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dynamics.hpp
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/*
File: dynamics.hpp
Function: Simulate dynamics of chromosomes and nuclear envelope
Model: chromoCell
Created: 11 December, 2017 (XF)
*/
#ifndef DYNAMICS_HPP_INCLUDED
#define DYNAMICS_HPP_INCLUDED
#include "initConfig.hpp"
// ===================== Functions =========================
void oneIter(vector<Chromosome> & vecChromosome, vector<Node> & vecNode, vector<iPair> vecBeadPairInteract,
vector<double> & vecBeadPairInteractFreq, vector<int> & vecFluoroSite,
unordered_map<string, double> & energy, VoxMap & voxMap, bool FLAG_INTERACT_ON, vector<double> & randNormNum0, bool flagIsPrep); // if using VoxMap
//void oneIter(vector<Chromosome> & vecChromosome, vector<Node> & vecNode, vector<iPair> vecBeadPairInteract,
// unordered_map<string, double> & energy, Octree & octree, bool FLAG_INTERACT_ON); // if using Octree
void oneIterBrownianSimulation(vector<Chromosome> & vecChromosome, vector<Node> & vecNode,
vector<int> & vecCondensinSite, vector<int> & vecFluoroSite,
unordered_map<string, double> & energy, VoxMap & voxMap,
vector<double> & randNormNum0, bool flagIsPrep);
void oneIterBrownianSimulationOverdamp(vector<Chromosome> & vecChromosome, vector<Node> & vecNode,
vector<int> & vecCondensinSite, vector<int> & vecBinderBlockSite, vector<int> & vecFluoroSite,
vector<Binder> & vecBinder,
unordered_map<string, double> & energy, VoxMap & voxMap,
vector<double> & randNormNum0, bool flagIsPrep, bool flagIsInitConfig, vector<iPair> & capturer, vector<int> & hit_valence, map<int, vector<int>> & Domain_CSB, bool flagLE_ON, bool flagIsInterphase);
// STEP 1
void updateCoord(vector<Node> & vecNode, vector<double> & randNormNum0, bool flagTetherEnds, bool flagFreezeFluoro, vector<int> & vecFluoroSite, bool flagIsPrep);
void updateCoord_OMP(vector<Node> & vecNode); // not optimized
// STEP 2
// --- following functions are for RECONSTRUCTION objective ---
void updateAccel(vector<Chromosome> & vecChromosome, vector<Node> & vecNode,
vector<iPair> vecBeadPairInteract, vector<double> & vecBeadPairInteractFreq,
VoxMap & voxMap, unordered_map<string, double> & energy, bool FLAG_INTERACT_ON);
// --- following functions are for Brownian SIMULATION objective ---
void updateAccelBrownianSimulation(vector<Chromosome> & vecChromosome, vector<Node> & vecNode, vector<int> & vecCondensinSite,
VoxMap & voxMap, unordered_map<string, double> & energy, vector<double> & randNormNum0);
void updateVelocBrownianSimulationOverdamp(vector<Chromosome> & vecChromosome, vector<Node> & vecNode, vector<int> & vecCondensinSite,
vector<int> & vecBinderBlockSite, vector<Binder> & vecBinder,
VoxMap & voxMap, unordered_map<string, double> & energy, vector<double> & randNormNum0, bool flagIsPrep, vector<iPair> & capturer, vector<int> & hit_valence, map<int, vector<int>> & Domain_CSB, bool flagLE_ON, bool flagIsInterphase);
// STEP 3
void updateVeloc(vector<Node> & vecNode, unordered_map<string, double> & energy);
void updateVelocLinearDamp(vector<Node> & vecNode, unordered_map<string, double> & energy);
double dVecDist(dVec & p1, dVec & p2);
// VoxMap algorithm
void updateVoxMap(VoxMap & voxMap, vector<Node> & vecNode);
// Octree algorithm
void updateOctree(Octree & octree, vector<Node> & vecNode, int depth_init = 2);
void branchLeaf(vector<Leaf> & vecLeaf, vector<bVec> position_child0);
bool coord2position(double fracX);
#endif // DYNAMICS_HPP_INCLUDED