add adaptive ts simulator

AEDESINTER_AUTOROUTES_ADAPTIV/BinaryIO.cpp

+
+#include  <iostream>
+#include  <cfloat>
+using namespace std;
+#include "error.hpp"
+#include "AFunction.hpp"
+#include "rgraph.hpp"
+#include "RNM.hpp"
+#include "fem.hpp"
+#include "FESpace.hpp" 
+#include "MeshPoint.hpp"
+#include "AFunction_ext.hpp" // Extension of "AFunction.hpp" to deal with more than 3 parameters function
+using namespace Fem2D;
+
+
+double SaveVecAppend(KN<double> *const & f, string *const & nome){
+  std::ofstream outfile (nome->data(),ios_base::binary | std::ofstream::app);
+ 
+  long int nn = f->N(); // get number of nodes
+  long int dim=nn;
+  long pos = outfile.tellp();
+  if (!pos)
+    outfile.write ((char*) &dim, sizeof(long int));//write the dimension of the vector
+  double ftemp ;
+  for(long int i=0; i<nn; i++) {
+    
+    ftemp = *(f[0]+i) ;
+    outfile.write ((char*) &ftemp, sizeof(double));
+  }
+  outfile.close();
+  return 0.0;  // dummy return value.
+}
+
+double SetSizeVec(long int *const & size, string *const & nome){
+  //std::ofstream outfile (nome->data(),ios_base::binary | std::ofstream::app);
+  std::fstream outfile(nome->data(), ios_base::binary | std::fstream::out | std::fstream::in);
+  
+  long int N=*size;
+  
+  outfile.write ((char*) &N, sizeof(long int));//write the dimension of the vector
+  outfile.close();
+  return 0.0;  // dummy return value.
+}
+
+double SaveVec(KN<double> *const & f, string *const & nome)   
+{
+  std::ofstream outfile (nome->data(),ios_base::binary);
+  // To access value at node i of vector N, do as follow: *(N[0]+i)
+  // Explanation (C++ for dummies as I am ;-):
+  //   N         is an alias to the KN object.
+  //   N[0]      is a pointer to the first element of the vector.
+  //   N[0]+i    is a pointer to the ith element of the vector.
+  //   *(N[0]+i) is the value of the ith element of the vector.
+ 
+  long int nn = f->N(); // get number of nodes
+  long int dim=nn;
+  outfile.write ((char*) &dim, sizeof(long int));//write the dimension of the vector
+  double ftemp ;
+  for(long int i=0; i<nn; i++) {
+    
+    ftemp = *(f[0]+i) ;
+    outfile.write ((char*) &ftemp, sizeof(double));
+  }
+  outfile.close();
+  return 0.0;  // dummy return value.
+}
+
+double GetSizeVec(long int *const & size,string *const & nome){
+  std::ifstream infile (nome->data(),ios_base::binary);
+  long int dim;
+  infile.read((char *) &dim, sizeof(long int));
+  *size=dim;
+  infile.close();
+  return 0.0;
+}
+double LoadVec(KN<double> *const & ww, string *const & nome)   
+{
+  std::ifstream infile (nome->data(),ios_base::binary);
+  long int dim;
+  infile.read((char *) &dim, sizeof(long int));
+  double dtemp;
+  for(long int i=0; i<dim; i++)
+   {
+   infile.read((char *) &dtemp, sizeof(double));
+    *(ww[0]+i)=dtemp ;
+    }
+  return 0.0;  // dummy return value.
+}
+
+ 
+double LoadFlag(long int *const & ww, string *const & nome)   
+{
+  std::ifstream infile (nome->data(),ios_base::binary);
+  long int flag;
+  infile.read((char *) &flag, sizeof(long int));
+  *ww=flag;
+  return 0.0;  // dummy return value.
+}
+
+double flag(long int *const & FLAG,string *const &nome)   
+{
+  std::ofstream outfile (nome->data(),ios_base::binary);
+long int Flag;
+ Flag= *FLAG;   
+ outfile.write ((char*) &Flag, sizeof(long int));
+outfile.close();
+ return 0.0;
+}
+
+
+
+//   add the function name to the freefem++ table 
+/*  class Init { public:
+  Init();
+};	
+$1 */
+static void Load_Init(){	
+		
+  Global.Add("LoadVec","(",new OneOperator2_<double,  KN<double>*, string* >(LoadVec)); 
+  Global.Add("LoadFlag","(",new OneOperator2_<double,long int*, string* >(LoadFlag));
+  Global.Add("SaveVec","(",new OneOperator2_<double,KN<double>*, string* >(SaveVec));
+  Global.Add("flag","(",new OneOperator2_<double,long int*,string* >(flag));  
+  Global.Add("GetSizeVec","(",new OneOperator2_<double,long int*,string* >(GetSizeVec));
+  Global.Add("SaveVecAppend","(",new OneOperator2_<double,KN<double>*, string* >(SaveVecAppend));
+  Global.Add("SetSizeVec","(",new OneOperator2_<double,long int*, string* >(SetSizeVec));
+  
+  
+}
+
+LOADFUNC(Load_Init)

