From 634fc7caf1e94c151e27e53a6c05c4bbc5106c4f Mon Sep 17 00:00:00 2001
From: capomav <chinmaypabshettiwar@gmail.com>
Date: Wed, 6 Dec 2023 02:53:20 +0100
Subject: [PATCH] addition of cutoff parameters to bond and energy criterion

---
 src/core/pair_criteria/BondCriterion.hpp            | 13 +++++++++++--
 src/core/pair_criteria/EnergyCriterion.hpp          |  9 +++++++--
 src/core/pair_criteria/PairCriterion.hpp            |  2 ++
 .../pair_criteria/BondCriterion.hpp                 |  5 ++++-
 .../pair_criteria/EnergyCriterion.hpp               |  7 +++++--
 5 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/src/core/pair_criteria/BondCriterion.hpp b/src/core/pair_criteria/BondCriterion.hpp
index d1bd387a1c..b4a976384e 100644
--- a/src/core/pair_criteria/BondCriterion.hpp
+++ b/src/core/pair_criteria/BondCriterion.hpp
@@ -28,14 +28,23 @@ namespace PairCriteria {
 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;
+  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; }
 
+  int 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
 
diff --git a/src/core/pair_criteria/EnergyCriterion.hpp b/src/core/pair_criteria/EnergyCriterion.hpp
index e81a59dd66..5fc188f422 100644
--- a/src/core/pair_criteria/EnergyCriterion.hpp
+++ b/src/core/pair_criteria/EnergyCriterion.hpp
@@ -46,13 +46,18 @@ 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
diff --git a/src/core/pair_criteria/PairCriterion.hpp b/src/core/pair_criteria/PairCriterion.hpp
index c5ac88bdf7..c611c427ca 100644
--- a/src/core/pair_criteria/PairCriterion.hpp
+++ b/src/core/pair_criteria/PairCriterion.hpp
@@ -41,6 +41,8 @@ class PairCriterion {
     const bool res = decide(p1, p2);
     return res;
   }
+  
+  virtual double cutoff(Particle const &p1, Particle const &p2) const = 0;
   virtual ~PairCriterion() = default;
 };
 } // namespace PairCriteria
diff --git a/src/script_interface/pair_criteria/BondCriterion.hpp b/src/script_interface/pair_criteria/BondCriterion.hpp
index b59e9303d5..bbb4e48dcd 100644
--- a/src/script_interface/pair_criteria/BondCriterion.hpp
+++ b/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>
diff --git a/src/script_interface/pair_criteria/EnergyCriterion.hpp b/src/script_interface/pair_criteria/EnergyCriterion.hpp
index e5ec358270..99632c2b0c 100644
--- a/src/script_interface/pair_criteria/EnergyCriterion.hpp
+++ b/src/script_interface/pair_criteria/EnergyCriterion.hpp
@@ -41,9 +41,12 @@ 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>