Merge branch 'python' into rocm

src/core/CellStructure.hpp

@@ -53,25 +53,16 @@ enum Resort : unsigned {
 };
 }
 
-/** List of cell pointers. */
-struct CellPList {
-  ParticleRange particles() const {
-    /* Find first non-empty cell */
-    auto first = std::find_if(cell, cell + n,
-                              [](const Cell *c) { return not c->empty(); });
-
-    return {CellParticleIterator(first, cell + n),
-            CellParticleIterator(cell + n)};
-  }
-
-  Cell **begin() { return cell; }
-  Cell **end() { return cell + n; }
-
-  Cell *operator[](int i) { return assert(i < n), cell[i]; }
+namespace Cells {
+inline ParticleRange particles(Utils::Span<Cell *> cells) {
+  /* Find first non-empty cell */
+  auto first_non_empty = std::find_if(
+      cells.begin(), cells.end(), [](const Cell *c) { return not c->empty(); });
 
-  Cell **cell = nullptr;
-  int n = 0;
-};
+  return {CellParticleIterator(first_non_empty, cells.end()),
+          CellParticleIterator(cells.end())};
+}
+} // namespace Cells
 
 /** Describes a cell structure / cell system. Contains information
  *  about the communication of cell contents (particles, ghosts, ...)
@@ -199,12 +190,15 @@ struct CellStructure {
   double min_range;
 
   /** Return the global local_cells */
-  CellPList local_cells() {
-    return {m_local_cells.data(), static_cast<int>(m_local_cells.size())};
+  Utils::Span<Cell *> local_cells() {
+    return {m_local_cells.data(), m_local_cells.size()};
+  }
+
+  ParticleRange local_particles() {
+    return Cells::particles(Utils::make_span(m_local_cells));
   }
-  /** Return the global ghost_cells */
-  CellPList ghost_cells() {
-    return {m_ghost_cells.data(), static_cast<int>(m_ghost_cells.size())};
+  ParticleRange ghost_particles() {
+    return Cells::particles(Utils::make_span(m_ghost_cells));
   }
 
   /** Communicator to exchange ghost particles. */

src/core/EspressoSystemInterface.cpp

@@ -33,7 +33,7 @@ void EspressoSystemInterface::gatherParticles() {
 #ifdef CUDA
   if (m_gpu) {
     if (gpu_get_global_particle_vars_pointer_host()->communication_enabled) {
-      copy_part_data_to_gpu(cell_structure.local_cells().particles());
+      copy_part_data_to_gpu(cell_structure.local_particles());
       reallocDeviceMemory(gpu_get_particle_pointer().size());
       if (m_splitParticleStructGpu && (this_node == 0))
         split_particle_struct();

src/core/cells.cpp

@@ -198,7 +198,7 @@ unsigned topology_check_resort(int cs, unsigned local_resort) {
 /** Go through ghost cells and remove the ghost entries from the
     local particle index. */
 static void invalidate_ghosts() {
-  for (auto const &p : cell_structure.ghost_cells().particles()) {
+  for (auto const &p : cell_structure.ghost_particles()) {
     if (cell_structure.get_local_particle(p.identity()) == &p) {
       cell_structure.update_particle_index(p.identity(), nullptr);
     }
@@ -233,9 +233,7 @@ void cells_re_init(int new_cs, double range) {
 
   clear_particle_node();
 
-  for (auto &p : CellPList{old_local_cells.data(),
-                           static_cast<int>(old_local_cells.size())}
-                     .particles()) {
+  for (auto &p : Cells::particles(Utils::make_span(old_local_cells))) {
     cell_structure.add_particle(std::move(p));
   }
 
@@ -281,7 +279,8 @@ void fold_and_reset(Particle &p) {
  *
  * @returns List of Particles that do not belong on this node.
  */
-ParticleList sort_and_fold_parts(const CellStructure &cs, CellPList cells,
+ParticleList sort_and_fold_parts(const CellStructure &cs,
+                                 Utils::Span<Cell *> cells,
                                  std::vector<Cell *> &modified_cells) {
   ParticleList displaced_parts;
 
@@ -379,7 +378,7 @@ void cells_resort_particles(int global_flag) {
 
   displaced_parts.clear();
 
-  on_resort_particles(cell_structure.local_cells().particles());
+  on_resort_particles(cell_structure.local_particles());
 }
 
 /*************************************************/
@@ -404,14 +403,13 @@ void cells_on_geometry_change(int flags) {
 void check_resort_particles() {
   const double skin2 = Utils::sqr(skin / 2.0);
 
