Geant4 Cross Reference

Cross-Referencing   Geant4
Geant4/examples/advanced/dna/dsbandrepair/analysis/src/ODESolver.cc

Version: [ ReleaseNotes ] [ 1.0 ] [ 1.1 ] [ 2.0 ] [ 3.0 ] [ 3.1 ] [ 3.2 ] [ 4.0 ] [ 4.0.p1 ] [ 4.0.p2 ] [ 4.1 ] [ 4.1.p1 ] [ 5.0 ] [ 5.0.p1 ] [ 5.1 ] [ 5.1.p1 ] [ 5.2 ] [ 5.2.p1 ] [ 5.2.p2 ] [ 6.0 ] [ 6.0.p1 ] [ 6.1 ] [ 6.2 ] [ 6.2.p1 ] [ 6.2.p2 ] [ 7.0 ] [ 7.0.p1 ] [ 7.1 ] [ 7.1.p1 ] [ 8.0 ] [ 8.0.p1 ] [ 8.1 ] [ 8.1.p1 ] [ 8.1.p2 ] [ 8.2 ] [ 8.2.p1 ] [ 8.3 ] [ 8.3.p1 ] [ 8.3.p2 ] [ 9.0 ] [ 9.0.p1 ] [ 9.0.p2 ] [ 9.1 ] [ 9.1.p1 ] [ 9.1.p2 ] [ 9.1.p3 ] [ 9.2 ] [ 9.2.p1 ] [ 9.2.p2 ] [ 9.2.p3 ] [ 9.2.p4 ] [ 9.3 ] [ 9.3.p1 ] [ 9.3.p2 ] [ 9.4 ] [ 9.4.p1 ] [ 9.4.p2 ] [ 9.4.p3 ] [ 9.4.p4 ] [ 9.5 ] [ 9.5.p1 ] [ 9.5.p2 ] [ 9.6 ] [ 9.6.p1 ] [ 9.6.p2 ] [ 9.6.p3 ] [ 9.6.p4 ] [ 10.0 ] [ 10.0.p1 ] [ 10.0.p2 ] [ 10.0.p3 ] [ 10.0.p4 ] [ 10.1 ] [ 10.1.p1 ] [ 10.1.p2 ] [ 10.1.p3 ] [ 10.2 ] [ 10.2.p1 ] [ 10.2.p2 ] [ 10.2.p3 ] [ 10.3 ] [ 10.3.p1 ] [ 10.3.p2 ] [ 10.3.p3 ] [ 10.4 ] [ 10.4.p1 ] [ 10.4.p2 ] [ 10.4.p3 ] [ 10.5 ] [ 10.5.p1 ] [ 10.6 ] [ 10.6.p1 ] [ 10.6.p2 ] [ 10.6.p3 ] [ 10.7 ] [ 10.7.p1 ] [ 10.7.p2 ] [ 10.7.p3 ] [ 10.7.p4 ] [ 11.0 ] [ 11.0.p1 ] [ 11.0.p2 ] [ 11.0.p3, ] [ 11.0.p4 ] [ 11.1 ] [ 11.1.1 ] [ 11.1.2 ] [ 11.1.3 ] [ 11.2 ] [ 11.2.1 ] [ 11.2.2 ] [ 11.3.0 ]

Diff markup

Differences between /examples/advanced/dna/dsbandrepair/analysis/src/ODESolver.cc (Version 11.3.0) and /examples/advanced/dna/dsbandrepair/analysis/src/ODESolver.cc (Version 9.1.p3)


