X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fnlsop.git;a=blobdiff_plain;f=nlsop.c;h=350868e536751af130b839c9f4f87f9140c24b81;hp=ec8e4d32946cc5219f526237d73b7797dd93c3fa;hb=f8eab7046ff397059600f9f25181b38c101e6f81;hpb=385dd1d28c455f57ecdbdc61766607123a0c5063

diff --git a/nlsop.c b/nlsop.c
index ec8e4d3..350868e 100644
--- a/nlsop.c
+++ b/nlsop.c
@@ -1,6 +1,8 @@
 /*
  * nlsop.c 
  *
+ * author: frank zirkelbach (frank.zirkelbach@physik.uni-augsburg.de)
+ *
  * this program tries helping to understand the amorphous depuration
  * and recrystallization of SiCx while ion implantation at temperatures
  * below 400 degree celsius.
@@ -8,8 +10,25 @@
  * selforganizing lamella structure in the observed behaviour.
  *
  * refs: 
- *  - J. K. N. Lindner. Habilationsschrift, Universitaet Augsburg.
+ *  - J. K. N. Lindner. Habil.Schrift, Universitaet Augsburg.
  *  - Maik Haeberlen. Diplomarbeit, Universitaet Augsburg.
+ *
+ * Copyright (C) 2004 Frank Zirkelbach
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ *
  */
 
 #define _GNU_SOURCE
@@ -29,18 +48,13 @@
 #define MAKE_AMORPH(N) *(N)|=AMORPH
 #define MAKE_CRYST(N) *(N)&=~AMORPH
 
-/* test globals - get removed or included in my_info struct later */
-int amorph_count;
-int cryst_count;
-
 int usage(void)
 {
  puts("usage:");
  puts("-h \t\t help");
  puts("-n \t\t no user interaction");
  puts("-Z \t\t cryst -> amorph c diffusion in z direction");
- printf("-a <value> \t slope of nuclear energy loss (default %f)\n",A_EL);
- printf("-b <value> \t nuclear energy loss offset (default %f)\n",B_EL);
+ puts("-i \t\t no cryst to cryst diffusion");
  printf("-x <value> \t # x cells (default %d)\n",X);
  printf("-y <value> \t # y cells (default %d)\n",Y);
  printf("-z <value> \t # z cells (default %d)\n",Z);
@@ -50,32 +64,34 @@ int usage(void)
  printf("-f <value> \t pressure = <value> * 1/distance^2 (default %f)\n",A_AP);
  printf("-p <value> \t pressure offset (default %f)\n",B_AP);
  printf("-F <value> \t proportionality constant between c conc and ability to get amorphous (default %f)\n",A_CP);
- printf("-A <value> \t slope of linear c distribution (default %f)\n",A_CD);
- printf("-B <value> \t linear c distribution offset (default %f)\n",B_CD);
  printf("-D <value> \t diffusion rate from cryst to amorph cells (default %f)\n",DR_AC);
  printf("-c <value> \t diffusion rate in cryst cells (default %f)\n",DR_CC);
  printf("-e <value> \t do diffusion every <value> steps (default %d)\n",DIFF_RATE);
+ puts("-g <file> <step> continue simulation from file and step (step > 0)!");
  printf("-W <value> \t write every <value> steps to save file (default %d)\n",RESAVE);
  puts("-C <file> \t convert file to gnuplot format");
  puts("-L <file> \t load from file");
  puts("-S <file> \t save to file");
  puts("-R <file> \t read from random file");
- puts("-P <file> \t specify implantatin profile file");
+ puts("-P <file> \t specify implantation profile file");
+ puts("-N <file> \t specify nuclear energy loss profile file");
+ printf("-H <value> \t collisions per ion in simulation window (default %d)\n",CPI);
+ puts("-m <value> \t specify c->a carbon saturation");
  
  return 1;
 }
 
-int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,info *my_info)
+int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,info *my_info,u32 nel_z)
 {
  unsigned char *thiz;
  int *conc;
  int i,j;
  int off;
- double p;
+ double p,q;
 
