4 * author: frank zirkelbach (frank.zirkelbach@physik.uni-augsburg.de)
6 * this program tries helping to understand the amorphous depuration
7 * and recrystallization of SiCx while ion implantation at temperatures
8 * below 400 degree celsius.
9 * hopefully the program will simulate the stabilization of the
10 * selforganizing lamella structure in the observed behaviour.
13 * - J. K. N. Lindner. Habil.Schrift, Universitaet Augsburg.
14 * - Maik Haeberlen. Diplomarbeit, Universitaet Augsburg.
16 * Copyright (C) 2004 Frank Zirkelbach
18 * This program is free software; you can redistribute it and/or modify
19 * it under the terms of the GNU General Public License as published by
20 * the Free Software Foundation; either version 2 of the License, or
21 * (at your option) any later version.
23 * This program is distributed in the hope that it will be useful,
24 * but WITHOUT ANY WARRANTY; without even the implied warranty of
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 * GNU General Public License for more details.
28 * You should have received a copy of the GNU General Public License
29 * along with this program; if not, write to the Free Software
30 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
38 #include <sys/types.h>
48 #define MAKE_AMORPH(N) *(N)|=AMORPH
49 #define MAKE_CRYST(N) *(N)&=~AMORPH
55 puts("-n \t\t no user interaction");
56 puts("-Z \t\t cryst -> amorph c diffusion in z direction");
57 puts("-i \t\t no cryst to cryst diffusion");
58 printf("-x <value> \t # x cells (default %d)\n",_X);
59 printf("-y <value> \t # y cells (default %d)\n",_Y);
60 printf("-z <value> \t # z cells (default %d)\n",_Z);
61 printf("-s <value> \t steps (default %d)\n",STEPS);
62 printf("-d <value> \t refresh display (default %d)\n",REFRESH);
63 printf("-r <value> \t amorphous influence range (default %d)\n",RANGE);
64 printf("-f <value> \t stress induced amorphization influence (default %f)\n",S_D);
65 printf("-p <value> \t ballistic amorphization influence (default %f)\n",B_D);
66 printf("-F <value> \t carbon induced amorphization influence (default %f)\n",C_D);
67 printf("-D <value> \t diffusion rate from cryst to amorph cells (default %f)\n",DR_AC);
68 printf("-e <value> \t do diffusion every <value> steps (default %d)\n",DIFF_RATE);
69 puts("-g <file> <step> continue simulation from file and step (step > 0)!");
70 printf("-W <value> \t write every <value> steps to save file (default %d)\n",RESAVE);
71 puts("-C <file> \t convert file to gnuplot format");
72 puts("-L <file> \t load from file");
73 puts("-S <file> \t save to file");
74 puts("-R <file> \t read from random file");
75 puts("-P <file> \t specify implantation profile file");
76 puts("-N <file> \t specify nuclear energy loss profile file");
77 printf("-H <value> \t collisions per ion in simulation window (default %d)\n",CPI);
78 printf("-m <value> \t number of ion hits sputtering 3nm (default %d)\n",S_RATE);
83 int sputter(d3_lattice *d3_l)