AEDESINTER_AUTOROUTES_ADAPTIV/BinaryIO.edp

+load "BinaryIO"
+// test of BinaryIO tools ...
+
+real[int] buffer1(5);
+real[int] buffer2(5);
+
+for (int ii=0;ii<5;ii++)
+  buffer1[ii]=ii;
+
+SaveVec(buffer1,"saveBuff");
+int size=0;
+GetSizeVec(size,"saveBuff");
+cout<<"size ="<<size<<endl;
+
+LoadVec(buffer2,"saveBuff");
+for (int ii=0;ii<size;ii++)
+  cout<<buffer2[ii]<<" ";
+cout<<endl;
+
+for (int jj=0;jj<4;jj++){
+  for (int ii=0;ii<5;ii++)
+    buffer1[ii]=buffer1[ii]+5;
+  SaveVecAppend(buffer1,"saveBuff");
+}
+int newSize=25;
+
+
+SetSizeVec(newSize,"saveBuff");
+GetSizeVec(size,"saveBuff");
+real[int] buffer3(size);
+cout<<"now size ="<<size<<endl;
+LoadVec(buffer3,"saveBuff");
+for (int ii=0;ii<size;ii++)
+  cout<<buffer3[ii]<<" ";
+cout<<endl;

AEDESINTER_AUTOROUTES_ADAPTIV/BinaryIOb.edp

+load "BinaryIO"
+int size;
+GetSizeVec(size,"SAVE/u2d0__rep_0");
+
+cout<<"now size ="<<size<<endl;

AEDESINTER_AUTOROUTES_ADAPTIV/Readme.txt

+This file is copied during the execution of the C prog gen2speciesNL.c.
+It contains the command that must be done to allow the simulation.
+
+This commands are necessary to run the simulation:
+1) more userFDef0.txt
+  Just to check the dynamic on each patch
+2) chmod +x genSetFunc.sh
+3) ./genSetFunc.sh
+  To generate the dynamic on each patch
+
+
+The simuated must be ready to run:
+FreeFem++ cas1.edp
+
+Finaly, visualized with 'python vtktopng.py'

AEDESINTER_AUTOROUTES_ADAPTIV/Surfaces.txt

+Surf0=1.36556e+11
+Surf1=3.34226e+10
+Surf2=5.28336e+10
+Surf3=2.35296e+10
+Surf4=4.77306e+10
+Surf5=4.20849e+10
+Surf6=3.22273e+10
+Surf7=1.99198e+10
+Surf8=4.59006e+10
+Surf9=2.2696e+10
+Surf10=2.2557e+10
+Surf11=2.88487e+10
+Surf12=5.73733e+09
+Surf13=3.18954e+09
+Surf14=2.29261e+10

AEDESINTER_AUTOROUTES_ADAPTIV/VISU/README

+ce repeertoire contient les scripts de post tratement de simulation.
+1) checkSimu.edp : verifie que la presence et la taille des fichiers de sortie des 100 iterations du simulateur.
+2) postT.cpp : calcul les trajectoire min et max
+3) visuSimuMax.edp: creer les sorties VTK des trajectoires min max, doit etre lancer une fois avec "max" et une fois avec "min"
+4)vtktopng.py et vtktopngGen.py: creer les images a partir des sorties vtk.
+
+Attention, il convient de s'assurer que les scrits et programme pointe bien vers le repertoire de sorties que simulations visé.
\ No newline at end of file

AEDESINTER_AUTOROUTES_ADAPTIV/VISU/checkSimu.edp

+load "BinaryIO";
+include "paramsTS.edp";
+//string BASEREP="../SAVE/MEDIAN/";
+string BASEREP="../SAVE/HIGHT/";
+int curStep=0;
+verbosity=0;
+int[int] sizeBinary(15);
+for (int ii=0;ii<15;ii++)
+  sizeBinary[ii]=0;
+int sizeBinaryAux=0;
+macro checkFile(XXINT){
+  string FILENAME=BASEREP+"u2d"+string(XXINT)+"__rep_"+string(numRun);
+  if (exec("ls "+FILENAME+" 2>/dev/null >/dev/null")){
+    nofile=1;
+  }else{
+    if (!sizeBinary[XXINT]){
+      GetSizeVec(sizeBinary[XXINT],FILENAME);
+    }else{
+      GetSizeVec(sizeBinaryAux,FILENAME);
+      if (sizeBinaryAux != sizeBinary[XXINT])
+        cout<<"ERROR "+FILENAME+" size is "<<sizeBinaryAux<<" and should be "<<sizeBinary[XXINT]<<endl;
+    }
+    
+  }
+}//
+
+for( int numRun=0;numRun<100;numRun++){
+  int nofile=0;
+  //for (CURYEAR=FIRSTYEAR; CURYEAR<=LASTYEAR; CURYEAR++){
+  //  for ( curStep=0;curStep<nbSteps;curStep++){
+  for (int ii=0;ii<15;ii++)
+    checkFile(ii);
+  if (!nofile){
+    cout<<"numRun="<<numRun<<" ok"<<endl;
+  }else{
+    cout<<"numRun="<<numRun<<" missing"<<endl;
+  }
+        
+}