  thiz=d3_l->status+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
  conc=d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
- p=my_info->b_ap*URAND_MAX;
+ p=my_info->b_ap*nel_z;
  for(i=-(my_info->range);i<=my_info->range;i++)
  {
   for(j=-(my_info->range);j<=my_info->range;j++)
@@ -90,25 +106,28 @@ int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,info *my_info)
  p+=*conc*my_info->a_cp*URAND_MAX;
  if(!(*thiz&AMORPH))
  {
-  if(get_rand(URAND_MAX)<=p)
-  {
-   MAKE_AMORPH(thiz);
-   amorph_count++;
-  }
+  if(get_rand(URAND_MAX)<=p) MAKE_AMORPH(thiz);
  } else
  {
   /* assume 1-p probability */
-  if(get_rand(URAND_MAX)>p)
-  {
-   MAKE_CRYST(thiz);
-   cryst_count++;
-  }
+  /* also look for neighbours ! */
+  q=(URAND_MAX-p)>0?URAND_MAX-p:0;
+  j=0;
+  j+=(*(d3_l->status+((x+d3_l->max_x+1)%d3_l->max_x)+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&AMORPH)?1:0;
+  j+=(*(d3_l->status+((x+d3_l->max_x-1)%d3_l->max_x)+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&AMORPH)?1:0;
+  j+=(*(d3_l->status+x+((y+1+d3_l->max_y)%d3_l->max_y)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&AMORPH)?1:0;
+  j+=(*(d3_l->status+x+((y-1+d3_l->max_y)%d3_l->max_y)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&AMORPH)?1:0;
+  j+=(*(d3_l->status+x+y*d3_l->max_x+((z+1+d3_l->max_z)%d3_l->max_z)*d3_l->max_x*d3_l->max_y)&AMORPH)?1:0;
+  j+=(*(d3_l->status+x+y*d3_l->max_x+((z-1+d3_l->max_z)%d3_l->max_z)*d3_l->max_x*d3_l->max_y)&AMORPH)?1:0;
+
+  p+=((q/6)*j);
+  if(get_rand(URAND_MAX)>p) MAKE_CRYST(thiz);
  }
  
  return 1;
 }
 
-int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio)
+int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio,u32 rj_m,u32 *rj_g)
 {
  u32 x,y,z;
  int i,j,k,c;
@@ -120,7 +139,7 @@ int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio)
  {
   x=get_rand(d3_l->max_x);
   y=get_rand(d3_l->max_y);
-  z=get_rand_lgp(d3_l->max_z,my_info->a_cd,my_info->b_cd);
+  z=get_rand_reject(d3_l->max_z,rj_m,rj_g);
   *(d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)+=1;
   (my_info->cc)++;
  }
@@ -135,8 +154,8 @@ int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio)
    for(k=0;k<d3_l->max_z;k++)
    {
     offset=i+j*d3_l->max_x+k*d3_l->max_x*d3_l->max_y;
-    /* case amorph - amorph <-> cryst diffusion */
-    if(*(d3_l->status+offset)&AMORPH)
+    /* case amorph: amorph <- cryst diffusion */
+    if(*(d3_l->status+offset)&AMORPH && *(d3_l->extra+offset)<my_info->c_sat)
     {
      for(c=-1;c<=1;c++)
      {
@@ -158,7 +177,7 @@ int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio)
       {
        off=i+((j+c+d3_l->max_y)%d3_l->max_y)*d3_l->max_x+k*d3_l->max_x*d3_l->max_y;
        carry=0;
-       if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));                             
+       if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
        if(carry!=0)
        {
         *(d3_l->extra+offset)+=carry; 
@@ -168,23 +187,33 @@ int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio)
      }
      if(my_info->z_diff)
      {
-      for(c=-1;c<=1;c++)
+      if(k!=0)
       {
-       if(c!=0)
+       off=i+j*d3_l->max_x+(k-1)*d3_l->max_x*d3_l->max_y;
+       carry=0;
+       if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
+       if(carry!=0)
        {
-        off=i+j*d3_l->max_x+((k+c+d3_l->max_z)%d3_l->max_z)*d3_l->max_x*d3_l->max_y;
-        carry=0;
-        if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
-        if(carry!=0)
-        {
-         *(d3_l->extra+off)-=carry;
-         *(d3_l->extra+offset)+=carry;
-        }
+        *(d3_l->extra+off)-=carry;
+        *(d3_l->extra+offset)+=carry;
+       }
+      }
+      if(k!=d3_l->max_z-1)
+      {
+       off=i+j*d3_l->max_x+(k+1)*d3_l->max_x*d3_l->max_y;
+       carry=0;
+       if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
+       if(carry!=0)
+       {
+        *(d3_l->extra+off)-=carry;
+        *(d3_l->extra+offset)+=carry;
        }
       }
      }  
     } else
-    /* case not amorph - cryst <-> cryst diffusion */
+    /* case not amorph: cryst <-> cryst diffusion */
+    if(my_info->c_diff) {
+    /* if there is c diff, no diff in z-direction */
     {
      for(c=-1;c<=1;c++) 
      {
@@ -221,6 +250,9 @@ int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio)
       }
      }
     }
+    /* end test */
+    }
+    /* */
    } /* for z */
   } /* for y */
  } /* for x */
@@ -305,9 +337,53 @@ int calc_max_extra(d3_lattice *d3_l)
  return max;
 }
 