88 size=d3_l->max_x*d3_l->max_y;
92 for(i=0;i<d3_l->max_z-1;i++)
94 memcpy(d3_l->status+offl,d3_l->status+offh,size);
95 memcpy(d3_l->extra+offl,d3_l->extra+offh,size*sizeof(int));
99 memset(d3_l->status+offl,0,size);
100 memset(d3_l->extra+offl,0,size);
105 int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,info *my_info,u32 nel_z)
113 thiz=d3_l->status+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
114 conc=d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
116 for(i=-(my_info->range);i<=my_info->range;i++)
118 for(j=-(my_info->range);j<=my_info->range;j++)
122 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;
123 if(*(d3_l->status+off)&AMORPH) p+=my_info->s*(*(d3_l->extra+off))*URAND_MAX/(i*i+j*j);
127 p+=*conc*my_info->c*URAND_MAX;
130 if(get_rand(URAND_MAX)<=p) MAKE_AMORPH(thiz);
133 /* assume 1-p probability */
134 /* also look for neighbours ! */
135 q=(URAND_MAX-p)>0?URAND_MAX-p:0;
137 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;
138 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;
139 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;
140 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;
141 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;
142 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;
145 if(get_rand(URAND_MAX)>p) MAKE_CRYST(thiz);
151 int distrib_c(d3_lattice *d3_l,info *my_info,int step,u32 rj_m,u32 *rj_g)
158 /* put one c ion somewhere in the lattice */
159 x=get_rand(d3_l->max_x);
160 y=get_rand(d3_l->max_y);
161 z=get_rand_reject(d3_l->max_z,rj_m,rj_g);
162 *(d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)+=1;
165 if(step%my_info->diff_rate==0)
168 for(i=0;i<d3_l->max_x;i++)
170 for(j=0;j<d3_l->max_y;j++)
172 for(k=0;k<d3_l->max_z;k++)
174 offset=i+j*d3_l->max_x+k*d3_l->max_x*d3_l->max_y;
175 /* case amorph: amorph <- cryst diffusion */
176 if(*(d3_l->status+offset)&AMORPH)
182 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;
184 if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
187 *(d3_l->extra+offset)+=carry;
188 *(d3_l->extra+off)-=carry;
196 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;
198 if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
201 *(d3_l->extra+offset)+=carry;
202 *(d3_l->extra+off)-=carry;
209 off=i+j*d3_l->max_x+(k-1)*d3_l->max_x*d3_l->max_y;
211 if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
214 *(d3_l->extra+off)-=carry;
215 *(d3_l->extra+offset)+=carry;
220 off=i+j*d3_l->max_x+(k+1)*d3_l->max_x*d3_l->max_y;
222 if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
225 *(d3_l->extra+off)-=carry;
226 *(d3_l->extra+offset)+=carry;
234 } /* if step modulo diff_rate == 0 */
239 int calc_pressure(d3_lattice *d3_l,int range)
245 for(x=0;x<d3_l->max_x;x++)
247 for(y=0;y<d3_l->max_y;y++)
249 for(z=0;z<d3_l->max_z;z++)
252 for(i=-range;i<=range;i++)
254 for(j=-range;j<=range;j++)
258 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;