-  auto const level =
-      (std::any_of(cell_structure.local_cells().particles().begin(),
-                   cell_structure.local_cells().particles().end(),
-                   [&skin2](Particle const &p) {
-                     return (p.r.p - p.l.p_old).norm2() > skin2;
-                   }))
-          ? Cells::RESORT_LOCAL
-          : Cells::RESORT_NONE;
+  auto const level = (std::any_of(cell_structure.local_particles().begin(),
+                                  cell_structure.local_particles().end(),
+                                  [&skin2](Particle const &p) {
+                                    return (p.r.p - p.l.p_old).norm2() > skin2;
+                                  }))
+                         ? Cells::RESORT_LOCAL
+                         : Cells::RESORT_NONE;
 
   cell_structure.set_resort_particles(level);
 }
@@ -439,7 +437,7 @@ void cells_update_ghosts(unsigned data_parts) {
 
     /* Add the ghost particles to the index if we don't already
      * have them. */
-    for (auto &part : cell_structure.ghost_cells().particles()) {
+    for (auto &part : cell_structure.ghost_particles()) {
       if (cell_structure.get_local_particle(part.p.identity) == nullptr) {
         cell_structure.update_particle_index(part.identity(), &part);
       }

src/core/communication.cpp

@@ -598,8 +598,7 @@ void mpi_bcast_max_mu() { mpi_call_all(calc_mu_max); }
 
 /***** GALILEI TRANSFORM AND ASSOCIATED FUNCTIONS ****/
 void mpi_kill_particle_motion_slave(int rotation) {
-  local_kill_particle_motion(rotation,
-                             cell_structure.local_cells().particles());
+  local_kill_particle_motion(rotation, cell_structure.local_particles());
   on_particle_change();
 }
 
@@ -610,7 +609,7 @@ void mpi_kill_particle_motion(int rotation) {
 }
 
 void mpi_kill_particle_forces_slave(int torque) {
-  local_kill_particle_forces(torque, cell_structure.local_cells().particles());
+  local_kill_particle_forces(torque, cell_structure.local_particles());
   on_particle_change();
 }
 

src/core/debug.cpp

@@ -29,12 +29,12 @@
 #include <stdexcept>
 
 void check_particle_consistency() {
-  auto local_cells = cell_structure.local_cells();
-  auto const cell_part_cnt = local_cells.particles().size();
+  auto local_particles = cell_structure.local_particles();
+  auto const cell_part_cnt = local_particles.size();
 
   auto const max_id = cell_structure.get_max_local_particle_id();
 
-  for (auto const &p : local_cells.particles()) {
+  for (auto const &p : local_particles) {
     auto const id = p.identity();
 
     if (id < 0 || id > max_id) {

src/core/electrostatics_magnetostatics/coulomb.cpp

@@ -185,8 +185,8 @@ void integrate_sanity_check() {
 }
 
 void update_dependent_particles() {
-  iccp3m_iteration(cell_structure.local_cells().particles(),
-                   cell_structure.ghost_cells().particles());
+  iccp3m_iteration(cell_structure.local_particles(),
+                   cell_structure.ghost_particles());
 }
 
 void on_observable_calc() {

src/core/electrostatics_magnetostatics/mdlc_correction.cpp

@@ -39,7 +39,7 @@ DLC_struct dlc_params = {1e100, 0, 0, 0, 0};
 static double mu_max;
 
 void calc_mu_max() {
-  auto local_particles = cell_structure.local_cells().particles();
+  auto local_particles = cell_structure.local_particles();
   mu_max = std::accumulate(
       local_particles.begin(), local_particles.end(), 0.0,
       [](double mu, Particle const &p) { return std::max(mu, p.p.dipm); });

src/core/electrostatics_magnetostatics/p3m-dipolar.cpp

@@ -1795,7 +1795,7 @@ void dp3m_count_magnetic_particles() {
     tot_sums[i] = 0.0;
   }
 
-  for (auto const &p : cell_structure.local_cells().particles()) {
+  for (auto const &p : cell_structure.local_particles()) {
     if (p.p.dipm != 0.0) {
       node_sums[0] += p.calc_dip().norm2();
       node_sums[1] += 1.0;

src/core/electrostatics_magnetostatics/p3m.cpp

@@ -1697,7 +1697,7 @@ void p3m_count_charged_particles() {
     tot_sums[i] = 0.0;
   }
 