-int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
+int write_ac_distr(d3_lattice *d3_l,int ac_distr)
+{
+ int fd,x,y,z;
+ int count,offset;
+ char file[32];
+ int si_count;
+ 
+ si_count=d3_l->max_x*d3_l->max_y*SI_PER_VOLUME;
+ if(ac_distr==1) strcpy(file,"carbon_in_av.plot");
+ if(ac_distr==2) strcpy(file,"carbon_in_cv.plot");
+ if(ac_distr==3) strcpy(file,"carbon.plot");
+ if(ac_distr==4) strcpy(file,"amorphous_volumes.plot");
+
+ if((fd=open(file,O_WRONLY|O_CREAT))<0)
+ {
+  puts("cannot open plot file");
+  return -1;
+ }
+
+ for(z=0;z<d3_l->max_z;z++)
+ {
+  count=0;
+  for(x=0;x<d3_l->max_x;x++)
+  {
+   for(y=0;y<d3_l->max_y;y++)
+   {
+    offset=x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
+    if(ac_distr==1)
+     if(*(d3_l->status+offset)&AMORPH) count+=*(d3_l->extra+offset);
+    if(ac_distr==2)
+     if(!(*(d3_l->status+offset)&AMORPH)) count+=*(d3_l->extra+offset);
+    if(ac_distr==3) count+=*(d3_l->extra+offset);
+    if(ac_distr==4)
+     if(*(d3_l->status+offset)&AMORPH) count+=1;
+   }
+  }
+  if(ac_distr==4) dprintf(fd,"%d %d\n",z*CELL_LENGTH,count);
+  else dprintf(fd,"%d %f\n",z*CELL_LENGTH,100.0*count/si_count);
+ }
+ close(fd);
+ 
+ return 1;
+}
+
+int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z,int max)
 {
- int fd,i,j,size=0,foo=0;
+ int fd,i,j,size=0,foo=0,k,sum;
  int width=0,height=0;
  char bmpfile[MAX_CHARS];
  char buf[128];
@@ -317,16 +393,16 @@ int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
   sprintf(bmpfile,"x-z_%d.bmp",y);
   foo=3*d3_l->max_x;
   size=(foo+(4-foo%4))*d3_l->max_z;
-  width=d3_l->max_x;
   height=d3_l->max_z;
+  width=d3_l->max_x;
  }
  if(window==2)
  {
   sprintf(bmpfile,"y-z_%d.bmp",x);
   foo=3*d3_l->max_y;
   size=(foo+(4-foo%4))*d3_l->max_z;
-  width=d3_l->max_y;
   height=d3_l->max_z;
+  width=d3_l->max_y;
  }
  if(window==3)
  {
@@ -336,7 +412,78 @@ int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
   width=d3_l->max_x;
   height=d3_l->max_y;
  }
-
+ if(window==4)
+ {
+  sprintf(bmpfile,"x-z_cdistr_%d.bmp",y);
+  foo=3*d3_l->max_x;
+  size=(foo+(4-foo%4))*d3_l->max_z;
+  height=d3_l->max_z;
+  width=d3_l->max_x;
+ }
+ if(window==5)
+ {
+  sprintf(bmpfile,"y-z_cdistr_%d.bmp",x);
+  foo=3*d3_l->max_y;
+  size=(foo+(4-foo%4))*d3_l->max_z;
+  height=d3_l->max_z;
+  width=d3_l->max_y;
+ }
+ if(window==6)
+ {
+  sprintf(bmpfile,"x-y_cdistr_%d.bmp",z);
+  foo=3*d3_l->max_x;
+  size=(foo+(4-foo%4))*d3_l->max_y;
+  width=d3_l->max_x;
+  height=d3_l->max_y;
+ }
+ if(window==7)
+ {
+  sprintf(bmpfile,"x-z_a_cdistr_%d.bmp",y);
+  foo=3*d3_l->max_x;
+  size=(foo+(4-foo%4))*d3_l->max_z;
+  height=d3_l->max_z;
+  width=d3_l->max_x;
+ }
+ if(window==8)
+ {
+  sprintf(bmpfile,"y-z_a_cdistr_%d.bmp",x);
+  foo=3*d3_l->max_y;
+  size=(foo+(4-foo%4))*d3_l->max_z;
+  height=d3_l->max_z;
+  width=d3_l->max_y;
+ }
+ if(window==9)
+ {
+  sprintf(bmpfile,"x-y_a_cdistr_%d.bmp",z);
+  foo=3*d3_l->max_x;
+  size=(foo+(4-foo%4))*d3_l->max_y;
+  height=d3_l->max_y;
+  width=d3_l->max_x;
+ }
+ if(window==10)
+ {
+  sprintf(bmpfile,"x-z_c_cdistr_%d.bmp",y);
+  foo=3*d3_l->max_x;
+  size=(foo+(4-foo%4))*d3_l->max_z;
+  height=d3_l->max_z;
+  width=d3_l->max_x;
+ }
+ if(window==11)
+ {
+  sprintf(bmpfile,"y-z_c_cdistr_%d.bmp",x);
+  foo=3*d3_l->max_y;
+  size=(foo+(4-foo%4))*d3_l->max_z;
+  height=d3_l->max_z;
+  width=d3_l->max_y;
+ }
+ if(window==12)
+ {
+  sprintf(bmpfile,"x-y_c_cdistr_%d.bmp",z);
+  foo=3*d3_l->max_x;
+  size=(foo+(4-foo%4))*d3_l->max_y;
+  height=d3_l->max_y;
+  width=d3_l->max_x;
+ }
  if((fd=open(bmpfile,O_WRONLY|O_CREAT))<0)
  {
   puts("cannot open bmp file");
@@ -386,8 +533,11 @@ int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
   {
    for(i=0;i<d3_l->max_x;i++)
    {
-    if(*(d3_l->status+i+y*d3_l->max_x+(d3_l->max_z-j)*d3_l->max_x*d3_l->max_y)&RED) memset(buf,0xff,3);
-    else memset(buf,0,3);
+    sum=0;
+    for(k=-2;k<=2;k++)
+     if(*(d3_l->status+i+(((y+k+d3_l->max_y)%d3_l->max_y)*d3_l->max_x)+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y)&RED) sum+=0xff;
+    sum/=5;
+    memset(buf,(unsigned char)sum,3);
     if(write(fd,buf,3)<3)
     {
      puts("failed writing rgb values to bmp file");
@@ -411,8 +561,11 @@ int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
   {
    for(i=0;i<d3_l->max_y;i++)
    {
-    if(*(d3_l->status+x+i*d3_l->max_x+(d3_l->max_z-j)*d3_l->max_x*d3_l->max_y)&RED) memset(buf,0xff,3);
-    else memset(buf,0,3);
+    sum=0;
+    for(k=-2;k<=2;k++)