259 if(*(d3_l->status+off)&AMORPH) count+=((double)*(d3_l->extra+off))/(i*i+j*j);
263 if(count>max) max=count;
268 for(x=0;x<d3_l->max_x;x++)
270 for(y=0;y<d3_l->max_y;y++)
272 for(z=0;z<d3_l->max_z;z++)
275 for(i=-range;i<=range;i++)
277 for(j=-range;j<=range;j++)
281 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;
282 if(*(d3_l->status+off)&AMORPH) count+=((double)*(d3_l->extra+off))/(i*i+j*j);
286 *(unsigned char *)(d3_l->v_ptr+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)=(unsigned char)(count*255/max);
294 int calc_max_extra(d3_lattice *d3_l)
299 for(x=0;x<d3_l->max_x;x++)
301 for(y=0;y<d3_l->max_y;y++)
303 for(z=0;z<d3_l->max_z;z++)
305 off=x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
306 if(*(d3_l->extra+off)>max) max=*(d3_l->extra+off);
314 int write_ac_distr(d3_lattice *d3_l,int ac_distr)
321 si_count=d3_l->max_x*d3_l->max_y*SI_PER_VOLUME;
322 if(ac_distr==1) strcpy(file,"carbon_in_av.plot");
323 if(ac_distr==2) strcpy(file,"carbon_in_cv.plot");
324 if(ac_distr==3) strcpy(file,"carbon.plot");
325 if(ac_distr==4) strcpy(file,"amorphous_volumes.plot");
327 if((fd=open(file,O_WRONLY|O_CREAT))<0)
329 puts("cannot open plot file");
333 for(z=0;z<d3_l->max_z;z++)
336 for(x=0;x<d3_l->max_x;x++)
338 for(y=0;y<d3_l->max_y;y++)
340 offset=x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
342 if(*(d3_l->status+offset)&AMORPH) count+=*(d3_l->extra+offset);
344 if(!(*(d3_l->status+offset)&AMORPH)) count+=*(d3_l->extra+offset);
345 if(ac_distr==3) count+=*(d3_l->extra+offset);
347 if(*(d3_l->status+offset)&AMORPH) count+=1;
350 if(ac_distr==4) dprintf(fd,"%d %d\n",z*CELL_LENGTH,count);
352 else dprintf(fd,"%d %f\n",z*CELL_LENGTH,100.0*count/si_count);
354 else dprintf(fd,"%d %d\n",z*CELL_LENGTH,count/(d3_l->max_x*d3_l->max_y));
362 int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z,int max)
364 int fd,i,j,size=0,foo=0,k,sum;
365 int width=0,height=0;
366 char bmpfile[MAX_CHARS];
371 sprintf(bmpfile,"x-z_%d.bmp",y);
373 size=(foo+(4-foo%4))*d3_l->max_z;
379 sprintf(bmpfile,"y-z_%d.bmp",x);
381 size=(foo+(4-foo%4))*d3_l->max_z;
387 sprintf(bmpfile,"x-y_%d.bmp",z);
389 size=(foo+(4-foo%4))*d3_l->max_y;
395 sprintf(bmpfile,"x-z_cdistr_%d.bmp",y);
397 size=(foo+(4-foo%4))*d3_l->max_z;
403 sprintf(bmpfile,"y-z_cdistr_%d.bmp",x);
405 size=(foo+(4-foo%4))*d3_l->max_z;
411 sprintf(bmpfile,"x-y_cdistr_%d.bmp",z);
413 size=(foo+(4-foo%4))*d3_l->max_y;
419 sprintf(bmpfile,"x-z_a_cdistr_%d.bmp",y);
421 size=(foo+(4-foo%4))*d3_l->max_z;
427 sprintf(bmpfile,"y-z_a_cdistr_%d.bmp",x);
429 size=(foo+(4-foo%4))*d3_l->max_z;
435 sprintf(bmpfile,"x-y_a_cdistr_%d.bmp",z);
437 size=(foo+(4-foo%4))*d3_l->max_y;
443 sprintf(bmpfile,"x-z_c_cdistr_%d.bmp",y);
445 size=(foo+(4-foo%4))*d3_l->max_z;
451 sprintf(bmpfile,"y-z_c_cdistr_%d.bmp",x);
453 size=(foo+(4-foo%4))*d3_l->max_z;
459 sprintf(bmpfile,"x-y_c_cdistr_%d.bmp",z);
461 size=(foo+(4-foo%4))*d3_l->max_y;
