added diffusion of c ions

diff --git a/nlsop.c b/nlsop.c
index 87b551b..c4fc825 100644 (file)
--- a/nlsop.c
+++ b/nlsop.c
@@ -50,7 +50,10 @@ int usage(void)
  printf("-p <value> \t pressure offset (default %f)\n",B_AP);
  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("-C <value> \t initial c concentration (default %d)\n",CC);
+ */
+ printf("-D <value> \t diffusion rate from cryst to amorph cells (default %f)\n",D_R);
  puts("-L <file> \t load from file");
  puts("-S <file> \t save to file");
  puts("-R <file> \t read from random file");
@@ -83,22 +86,110 @@ int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,int r,double a,double b,int
   if(get_rand(URAND_MAX)<=p)
   {
    MAKE_AMORPH(thiz);
-   *t_c=*t_c+1-*conc;
-  } else *t_c+=1;
+   // *t_c=*t_c+1-*conc;
+  } // else *t_c+=1;
  } else
  {
   /* assume 1-p probability */
   if(get_rand(URAND_MAX)>p)
   {
    MAKE_CRYST(thiz);
-   *t_c=*t_c+1+*conc;
-  } else *t_c+=1;
+   // *t_c=*t_c+1+*conc;
+  } // else *t_c+=1;
  }
+ 
+ *t_c+=1;
 
  return 1;
 }
 
-int distrib_c(d3_lattice *d3_l,int t_c,double a,double b)
+int distrib_c(d3_lattice *d3_l,double d_r,double a,double b)
+{
+ u32 x,y,z;
+ int i,j,k,c;
+ int offset,off;
+ int carry;
+
+ /* put one c ion somewhere in the lattice */
+ x=get_rand(d3_l->max_x);
+ y=get_rand(d3_l->max_y);
+ z=get_rand_lgp(d3_l->max_z,a,b);
+ *(d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)+=1;
+
+ /* diffusion in layer */
+ for(i=0;i<d3_l->max_x;i++)
+ {
+  for(j=0;j<d3_l->max_y;j++)
+  {
+   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 */
+    if(*(d3_l->status+offset)&AMORPH)
+    {
+     /* look at neighbours and move c ions */
+     for(c=-1;c<=1;c++)
+     {
+      if(c!=0)
+      {
+       off=((i+d3_l->max_x+c)%d3_l->max_x)+j*d3_l->max_x+k*d3_l->max_x*d3_l->max_y;
+       /* case neighbour not amorph */
+       if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(d_r*(*(d3_l->extra+off)));
+       /* case neighbour amorph */
+       else carry=(*(d3_l->extra+off)-*(d3_l->extra+offset))/2;
+       if(carry!=0)
+       {
+        *(d3_l->extra+offset)+=carry;
+        *(d3_l->extra+off)-=carry;
+       }
+      }
+     }
+     for(c=-1;c<=1;c++)
+     {
+      if(c!=0)
+      {
+       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;
+       /* case neighbour not amorph */  
+       if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(d_r*(*(d3_l->extra+off)));                             
+       /* case neighbour amorph */
+       else carry=(*(d3_l->extra+off)-*(d3_l->extra+offset))/2;
+       if(carry!=0)
+       {
+        *(d3_l->extra+offset)+=carry; 
+        *(d3_l->extra+off)-=carry; 
+       }
+      }
+     }
+    } else
+    /* case not amorph */
+    {
+     /* look at neighbours and move c ions */     
+     for(c=-1;c<=1;c++) 
+     {
+      if(c!=0)
+      {
+       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;
+       /* case neighbour not amorph */
+       if(!(*(d3_l->status+off)&AMORPH))
+       {
+        carry=(*(d3_l->extra+off)-*(d3_l->extra+offset))/2;
+        if(carry!=0)
+        {
+         *(d3_l->extra+offset)+=carry;
+         *(d3_l->extra+off)-=carry;
+        }
+       }
+      }
+     }
+    }
+   } /* for z */
+  } /* for y */
+ } /* for x */
+
+ return 1;
+}
+
+int distrib_c_old(d3_lattice *d3_l,int t_c,double a,double b)
 {
  int i,j,k,total,area;
  double sum;
@@ -264,6 +355,7 @@ int main(int argc,char **argv)
  char ap2_txt[MAX_TXT];
  char cd2_txt[MAX_TXT];
  char el2_txt[MAX_TXT];
+ char dr_txt[MAX_TXT];
  char *arg_v[MAX_ARGV];
  d3_lattice d3_l;
  info my_info;
@@ -281,6 +373,7 @@ int main(int argc,char **argv)
  my_info.a_ap=A_AP;
  my_info.b_ap=B_AP;
  my_info.cc=CC;
+ my_info.d_r=D_R;
  nowait=0;
  quit=0;
  escape=0;
@@ -347,9 +440,14 @@ int main(int argc,char **argv)
     case 'B':
      my_info.b_cd=atof(argv[++i]);
      break;
+    /*
     case 'C':
      my_info.cc=atoi(argv[++i]);
      break;
+    */
+    case 'D':
+     my_info.d_r=atof(argv[++i]);
+     break;
     case 'L':
      strcpy(l_file,argv[++i]);
      break;
@@ -408,6 +506,7 @@ int main(int argc,char **argv)
  sprintf(el2_txt,"energy loss offset: %.2f",my_info.b_el);
  sprintf(cd_txt,"c distrib slope: %.2f",my_info.a_cd);
  sprintf(cd2_txt,"c distrib offset: %.2f",my_info.b_cd);
+ sprintf(dr_txt,"diffusion rate: %.2f",my_info.d_r);
  arg_v[1]=x_txt;
  arg_v[2]=y_txt;
  arg_v[3]=z_txt;
@@ -431,6 +530,7 @@ int main(int argc,char **argv)
  arg_v[21]=el2_txt;
  arg_v[22]=cd_txt;
  arg_v[23]=cd2_txt;
+ arg_v[24]=dr_txt;
 
  if(!strcmp(l_file,""))
  {
@@ -440,7 +540,7 @@ int main(int argc,char **argv)
    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.cc,my_info.a_cd,my_info.b_cd);
+   distrib_c(&d3_l,my_info.d_r,my_info.a_cd,my_info.b_cd);
    process_cell(&d3_l,x_c,y_c,z_c,my_info.range,my_info.a_ap,my_info.b_ap,&(my_info.cc));
    if(i%refresh==0)
    {
@@ -451,7 +551,7 @@ int main(int argc,char **argv)
     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",i);
     sprintf(cc_txt,"total c: %d",my_info.cc);
-    d3_lattice_draw(&d3_l,x,y,z,23,arg_v);
+    d3_lattice_draw(&d3_l,x,y,z,24,arg_v);
     // scan_event(&d3_l,&x,&y,&z,&quit,&escape);
    }
    i++;
@@ -469,7 +569,7 @@ int main(int argc,char **argv)
   sprintf(conc_txt,"conc: %d",*(d3_l.extra+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y));
   strcpy(steps_txt,"step: end!");
   sprintf(cc_txt,"total c: %d",my_info.cc);
-  d3_lattice_draw(&d3_l,x,y,z,23,arg_v);
+  d3_lattice_draw(&d3_l,x,y,z,24,arg_v);
   scan_event(&d3_l,&x,&y,&z,&quit,&escape);
  }