Make header files self-contained (#3990)

Fixes #3977, closes #3905 (ESPResSo 4.2-dev now compiles on GCC 11) Explicitly include used header files to make source files self-contained and improve portability (see C++ Core Guidelines: [SF.11: Header files should be self-contained](https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#sf11-header-files-should-be-self-contained), [SF.10: Avoid dependencies on implicitly #included names](https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#sf10-avoid-dependencies-on-implicitly-included-names)). Description of changes: * apply suggestions from IWYU 10 * add missing includes revealed by an implementation of the `compile_commands.json`-based algorithm outlined in #3977 * remove unused includes and reduce visibility of large header files: * `Particle.hpp`: from 332 includes to 245 * `particle_data.hpp`: from 36 includes to 28 * address several issues: * remove a broken ifdef * register a unit test in CMake so it can run * remove unnecessary static globals in MMM1D GPU * dependency inversion for DPD interaction
espressomd · Nov 13, 2020 · 78bf03d · 78bf03d
2 parents 4f04a5b + 633302b
commit 78bf03d
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diff --git a/src/core/AtomDecomposition.cpp b/src/core/AtomDecomposition.cpp
@@ -21,11 +21,13 @@
 
 #include "AtomDecomposition.hpp"
 
+#include <utils/Vector.hpp>
+
 #include <boost/mpi/collectives/all_to_all.hpp>
-#include <boost/serialization/vector.hpp>
 
-#include <cassert>
+#include <cstddef>
 #include <limits>
+#include <vector>
 
 void AtomDecomposition::configure_neighbors() {
  std::vector<Cell *> red_neighbors;

diff --git a/src/core/AtomDecomposition.hpp b/src/core/AtomDecomposition.hpp
@@ -22,12 +22,17 @@
 #ifndef ESPRESSO_ATOM_DECOMPOSITION_HPP
 #define ESPRESSO_ATOM_DECOMPOSITION_HPP
 
+#include "Particle.hpp"
 #include "ParticleDecomposition.hpp"
+#include "ghosts.hpp"
 
+#include <utils/Span.hpp>
 #include <utils/Vector.hpp>
 
 #include <boost/mpi/communicator.hpp>
+#include <boost/optional.hpp>
 
+#include <utility>
 #include <vector>
 
 /**

diff --git a/src/core/BondList.hpp b/src/core/BondList.hpp
@@ -28,6 +28,8 @@
 #include <boost/serialization/access.hpp>
 #include <boost/serialization/array.hpp>
 #include <boost/version.hpp>
+
+#include <cstddef>
 #include <type_traits>
 
 /**

diff --git a/src/core/CudaDeviceAllocator.hpp b/src/core/CudaDeviceAllocator.hpp
@@ -1,3 +1,21 @@
+/*
+ * Copyright (C) 2010-2020 The ESPResSo project
+ *
+ * This file is part of ESPResSo.
+ *
+ * ESPResSo is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ESPResSo is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * 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_CUDA_DEVICE_ALLOCATOR_HPP
 #define ESPRESSO_CUDA_DEVICE_ALLOCATOR_HPP
 
@@ -12,6 +30,8 @@
 #include <thrust/device_ptr.h>
 #include <thrust/device_reference.h>
 
+#include <cstddef>
+
 /**
  * @brief Allocator that uses CUDA to allocate GPU memory.
  *

diff --git a/src/core/CudaHostAllocator.cu b/src/core/CudaHostAllocator.cu
@@ -1,7 +1,26 @@
+/*
+ * Copyright (C) 2010-2020 The ESPResSo project
+ *
+ * This file is part of ESPResSo.
+ *
+ * ESPResSo is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ESPResSo is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
 #include "CudaHostAllocator.hpp"
 
 #include <cuda.h>
 
+#include <cstddef>
 #include <stdexcept>
 
 void cuda_malloc_host(void **p, std::size_t n) {

diff --git a/src/core/CudaHostAllocator.hpp b/src/core/CudaHostAllocator.hpp
@@ -1,6 +1,25 @@
+/*
+ * Copyright (C) 2010-2020 The ESPResSo project
+ *
+ * This file is part of ESPResSo.
+ *
+ * ESPResSo is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ESPResSo is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * 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_CUDA_HOST_ALLOCATOR_HPP
 #define ESPRESSO_CUDA_HOST_ALLOCATOR_HPP
 
+#include <cstddef>
 #include <type_traits>
 #include <vector>
 

diff --git a/src/core/DomainDecomposition.cpp b/src/core/DomainDecomposition.cpp
@@ -21,8 +21,10 @@
 