465 if((fd=open(bmpfile,O_WRONLY|O_CREAT))<0)
467 puts("cannot open bmp file");
472 buf[0]='B'; /* std header start */
474 buf[2]=(size+0x36)&0xff; /* file size */
475 buf[3]=(size+0x36)>>8;
477 buf[10]=0x36; /* offset to data */
479 buf[14]=0x28; /* length of bmp info header */
481 buf[18]=width&0xff; /* width and height */
487 buf[26]=1; /* # planes -> 1 */
489 buf[28]=24; /* bits per pixel -> 2^24 (true color) */
491 memset(buf+30,0,4); /* compression -> none */
492 buf[34]=size&0xff; /* data size */
495 buf[38]=0x12; /* res: pixel/meter */
501 memset(buf+46,0,8); /* no colors, no important colors */
503 if(write(fd,buf,54)<54)
505 puts("failed writing bmp header");
510 for(j=0;j<d3_l->max_z;j++)
512 for(i=0;i<d3_l->max_x;i++)
516 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;
518 memset(buf,(unsigned char)sum,3);
519 if(write(fd,buf,3)<3)
521 puts("failed writing rgb values to bmp file");
527 memset(buf,0,4-foo%4);
528 if(write(fd,buf,4-foo%4)<4-foo%4)
530 puts("failed writing 4 byte ending");
538 for(j=0;j<d3_l->max_z;j++)
540 for(i=0;i<d3_l->max_y;i++)
544 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;
546 memset(buf,(unsigned char)sum,3);
547 if(write(fd,buf,3)<3)
549 puts("failed writing rgb values to bmp file");
555 memset(buf,0,4-foo%4);
556 if(write(fd,buf,4-foo%4)<4-foo%4)
558 puts("failed writing 4 byte ending");
566 for(j=0;j<d3_l->max_y;j++)
568 for(i=0;i<d3_l->max_x;i++)
570 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);
571 else memset(buf,0,3);
572 if(write(fd,buf,3)<3)
574 puts("failed writing rgb values to bmp file");
580 memset(buf,0,4-foo%4);
581 if(write(fd,buf,4-foo%4)<4-foo%4)
583 puts("failed writing 4 byte ending");
591 for(j=0;j<d3_l->max_z;j++)
593 for(i=0;i<d3_l->max_x;i++)
595 sum=*(d3_l->extra+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
597 memset(buf,(unsigned char)sum,3);
598 if(write(fd,buf,3)<3)
600 puts("failed writing rgb values to bmp file");
606 memset(buf,0,4-foo%4);
607 if(write(fd,buf,4-foo%4)<4-foo%4)
609 puts("failed writing 4 byte ending");
617 for(j=0;j<d3_l->max_z;j++)
619 for(i=0;i<d3_l->max_x;i++)
621 sum=*(d3_l->extra+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
623 memset(buf,(unsigned char)sum,3);
624 if(write(fd,buf,3)<3)
626 puts("failed writing rgb values to bmp file");
632 memset(buf,0,4-foo%4);
633 if(write(fd,buf,4-foo%4)<4-foo%4)
635 puts("failed writing 4 byte ending");
643 for(j=0;j<d3_l->max_y;j++)
645 for(i=0;i<d3_l->max_x;i++)
647 sum=*(d3_l->extra+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y);
649 memset(buf,(unsigned char)sum,3);
650 if(write(fd,buf,3)<3)
652 puts("failed writing rgb values to bmp file");
658 memset(buf,0,4-foo%4);
659 if(write(fd,buf,4-foo%4)<4-foo%4)
661 puts("failed writing 4 byte ending");
669 for(j=0;j<d3_l->max_z;j++)
671 for(i=0;i<d3_l->max_x;i++)
673 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);
676 memset(buf,(unsigned char)sum,3);
677 if(write(fd,buf,3)<3)
