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Co-authored-by: Jean-Noël Grad <[email protected]>
espressomd · Apr 8, 2022 · d039c79 · d039c79
1 parent 1669db6
commit d039c79
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Showing 6 changed files with 20 additions and 20 deletions.
diff --git a/src/core/CellStructure.hpp b/src/core/CellStructure.hpp
@@ -669,11 +669,12 @@ struct CellStructure {
    * @brief Run kernel on all particles inside cell and neighbors.
    *
    * @param p Particle to identify cell and neighbors
-   * @param kernel Function with (Particle, Particle, Vector)
-   * @return false if cell is not found via particle_to_cell, otherwise true
+   * @param kernel Function with signature <tt>double(Particle, Particle, Vector)</tt>
+   * @return false if cell is not found via @ref particle_to_cell, otherwise true
    */
   template <class Kernel>
-  bool run_on_particle_short_range_neighbors(Particle const &p, Kernel kernel) {
+  bool run_on_particle_short_range_neighbors(Particle const &p,
+                                             Kernel &kernel) {
     auto const cell = find_current_cell(p);
 
     if (cell == nullptr) {
@@ -694,8 +695,8 @@ struct CellStructure {
 
 private:
   template <class Kernel, class DistanceFunc>
-  void short_range_neighbor_loop(Particle const &p, Cell *cell, Kernel kernel,
-                                 DistanceFunc df) {
+  void short_range_neighbor_loop(Particle const &p, Cell *const cell,
+                                 Kernel &kernel, DistanceFunc const &df) {
     /* Iterate over particles inside cell */
     for (auto const &part : cell->particles()) {
       if (&part == &p) {

diff --git a/src/core/cells.cpp b/src/core/cells.cpp
@@ -129,8 +129,8 @@ mpi_get_short_range_neighbors_local(int const pid, double const distance) {
   auto kernel = [&ret, cutoff2](Particle const &p, Particle const &p1,
                                 Utils::Vector3d const &vec) {
     if (vec.norm2() < cutoff2) {
-      ret.emplace_back(p1.p.identity);
-    };
+      ret.emplace_back(p1.id());
+    }
   };
   cell_structure.run_on_particle_short_range_neighbors(*p, kernel);
   return ret;

diff --git a/src/core/energy.cpp b/src/core/energy.cpp
@@ -141,10 +141,13 @@ double particle_short_range_energy_contribution_local(int pid) {
   if (p) {
     auto kernel = [&ret](Particle const &p, Particle const &p1,
                          Utils::Vector3d const &vec) {
-      auto const dist = sqrt(vec.norm2());
-      auto const &ia_params = *get_ia_param(p.p.type, p1.p.type);
+#ifdef EXCLUSIONS
+      if (not do_nonbonded(p, p1))
+        return;
+#endif
+      auto const &ia_params = *get_ia_param(p.type(), p1.type());
       // Add energy for current particle pair to result
-      ret += calc_non_bonded_pair_energy(p, p1, ia_params, vec, dist);
+      ret += calc_non_bonded_pair_energy(p, p1, ia_params, vec, vec.norm());
     };
     cell_structure.run_on_particle_short_range_neighbors(*p, kernel);
   }

diff --git a/src/python/espressomd/analyze.pyx b/src/python/espressomd/analyze.pyx
@@ -345,17 +345,18 @@ class Analysis:
         utils.handle_errors("calculate_energy() failed")
         return obs
 
-    def particle_energy(self, ParticleHandle particle):
+    def particle_energy(self, particle):
         """
         Calculate the non-bonded energy of a single given particle.
 
         Parameters
         ----------
-        particle : :attr:`~espressomd.particle_data.ParticleHandle.type`
+        particle : :class:`~espressomd.particle_data.ParticleHandle`
 
         Returns
         -------
-        :obj: `float` non-bonded energy of that particle
+        :obj: `float`
+            non-bonded energy of that particle
 
         """
         energy_contribution = particle_short_range_energy_contribution(

diff --git a/src/python/espressomd/cellsystem.pxd b/src/python/espressomd/cellsystem.pxd
@@ -39,11 +39,6 @@ cdef extern from "CellStructureType.hpp":
         CELL_STRUCTURE_REGULAR "CellStructureType::CELL_STRUCTURE_REGULAR"
         CELL_STRUCTURE_NSQUARE "CellStructureType::CELL_STRUCTURE_NSQUARE"
 
-cdef extern from "particle_data.hpp":
-    ctypedef struct particle "Particle"
-    const particle & get_particle_data(int pid) except +
-
-
 cdef extern from "cells.hpp":
     ctypedef struct CellStructure:
         CellStructureType decomposition_type()

diff --git a/src/python/espressomd/cellsystem.pyx b/src/python/espressomd/cellsystem.pyx
@@ -130,13 +130,13 @@ cdef class CellSystem:
         handle_errors("Error in get_pairs()")
         return pairs
 
-    def get_neighbors(self, ParticleHandle particle, distance):
+    def get_neighbors(self, particle, distance):
         """
         Get neighbors of a given particle up to distance
 
         Parameters
         ----------
-        particle : :attr:`~espressomd.particle_data.ParticleHandle.type`
+        particle : :class:`~espressomd.particle_data.ParticleHandle`
         distance : :obj:`float`
             Pairs of particles closer than ``distance`` are found.