  1 //                                                  1 
  2 // *******************************************    
  3 // * License and Disclaimer                       
  4 // *                                              
  5 // * The  Geant4 software  is  copyright of th    
  6 // * the Geant4 Collaboration.  It is provided    
  7 // * conditions of the Geant4 Software License    
  8 // * LICENSE and available at  http://cern.ch/    
  9 // * include a list of copyright holders.         
 10 // *                                              
 11 // * Neither the authors of this software syst    
 12 // * institutes,nor the agencies providing fin    
 13 // * work  make  any representation or  warran    
 14 // * regarding  this  software system or assum    
 15 // * use.  Please see the license in the file     
 16 // * for the full disclaimer and the limitatio    
 17 // *                                              
 18 // * This  code  implementation is the result     
 19 // * technical work of the GEANT4 collaboratio    
 20 // * By using,  copying,  modifying or  distri    
 21 // * any work based  on the software)  you  ag    
 22 // * use  in  resulting  scientific  publicati    
 23 // * acceptance of all terms of the Geant4 Sof    
 24 // *******************************************    
 25 //                                                
 26 //                                                
 27 /// \file ODESolver.cc                            
 28 /// \brief Implementation of the ODESolver cla    
 29                                                   
 30 #include "ODESolver.hh"                           
 31 #include <iostream>                               
 32 #include <cmath>                                  
 33                                                   
 34 //....oooOO0OOooo........oooOO0OOooo........oo    
 35                                                   
 36 std::vector<double> operator*(const std::vecto    
 37 {                                                 
 38   std::vector<double> vout;                       
 39   for (auto const val : v) vout.push_back(val*    
 40   return vout;                                    
 41 }                                                 
 42                                                   
 43 //....oooOO0OOooo........oooOO0OOooo........oo    
 44                                                   
 45 std::vector<double> operator+(const std::vecto    
 46 {                                                 
 47   std::vector<double> vout;                       
 48   for (auto const val : v) vout.push_back(val     
 49   return vout;                                    
 50 }                                                 
 51                                                   
 52 //....oooOO0OOooo........oooOO0OOooo........oo    
 53                                                   
 54 std::vector<double> operator+(const std::vecto    
 55 {                                                 
 56   std::vector<double> vout;                       
 57   for (size_t i=0;i<v1.size();i++) vout.push_b    
 58   return vout;                                    
 59 }                                                 
 60                                                   
 61 //....oooOO0OOooo........oooOO0OOooo........oo    
 62                                                   
 63 ODESolver::ODESolver(): fNstepsForObserver(1)     
 64 {}                                                
 65                                                   
 66 //....oooOO0OOooo........oooOO0OOooo........oo    
 67                                                   
 68 double ODESolver::RungeKutta_Fehlberg( std::fu    
 69 func,std::vector<double> &y, double t, double     
 70 {                                                 
 71   //based on https://en.wikipedia.org/wiki/Run    
 72   const int nk=6;                                 
 73   double h = stepsize;                            
 74   double CH[nk]={47./450.,0,12./25.,32./255.,1    
 75   double CT[nk]={-1./150.,0.,3./100.,-16./75.,    
 76   double A[nk]={0.,2./9.,1./3.,3./4.,1.,5./6.}    
 77   double B21=2./9., B31=1./12., B41=69./128.,     
 78   double B32=1./4., B42=-243./128., B52=27./5.    
 79   double B43=135./64., B53=-27./5., B63=13./16    
 80   double B54=16./15., B64=4./27.;                 
 81   double B65=5./144.;                             
 82   double maxError = 1.;                           
 83   std::vector<double> k1 = func(t+A[0]*h,y)*h;    
 84   std::vector<double> k2 = func(t+A[1]*h,y + k    
 85   std::vector<double> k3 = func(t+A[2]*h,y + k    
 86   std::vector<double> k4 = func(t+A[3]*h,y + k    
 87   std::vector<double> k5 = func(t+A[4]*h,y + k    
 88   std::vector<double> k6 = func(t+A[5]*h,y + k    
 89   y = y + k1*CH[0] + k2*CH[1] + k3*CH[2] + k4*    
 90   auto TE = k1*CT[0] + k2*CT[1] + k3*CT[2] + k    
 91   absValuesVector(TE);                            
 92   maxError = *std::max_element(TE.begin(),TE.e    
 93                                                   
