Merge branch 'ci-salva' into midterm_code_push

Author: salva24

CMakeLists.txt

@@ -1,5 +1,19 @@
+# -----------------------------------------------------------------------------
+#
+# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
+# BioDynaMo collaboration. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# See the LICENSE file distributed with this work for details.
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# -----------------------------------------------------------------------------
 cmake_minimum_required(VERSION 3.19.3)
-project(CARTopiaX)
+project(cart_tumor)
+
 
 # BioDynaMo curretly uses the C++17 standard.
 set(CMAKE_CXX_STANDARD 17)

README.md

@@ -18,6 +18,7 @@ The simulation integrates computational modeling and biological insights to expl
 7. [Acknowledgments](#acknowledgments)
 8. [License](#license)
 
+
 ---
 
 ## Project Overview
@@ -51,6 +52,7 @@ Clone the repository:
 ```bash
 git clone https://github.com/compiler-research/CARTopiaX.git
 cd CARTopiaX
+
 ```
 
 ---
@@ -86,6 +88,7 @@ biodynamo run
 **Option 2:**  
 Directly from the build directory:
 ```bash
+
 ./build/CARTopiaX
 ```
 
@@ -98,6 +101,7 @@ Data about tumor growth and diffrent types of cell populations is output in ./ou
 To visualize the results in paraview use:
 ```bash
 paraview ./output/CARTopiaX/CARTopiaX.pvsm
+
 ```
 
 ---

src/cart_cell.cc

@@ -38,11 +38,12 @@ CartCell::CartCell(const Real3& position) {
   SetNuclearVolume(kDefaultVolumeNucleusCartCell);
 
 
+
+  ResourceManager &rm = *Simulation::GetActive()->GetResourceManager();
   // Pointer to oxygen diffusion grid
-  auto &rm = *Simulation::GetActive()->GetResourceManager();
   oxygen_dgrid_ = rm.GetDiffusionGrid("oxygen");
   // Pointer to immunostimulatory_factor diffusion grid
-  immunostimulatory_factor_dgrid_ = rm.GetDiffusionGrid("immunostimulatory_factor");
+  immunostimulatory_factor_dgrid_ = rm.GetDiffusionGrid("immunostimulatory_factor"); 
   // Initially not attached to a tumor cell
   attached_to_tumor_cell_ = false; 
   // Initialize attached cell pointer to null
@@ -64,7 +65,9 @@ CartCell::CartCell(const Real3& position) {
 
 // Cart cells can move if they are alive and not attached to a tumor cell
 bool CartCell::DoesCellMove() {
-  return state_ == CartCellState::kAlive && !attached_to_tumor_cell_; 
+
+  return (state_ == CartCellState::kAlive && !attached_to_tumor_cell_); 
+
 }
 
 
@@ -138,11 +141,10 @@ Real3 CartCell::CalculateDisplacement(const InteractionForce* force,
 
   Real3 translation_velocity_on_point_mass{0, 0, 0};
 
-  //--------------------------------------------
-  //Adhesion and repulsion forces
-  //--------------------------------------------
   // We check for every neighbor object if they touch us, i.e. push us
   // away and agreagate the velocities
+
+
   uint64_t non_zero_neighbor_forces = 0;
   if (!IsStatic()) {
     auto* ctxt = Simulation::GetActive()->GetExecutionContext();
@@ -164,31 +166,11 @@ Real3 CartCell::CalculateDisplacement(const InteractionForce* force,
     }
   }
 
-  //--------------------------------------------
-
-  //Still in progress
-  Real3 motility{0, 0, 0};
-
-  if (DoesCellMove()){
-    //compute motility
-  }
-
-
 
-
-
-
-
-
-
-
-  //--------------------------------------------
   // Two step Adams-Bashforth approximation of the time derivative for position
   // position(t + dt) ≈ position(t) + dt * [ 1.5 * velocity(t) - 0.5 * velocity(t - dt) ]
-  //--------------------------------------------
   movement_at_next_step += translation_velocity_on_point_mass * kDnew + older_velocity_ * kDold;
 
-
   older_velocity_ = translation_velocity_on_point_mass;
 
   // Displacement
@@ -204,7 +186,6 @@ real_t CartCell::ConsumeSecreteSubstance(int substance_id, real_t old_concentrat
   } else if (substance_id == immunostimulatory_factor_dgrid_->GetContinuumId()) {
     // This point should never be reached
     res= old_concentration;
-
   } else {
     throw std::invalid_argument("Unknown substance id: " + std::to_string(substance_id));
   }
@@ -291,4 +272,4 @@ void StateControlCart::Run(Agent* agent) {
   }
 }
 
-}  // namespace bdm
+}  // namespace bdm

src/cart_cell.h

@@ -221,4 +221,4 @@ struct StateControlCart : public Behavior {
 
 }  // namespace bdm
 
-#endif
+#endif  // CART_CELL_H_

src/cart_tumor.h

@@ -30,7 +30,6 @@ enum Substances { kImmunostimulatoryFactor, kOxygen };
 /// Function declaration for the main simulation
 int Simulate(int argc, const char** argv);
 
-
 }  // namespace bdm
 
 #endif  // CART_TUMOR_H_

src/hyperparams.h

@@ -81,7 +81,6 @@ constexpr real_t kVolumeRelaxarionRateFluidNecroticLysed = 0.050/60.0;
 ///
 /// General Hyperparameters
 ///
-
 /// Seed for random number generation
 constexpr int kSeed =3; 
 
@@ -193,4 +192,4 @@ constexpr real_t kDefaultFractionFluidCartCell = 0.75;
 
 }  // namespace bdm
 
-#endif  // TUMOR_HYPERPARAMS_H_
+#endif  // TUMOR_HYPERPARAMS_H_

src/tumor_cell.cc

@@ -435,7 +435,7 @@ void StateControlGrowProliferate::Run(Agent* agent) {
         break;
       }
       case TumorCellState::kApoptotic:{
-        //CHANGE write this in the function that causes apoptosis
+      //CHANGE write this in the function that causes apoptosis
         // //Stop Secretion and reduce consumption
         //   for (auto* beh : cell->GetAllBehaviors()) {
         //     if (auto* c = dynamic_cast<Consumption*>(beh)) {c->SetQuantity(c->GetQuantity()*kReductionConsumptionDeadCells);}// Reduce consumption rate