 #include "DomainDecomposition.hpp"
 
+#include "RuntimeErrorStream.hpp"
 #include "errorhandling.hpp"
 
+#include <utils/Vector.hpp>
 #include <utils/index.hpp>
 #include <utils/mpi/cart_comm.hpp>
 #include <utils/mpi/sendrecv.hpp>
@@ -31,6 +33,14 @@
 #include <boost/range/algorithm/reverse.hpp>
 #include <boost/range/numeric.hpp>
 
+#include <algorithm>
+#include <array>
+#include <cmath>
+#include <cstddef>
+#include <functional>
+#include <iterator>
+#include <utility>
+
 /** Returns pointer to the cell which corresponds to the position if the
  * position is in the nodes spatial domain otherwise a nullptr pointer.
  */

diff --git a/src/core/DomainDecomposition.hpp b/src/core/DomainDecomposition.hpp
@@ -27,6 +27,18 @@
 #include "BoxGeometry.hpp"
 #include "LocalBox.hpp"
 
+#include "Cell.hpp"
+#include "Particle.hpp"
+#include "ParticleList.hpp"
+#include "ghosts.hpp"
+
+#include <utils/Span.hpp>
+#include <utils/Vector.hpp>
+
+#include <boost/optional.hpp>
+
+#include <vector>
+
 /** @brief Structure containing the information about the cell grid used for
  * domain decomposition.
  *

diff --git a/src/core/EspressoSystemInterface_cuda.cu b/src/core/EspressoSystemInterface_cuda.cu
@@ -17,13 +17,13 @@
  * along with this program. If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <cuda.h>
-
 #include "EspressoSystemInterface.hpp"
 #include "cuda_interface.hpp"
 #include "cuda_utils.hpp"
 #include "errorhandling.hpp"
 
+#include <cuda.h>
+
 #if defined(OMPI_MPI_H) || defined(_MPI_H)
 #error CU-file includes mpi.h! This should not happen!
 #endif

diff --git a/src/core/MpiCallbacks.hpp b/src/core/MpiCallbacks.hpp
@@ -30,11 +30,14 @@
 #include <boost/mpi/collectives/all_reduce.hpp>
 #include <boost/mpi/collectives/broadcast.hpp>
 #include <boost/mpi/communicator.hpp>
+#include <boost/optional.hpp>
 #include <boost/range/algorithm/remove_if.hpp>
 
 #include <functional>
 #include <initializer_list>
+#include <memory>
 #include <tuple>
+#include <type_traits>
 #include <utility>
 
 namespace Communication {

diff --git a/src/core/Observable_stat.cpp b/src/core/Observable_stat.cpp
@@ -25,6 +25,10 @@
 
 #include "bonded_interactions/bonded_interaction_data.hpp"
 
+#include <utils/Span.hpp>
+
+#include <cstddef>
+
 Observable_stat::Observable_stat(size_t chunk_size) : m_chunk_size(chunk_size) {
  // number of chunks for different interaction types
  auto constexpr n_coulomb = 2;

diff --git a/src/core/Observable_stat.hpp b/src/core/Observable_stat.hpp
@@ -26,7 +26,9 @@
 #include <utils/index.hpp>
 
 #include <algorithm>
-#include <utility>
+#include <cassert>
+#include <cstddef>
+#include <functional>
 #include <vector>
 
 /** Observable for the pressure and energy. */

diff --git a/src/core/PartCfg.cpp b/src/core/PartCfg.cpp
@@ -22,8 +22,13 @@
 #include "grid.hpp"
 #include "particle_data.hpp"
 
+#include <utils/Span.hpp>
+
 #include <boost/algorithm/clamp.hpp>
 
+#include <algorithm>
+#include <cstddef>
+
 void PartCfg::update() {
  if (m_valid)
  return;

diff --git a/src/core/PartCfg.hpp b/src/core/PartCfg.hpp
@@ -21,6 +21,7 @@
 
 #include "Particle.hpp"
 
+#include <cstddef>
 #include <vector>
 
 /**

diff --git a/src/core/Particle.hpp b/src/core/Particle.hpp
@@ -37,6 +37,19 @@ enum : uint8_t {
  ROTATION_Z = 4u
 };
 