+     if(*(d3_l->status+((x+k+d3_l->max_x)%d3_l->max_x)+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y)&RED) sum+=0xff;
+    sum/=5;
+    memset(buf,(unsigned char)sum,3);
     if(write(fd,buf,3)<3)
     {
      puts("failed writing rgb values to bmp file");
@@ -436,7 +589,7 @@ int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
   {
    for(i=0;i<d3_l->max_x;i++)
    {
-    if(*(d3_l->status+i+(d3_l->max_y-j)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&RED) memset(buf,0xff,3);
+    if(*(d3_l->status+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&RED) memset(buf,0xff,3);
     else memset(buf,0,3);
     if(write(fd,buf,3)<3)
     {
@@ -455,6 +608,246 @@ int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
    }
   }
  }
+ if(window==4)
+ {
+  for(j=0;j<d3_l->max_z;j++)
+  {
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    sum=*(d3_l->extra+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;
+    }
+   }
+   if(foo%4)
+   {
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
+ if(window==5)
+ { 
+  for(j=0;j<d3_l->max_z;j++) 
+  {                     
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    sum=*(d3_l->extra+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;  
+    }
+   }
+   if(foo%4)
+   {
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
+ if(window==6)
+ {   
+  for(j=0;j<d3_l->max_y;j++)
+  {  
+   for(i=0;i<d3_l->max_x;i++)
+   { 
+    sum=*(d3_l->extra+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y);
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;
+    }
+   } 
+   if(foo%4)
+   { 
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   } 
+  }
+ }
+ if(window==7)
+ {
+  for(j=0;j<d3_l->max_z;j++)
+  {
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    if(*(d3_l->status+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y)&RED) sum=*(d3_l->extra+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
+    else sum=0;
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;
+    }
+   }
+   if(foo%4)
+   {
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
+ if(window==8)
+ { 
+  for(j=0;j<d3_l->max_z;j++) 
+  {                     
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    if(*(d3_l->status+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y)&RED) sum=*(d3_l->extra+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
+    else sum=0;
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;  
+    }
+   }
+   if(foo%4)
+   {
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
+ if(window==9)
+ {   
+  for(j=0;j<d3_l->max_y;j++)
+  {  
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    if(*(d3_l->status+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&RED) sum=*(d3_l->extra+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y);
+    else sum=0;
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;
+    }
+   } 
+   if(foo%4)
+   { 
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   } 
+  }
+ }
+ if(window==10)
+ {
+  for(j=0;j<d3_l->max_z;j++)
+  {
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    if(!(*(d3_l->status+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y)&RED)) sum=*(d3_l->extra+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
+    else sum=0;
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;
+    }
+   }
+   if(foo%4)
+   {
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
+ if(window==11)
+ { 
+  for(j=0;j<d3_l->max_z;j++) 
+  {                     
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    if(!(*(d3_l->status+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y)&RED)) sum=*(d3_l->extra+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
+    else sum=0;
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;  
+    }
+   }
+   if(foo%4)
+   {
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
+ if(window==12)
+ {   
+  for(j=0;j<d3_l->max_y;j++)
+  {  
+   for(i=0;i<d3_l->max_x;i++)
+   {
+    if(!(*(d3_l->status+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&RED)) sum=*(d3_l->extra+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y);
+    else sum=0;
+    sum=sum*255/max;
+    memset(buf,(unsigned char)sum,3);
+    if(write(fd,buf,3)<3)
+    {
+     puts("failed writing rgb values to bmp file");
+     return-1;
+    }
+   } 
+   if(foo%4)
+   { 
+    memset(buf,0,4-foo%4);
+    if(write(fd,buf,4-foo%4)<4-foo%4)
+    {
+     puts("failed writing 4 byte ending");
+     return -1;
+    }
+   }
+  }
+ }
  close(fd);
 
