core: Split of non-head-node exclusion code

src/core/CMakeLists.txt

@@ -42,7 +42,7 @@ set(EspressoCore_SRC
     thermostat.cpp
     tuning.cpp
     virtual_sites.cpp
-)
+    exclusions.cpp)
 
 if(CUDA)
   set(EspressoCuda_SRC

src/core/bonded_interactions/bonded_interaction_data.cpp

@@ -19,7 +19,9 @@
 #include "bonded_interaction_data.hpp"
 #include "communication.hpp"
 
+#include <boost/range/algorithm/copy.hpp>
 #include <boost/range/numeric.hpp>
+
 #include <utils/constants.hpp>
 
 std::vector<Bonded_ia_parameters> bonded_ia_params;
@@ -146,3 +148,48 @@ void remove_all_bonds_to(Particle &p, int id) {
   }
   assert(i == bl->n);
 }
+
+void add_bond(Particle &p, Utils::Span<const int> bond) {
+  boost::copy(bond, std::back_inserter(p.bl));
+}
+
+int delete_bond(Particle *part, const int *bond) {
+  IntList *bl = &part->bl;
+  int i, j, type, partners;
+
+  // Empty bond means: delete all bonds
+  if (!bond) {
+    bl->clear();
+
+    return ES_OK;
+  }
+
+  // Go over the bond list to find the bond to delete
+  for (i = 0; i < bl->n;) {
+    type = bl->e[i];
+    partners = bonded_ia_params[type].num;
+
+    // If the bond type does not match the one, we want to delete, skip
+    if (type != bond[0])
+      i += 1 + partners;
+    else {
+      // Go over the bond partners
+      for (j = 1; j <= partners; j++) {
+        // Leave the loop early, if the bond to delete and the bond with in the
+        // particle don't match
+        if (bond[j] != bl->e[i + j])
+          break;
+      }
+      // If we did not exit from the loop early, all parameters matched
+      // and we go on with deleting
+      if (j > partners) {
+        // New length of bond list
+        bl->erase(bl->begin() + i, bl->begin() + i + 1 + partners);
+
+        return ES_OK;
+      }
+      i += 1 + partners;
+    }
+  }
+  return ES_ERROR;
+}

src/core/collision.cpp

@@ -27,9 +27,7 @@
 #include "event.hpp"
 #include "grid.hpp"
 #include "nonbonded_interactions/nonbonded_interaction_data.hpp"
-#include "particle_data.hpp"
 #include "particle_index.hpp"
-#include "rotation.hpp"
 #include "virtual_sites/VirtualSitesRelative.hpp"
 
 #include <utils/mpi/all_compare.hpp>

src/core/electrostatics_magnetostatics/magnetic_non_p3m_methods.cpp

@@ -28,8 +28,6 @@
 #include "electrostatics_magnetostatics/dipole.hpp"
 #include "errorhandling.hpp"
 #include "grid.hpp"
-#include "nonbonded_interactions/nonbonded_interaction_data.hpp"
-#include "particle_data.hpp"
 
 #include <utils/constants.hpp>
 

src/core/energy_inline.hpp

@@ -61,7 +61,7 @@
 #include "bonded_interactions/bonded_coulomb_sr.hpp"
 #include "electrostatics_magnetostatics/coulomb_inline.hpp"
 #endif
-#include "particle_data.hpp"
+#include "exclusions.hpp"
 #include "particle_index.hpp"
 #include "statistics.hpp"
 

src/core/exclusions.cpp

@@ -0,0 +1,19 @@
+#include "exclusions.hpp"
+
+#ifdef EXCLUSIONS
+void add_exclusion(Particle *part, int part2) {
+  for (int i = 0; i < part->el.n; i++)
+    if (part->el.e[i] == part2)
+      return;
+
+  part->el.push_back(part2);
+}
+
+void delete_exclusion(Particle *part, int part2) {
+  IntList &el = part->el;
+
+  if (!el.empty()) {
+    el.erase(std::remove(el.begin(), el.end(), part2), el.end());
+  };
+}
+#endif

src/core/exclusions.hpp

@@ -0,0 +1,23 @@
+#ifndef ESPRESSO_EXCLUSIONS_HPP
+#define ESPRESSO_EXCLUSIONS_HPP
+
+#include "Particle.hpp"
+
+#ifdef EXCLUSIONS
+/** Determine if the non-bonded interactions between @p p1 and @p p2 should be
+ *  calculated.
+ */
+inline bool do_nonbonded(Particle const &p1, Particle const &p2) {
+  /* check for particle 2 in particle 1's exclusion list. The exclusion list is
+   * symmetric, so this is sufficient. */
+  return std::none_of(p1.el.begin(), p1.el.end(),
+                      [&p2](int id) { return p2.p.identity == id; });
+}
+
+/** Remove exclusion from particle if possible */
+void delete_exclusion(Particle *part, int part2);
+
+/** Insert an exclusion if not already set */
+void add_exclusion(Particle *part, int part2);
+#endif
+#endif // ESPRESSO_EXCLUSIONS_HPP

src/core/forces_inline.hpp

@@ -36,6 +36,7 @@
 #include "bonded_interactions/thermalized_bond.hpp"
 #include "bonded_interactions/umbrella.hpp"
 #include "errorhandling.hpp"
+#include "exclusions.hpp"
 #include "forces.hpp"
 #include "immersed_boundary/ibm_tribend.hpp"
 #include "immersed_boundary/ibm_triel.hpp"
@@ -59,7 +60,6 @@
 #include "npt.hpp"
 #include "object-in-fluid/oif_global_forces.hpp"
 #include "object-in-fluid/oif_local_forces.hpp"
-#include "particle_data.hpp"
 #include "particle_index.hpp"
 #include "rotation.hpp"
 #include "thermostat.hpp"

src/core/global.cpp

@@ -33,7 +33,6 @@
 #include "nonbonded_interactions/nonbonded_interaction_data.hpp"
 #include "npt.hpp"
 #include "object-in-fluid/oif_global_forces.hpp"
-#include "particle_data.hpp"
 #include "rattle.hpp"
 #include "thermostat.hpp"
 #include "tuning.hpp"

src/core/grid_based_algorithms/lbgpu.cpp

@@ -36,7 +36,6 @@
 #include "grid_based_algorithms/lbgpu.hpp"
 #include "integrate.hpp"
 #include "nonbonded_interactions/nonbonded_interaction_data.hpp"
-#include "particle_data.hpp"
 #include "statistics.hpp"
 