AEDESINTER_AUTOROUTES_ADAPTIV/VISU/freefem++.pref

+includepath += ".."
+includepath += "../../Tools1D/"
+includepath += "../../Recorder/"
+includepath += "../../examples1D/"
+loadpath += "/opt/freefem++-3.58/examples++-load/"

AEDESINTER_AUTOROUTES_ADAPTIV/VISU/postT.cpp

+#include <fstream>
+#include  <iostream>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+using namespace std;
+#define BASEREP "../SAVE/HIGHT/"
+
+long int GetSizeVec(char* name){
+  std::ifstream infile (name,ios_base::binary);
+  long int dim;
+  infile.read((char *) &dim, sizeof(long int));
+  infile.close();
+  return dim;
+}
+void LoadVec(char* name,double *pD)   
+{
+  std::ifstream infile (name,ios_base::binary);
+  long int dim;
+  infile.read((char *) &dim, sizeof(long int));
+  double dtemp;
+  for(long int i=0; i<dim; i++)
+  {
+   infile.read((char *) &dtemp, sizeof(double));
+    *(pD++)=dtemp ;
+  }
+  infile.close();
+}
+void SaveVec(double * pD, long int N, char* name)   
+{
+  std::ofstream outfile (name,ios_base::binary);
+  
+  
+  outfile.write ((char*) &N, sizeof(long int));//write the dimension of the vector
+  double ftemp ;
+  for(long int i=0; i<N; i++) {
+    
+    ftemp = pD[i] ;
+    outfile.write ((char*) &ftemp, sizeof(double));
+  }
+  outfile.close();
+}
+
+int main(){
+  char filename[256];
+  int N=4;
+  double * pBufTraj[15];
+  double * pMaxTraj[15];
+  double * pMinTraj[15];
+  long int size[15];
+  for (int j=0;j<15;j++){
+    sprintf(filename,"%su2d%i__rep_0",BASEREP,j);
+    size[j]=GetSizeVec(filename);
+    pBufTraj[j]=(double *)malloc(size[j]*sizeof(double));
+    pMaxTraj[j]=(double *)malloc(size[j]*sizeof(double));
+    pMinTraj[j]=(double *)malloc(size[j]*sizeof(double));
+    LoadVec(filename,pMaxTraj[j]);
+    memcpy(pMinTraj[j],pMaxTraj[j],size[j]*sizeof(double));
+  }
+  
+  for(int numRun=1;numRun<N;numRun++){
+    for (int j=0;j<15;j++){
+      sprintf(filename,"%su2d%i__rep_%i",BASEREP,j,numRun);
+      LoadVec(filename,pBufTraj[j]);
+      for (int k=0;k<size[j];k++){
+        if (pBufTraj[j][k]>pMaxTraj[j][k])
+          pMaxTraj[j][k]=pBufTraj[j][k];
+        if (pBufTraj[j][k]<pMinTraj[j][k])
+          pMinTraj[j][k]=pBufTraj[j][k];
+      }
+    }
+  }
+
+  for (int j=0;j<15;j++){
+    sprintf(filename,"%su2d%i__max",BASEREP,j);
+    SaveVec(pMaxTraj[j],size[j],filename);
+    sprintf(filename,"%su2d%i__min",BASEREP,j);
+    SaveVec(pMinTraj[j],size[j],filename);
+  }
+  for (int j=0;j<15;j++){
+    free(pBufTraj[j]);
+    free(pMaxTraj[j]);
+    free(pMinTraj[j]);
+    
+  }
+  
+  return 0;
+}

AEDESINTER_AUTOROUTES_ADAPTIV/VISU/saveVtk.edp

+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"0s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th0,utm12d0,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"1s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th1,utm12d1,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"2s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th2,utm12d2,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"3s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th3,utm12d3,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"4s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th4,utm12d4,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"5s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th5,utm12d5,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"6s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th6,utm12d6,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"7s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th7,utm12d7,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"8s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th8,utm12d8,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"9s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th9,utm12d9,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"10s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th10,utm12d10,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"11s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th11,utm12d11,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"12s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th12,utm12d12,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"13s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th13,utm12d13,dataname="UU");
+		savevtk(OUTPUTDIR+"D2/u"+maxormin+"14s"+string(CURYEAR)+"_"+string(curStep)+".vtk",Th14,utm12d14,dataname="UU");

AEDESINTER_AUTOROUTES_ADAPTIV/VISU/traju0.txt

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