679 puts("failed writing rgb values to bmp file");
685 memset(buf,0,4-foo%4);
686 if(write(fd,buf,4-foo%4)<4-foo%4)
688 puts("failed writing 4 byte ending");
696 for(j=0;j<d3_l->max_z;j++)
698 for(i=0;i<d3_l->max_x;i++)
700 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);
703 memset(buf,(unsigned char)sum,3);
704 if(write(fd,buf,3)<3)
706 puts("failed writing rgb values to bmp file");
712 memset(buf,0,4-foo%4);
713 if(write(fd,buf,4-foo%4)<4-foo%4)
715 puts("failed writing 4 byte ending");
723 for(j=0;j<d3_l->max_y;j++)
725 for(i=0;i<d3_l->max_x;i++)
727 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);
730 memset(buf,(unsigned char)sum,3);
731 if(write(fd,buf,3)<3)
733 puts("failed writing rgb values to bmp file");
739 memset(buf,0,4-foo%4);
740 if(write(fd,buf,4-foo%4)<4-foo%4)
742 puts("failed writing 4 byte ending");
750 for(j=0;j<d3_l->max_z;j++)
752 for(i=0;i<d3_l->max_x;i++)
754 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);
757 memset(buf,(unsigned char)sum,3);
758 if(write(fd,buf,3)<3)
760 puts("failed writing rgb values to bmp file");
766 memset(buf,0,4-foo%4);
767 if(write(fd,buf,4-foo%4)<4-foo%4)
769 puts("failed writing 4 byte ending");
777 for(j=0;j<d3_l->max_z;j++)
779 for(i=0;i<d3_l->max_x;i++)
781 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);
784 memset(buf,(unsigned char)sum,3);
785 if(write(fd,buf,3)<3)
787 puts("failed writing rgb values to bmp file");
793 memset(buf,0,4-foo%4);
794 if(write(fd,buf,4-foo%4)<4-foo%4)
796 puts("failed writing 4 byte ending");
804 for(j=0;j<d3_l->max_y;j++)
806 for(i=0;i<d3_l->max_x;i++)
808 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);
811 memset(buf,(unsigned char)sum,3);
812 if(write(fd,buf,3)<3)
814 puts("failed writing rgb values to bmp file");
820 memset(buf,0,4-foo%4);
821 if(write(fd,buf,4-foo%4)<4-foo%4)
823 puts("failed writing 4 byte ending");
834 int save_to_file(char *sf,d3_lattice *d3_l,info *my_inf)
838 if((sf_fd=open(sf,O_WRONLY|O_CREAT))<0)
840 puts("cannot open save file");
843 if(write(sf_fd,d3_l,sizeof(d3_lattice))<sizeof(d3_lattice))
845 puts("failed saving d3 lattice struct");
848 if(write(sf_fd,my_inf,sizeof(info))<sizeof(info))
850 puts("failed saving info struct");
853 c=d3_l->max_x*d3_l->max_y*d3_l->max_z;
854 if(write(sf_fd,d3_l->status,c*sizeof(unsigned char))<c*sizeof(unsigned char))
856 puts("failed saving status of d3 lattice sites");
859 if(write(sf_fd,d3_l->extra,c*sizeof(int))<c*sizeof(int))
861 puts("failed saving sites concentration");
869 int load_from_file(char *lf,d3_lattice *d3_l,info *my_inf)
872 int lf_fd,c,pos,end,data,data_len,strip;
874 if((lf_fd=open(lf,O_RDONLY))<0)
876 puts("cannot open load file");
879 if(read(lf_fd,d3_l,sizeof(d3_lattice))<sizeof(d3_lattice))
881 puts("failed reading d3 lattice struct");
884 pos=lseek(lf_fd,0,SEEK_CUR);
885 printf("psition: %d (%d)\n",pos,sizeof(d3_lattice));
886 data=d3_l->max_x*d3_l->max_y*d3_l->max_z;