 94   k1.clear(); k1.shrink_to_fit();                 
 95   k2.clear(); k2.shrink_to_fit();                 
 96   k3.clear(); k3.shrink_to_fit();                 
 97   k4.clear(); k4.shrink_to_fit();                 
 98   k5.clear(); k5.shrink_to_fit();                 
 99   k6.clear(); k6.shrink_to_fit();                 
100   TE.clear(); TE.shrink_to_fit();                 
101   return  maxError;                               
102 }                                                 
103                                                   
104 //....oooOO0OOooo........oooOO0OOooo........oo    
105                                                   
106 void ODESolver::Embedded_RungeKutta_Fehlberg(     
107   std::function<std::vector<double>(double,std    
108   double start,double end,double stepsize,doub    
109   std::vector<double> *time_observer,std::vect    
110 {                                                 
111   double t = start;                               
112   double h = stepsize;                            
113   int nsteps = 0;                                 
114   if (h < 0) h = (end -  start)/(10000.);         
115   if (time_observer) time_observer->push_back(    
116   if (state_observer) state_observer->push_bac    
117   auto ytemp = y;                                 
118   while (t < end)                                 
119   {                                               
120     ytemp = y;                                    
121     double maxerror = RungeKutta_Fehlberg(func    
122     double scale = 0.9*std::pow(epsilon/maxerr    
123                                                   
124     double hnew = h*scale;                        
125     while (maxerror > epsilon)                    
126     {                                             
127       ytemp = y;                                  
128       maxerror = RungeKutta_Fehlberg(func,ytem    
129       scale = 0.9*std::pow(epsilon/maxerror,1.    
130       hnew = hnew*scale;                          
131     }                                             
132     h = hnew;                                     
133     y = ytemp;                                    
134     t += h;                                       
135     if (t > end) break;                           
136     if ( time_observer || state_observer) {       
137       nsteps++;                                   
138       if (nsteps%fNstepsForObserver == 0) {       
139         if (time_observer) time_observer->push    
140         if (state_observer) state_observer->pu    
141         nsteps = 0;                               
142       }                                           
143     }                                             
144   }                                               
145                                                   
146   ytemp.clear(); ytemp.shrink_to_fit();           
147 }                                                 
148                                                   
149 //....oooOO0OOooo........oooOO0OOooo........oo    
150                                                   
151 void ODESolver::RungeKutta4(                      
152   std::function<std::vector<double>(double,std    
153     double start,double end,double stepsize,      
154     std::vector<double> *time_observer,std::ve    
155 {                                                 
156   double t = start;                               
157   double h = stepsize;                            
158   int nsteps = 0;                                 
159   if (h < 0) h = (end -  start)/(10000.);         
160   if (time_observer) time_observer->push_back(    
161   if (state_observer) state_observer->push_bac    
162   while (t < end)                                 
163   {                                               
164     std::vector<double> k1 = func(t,y)*h;         
165     std::vector<double> k2 = func(t+0.5*h,y +     
166     std::vector<double> k3 = func(t+0.5*h,y +     
167     std::vector<double> k4 = func(t+h,y + k3)*    
168     t += h;                                       
169     if (t > end) break;                           
170     y = y +(k1 +k2*2+k3*2+k4)*(1./6.0);           
171     if ( time_observer || state_observer) {       
172       nsteps++;                                   
173       if (nsteps%fNstepsForObserver == 0) {       
174         if (time_observer) time_observer->push    
175         if (state_observer) state_observer->pu    
176         nsteps = 0;                               
177       }                                           
178     }                                             
179     k1.clear(); k1.shrink_to_fit();               
180     k2.clear(); k2.shrink_to_fit();               
181     k3.clear(); k3.shrink_to_fit();               
182     k4.clear(); k4.shrink_to_fit();               
183   }                                               
184 }                                                 
185                                                   
186 //....oooOO0OOooo........oooOO0OOooo........oo