-  for (auto const &p : cell_structure.local_cells().particles()) {
+  for (auto const &p : cell_structure.local_particles()) {
     if (p.p.q != 0.0) {
       node_sums[0] += 1.0;
       node_sums[1] += Utils::sqr(p.p.q);

src/core/electrostatics_magnetostatics/scafacos.cpp

@@ -86,7 +86,7 @@ int ScafacosData::update_particle_data() {
 #endif
   }
 
-  for (auto const &p : cell_structure.local_cells().particles()) {
+  for (auto const &p : cell_structure.local_particles()) {
     auto const pos = folded_position(p.r.p, box_geo);
     positions.push_back(pos[0]);
     positions.push_back(pos[1]);
@@ -113,7 +113,7 @@ void ScafacosData::update_particle_forces() const {
   if (positions.empty())
     return;
 
-  for (auto &p : cell_structure.local_cells().particles()) {
+  for (auto &p : cell_structure.local_particles()) {
     if (!dipolar()) {
       p.f.f += coulomb.prefactor * p.p.q *
                Utils::Vector3d(Utils::Span<const double>(&(fields[it]), 3));

src/core/energy.cpp

@@ -97,9 +97,9 @@ void energy_calc(double *result, const double time) {
         add_non_bonded_pair_energy(p1, p2, d.vec21, sqrt(d.dist2), d.dist2);
       });
 
-  calc_long_range_energies(cell_structure.local_cells().particles());
+  calc_long_range_energies(cell_structure.local_particles());
 
-  auto local_parts = cell_structure.local_cells().particles();
+  auto local_parts = cell_structure.local_particles();
   Constraints::constraints.add_energy(local_parts, time, energy);
 
 #ifdef CUDA

src/core/forces.cpp

@@ -68,7 +68,7 @@ void init_forces(const ParticleRange &particles) {
   /* initialize ghost forces with zero
      set torque to zero for all and rescale quaternions
   */
-  for (auto &p : cell_structure.ghost_cells().particles()) {
+  for (auto &p : cell_structure.ghost_particles()) {
     p.f = init_ghost_force(p);
   }
 }
@@ -88,10 +88,10 @@ void force_calc(CellStructure &cell_structure) {
   prepare_local_collision_queue();
 #endif
 
-  auto particles = cell_structure.local_cells().particles();
-  auto ghost_particles = cell_structure.ghost_cells().particles();
+  auto particles = cell_structure.local_particles();
+  auto ghost_particles = cell_structure.ghost_particles();
 #ifdef ELECTROSTATICS
-  iccp3m_iteration(particles, cell_structure.ghost_cells().particles());
+  iccp3m_iteration(particles, cell_structure.ghost_particles());
 #endif
   init_forces(particles);
 

src/core/galilei.cpp

@@ -56,8 +56,8 @@ void local_kill_particle_forces(int torque, const ParticleRange &particles) {
 /* Calculate the CMS of the system */
 std::pair<Utils::Vector3d, double> local_system_CMS() {
   return boost::accumulate(
-      cell_structure.local_cells().particles(),
-      std::pair<Utils::Vector3d, double>{}, [](auto sum, const Particle &p) {
+      cell_structure.local_particles(), std::pair<Utils::Vector3d, double>{},
+      [](auto sum, const Particle &p) {
         if (not p.p.is_virtual) {
           return std::pair<Utils::Vector3d, double>{
               sum.first +
@@ -70,8 +70,8 @@ std::pair<Utils::Vector3d, double> local_system_CMS() {
 
 std::pair<Utils::Vector3d, double> local_system_CMS_velocity() {
   return boost::accumulate(
-      cell_structure.local_cells().particles(),
-      std::pair<Utils::Vector3d, double>{}, [](auto sum, const Particle &p) {
+      cell_structure.local_particles(), std::pair<Utils::Vector3d, double>{},
+      [](auto sum, const Particle &p) {
         if (not p.p.is_virtual) {
           return std::pair<Utils::Vector3d, double>{
               sum.first + p.p.mass * p.m.v, sum.second + p.p.mass};
@@ -82,7 +82,7 @@ std::pair<Utils::Vector3d, double> local_system_CMS_velocity() {
 
 /* Remove the CMS velocity */
 void local_galilei_transform(const Utils::Vector3d &cmsvel) {
-  for (auto &p : cell_structure.local_cells().particles()) {
+  for (auto &p : cell_structure.local_particles()) {
     p.m.v -= cmsvel;
   }
 }

src/core/immersed_boundary/ImmersedBoundaries.cpp

@@ -124,7 +124,7 @@ void ImmersedBoundaries::calc_volumes() {
   std::vector<double> tempVol(MaxNumIBM);
 