887 data_len=data*(sizeof(int)+sizeof(unsigned char));
888 printf("there are %d volumes so we need %d of bytes\n",data,data_len);
889 end=lseek(lf_fd,0,SEEK_END);
891 printf("end: %d => length: %d => guessed info size: %d bytes\n",end,end-pos,c);
892 strip=sizeof(info)-c;
893 printf("as real programs info size is %d, we strip %d bytes\n",sizeof(info),strip);
894 lseek(lf_fd,pos,SEEK_SET);
896 if(strip>0) c-=strip;
899 puts("info smaller then strip size");
902 if(read(lf_fd,my_inf,c)<c)
904 puts("failed reading info struct");
907 if(strip>0) memset(my_inf+c,0,strip);
908 if(strip<0) lseek(lf_fd,(-1*strip),SEEK_CUR);
909 c=d3_l->max_x*d3_l->max_y*d3_l->max_z;
910 if((d3_l->status=(unsigned char*)malloc(c*sizeof(unsigned char)))==NULL)
912 puts("cannot allocate status buffer");
915 if((d3_l->extra=(int *)malloc(c*sizeof(int)))==NULL)
917 puts("cannot allocate concentration buffer");
920 if(read(lf_fd,d3_l->status,c*sizeof(unsigned char))<c*sizeof(unsigned char))
922 puts("failed reading status of d3 lattice sites");
925 if(read(lf_fd,d3_l->extra,c*sizeof(int))<c*sizeof(int))
927 puts("failed reading sites concentration");
935 int convert_file(char *cf,d3_lattice *d3_l)
940 if((c_fd=open(cf,O_WRONLY|O_CREAT))<0)
942 puts("cannot open convert file");
945 dprintf(c_fd,"# created by nlsop (gnuplot format)\n");
946 for(x=0;x<d3_l->max_x;x++)
948 for(y=0;y<d3_l->max_y;y++)
950 for(z=0;z<d3_l->max_z;z++)
952 if(*(d3_l->status+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)&AMORPH) dprintf(c_fd,"%d %d %d\n",x,y,z);
961 int get_c_ratio(double *c_ratio,char *pfile,info *my_info,d3_lattice *d3_l)
966 unsigned char buf[32];
970 if((p_fd=open(pfile,O_RDONLY))<0)
972 puts("cannot open profile file");
989 a=atof(p)/10; /* nm */
992 if(a<=d3_l->max_z*CELL_LENGTH) d+=b;
1002 u32 get_reject_graph(info *my_info,d3_lattice *d3_l,char *file,u32 *graph) {
1007 unsigned char *flag;
1011 if((fd=open(file,O_RDONLY))<0)
1013 puts("cannot open file to calculate rejection graph");
1016 if((flag=(unsigned char *)malloc(d3_l->max_z))==NULL)
1018 puts("cannot malloc flag memory for rejection graph");
1021 memset(flag,0,d3_l->max_z);
1022 memset(graph,0,d3_l->max_z*sizeof(u32));
1029 k=read(fd,&buf[i],1);
1030 if((buf[i]=='\n')||(k==0)) break;
1035 a=atof(p)/10; /* nm */
1038 if(a>d3_l->max_z*CELL_LENGTH) k=0;
1041 graph[(int)(a/CELL_LENGTH)]=(int)(URAND_MAX/100*b);
1042 flag[(int)(a/CELL_LENGTH)]=1;
1046 /* do (linear) interpolation here! */
1049 while(i<d3_l->max_z)
1051 /* graph[0] is 0! */
1054 while(flag[i]==0&&i<d3_l->max_z) i++;
1055 for(k=j+1;k<i;k++) graph[k]=(int)((k-j)*((int)graph[i]-(int)graph[j])/(i-j))+graph[j];
1056 if(graph[i]>max) max=graph[i];
1061 #ifdef DEBUG_INTERPOL_PROFILE
1062 printf("debug: %s (interpolated profile)\n",file);
1063 for(i=0;i<d3_l->max_z;i++) printf("%d %d\n",i,graph[i]);
1069 int get_amorphous_layer_info(d3_lattice *d3_l,int *sai,int *sacl,int *eacl) {
1070 int i,j,a,oend,nend,count;
