-

diff --git a/nlsop.c b/nlsop.c
index e9d72ab..2d09306 100644 (file)
--- a/nlsop.c
+++ b/nlsop.c
@@ -55,17 +55,19 @@ int usage(void)
  /*
  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);
+ 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("-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");
  
  return 1;
 }
 
-int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,int r,double a,double b,int *t_c)
+int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,info *my_info)
 {
  unsigned char *thiz;
  int *conc;
@@ -75,18 +77,19 @@ int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,int r,double a,double b,int
 
  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=b*URAND_MAX;
- for(i=-r;i<=r;i++)
+ p=my_info->b_ap*URAND_MAX;
+ for(i=-(my_info->range);i<=my_info->range;i++)
  {
-  for(j=-r;j<=r;j++)
+  for(j=-(my_info->range);j<=my_info->range;j++)
   {
    if(!(i==0 && j==0))
    {
     off=((x+d3_l->max_x+i)%d3_l->max_x)+((y+d3_l->max_y+j)%d3_l->max_x)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
-    if(*(d3_l->status+off)&AMORPH) p+=a*(*(d3_l->extra+off))*URAND_MAX/(i*i+j*j);
+    if(*(d3_l->status+off)&AMORPH) p+=my_info->a_ap*(*(d3_l->extra+off))*URAND_MAX/(i*i+j*j);
    } 
   }
  }
+ p+=*conc*my_info->a_cp*URAND_MAX;
  printf("debug: p = %f\n",p);
  if(!(*thiz&AMORPH))
  {
@@ -97,12 +100,12 @@ 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_CRYST(thiz);
  }
  
- *t_c+=1;
+ my_info->cc+=1;
 
  return 1;
 }
 
-int distrib_c(d3_lattice *d3_l,double d_r,double a,double b,char z_diff)
+int distrib_c(d3_lattice *d3_l,info *my_info) /* double d_r,double a,double b,char z_diff) */
 {
  u32 x,y,z;
  int i,j,k,c;
@@ -265,68 +268,6 @@ int calc_pressure(d3_lattice *d3_l,int range)
  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;
- int temp,left;
- int *area_h;
- u32 x,y,z;
-
- area=d3_l->max_x*d3_l->max_y;
- area_h=(int *)malloc(d3_l->max_z*sizeof(int));
-
- total=0;
- sum=b*d3_l->max_z+a*d3_l->max_z*(d3_l->max_z+1)/2;
- for(i=0;i<d3_l->max_z;i++)
- {
-  area_h[i]=0;
-  for(j=0;j<area;j++)
-  {
-   if(!(*(d3_l->status+(i*area)+j)&AMORPH))
-   {
-    area_h[i]+=1;
-   }
-  }
-  temp=(int)((i+1)*a+b)*t_c/(sum*area_h[i]);
-  for(j=0;j<area;j++)
-  {
-   if(!(*(d3_l->status+(i*area)+j)&AMORPH))
-   {
-    *(d3_l->extra+(i*area)+j)=temp;
-    total+=temp;
-   }
-  }
-  left=(int)(((i+1)*a+b)*t_c/sum)%area_h[i];
-  while(left)
-  {
-   x=get_rand(d3_l->max_x);
-   y=get_rand(d3_l->max_y);
-   if(!(*(d3_l->status+(i*area)+x+y*d3_l->max_x)&AMORPH))
-   {
-    *(d3_l->extra+(i*area)+x+y*d3_l->max_x)+=1;
-    total+=1;
-    left-=1;
-   }
-  }
- }
- left=t_c-total;
- while(left)
- {
-  x=get_rand(d3_l->max_x);
-  y=get_rand(d3_l->max_y);
-  z=get_rand_lgp(d3_l->max_z,a,b);
-  if(!(*(d3_l->status+x+y*d3_l->max_x+z*area)&AMORPH))
-  {
-   *(d3_l->extra+x+y*d3_l->max_x+z*area)+=1;
-   left-=1;
-  }
- }
- free(area_h);
-
- return 1;
-}
-
 int save_to_file(char *sf,d3_lattice *d3_l,info *my_inf)
 {
  int sf_fd,c;
@@ -438,17 +379,15 @@ int main(int argc,char **argv)
  u32 x,y,z,x_c,y_c,z_c;
  int i,quit,escape,switchmode,nowait;
  int refresh,resave;
- char z_diff;
  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 convert;
  char r_file[MAX_CHARS];
 #ifdef USE_DFB_API
- char x_txt[MAX_TXT];
- char y_txt[MAX_TXT];
- char z_txt[MAX_TXT];
+ char xyz_txt[MAX_TXT];
  char status_txt[MAX_TXT];
  char conc_txt[MAX_TXT];
  char steps_txt[MAX_TXT];
@@ -462,7 +401,8 @@ 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 dr_ac_txt[MAX_TXT];
+ char dr_cc_txt[MAX_TXT];
  char mode_txt[MAX_TXT];
  char *arg_v[MAX_ARGV];
 #endif
@@ -477,7 +417,7 @@ int main(int argc,char **argv)
  my_info.range=RANGE;
  refresh=REFRESH;
  resave=RESAVE;
- z_diff=0;
+ my_info.z_diff=0;
  my_info.a_el=A_EL;
  my_info.b_el=B_EL;
  my_info.a_cd=A_CD;
@@ -485,7 +425,8 @@ 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;
+ my_info.dr_ac=DR_AC;
+ my_info.dr_cc=DR_CC;
  nowait=0;
  quit=0;
  escape=0;
@@ -493,6 +434,7 @@ int main(int argc,char **argv)
  strcpy(s_file,"");
  strcpy(l_file,"");
  strcpy(c_file,"");
+ strcpy(p_file,IMP_PROFILE);
  convert=0;
  strcpy(r_file,"");
  mode=0;
@@ -533,7 +475,7 @@ int main(int argc,char **argv)
      break;
     */
     case 'Z':
-     z_diff=1;
+     my_info.z_diff=1;
      break;
     /* */
     case 's':
@@ -571,7 +513,10 @@ int main(int argc,char **argv)
      convert=1;
      break;
     case 'D':
-     my_info.d_r=atof(argv[++i]);
+     my_info.dr_ac=atof(argv[++i]);
+     break;
+    case 'c':
+     my_info.dr_cc=atof(argv[++i]);
      break;
     case 'L':
      strcpy(l_file,argv[++i]);
@@ -582,6 +527,9 @@ int main(int argc,char **argv)
     case 'R':
      strcpy(r_file,argv[++i]);
      break;
+    case 'P':
+     strcpy(p_file,argv[++i]);
+     break;
     default:
      usage();
      return -1;
@@ -652,32 +600,33 @@ 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);
+ sprintf(dr_ac_txt,"a/c diffusion rate: %.2f",my_info.dr_ac);
+ sprintf(dr_cc_txt,"c/c diffusion rate: %.2f",my_info-dr_cc);
  strcpy(mode_txt,"view: a/c mode");
- arg_v[1]=x_txt;
- arg_v[2]=y_txt;
- arg_v[3]=z_txt;
- arg_v[4]=NULL;
- arg_v[5]=status_txt;
- arg_v[6]=conc_txt;
+ arg_v[1]=xyz_txt;
+ arg_v[2]=NULL;
+ 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]=mode_txt;
- arg_v[9]=NULL;
- arg_v[10]=steps_txt;;
- arg_v[11]=cc_txt;
+ arg_v[8]=steps_txt;
+ arg_v[9]=cc_txt;
+ arg_v[10]=NULL;
+ arg_v[11]=NULL;
  arg_v[12]=NULL;
  arg_v[13]=NULL;
  arg_v[14]=a_txt;
- arg_v[15]=NULL;
- arg_v[16]=s_txt;
- arg_v[17]=r_txt;
- arg_v[18]=ap_txt;
- arg_v[19]=ap2_txt;
- arg_v[20]=el_txt;
- arg_v[21]=el2_txt;
- arg_v[22]=cd_txt;
- arg_v[23]=cd2_txt;
- arg_v[24]=dr_txt;
+ arg_v[15]=s_txt;
+ arg_v[16]=r_txt;
+ arg_v[17]=ap_txt;
+ arg_v[18]=ap2_txt;
+ arg_v[19]=el_txt;
+ arg_v[20]=el2_txt;
+ arg_v[21]=cd_txt;
+ arg_v[22]=cd2_txt;
+ arg_v[23]=dr_ac_txt;
+ arg_v[24]=dr_cc_txt;
 #endif
 