   // Loop over all particles on local node
-  for (auto const &p1 : cell_structure.local_cells().particles()) {
+  for (auto const &p1 : cell_structure.local_particles()) {
     // Check if particle has a BONDED_IA_IBM_TRIEL and a
     // BONDED_IA_IBM_VOLUME_CONSERVATION Basically this loops over all
     // triangles, not all particles First round to check for volume
@@ -226,7 +226,7 @@ void ImmersedBoundaries::calc_volumes() {
 /** Calculate and add the volume force to each node */
 void ImmersedBoundaries::calc_volume_force() {
   // Loop over all particles on local node
-  for (auto &p1 : cell_structure.local_cells().particles()) {
+  for (auto &p1 : cell_structure.local_particles()) {
 
     // Check if particle has a BONDED_IA_IBM_TRIEL and a
     // BONDED_IA_IBM_VOLUME_CONSERVATION. Basically this loops over all

src/core/integrate.cpp

@@ -192,7 +192,7 @@ int integrate(int n_steps, int reuse_forces) {
 
     if (integ_switch != INTEG_METHOD_STEEPEST_DESCENT) {
 #ifdef ROTATION
-      convert_initial_torques(cell_structure.local_cells().particles());
+      convert_initial_torques(cell_structure.local_particles());
 #endif
     }
 
@@ -216,11 +216,11 @@ int integrate(int n_steps, int reuse_forces) {
   for (int step = 0; step < n_steps; step++) {
     ESPRESSO_PROFILER_CXX_MARK_LOOP_ITERATION(integration_loop, step);
 
-    auto particles = cell_structure.local_cells().particles();
+    auto particles = cell_structure.local_particles();
 
 #ifdef BOND_CONSTRAINT
     if (n_rigidbonds)
-      save_old_pos(particles, cell_structure.ghost_cells().particles());
+      save_old_pos(particles, cell_structure.ghost_particles());
 #endif
 
     bool early_exit = integrator_step_1(particles);
@@ -245,7 +245,7 @@ int integrate(int n_steps, int reuse_forces) {
     // Communication step: distribute ghost positions
     cells_update_ghosts(global_ghost_flags());
 
-    particles = cell_structure.local_cells().particles();
+    particles = cell_structure.local_particles();
 
     force_calc(cell_structure);
 

src/core/particle_data.cpp

@@ -404,10 +404,10 @@ void mpi_who_has_slave(int, int) {
 
   sendbuf.resize(n_part);
 
-  auto end = std::transform(cell_structure.local_cells().particles().begin(),
-                            cell_structure.local_cells().particles().end(),
-                            sendbuf.data(),
-                            [](Particle const &p) { return p.p.identity; });
+  auto end =
+      std::transform(cell_structure.local_particles().begin(),
+                     cell_structure.local_particles().end(), sendbuf.data(),
+                     [](Particle const &p) { return p.p.identity; });
 
   auto npart = std::distance(sendbuf.data(), end);
   MPI_Send(sendbuf.data(), npart, MPI_INT, 0, SOME_TAG, comm_cart);
@@ -444,9 +444,7 @@ void mpi_who_has(const ParticleRange &particles) {
 /**
  * @brief Rebuild the particle index.
  */
-void build_particle_node() {
-  mpi_who_has(cell_structure.local_cells().particles());
-}
+void build_particle_node() { mpi_who_has(cell_structure.local_particles()); }
 
 /**
  *  @brief Get the mpi rank which owns the particle with id.
@@ -890,7 +888,7 @@ Particle *local_place_particle(int id, const Utils::Vector3d &pos, int _new) {
 }
 
 void local_rescale_particles(int dir, double scale) {
-  for (auto &p : cell_structure.local_cells().particles()) {
+  for (auto &p : cell_structure.local_particles()) {
     if (dir < 3)
       p.r.p[dir] *= scale;
     else {
@@ -902,7 +900,7 @@ void local_rescale_particles(int dir, double scale) {
 #ifdef EXCLUSIONS
 void local_change_exclusion(int part1, int part2, int _delete) {
   if (part1 == -1 && part2 == -1) {
-    for (auto &p : cell_structure.local_cells().particles()) {
+    for (auto &p : cell_structure.local_particles()) {
       p.el.clear();
     }
 

src/core/pressure.cpp

@@ -125,7 +125,7 @@ void pressure_calc(double *result, double *result_t, double *result_nb,
   /* rescale kinetic energy (=ideal contribution) */
   virials.data.e[0] /= (3.0 * volume * time_step * time_step);
 
-  calc_long_range_virials(cell_structure.local_cells().particles());
+  calc_long_range_virials(cell_structure.local_particles());
 
 #ifdef VIRTUAL_SITES
   {