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Diff for /imach/src/imach.c between versions 1.190 and 1.191

version 1.190, 2015/05/05 08:51:13 version 1.191, 2015/07/14 10:00:33
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.191  2015/07/14 10:00:33  brouard
     Summary: Some fixes
   
   Revision 1.190  2015/05/05 08:51:13  brouard    Revision 1.190  2015/05/05 08:51:13  brouard
   Summary: Adding digits in output parameters (7 digits instead of 6)    Summary: Adding digits in output parameters (7 digits instead of 6)
   
Line 1450  values at the three points, fa, fb , and Line 1453  values at the three points, fa, fb , and
 #endif   #endif 
 #ifdef MNBRAKORIGINAL  #ifdef MNBRAKORIGINAL
 #else  #else
       if (fu > *fc) {  /*       if (fu > *fc) { */
 #ifdef DEBUG  /* #ifdef DEBUG */
       printf("mnbrak4  fu > fc \n");  /*       printf("mnbrak4  fu > fc \n"); */
       fprintf(ficlog, "mnbrak4 fu > fc\n");  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
 #endif  /* #endif */
         /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */  /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
         /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */  /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
         dum=u; /* Shifting c and u */  /*      dum=u; /\* Shifting c and u *\/ */
         u = *cx;  /*      u = *cx; */
         *cx = dum;  /*      *cx = dum; */
         dum = fu;  /*      dum = fu; */
         fu = *fc;  /*      fu = *fc; */
         *fc =dum;  /*      *fc =dum; */
       } else { /* end */  /*       } else { /\* end *\/ */
   /* #ifdef DEBUG */
   /*       printf("mnbrak3  fu < fc \n"); */
   /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
   /* #endif */
   /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
   /*      *cx = dum; */
   /*      dum = fu; */
   /*      fu = *fc; */
   /*      *fc =dum; */
   /*       } */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak3  fu < fc \n");        printf("mnbrak34  fu < or >= fc \n");
       fprintf(ficlog, "mnbrak3 fu < fc\n");        fprintf(ficlog, "mnbrak34 fu < fc\n");
 #endif  #endif
         dum=u; /* Shifting c and u */        dum=u; /* Shifting c and u */
         u = *cx;        u = *cx;
         *cx = dum;        *cx = dum;
         dum = fu;        dum = fu;
         fu = *fc;        fu = *fc;
         *fc =dum;        *fc =dum;
       }  
 #endif  #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 #ifdef DEBUG  #ifdef DEBUG
Line 1565  void linmin(double p[], double xi[], int Line 1578  void linmin(double p[], double xi[], int
     }      }
   }while(fx != fx);    }while(fx != fx);
   
   #ifdef DEBUGLINMIN
     printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
   #endif
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
   /* fmin = f(p[j] + xmin * xi[j]) */    /* fmin = f(p[j] + xmin * xi[j]) */
Line 1574  void linmin(double p[], double xi[], int Line 1590  void linmin(double p[], double xi[], int
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif  #endif
   /* printf("linmin end "); */  #ifdef DEBUGLINMIN
     printf("linmin end ");
   #endif
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     /* printf(" before xi[%d]=%12.8f", j,xi[j]); */      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
     xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */      xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
Line 1583  void linmin(double p[], double xi[], int Line 1601  void linmin(double p[], double xi[], int
     p[j] += xi[j]; /* Parameters values are updated accordingly */      p[j] += xi[j]; /* Parameters values are updated accordingly */
   }     } 
   /* printf("\n"); */    /* printf("\n"); */
   /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */  #ifdef DEBUGLINMIN
     printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
     for (j=1;j<=n;j++) { 
       printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
       if(j % ncovmodel == 0)
         printf("\n");
     }
   #endif
   free_vector(xicom,1,n);     free_vector(xicom,1,n); 
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
Line 1780  void powell(double p[], double **xi, int Line 1805  void powell(double p[], double **xi, int
     }       } 
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
 #endif  #endif
   #ifdef DEBUGLINMIN
           printf("Before linmin in direction P%d-P0\n",n);
           for (j=1;j<=n;j++) { 
             printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
               printf("\n");
           }
   #endif
         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
   #ifdef DEBUGLINMIN
           for (j=1;j<=n;j++) { 
             printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
               printf("\n");
           }
   #endif
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
Line 5865  BOOL IsWow64() Line 5905  BOOL IsWow64()
 }  }
 #endif  #endif
   
 void syscompilerinfo()  void syscompilerinfo(int logged)
  {   {
    /* #include "syscompilerinfo.h"*/     /* #include "syscompilerinfo.h"*/
    /* command line Intel compiler 32bit windows, XP compatible:*/     /* command line Intel compiler 32bit windows, XP compatible:*/
Line 5914  void syscompilerinfo() Line 5954  void syscompilerinfo()
    int cross = CROSS;     int cross = CROSS;
    if (cross){     if (cross){
            printf("Cross-");             printf("Cross-");
            fprintf(ficlog, "Cross-");             if(logged) fprintf(ficlog, "Cross-");
    }     }
 #endif  #endif
   