+#ifdef EXTERNAL_FORCES
+/**
+ * \ref ParticleProperties::ext_flag "ext_flag" value for fixed coordinate
+ * @c coord.
+ */
+#define COORD_FIXED(coord) (2u << (coord))
+/** \ref ParticleProperties::ext_flag "ext_flag" mask to check whether any of
+ * the coordinates is fixed. */
+#define COORDS_FIX_MASK (COORD_FIXED(0) | COORD_FIXED(1) | COORD_FIXED(2))
+#else
+#define COORD_FIXED(coord) (0)
+#endif
+
 struct ParticleParametersSwimming {
  bool swimming = false;
  double f_swim = 0.;

diff --git a/src/core/ParticleDecomposition.hpp b/src/core/ParticleDecomposition.hpp
@@ -27,8 +27,11 @@
 #include <utils/Span.hpp>
 #include <utils/Vector.hpp>
 
+#include <boost/optional.hpp>
 #include <boost/variant.hpp>
 
+#include <vector>
+
 struct RemovedParticle {
  int id;
 };

diff --git a/src/core/RuntimeError.cpp b/src/core/RuntimeError.cpp
@@ -21,6 +21,7 @@
 
 #include <iostream>
 #include <sstream>
+#include <string>
 
 namespace ErrorHandling {
 

diff --git a/src/core/RuntimeErrorCollector.cpp b/src/core/RuntimeErrorCollector.cpp
@@ -18,11 +18,12 @@
  */
 #include "RuntimeErrorCollector.hpp"
 
-#include "communication.hpp"
 #include <utils/mpi/gather_buffer.hpp>
 
 #include <boost/mpi/collectives.hpp>
 
+#include <algorithm>
+#include <functional>
 #include <iostream>
 #include <sstream>
 #include <utility>

diff --git a/src/core/RuntimeErrorCollector.hpp b/src/core/RuntimeErrorCollector.hpp
@@ -20,13 +20,13 @@
 #ifndef ERROR_HANDLING_RUNTIMEERRORCOLLECTOR_HPP
 #define ERROR_HANDLING_RUNTIMEERRORCOLLECTOR_HPP
 
-#include <sstream>
-#include <string>
-#include <vector>
+#include "RuntimeError.hpp"
 
 #include <boost/mpi/communicator.hpp>
 
-#include "RuntimeError.hpp"
+#include <sstream>
+#include <string>
+#include <vector>
 
 namespace ErrorHandling {
 

diff --git a/src/core/RuntimeErrorStream.hpp b/src/core/RuntimeErrorStream.hpp
@@ -19,11 +19,11 @@
 #ifndef ERROR_HANDLING_RUNTIME_ERROR_STREAM_HPP
 #define ERROR_HANDLING_RUNTIME_ERROR_STREAM_HPP
 
+#include "RuntimeError.hpp"
+
 #include <sstream>
 #include <string>
 
-#include "RuntimeError.hpp"
-
 namespace ErrorHandling {
 
 class RuntimeErrorCollector;

diff --git a/src/core/SystemInterface.hpp b/src/core/SystemInterface.hpp
@@ -21,7 +21,6 @@
 
 #include "config.hpp"
 #include <utils/Vector.hpp>
-#include <vector>
 
 /** @todo: Turn needsXY in getter/setter **/
 

diff --git a/src/core/accumulators.cpp b/src/core/accumulators.cpp
@@ -21,7 +21,9 @@
 #include <boost/range/algorithm/remove_if.hpp>
 #include <boost/range/numeric.hpp>
 
+#include <algorithm>
 #include <cassert>
+#include <limits>
 #include <vector>
 
 namespace Accumulators {

diff --git a/src/core/accumulators/Correlator.cpp b/src/core/accumulators/Correlator.cpp
@@ -17,8 +17,11 @@
  * along with this program. If not, see <http://www.gnu.org/licenses/>.
  */
 #include "Correlator.hpp"
+
 #include "integrate.hpp"
 
+#include <utils/Vector.hpp>
+#include <utils/math/sqr.hpp>
 #include <utils/serialization/multi_array.hpp>
 
 #include <boost/archive/binary_iarchive.hpp>
@@ -29,10 +32,15 @@
 #include <boost/serialization/string.hpp>
 #include <boost/serialization/vector.hpp>
 
-#include <utils/math/sqr.hpp>
-
 #include <algorithm>
-#include <limits>
+#include <array>
+#include <cassert>
+#include <cmath>
+#include <cstddef>
+#include <functional>
+#include <numeric>
+#include <sstream>
+#include <stdexcept>
 
 namespace {
 int min(int i, unsigned int j) { return std::min(i, static_cast<int>(j)); }