  return 1;
@@ -497,7 +890,8 @@ int save_to_file(char *sf,d3_lattice *d3_l,info *my_inf)
 
 int load_from_file(char *lf,d3_lattice *d3_l,info *my_inf)
 {
- int lf_fd,c;
+
+ int lf_fd,c,pos,end,data,data_len,strip;
 
  if((lf_fd=open(lf,O_RDONLY))<0)
  {
@@ -509,11 +903,31 @@ int load_from_file(char *lf,d3_lattice *d3_l,info *my_inf)
   puts("failed reading d3 lattice struct");
   return -1;
  }
- if(read(lf_fd,my_inf,sizeof(info))<sizeof(info))
+ pos=lseek(lf_fd,0,SEEK_CUR);
+ printf("psition: %d (%d)\n",pos,sizeof(d3_lattice));
+ data=d3_l->max_x*d3_l->max_y*d3_l->max_z;
+ data_len=data*(sizeof(int)+sizeof(unsigned char));
+ printf("there are %d volumes so we need %d of bytes\n",data,data_len);
+ end=lseek(lf_fd,0,SEEK_END);
+ c=end-pos-data_len;
+ printf("end: %d => length: %d => guessed info size: %d bytes\n",end,end-pos,c);
+ strip=sizeof(info)-c;
+ printf("as real programs info size is %d, we strip %d bytes\n",sizeof(info),strip);
+ lseek(lf_fd,pos,SEEK_SET);
+ c=sizeof(info);
+ if(strip>0) c-=strip;
+ if(c<0)
+ {
+  puts("info smaller then strip size");
+  return -1;
+ }
+ if(read(lf_fd,my_inf,c)<c)
  {
   puts("failed reading info struct");
   return-1;
  }
+ if(strip>0) memset(my_inf+c,0,strip);
+ if(strip<0) lseek(lf_fd,(-1*strip),SEEK_CUR);
  c=d3_l->max_x*d3_l->max_y*d3_l->max_z;
  if((d3_l->status=(unsigned char*)malloc(c*sizeof(unsigned char)))==NULL)
  {
@@ -597,7 +1011,7 @@ int get_c_ratio(double *c_ratio,char *pfile,info *my_info,d3_lattice *d3_l)
    a=atof(p)/10; /* nm */
    p=strtok(NULL," ");
    b=atof(p);
-   if(a>my_info->b_cd*CELL_LENGTH && a<(my_info->b_cd+d3_l->max_z)*CELL_LENGTH) d+=b;
+   if(a<=d3_l->max_z*CELL_LENGTH) d+=b;
    all+=b;
   }
  }
@@ -607,16 +1021,85 @@ int get_c_ratio(double *c_ratio,char *pfile,info *my_info,d3_lattice *d3_l)
  return 1;
 }
 