 #include <stdint.h>  #include <stdint.h>
   
    printf("Compiled with:");fprintf(ficlog,"Compiled with:");     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)  #if defined(__clang__)
    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
 #endif  #endif
 #if defined(__ICC) || defined(__INTEL_COMPILER)  #if defined(__ICC) || defined(__INTEL_COMPILER)
    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */     printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
 #endif  #endif
 #if defined(__GNUC__) || defined(__GNUG__)  #if defined(__GNUC__) || defined(__GNUG__)
    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */     printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
 #endif  #endif
 #if defined(__HP_cc) || defined(__HP_aCC)  #if defined(__HP_cc) || defined(__HP_aCC)
    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */     printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
 #endif  #endif
 #if defined(__IBMC__) || defined(__IBMCPP__)  #if defined(__IBMC__) || defined(__IBMCPP__)
    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */     printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
 #endif  #endif
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */     printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
 #endif  #endif
 #if defined(__PGI)  #if defined(__PGI)
    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */     printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
 #endif  #endif
 #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)  #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */     printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
 #endif  #endif
    printf(" for ");fprintf(ficlog," for ");     printf(" for "); if (logged) fprintf(ficlog, " for ");
         
 // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros  // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
 #ifdef _WIN32 // note the underscore: without it, it's not msdn official!  #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
     // Windows (x64 and x86)      // Windows (x64 and x86)
    printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");     printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
 #elif __unix__ // all unices, not all compilers  #elif __unix__ // all unices, not all compilers
     // Unix      // Unix
    printf("Unix ");fprintf(ficlog,"Unix ");     printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
 #elif __linux__  #elif __linux__
     // linux      // linux
    printf("linux ");fprintf(ficlog,"linux ");     printf("linux ");if(logged) fprintf(ficlog,"linux ");
 #elif __APPLE__  #elif __APPLE__
     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..      // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
    printf("Mac OS ");fprintf(ficlog,"Mac OS ");     printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
 #endif  #endif
   
 /*  __MINGW32__   */  /*  __MINGW32__   */
Line 5973  void syscompilerinfo() Line 6013  void syscompilerinfo()
 /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */  /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
 #if UINTPTR_MAX == 0xffffffff  #if UINTPTR_MAX == 0xffffffff
    printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */     printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
 #elif UINTPTR_MAX == 0xffffffffffffffff  #elif UINTPTR_MAX == 0xffffffffffffffff
    printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */     printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
 #else  #else
    printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */     printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
 #endif  #endif
   
 #if defined(__GNUC__)  #if defined(__GNUC__)
Line 5990  void syscompilerinfo() Line 6030  void syscompilerinfo()
                             + __GNUC_MINOR__ * 100)                              + __GNUC_MINOR__ * 100)
 # endif  # endif
    printf(" using GNU C version %d.\n", __GNUC_VERSION__);     printf(" using GNU C version %d.\n", __GNUC_VERSION__);
    fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);     if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
    if (uname(&sysInfo) != -1) {     if (uname(&sysInfo) != -1) {
      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);       printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);           if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
    }     }
    else     else
       perror("uname() error");        perror("uname() error");
    //#ifndef __INTEL_COMPILER      //#ifndef __INTEL_COMPILER 
 #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)  #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
    printf("GNU libc version: %s\n", gnu_get_libc_version());      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
    fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());     if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
 #endif  #endif
 #endif  #endif
   
Line 6009  void syscompilerinfo() Line 6049  void syscompilerinfo()
    //   {     //   {
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    if (IsWow64()){     if (IsWow64()){
            printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");             printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
            fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");             if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
    }     }
    else{     else{
            printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");             printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
            fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");             if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
    }     }
    //      printf("\nPress Enter to continue...");     //      printf("\nPress Enter to continue...");
    //      getchar();     //      getchar();
Line 6190  int main(int argc, char *argv[]) Line 6230  int main(int argc, char *argv[])
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb;    double agedeb=0.;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
   double fret;    double fret;
   double dum; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   
Line 6204  int main(int argc, char *argv[]) Line 6244  int main(int argc, char *argv[])
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int c,  h , cpt;    int c,  h , cpt;
   int jl;    int jl=0;
   int i1, j1, jk, stepsize;    int i1, j1, jk, stepsize=0;
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
   float  sumlpop=0.;    float  sumlpop=0.;
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
   double bage=0, fage=110, age, agelim, agebase;    double bage=0, fage=110., age, agelim=0., agebase=0.;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
Line 6276  int main(int argc, char *argv[]) Line 6316  int main(int argc, char *argv[])
 #else  #else
   getcwd(pathcd, size);    getcwd(pathcd, size);
 #endif  #endif
     syscompilerinfo(0);
   printf("\n%s\n%s",version,fullversion);    printf("\n%s\n%s",version,fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
Line 6349  int main(int argc, char *argv[]) Line 6389  int main(int argc, char *argv[])
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   syscompilerinfo();    syscompilerinfo(0);
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
Line 6448  int main(int argc, char *argv[]) Line 6488  int main(int argc, char *argv[])
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     fclose (ficparo);      fclose (ficparo);
     fclose (ficlog);      fclose (ficlog);
Removed from v.1.190  
changed lines
  Added in v.1.191

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