Update BDM_BRANCH to umar_neurite_test and make changes to Mechanical…

…ForcesOp and NeuriteElement

Singularity

@@ -59,7 +59,7 @@ From:ubuntu:20.04
   git config --system user.name "Test User"
   git config --system user.email user@test.com
 
-  export BDM_BRANCH="master"
+  export BDM_BRANCH="umar_neurite_test"
   git clone https://github.com/BioDynaMo/biodynamo.git
   cd biodynamo
   git checkout $BDM_BRANCH
@@ -70,6 +70,6 @@ From:ubuntu:20.04
   cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ..
 
   ninja -j $(($(nproc) - 1)) 
-
+  export XVFBARGS=":99 -ac -screen 0 2560x1440x24"
 
-%runscript
+%runscript

src/core/operation/mechanical_forces_op.h

@@ -93,6 +93,10 @@ class MechanicalForcesOp : public AgentOperationImpl {
       last_time_run_[tid] = current_time;
     }
 
+    if (agent->GetShape() == Shape::kCylinder) {
+      squared_radius_ = 0.0001;
+    }
+
     const auto& displacement =
         agent->CalculateDisplacement(force_, squared_radius_, delta_time_[tid]);
     agent->ApplyDisplacement(displacement);

src/neuroscience/neurite_element.cc

@@ -132,7 +132,8 @@ void NeuriteElement::CriticalRegion(std::vector<AgentPointer<>>* aptrs) {
 }
 
 std::set<std::string> NeuriteElement::GetRequiredVisDataMembers() const {
-  return {"mass_location_", "diameter_", "actual_length_", "spring_axis_"};
+  return {"mass_location_", "diameter_",         "actual_length_",
+          "spring_axis_",   "mother_cell_type_", "mother_uid_"};
 }
 
 void NeuriteElement::SetDiameter(real_t diameter) {

src/neuroscience/neurite_element.h

@@ -90,6 +90,18 @@ class NeuriteElement : public Agent, public NeuronOrNeurite {
 
   void SetMassLocation(const Real3& mass_location);
 
+  // Getter and setter for mother_cell_type_ (used for visualization)
+  real_t GetMotherCellType() const { return mother_cell_type_; }
+
+  void SetMotherCellType(real_t mother_cell_type) {
+    mother_cell_type_ = mother_cell_type;
+  }
+
+  // Getter and setter for mother_uid_ (used for synapses)
+  AgentUid GetMotherUid() { return mother_uid_; }
+
+  void SetMotherUid(AgentUid mother_uid) { mother_uid_ = mother_uid; }
+
   real_t GetAdherence() const { return adherence_; }
 
   void SetAdherence(real_t adherence);
@@ -465,6 +477,12 @@ class NeuriteElement : public Agent, public NeuronOrNeurite {
   /// position_ is the middle point of cylinder
   Real3 position_ = {{0.0, 0.0, 0.0}};
 
+  /// This is the type of the mother neuron
+  real_t mother_cell_type_;
+
+  /// The uid of the mother neuron
+  AgentUid mother_uid_;
+
   real_t volume_;
   /// NB: Use setter and don't assign values directly
   real_t diameter_ = 1;