  if(!strcmp(l_file,""))
@@ -689,13 +638,11 @@ int main(int argc,char **argv)
    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.d_r,my_info.a_cd,my_info.b_cd,z_diff);
-   process_cell(&d3_l,x_c,y_c,z_c,my_info.range,my_info.a_ap,my_info.b_ap,&(my_info.cc));
+   process_cell(&d3_l,x_c,y_c,z_c,&my_info);
 #ifdef USE_DFB_API
    if(i%refresh==0)
    {
-    sprintf(x_txt,"x: %d",x+1);
-    sprintf(y_txt,"y: %d",y+1);
-    sprintf(z_txt,"z: %d",z+1);
+    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",i);
@@ -703,7 +650,7 @@ int main(int argc,char **argv)
     d3_lattice_draw(&d3_l,x,y,z,24,arg_v,mode);
    }
 #endif
-   if(i%resave==0 && strcmp(s_file,"") && resave!=0)
+   if(i%resave==0 && strcmp(s_file,"") && resave!=0 && i!=0)
    {
     sprintf(s_file_tmp,"%s_%d_of_%d",s_file,i,my_info.steps);
     save_to_file(s_file_tmp,&d3_l,&my_info);

diff --git a/nlsop.h b/nlsop.h
index 1b8e4ca..3cd94e6 100644 (file)
--- a/nlsop.h
+++ b/nlsop.h
@@ -13,7 +13,8 @@ typedef unsigned int u32;
 typedef struct __info
 {
  int cc,steps,range;
- double a_el,b_el,a_cd,b_cd,a_ap,b_ap,d_r;
+ double a_el,b_el,a_cd,b_cd,a_ap,b_ap,a_cp,dr_ac,dr_cc;
+ char z_diff;
 } info;
 
 #define AMORPH 1
@@ -35,15 +36,20 @@ typedef struct __info
 
 #define CC 0
 
-#define D_R .5
+#define DR_AC .5
+#define DR_CC .2
 
 #define A_AP .1
 #define B_AP .01
 
+#define A_CP .01
+
 #define MAX_CHARS 64
 #define MAX_TXT 32
 #define MAX_ARGV 27
 
 #define MAX_VPTR 50
 
+#define IMP_PROFILE "imp-profile.txt"
+
 #endif /* NLSOP_H */