+u32 get_reject_graph(info *my_info,d3_lattice *d3_l,char *file,u32 *graph) {
+ double a,b;
+ int i,j,k;
+ int fd;
+ char buf[32],*p;
+ unsigned char *flag;
+ u32 max;
+
+ max=0;
+ if((fd=open(file,O_RDONLY))<0)
+ {
+  puts("cannot open file to calculate rejection graph");
+  return -1;
+ }
+ if((flag=(unsigned char *)malloc(d3_l->max_z))==NULL)
+ {
+  puts("cannot malloc flag memory for rejection graph");
+  return -1;
+ }
+ memset(flag,0,d3_l->max_z);
+ memset(graph,0,d3_l->max_z*sizeof(u32));
+ /* get fixpoints */
+ k=1;
+ while(k)
+ {
+  for(i=0;i<32;i++)
+  {
+   k=read(fd,&buf[i],1);
+   if((buf[i]=='\n')||(k==0)) break;
+  }
+  if(k)
+  {
+   p=strtok(buf," ");
+   a=atof(p)/10; /* nm */
+   p=strtok(NULL," ");
+   b=atof(p);
+   if(a>d3_l->max_z*CELL_LENGTH) k=0;
+   else 
+   {
+    graph[(int)(a/CELL_LENGTH)]=(int)(URAND_MAX/100*b);
+    flag[(int)(a/CELL_LENGTH)]=1;
+   }
+  }
+ }
+ /* do (linear) interpolation here! */
+ i=0;
+ a=0;
+ while(i<d3_l->max_z)
+ {
+  /* graph[0] is 0! */
+  j=i;
+  i++;
+  while(flag[i]==0&&i<d3_l->max_z) i++;
+  for(k=j+1;k<i;k++) graph[k]=(int)((k-j)*((int)graph[i]-(int)graph[j])/(i-j))+graph[j];
+  if(graph[i]>max) max=graph[i];
+ }
+
+ free(flag);
+
+#ifdef DEBUG_INTERPOL_PROFILE
+ printf("debug: %s (interpolated profile)\n",file);
+ for(i=0;i<d3_l->max_z;i++) printf("%d %d\n",i,graph[i]);
+#endif
+
+ return max;
+}
+
 int main(int argc,char **argv)
 {
  u32 x,y,z,x_c,y_c,z_c;
- int i,quit,escape,switchmode,nowait,bmp;
+ int i,j,quit,escape,switchmode,nowait,bmp,ac_distr;
  int refresh,resave;
+ int c_step;
  char s_file[MAX_CHARS];
  char s_file_tmp[MAX_CHARS];
  char l_file[MAX_CHARS];
  char c_file[MAX_CHARS];
  char p_file[MAX_CHARS];
+ char n_e_file[MAX_CHARS];
  char convert;
  char r_file[MAX_CHARS];
 #ifdef USE_DFB_API
@@ -627,17 +1110,18 @@ int main(int argc,char **argv)
  char cc_txt[MAX_TXT];
  char a_txt[MAX_TXT];
  char s_txt[MAX_TXT];
- char ap_txt[MAX_TXT];
- char el_txt[MAX_TXT];
- char cd_txt[MAX_TXT];
+ char ballistic_txt[MAX_TXT];
+ char carbon_txt[MAX_TXT];
+ char stress_txt[MAX_TXT];
  char r_txt[MAX_TXT];
- char cp_txt[MAX_TXT];
  char zdiff_txt[MAX_TXT];
  char diff_txt[MAX_TXT];
  char dr_ac_txt[MAX_TXT];
  char dr_cc_txt[MAX_TXT];
  char dose_txt[MAX_TXT];
  char mode_txt[MAX_TXT];
+ char hpi_txt[MAX_TXT];
+ char csat_txt[MAX_TXT];
  char *arg_v[MAX_ARGV];
 #endif
  d3_lattice d3_l;
@@ -647,6 +1131,10 @@ int main(int argc,char **argv)
 #ifdef USE_DFB_API
  int max_extra;
 #endif
+ u32 *c_profile;
+ u32 *n_e_loss;
+ u32 ne_max,ip_max;
+ u32 nel_z;
 
  d3_l.max_x=X;
  d3_l.max_y=Y;
@@ -656,10 +1144,7 @@ int main(int argc,char **argv)
  refresh=REFRESH;
  resave=RESAVE;
  my_info.z_diff=0;
- my_info.a_el=A_EL;
- my_info.b_el=B_EL;
- my_info.a_cd=A_CD;
- my_info.b_cd=B_CD;
+ my_info.c_diff=1;
  my_info.a_ap=A_AP;
  my_info.b_ap=B_AP;
  my_info.a_cp=A_CP;
@@ -667,20 +1152,23 @@ int main(int argc,char **argv)
  my_info.dr_ac=DR_AC;
  my_info.dr_cc=DR_CC;
  my_info.diff_rate=DIFF_RATE;
+ my_info.cpi=CPI;
+ my_info.c_sat=C_SAT;
  nowait=0;
  quit=0;
  escape=0;
  switchmode=0;
+ c_step=0;
  strcpy(s_file,"");
  strcpy(l_file,"");
  strcpy(c_file,"");
  strcpy(p_file,IMP_PROFILE);
+ strcpy(n_e_file,NEL_PROFILE);
  convert=0;
  strcpy(r_file,"");
  mode=0;
-
- amorph_count=0;
- cryst_count=0;
+ ne_max=0;
+ ip_max=0;
 
  for(i=1;i<argc;i++)
  {
@@ -694,12 +1182,6 @@ int main(int argc,char **argv)
     case 'n':
      nowait=1;
      break;
-    case 'a':
-     my_info.a_el=atof(argv[++i]);
-     break;
-    case 'b':
-     my_info.b_el=atof(argv[++i]);
-     break;
     case 'x':
      d3_l.max_x=atoi(argv[++i]);
      break;
@@ -712,6 +1194,10 @@ int main(int argc,char **argv)
     case 'Z':
      my_info.z_diff=1;
      break;
+    case 'i':
+     my_info.c_diff=0;
+     my_info.dr_cc=0;
+     break;
     case 's':
      my_info.steps=atoi(argv[++i]);
      break;
@@ -730,12 +1216,6 @@ int main(int argc,char **argv)
     case 'F':
      my_info.a_cp=atof(argv[++i]);
      break;
-    case 'A':
-     my_info.a_cd=atof(argv[++i]);
-     break;
-    case 'B':
-     my_info.b_cd=atof(argv[++i]);
-     break;
     case 'W':
      resave=atoi(argv[++i]);
      break;
@@ -765,6 +1245,19 @@ int main(int argc,char **argv)
     case 'P':
      strcpy(p_file,argv[++i]);
      break;
+    case 'N':
+     strcpy(n_e_file,argv[++i]);
+     break;
+    case 'g':
+     strcpy(l_file,argv[++i]);
+     if(i<argc-1) if(argv[i+1][0]!='-') c_step=atoi(argv[++i]);
+     break;
+    case 'H':
+     my_info.cpi=atoi(argv[++i]);
+     break;
+    case 'm':
+     my_info.c_sat=atoi(argv[++i]);
+     break;
     default:
      usage();
      return -1;
@@ -817,7 +1310,7 @@ int main(int argc,char **argv)
    return 1;
   } 
 #ifdef USE_DFB_API
-    else d3_lattice_init(&argc,argv,&d3_l);
+  else d3_lattice_init(&argc,argv,&d3_l);
 #endif
  }
 