 #include <utils/constants.hpp>

src/core/pair_criteria/pair_criteria.hpp

@@ -21,6 +21,8 @@
 
 #include "Particle.hpp"
 #include "energy_inline.hpp"
+#include "particle_data.hpp"
+
 #include <stdexcept>
 
 namespace PairCriteria {

src/core/particle_data.cpp

@@ -391,9 +391,9 @@ std::unordered_map<int, int> particle_node;
 
 int delete_bond(Particle *part, const int *bond);
 
-void try_delete_exclusion(Particle *part, int part2);
+void delete_exclusion(Particle *part, int part2);
 
-void try_add_exclusion(Particle *part, int part2);
+void add_exclusion(Particle *part, int part2);
 
 void auto_exclusion(int distance);
 
@@ -955,51 +955,6 @@ void local_rescale_particles(int dir, double scale) {
   }
 }
 
-void add_bond(Particle &p, Utils::Span<const int> bond) {
-  boost::copy(bond, std::back_inserter(p.bl));
-}
-
-int delete_bond(Particle *part, const int *bond) {
-  IntList *bl = &part->bl;
-  int i, j, type, partners;
-
-  // Empty bond means: delete all bonds
-  if (!bond) {
-    bl->clear();
-
-    return ES_OK;
-  }
-
-  // Go over the bond list to find the bond to delete
-  for (i = 0; i < bl->n;) {
-    type = bl->e[i];
-    partners = bonded_ia_params[type].num;
-
-    // If the bond type does not match the one, we want to delete, skip
-    if (type != bond[0])
-      i += 1 + partners;
-    else {
-      // Go over the bond partners
-      for (j = 1; j <= partners; j++) {
-        // Leave the loop early, if the bond to delete and the bond with in the
-        // particle don't match
-        if (bond[j] != bl->e[i + j])
-          break;
-      }
-      // If we did not exit from the loop early, all parameters matched
-      // and we go on with deleting
-      if (j > partners) {
-        // New length of bond list
-        bl->erase(bl->begin() + i, bl->begin() + i + 1 + partners);
-
-        return ES_OK;
-      }
-      i += 1 + partners;
-    }
-  }
-  return ES_ERROR;
-}
-
 #ifdef EXCLUSIONS
 void local_change_exclusion(int part1, int part2, int _delete) {
   if (part1 == -1 && part2 == -1) {
@@ -1014,39 +969,21 @@ void local_change_exclusion(int part1, int part2, int _delete) {
   auto part = get_local_particle_data(part1);
   if (part) {
     if (_delete)
-      try_delete_exclusion(part, part2);
+      delete_exclusion(part, part2);
     else
-      try_add_exclusion(part, part2);
+      add_exclusion(part, part2);
   }
 
   /* part2, if here */
   part = get_local_particle_data(part2);
   if (part) {
     if (_delete)
-      try_delete_exclusion(part, part1);
+      delete_exclusion(part, part1);
     else
-      try_add_exclusion(part, part1);
+      add_exclusion(part, part1);
   }
 }
 
-void try_add_exclusion(Particle *part, int part2) {
-  for (int i = 0; i < part->el.n; i++)
-    if (part->el.e[i] == part2)
-      return;
-
-  part->el.push_back(part2);
-}
-
-void try_delete_exclusion(Particle *part, int part2) {
-  IntList &el = part->el;
-
-  if (!el.empty()) {
-    el.erase(std::remove(el.begin(), el.end(), part2), el.end());
-  };
-}
-#endif
-
-#ifdef EXCLUSIONS
 namespace {
 /* keep a unique list for particle i. Particle j is only added if it is not i
    and not already in the list. */

src/core/particle_data.hpp

@@ -384,24 +384,6 @@ void local_remove_all_particles();
  */
 void local_rescale_particles(int dir, double scale);
 
-#ifdef EXCLUSIONS
-/** Determine if the non-bonded interactions between @p p1 and @p p2 should be
- *  calculated.
- */
-inline bool do_nonbonded(Particle const &p1, Particle const &p2) {
-  /* check for particle 2 in particle 1's exclusion list. The exclusion list is
-   * symmetric, so this is sufficient. */
-  return std::none_of(p1.el.begin(), p1.el.end(),
-                      [&p2](int id) { return p2.p.identity == id; });
-}
-#endif
-
-/** Remove exclusion from particle if possible */
-void try_delete_exclusion(Particle *part, int part2);
-
-/** Insert an exclusion if not already set */
-void try_add_exclusion(Particle *part, int part2);
-
 /** Automatically add the next \<distance\> neighbors in each molecule to the
  *  exclusion list.
  *  This uses the bond topology obtained directly from the particles.

src/core/pressure_inline.hpp

@@ -25,6 +25,7 @@
 #ifndef CORE_PRESSURE_INLINE_HPP
 #define CORE_PRESSURE_INLINE_HPP
 
+#include "exclusions.hpp"
 #include "forces_inline.hpp"
 #include "integrate.hpp"
 #include "npt.hpp"