Refactor particle insertion code

src/core/CMakeLists.txt

@@ -22,6 +22,7 @@ set(EspressoCore_SRC
     npt.cpp
     partCfg_global.cpp
     particle_data.cpp
+    particle_node.cpp
     polymer.cpp
     pressure.cpp
     rattle.cpp

src/core/PartCfg.cpp

@@ -20,7 +20,7 @@
 #include "PartCfg.hpp"
 
 #include "grid.hpp"
-#include "particle_data.hpp"
+#include "particle_node.hpp"
 
 #include <utils/Span.hpp>
 

src/core/cells.cpp

@@ -32,7 +32,7 @@
 #include "event.hpp"
 #include "grid.hpp"
 #include "integrate.hpp"
-#include "particle_data.hpp"
+#include "particle_node.hpp"
 
 #include "ParticleDecomposition.hpp"
 #include "RegularDecomposition.hpp"

src/core/cluster_analysis/Cluster.cpp

@@ -29,7 +29,7 @@
 #include "Particle.hpp"
 #include "errorhandling.hpp"
 #include "grid.hpp"
-#include "particle_data.hpp"
+#include "particle_node.hpp"
 
 #include <utils/Vector.hpp>
 

src/core/cluster_analysis/ClusterStructure.cpp

@@ -22,6 +22,7 @@
 #include "PartCfg.hpp"
 #include "errorhandling.hpp"
 #include "partCfg_global.hpp"
+#include "particle_node.hpp"
 
 #include <utils/for_each_pair.hpp>
 

src/core/electrostatics_magnetostatics/mdlc_correction.cpp

@@ -33,6 +33,7 @@
 #include "errorhandling.hpp"
 #include "grid.hpp"
 #include "particle_data.hpp"
+#include "particle_node.hpp"
 
 #include <utils/constants.hpp>
 #include <utils/math/sqr.hpp>

src/core/event.cpp

@@ -47,7 +47,7 @@
 #include "nonbonded_interactions/nonbonded_interaction_data.hpp"
 #include "npt.hpp"
 #include "partCfg_global.hpp"
-#include "particle_data.hpp"
+#include "particle_node.hpp"
 #include "thermostat.hpp"
 #include "virtual_sites.hpp"
 

src/core/exclusions.cpp

@@ -25,20 +25,23 @@
 
 #include "exclusions.hpp"
 
+#include "Particle.hpp"
+
 #include <utils/contains.hpp>
 
 #include <algorithm>
 
-void add_exclusion(Particle *part, int part2) {
-  if (Utils::contains(part->exclusions(), part2))
+void add_exclusion(Particle &p, int p_id) {
+  if (Utils::contains(p.exclusions(), p_id))
     return;
 
-  part->exclusions().push_back(part2);
+  p.exclusions().push_back(p_id);
 }
 
-void delete_exclusion(Particle *part, int part2) {
-  auto &el = part->exclusions();
+void delete_exclusion(Particle &p, int p_id) {
+  auto &el = p.exclusions();
 
-  el.erase(std::remove(el.begin(), el.end(), part2), el.end());
+  el.erase(std::remove(el.begin(), el.end(), p_id), el.end());
 }
-#endif
+
+#endif // EXCLUSIONS

src/core/exclusions.hpp

@@ -28,6 +28,7 @@
 #include <algorithm>
 
 #ifdef EXCLUSIONS
+
 /** Determine if the non-bonded interactions between @p p1 and @p p2 should be
  *  calculated.
  */
@@ -39,9 +40,10 @@ inline bool do_nonbonded(Particle const &p1, Particle const &p2) {
 }
 
 /** Remove exclusion from particle if possible */
-void delete_exclusion(Particle *part, int part2);
+void delete_exclusion(Particle &p, int p_id);
 
 /** Insert an exclusion if not already set */
-void add_exclusion(Particle *part, int part2);
-#endif
+void add_exclusion(Particle &p, int p_id);
+
+#endif // EXCLUSIONS
 #endif // ESPRESSO_EXCLUSIONS_HPP

src/core/observables/fetch_particles.hpp

@@ -21,7 +21,7 @@
 #define FETCH_PARTICLES_HPP
 
 #include "grid.hpp"
-#include "particle_data.hpp"
+#include "particle_node.hpp"
 
 #include <utils/Span.hpp>
 

src/core/pair_criteria/pair_criteria.hpp

@@ -22,7 +22,7 @@
 #include "Particle.hpp"
 #include "energy_inline.hpp"
 #include "grid.hpp"
-#include "particle_data.hpp"
+#include "particle_node.hpp"
 
 namespace PairCriteria {
 /** @brief Criterion which provides a true/false for a pair of particles */