@@ -830,66 +1323,107 @@ int main(int argc,char **argv)
  sprintf(s_txt,"steps: %d",my_info.steps);
  sprintf(dose_txt,"dose: %.2fe+17 C/cm²",my_info.steps*1.0/(d3_l.max_x*d3_l.max_y*CELL_LENGTH*CELL_LENGTH*1000));
  sprintf(r_txt,"pressure range: %d",my_info.range);
- sprintf(ap_txt,"a_ap: %.3f  b_ap: %.3f",my_info.a_ap,my_info.b_ap);
- sprintf(el_txt,"a_el: %.3f  b_el: %.3f",my_info.a_el,my_info.b_el);
- sprintf(cd_txt,"a_cd: %.3f  b_cd: %.3f",my_info.a_cd,my_info.b_cd);
- sprintf(cp_txt,"a_cp: %.4f",my_info.a_cp);
- sprintf(dr_ac_txt,"a/c diffusion rate: %.4f",my_info.dr_ac);
- sprintf(dr_cc_txt,"c/c diffusion rate: %.4f",my_info.dr_cc);
+ sprintf(stress_txt,"stress term: %f",my_info.a_ap);
+ sprintf(ballistic_txt,"ballistic term: %f",my_info.b_ap);
+ sprintf(carbon_txt,"carbon term: %f",my_info.a_cp);
+ sprintf(dr_ac_txt,"a/c diffusion rate: %f",my_info.dr_ac);
+ if(my_info.c_diff!=0) sprintf(dr_cc_txt,"c/c diffusion rate: %f",my_info.dr_cc);
+ else sprintf(dr_cc_txt,"c/c diffusion rate: none");
  sprintf(zdiff_txt,"diffusion in z direction: %c",my_info.z_diff?'y':'n');
  sprintf(diff_txt,"diffusion every %d steps",my_info.diff_rate);
  strcpy(mode_txt,"view: a/c mode");
- arg_v[1]=xyz_txt;
- arg_v[2]=NULL;
+ sprintf(hpi_txt,"hits per ion: %d",my_info.cpi);
+ sprintf(csat_txt,"carbon saturation: %d",my_info.c_sat);
+ arg_v[1]=mode_txt;
+ arg_v[2]=xyz_txt;
  arg_v[3]=status_txt;
  arg_v[4]=conc_txt;
  arg_v[5]=NULL;
- arg_v[6]=mode_txt;
- arg_v[7]=NULL;
- arg_v[8]=steps_txt;
- arg_v[9]=cc_txt;
- arg_v[10]=NULL;
- arg_v[11]=diff_txt;
- arg_v[12]=zdiff_txt;
- arg_v[13]=NULL;
- arg_v[14]=a_txt;
- arg_v[15]=s_txt;
- arg_v[16]=dose_txt;
- arg_v[17]=NULL;
- arg_v[18]=r_txt;
- arg_v[19]=ap_txt;
- arg_v[20]=el_txt;
- arg_v[21]=cd_txt;
- arg_v[22]=cp_txt;
+ arg_v[6]=steps_txt;
+ arg_v[7]=cc_txt;
+ arg_v[8]=NULL;
+ arg_v[9]=a_txt;
+ arg_v[10]=s_txt;
+ arg_v[11]=dose_txt;
+ arg_v[12]=diff_txt;
+ arg_v[13]=zdiff_txt;
+ arg_v[14]=r_txt;
+ arg_v[15]=ballistic_txt;
+ arg_v[16]=carbon_txt;
+ arg_v[17]=stress_txt;
+ arg_v[18]=dr_ac_txt;
+ arg_v[19]=dr_cc_txt;
+ arg_v[20]=hpi_txt;
+ arg_v[21]=csat_txt;
+ arg_v[22]=NULL;
  arg_v[23]=NULL;
- arg_v[24]=dr_ac_txt;
- arg_v[25]=dr_cc_txt;
+ arg_v[24]=NULL;
+ arg_v[25]=NULL;
 #endif
 
