WIP - Cluster Analysis

src/core/pair_criteria/BondCriterion.hpp

@@ -22,20 +22,31 @@
 #include "pair_criteria/PairCriterion.hpp"
 
 #include "BondList.hpp"
+#include "BoxGeometry.hpp"
+#include "system/System.hpp"
 
 namespace PairCriteria {
 /** @brief True if a bond of given type exists between two particles. */
 class BondCriterion : public PairCriterion {
 public:
   bool decide(Particle const &p1, Particle const &p2) const override {
-    return pair_bond_exists_on(p1.bonds(), p2.id(), m_bond_type) ||
-           pair_bond_exists_on(p2.bonds(), p1.id(), m_bond_type);
+
+    auto const &box_geo = *System::get_system().box_geo;
+    auto const d = box_geo.get_mi_vector(p1.pos(), p2.pos()).norm();
+
+    return (pair_bond_exists_on(p1.bonds(), p2.id(), m_bond_type) ||
+            pair_bond_exists_on(p2.bonds(), p1.id(), m_bond_type)) &&
+           d <= m_cut_off;
   }
   int get_bond_type() { return m_bond_type; }
   void set_bond_type(int t) { m_bond_type = t; }
 
+  double get_cut_off() { return m_cut_off; }
+  void set_cut_off(double c) { m_cut_off = c; }
+
 private:
   int m_bond_type;
+  double m_cut_off;
 };
 } // namespace PairCriteria
 

src/core/pair_criteria/EnergyCriterion.hpp

@@ -46,13 +46,16 @@ class EnergyCriterion : public PairCriterion {
     auto const energy = calc_non_bonded_pair_energy(
         p1, p2, ia_params, d, d.norm(), get_ptr(coulomb_kernel));
 
-    return energy >= m_cut_off;
+    return energy >= e_cut_off && d.norm() <= m_cut_off;
   }
   double get_cut_off() { return m_cut_off; }
   void set_cut_off(double c) { m_cut_off = c; }
 
+  double get_e_cut_off() { return e_cut_off; }
+  void set_e_cut_off(double e) { e_cut_off = e; }
+
 private:
-  double m_cut_off;
+  double m_cut_off, e_cut_off;
   System::System const &m_system;
 };
 } // namespace PairCriteria

src/core/pair_criteria/PairCriterion.hpp

@@ -41,6 +41,7 @@ class PairCriterion {
     const bool res = decide(p1, p2);
     return res;
   }
+
   virtual ~PairCriterion() = default;
 };
 } // namespace PairCriteria

src/script_interface/pair_criteria/BondCriterion.hpp

@@ -40,7 +40,10 @@ class BondCriterion : public PairCriterion {
     add_parameters(
         {{"bond_type",
           [this](Variant const &v) { m_c->set_bond_type(get_value<int>(v)); },
-          [this]() { return m_c->get_bond_type(); }}});
+          [this]() { return m_c->get_bond_type(); }},
+         {"cut_off",
+          [this](Variant const &v2) { m_c->set_cut_off(get_value<int>(v2)); },
+          [this]() { return m_c->get_cut_off(); }}});
   }
 
   std::shared_ptr<::PairCriteria::PairCriterion>

src/script_interface/pair_criteria/EnergyCriterion.hpp

@@ -41,9 +41,14 @@ class EnergyCriterion : public PairCriterion {
       : m_c(std::make_shared<::PairCriteria::EnergyCriterion>(
             ::System::get_system())) {
     add_parameters(
-        {{"cut_off",
+        {{"d_cut_off",
           [this](Variant const &v) { m_c->set_cut_off(get_value<double>(v)); },
-          [this]() { return m_c->get_cut_off(); }}});
+          [this]() { return m_c->get_cut_off(); }},
+         {"e_cut_off",
+          [this](Variant const &v2) {
+            m_c->set_e_cut_off(get_value<double>(v2));
+          },
+          [this]() { return m_c->get_e_cut_off(); }}});
   }
 
   std::shared_ptr<::PairCriteria::PairCriterion>