Parameters.hpp

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#pragma once
 
#include <math.h>
#include <cmath>
#include <vector>
#include <string>
#include <iostream>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_linalg.h>
 
#include "energy_force/Energy.hpp"
#include "energy_force/Force.hpp"
 
#include "linalg/Linear_algebra.hpp"
 
 
enum class BoundaryType
{
    Fixed,
 
    Periodic,
 
    Free
};
 
struct DeformationCount
{
    int shapeDeformCount = 0; 
    int areaDeformCount = 0;  
    int noDeformCount = 0;    
};
 
struct SubdivisionMatrix
{
    Matrix irregM;
    Matrix irregM1;
    Matrix irregM2;
    Matrix irregM3;
    Matrix irregM4;
};
 
class Particle
{
public:
    int index;                   
    int faceIndex;               
    Matrix vwu = Matrix(3, 1);   
    Matrix coord = Matrix(3, 1); 
    double D = 0.0;              
};
 
struct Param
{
    // developer options
    bool VERBOSE_MODE = true; 
    int maxIterations = 1E5; 
    std::string restartInputFile = ""; 
    std::string checkpointOutputFile = "slimed_restart.chk"; 
    int checkpointOutputInterval = 1000; 
 
    // physical constants
    double kCurv = 83.4;  
    double uSurf = 250.0; 
    double uVol = 0.0;    
    double kReg = 83.4;    
    double kSpring;       
    bool setRelaxAreaToDefault = false; 
    double area0;         
    double area;          
    double vol0;        
    double vol;         
    double insertCurv;  
    double spontCurv;   
 
    // membrane size and axes division
    double sideX = 100.0;                           
    double sideY = 100.0;                           
    double radius = 25.0;                          
    double lFace = 5.0;                           
    int nFaceX = -1;                        
    int nFaceY = -1;                        
    double dFaceX;                          
    double dFaceY;                          
    double meanL;                           
    double sigma = 0.0;                     
    int subDivideTimes;                     
    bool isInsertionAreaConstraint = false; 
    bool isAdditiveScheme = false;          
    bool isGlobalConstraint = true;                
    double elementTriangleArea0;            
 
    // gauss quadrature
    int gaussQuadratureN = 2;    
    Matrix VWU;                  
    Matrix gaussQuadratureCoeff; 
 
    // shape function
    std::vector<Matrix> shapeFunctions; 
 
    // irregular patch
    SubdivisionMatrix subMatrix; 
 
    // boundary conditions
    BoundaryType boundaryCondition = BoundaryType::Periodic; 
 
    // optimization methods
    bool usingNCG = true;      
    bool isNCGstuck = false; 
 
    // convergence criteria
    double deltaEnergyConverge = 1e-5; 
    double deltaForceScaleConverge = 1e-5; 
 
    // regularization
    double gamaShape = 0.2;                       
    double gamaArea = 0.2;                        
    bool usingRpi = true;             
 
    // spline points
    bool xyzOutput = true;                                       
    bool meshpointOutput = true;                                 
    bool isEnergyHarmonicBondIncluded = false;                    
    std::vector<Matrix> scaffoldingPoints;                       
    std::vector<int> scaffoldingPoints_correspondingVertexIndex; 
    double scaffoldingSphereRaidus = 50.0;                       
    double springConst = 4.5;                                   
    double springConstScaler = 1.31607401;                              
    int springConstScalingInterv = 200;                          
    int springConstUpperBound = 1000.0;                          
    int propagateScaffoldingInterv = 7;                         
    int propagateScaffoldingNstep = 100;                         
    double splinePointsZcoordScaling = 0.0;                     // for z scaling
    double lbond = 9.0;                                          
    double relaxLengthRatioApproximation = 1.0;                  
    double scaffoldingZeroPlaneZ = 0.0;                          
    std::string scaffoldingFileName = "";
    bool isGagScaffoldingEnergyIncluded = false;                 
    std::string gagReferenceStateFileName = "";                  
    std::string gagReactionFileName = "";                        
    bool isIdealizedProteinLatticeEnergyIncluded = false;        
    std::string idealizedProteinLatticeFileName = "";            
    double gagKsigma = 0.0;                                      
    double gagKtheta = 0.0;                                      
    double gagKphi = 0.0;                                        
    double gagKomega = 0.0;                                      
    double gagFiniteDifferenceStep = 1.0e-4;                     
    double gagPropagationStepSize = 1.0e-6;                      
    int gagPreRelaxSteps = 200;                                  
    
 
    // dynamics
    double timeStep = 0.1;   // us
    double diffConst = 0.01; // um^2/us
    double KBT = 4.17;       // 1KbT = 4.17 pN.nm
    unsigned int randomSeed = 42; 
    bool surfacepointOutput = true; 
 
    // thermal fluctuation / annealing for equilibrium searches
    bool thermalFluctuationEnabled = false;           
    bool thermalFluctuationPureMMC = false;           
    int thermalFluctuationInterval = 50;              
    double thermalFluctuationTemperatureKelvin = 298.0;    
    double thermalFluctuationMinTemperatureKelvin = 298.0; 
    double thermalFluctuationCoolingRate = 1.0;       
    double thermalFluctuationStepScale = 0.02;        
 
    // insertion
    bool isInsertionIncluded = false;
    std::vector<std::vector<int>> insertionPatch;
 
    Energy energy;
    Energy energyPrev;
    DeformationCount deformationCount;
};
 
std::ostream& operator<<(std::ostream& os, const Param& param);