- if(!strcmp(l_file,""))
+ /* compute graphs for random number rejection method */
+ if((c_profile=(u32 *)malloc(d3_l.max_z*sizeof(unsigned int)))==NULL)
+ {
+  puts("failed allocating memory for carbon profile graph");
+  return -1;
+ }
+ if((n_e_loss=(u32 *)malloc(d3_l.max_z*sizeof(unsigned int)))==NULL)
+ {
+  puts("failed allocating memory for nuclear energy loss graph");
+  return -1;
+ }
+ ip_max=get_reject_graph(&my_info,&d3_l,p_file,c_profile);
+ ne_max=get_reject_graph(&my_info,&d3_l,n_e_file,n_e_loss);
+
+ if((!strcmp(l_file,""))||(c_step))
  {
+  /* calculate ratio of c_simwindow / c_total */
   if(get_c_ratio(&c_ratio,p_file,&my_info,&d3_l)!=1)
   {
    puts("failed calculating ratio");
    return -1;
   }
-  i=0;
+
+#ifdef DEBUG_RAND
+ i=0;
+ while(1)
+ {
+#ifdef DEBUG_CP
+  printf("%d\n",get_rand_reject(d3_l.max_z,ip_max,c_profile));
+#endif
+#ifdef DEBUG_NEL
+  printf("%d\n",get_rand_reject(d3_l.max_z,ne_max,n_e_loss));
+#endif
+#ifdef DEBUG_NORM
+  printf("%d\n",get_rand(d3_l.max_z));
+#endif
+ if(i==10000000) return 1;
+ i++;
+ }
+#endif
+
+  i=(c_step?c_step:0);
   while((i<my_info.steps) && (quit==0) && (escape==0))
   {
-   x_c=get_rand(d3_l.max_x);
-   y_c=get_rand(d3_l.max_y);
-   z_c=get_rand_lgp(d3_l.max_z,my_info.a_el,my_info.b_el);
-   distrib_c(&d3_l,&my_info,i,c_ratio);
-   process_cell(&d3_l,x_c,y_c,z_c,&my_info);
+   for(j=0;j<my_info.cpi;j++)
+   {
+    x_c=get_rand(d3_l.max_x);
+    y_c=get_rand(d3_l.max_y);
+    // z_c=get_rand_reject(d3_l.max_z,ne_max,n_e_loss);
+    z_c=get_rand(d3_l.max_z);
+    nel_z=URAND_MAX*(1.0*n_e_loss[z_c]/ne_max);
+    process_cell(&d3_l,x_c,y_c,z_c,&my_info,nel_z);
+   }
+   distrib_c(&d3_l,&my_info,i,c_ratio,ip_max,c_profile);
 #ifdef USE_DFB_API
    if(i%refresh==0)
    {
     sprintf(xyz_txt,"x: %d  y: %d  z: %d",x+1,y+1,z+1);
     sprintf(status_txt,"status: %c",(*(d3_l.status+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y)&AMORPH)?'a':'c');
     sprintf(conc_txt,"conc: %d",*(d3_l.extra+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y));
-    sprintf(steps_txt,"step: %d  a_count: %d",i,amorph_count);
-    sprintf(cc_txt,"total c: %d  c_count: %d",my_info.cc,cryst_count);
-    d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,0);
+    sprintf(steps_txt,"step: %d",i);
+    sprintf(cc_txt,"total c: %d",my_info.cc);
+    d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,0,NULL,0,NULL,0);
    }
 #endif
    if(i%resave==0 && strcmp(s_file,"") && resave!=0 && i!=0)
@@ -927,6 +1461,7 @@ int main(int argc,char **argv)
   if(switchmode==0) mode=0;
   if(switchmode==1) mode=1;
   if(switchmode==2) mode=2;
+  if(switchmode==3) mode=3;
   /* end of bahh! */
   sprintf(xyz_txt,"x: %d  y: %d  z: %d",x+1,y+1,z+1);
   sprintf(status_txt,"status: %c",(*(d3_l.status+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y)&AMORPH)?'a':'c');
@@ -936,11 +1471,13 @@ int main(int argc,char **argv)
   if(switchmode==0) strcpy(mode_txt,"view: a/c mode");
   if(switchmode==1) strcpy(mode_txt,"view: c conc mode");
   if(switchmode==2) strcpy(mode_txt,"view: a pressure mode");
-  d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,max_extra);
+  if(switchmode==3) strcpy(mode_txt,"view: a/c + profiles mode");
+  d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,max_extra,c_profile,ip_max,n_e_loss,ne_max);
   bmp=0;
-  scan_event(&d3_l,&x,&y,&z,&quit,&escape,&switchmode,&bmp);
-  if(bmp) write_bmp(&d3_l,bmp,x,y,z);
-
+  ac_distr=0;
+  scan_event(&d3_l,&x,&y,&z,&quit,&escape,&switchmode,&bmp,&ac_distr);
+  if(bmp) write_bmp(&d3_l,bmp,x,y,z,max_extra);
+  if(ac_distr) write_ac_distr(&d3_l,ac_distr);
  }
 
  d3_lattice_release(&d3_l);