numbers));
@@ -105,8 +117,8 @@ BOOST_AUTO_TEST_CASE(range_constructor_test) {
 }
 
 BOOST_AUTO_TEST_CASE(unit_vector_test) {
-  BOOST_CHECK((Utils::unit_vector<int>(2) == Utils::Vector3i{0, 0, 1}));
-  BOOST_CHECK_THROW(Utils::unit_vector<double>(3), std::domain_error);
+  BOOST_CHECK((Utils::unit_vector<int>(2u) == Utils::Vector3i{0, 0, 1}));
+  BOOST_CHECK_THROW(Utils::unit_vector<double>(3u), std::domain_error);
 }
 
 BOOST_AUTO_TEST_CASE(test_norm2) {
@@ -187,6 +199,13 @@ BOOST_AUTO_TEST_CASE(algebraic_operators) {
     BOOST_CHECK(v4 == (v3 /= 2));
   }
 
+  {
+    Utils::Vector3i v3{2, 12, 91};
+    Utils::Vector3i v4{180, 30, 3};
+    auto v5 = 360 / v3;
+    BOOST_CHECK(v5 == v4);
+  }
+
   BOOST_CHECK((sqrt(Utils::Vector3d{1., 2., 3.}) ==
                Utils::Vector3d{sqrt(1.), sqrt(2.), sqrt(3.)}));
 

src/walberla_bridge/src/lattice_boltzmann/LBWalberlaImpl.hpp

@@ -585,9 +585,9 @@ class LBWalberlaImpl : public LBWalberlaBase {
     auto const omega_odd = odd_mode_relaxation_rate(omega);
     auto const blocks = get_lattice().get_blocks();
     m_kT = FloatType_c(kT);
-    auto obj = CollisionModelThermalized(
-        m_last_applied_force_field_id, m_pdf_field_id, m_kT, omega, omega,
-        omega_odd, omega, seed, uint32_t{0u});
+    auto obj = CollisionModelThermalized(m_last_applied_force_field_id,
+                                         m_pdf_field_id, m_kT, omega, omega,
+                                         omega_odd, omega, seed, uint32_t{0u});
     m_collision_model = std::make_shared<CollisionModel>(std::move(obj));
     m_run_collide_sweep = CollideSweepVisitor(blocks);
   }

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepDoublePrecisionLeesEdwards.h

@@ -56,7 +56,7 @@ class CollideSweepDoublePrecisionLeesEdwards {
                                          BlockDataID pdfsID_, double grid_size,
                                          double omega_shear, double v_s)
       : forceID(forceID_), pdfsID(pdfsID_), grid_size_(grid_size),
-        omega_shear_(omega_shear), v_s_(v_s) {};
+        omega_shear_(omega_shear), v_s_(v_s){};
 
   void run(IBlock *block);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepDoublePrecisionLeesEdwardsAVX.h

@@ -57,7 +57,7 @@ class CollideSweepDoublePrecisionLeesEdwardsAVX {
                                             double grid_size,
                                             double omega_shear, double v_s)
       : forceID(forceID_), pdfsID(pdfsID_), grid_size_(grid_size),
-        omega_shear_(omega_shear), v_s_(v_s) {};
+        omega_shear_(omega_shear), v_s_(v_s){};
 
   void run(IBlock *block);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepDoublePrecisionLeesEdwardsCUDA.h

@@ -59,7 +59,7 @@ class CollideSweepDoublePrecisionLeesEdwardsCUDA {
                                              double grid_size,
                                              double omega_shear, double v_s)
       : forceID(forceID_), pdfsID(pdfsID_), grid_size_(grid_size),
-        omega_shear_(omega_shear), v_s_(v_s) {};
+        omega_shear_(omega_shear), v_s_(v_s){};
 
   void run(IBlock *block, gpuStream_t stream = nullptr);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepDoublePrecisionThermalized.h

@@ -60,7 +60,7 @@ class CollideSweepDoublePrecisionThermalized {
       : forceID(forceID_), pdfsID(pdfsID_), kT_(kT), omega_bulk_(omega_bulk),
         omega_even_(omega_even), omega_odd_(omega_odd),
         omega_shear_(omega_shear), seed_(seed), time_step_(time_step),
-        configured_(false) {};
+        configured_(false){};
 
   void run(IBlock *block);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepDoublePrecisionThermalizedAVX.h

@@ -61,7 +61,7 @@ class CollideSweepDoublePrecisionThermalizedAVX {
       : forceID(forceID_), pdfsID(pdfsID_), kT_(kT), omega_bulk_(omega_bulk),
         omega_even_(omega_even), omega_odd_(omega_odd),
         omega_shear_(omega_shear), seed_(seed), time_step_(time_step),
-        configured_(false) {};
+        configured_(false){};
 
   void run(IBlock *block);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepDoublePrecisionThermalizedCUDA.h

@@ -61,7 +61,7 @@ class CollideSweepDoublePrecisionThermalizedCUDA {
       : forceID(forceID_), pdfsID(pdfsID_), kT_(kT), omega_bulk_(omega_bulk),
         omega_even_(omega_even), omega_odd_(omega_odd),
         omega_shear_(omega_shear), seed_(seed), time_step_(time_step),
-        configured_(false) {};
+        configured_(false){};
 
   void run(IBlock *block, gpuStream_t stream = nullptr);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepSinglePrecisionLeesEdwards.h

@@ -56,7 +56,7 @@ class CollideSweepSinglePrecisionLeesEdwards {
                                          BlockDataID pdfsID_, float grid_size,
                                          float omega_shear, float v_s)
       : forceID(forceID_), pdfsID(pdfsID_), grid_size_(grid_size),
-        omega_shear_(omega_shear), v_s_(v_s) {};
+        omega_shear_(omega_shear), v_s_(v_s){};
 
   void run(IBlock *block);
 

src/walberla_bridge/src/lattice_boltzmann/generated_kernels/CollideSweepSinglePrecisionLeesEdwardsAVX.h

@@ -57,7 +57,7 @@ class CollideSweepSinglePrecisionLeesEdwardsAVX {
                                             float grid_size, float omega_shear,
                                             float v_s)
       : forceID(forceID_), pdfsID(pdfsID_), grid_size_(grid_size),
-        omega_shear_(omega_shear), v_s_(v_s) {};
+        omega_shear_(omega_shear), v_s_(v_s){};
 
   void run(IBlock *block);