1071 unsigned char sacl_is_set=0;
1072 unsigned char eacl_is_set=0;
1073 unsigned char sai_is_set=0;
1075 a=d3_l->max_x*d3_l->max_y;
1079 for(i=0;i<d3_l->max_z;i++) {
1081 for(j=oend;j<nend;j++) if(*(d3_l->status+j)&AMORPH) count++;
1084 if((count>=A_START*a)&&(!sai_is_set)) {
1088 if((count>=AC_START*a)&&(!sacl_is_set)) {
1092 if((count<=A_END*a)&&(sacl_is_set)&&(!eacl_is_set)) {
1096 if((eacl_is_set)&&(count>=A_END*a)) eacl_is_set=0;
1101 int main(int argc,char **argv)
1103 u32 x,y,z,x_c,y_c,z_c;
1104 int i,j,quit,escape,switchmode,nowait,bmp,ac_distr;
1108 char s_file[MAX_CHARS];
1109 char s_file_tmp[MAX_CHARS];
1110 char l_file[MAX_CHARS];
1111 char c_file[MAX_CHARS];
1112 char p_file[MAX_CHARS];
1113 char n_e_file[MAX_CHARS];
1115 char r_file[MAX_CHARS];
1117 char xyz_txt[MAX_TXT];
1118 char status_txt[MAX_TXT];
1119 char conc_txt[MAX_TXT];
1120 char steps_txt[MAX_TXT];
1121 char cc_txt[MAX_TXT];
1122 char a_txt[MAX_TXT];
1123 char s_txt[MAX_TXT];
1124 char ballistic_txt[MAX_TXT];
1125 char carbon_txt[MAX_TXT];
1126 char stress_txt[MAX_TXT];
1127 char r_txt[MAX_TXT];
1128 char zdiff_txt[MAX_TXT];
1129 char diff_txt[MAX_TXT];
1130 char dr_ac_txt[MAX_TXT];
1131 char dose_txt[MAX_TXT];
1132 char mode_txt[MAX_TXT];
1133 char hpi_txt[MAX_TXT];
1134 char srate_txt[MAX_TXT];
1135 char start_ai_txt[MAX_TXT];
1136 char start_acl_txt[MAX_TXT];
1137 char end_acl_txt[MAX_TXT];
1138 char *arg_v[MAX_ARGV];
1155 my_info.steps=STEPS;
1156 my_info.range=RANGE;
1163 my_info.dr_ac=DR_AC;
1164 my_info.diff_rate=DIFF_RATE;
1166 my_info.s_rate=S_RATE;
1175 strcpy(p_file,IMP_PROFILE);
1176 strcpy(n_e_file,NEL_PROFILE);
1187 printf("reading argv ...");
1203 d3_l.max_x=atoi(argv[++i]);
1206 d3_l.max_y=atoi(argv[++i]);
1209 d3_l.max_z=atoi(argv[++i]);
1212 my_info.steps=atoi(argv[++i]);
1215 refresh=atoi(argv[++i]);
1218 my_info.range=atoi(argv[++i]);
1221 my_info.s=atof(argv[++i]);
1224 my_info.b=atof(argv[++i]);
1227 my_info.c=atof(argv[++i]);
1230 resave=atoi(argv[++i]);
1233 strcpy(l_file,argv[++i]);
1234 if(i<argc-1) if(argv[i+1][0]!='-') strcpy(c_file,argv[++i]);
1238 my_info.dr_ac=atof(argv[++i]);
1241 my_info.diff_rate=atoi(argv[++i]);
1244 strcpy(l_file,argv[++i]);
1247 strcpy(s_file,argv[++i]);
1250 strcpy(r_file,argv[++i]);
1253 strcpy(p_file,argv[++i]);
1256 strcpy(n_e_file,argv[++i]);
1259 strcpy(l_file,argv[++i]);
1260 if(i<argc-1) if(argv[i+1][0]!='-') c_step=atoi(argv[++i]);
1263 my_info.cpi=atoi(argv[++i]);
1266 my_info.s_rate=atoi(argv[++i]);
1284 if(!strcmp(s_file,""))
1286 puts("NODFB defined, run with -S option");
1291 printf("random api init ...");
1292 if(!strcmp(r_file,"")) rand_init(NULL);
1293 else rand_init(r_file);
1296 if(!strcmp(l_file,""))
1298 i=d3_l.max_x*d3_l.max_y*d3_l.max_z;
1300 printf("d3 lattice init ...");
1301 d3_lattice_init(&argc,argv,&d3_l);
1304 if((d3_l.status=(unsigned char *)malloc(i*sizeof(unsigned char)))==NULL)
1306 puts("failed allocating status buffer");
1309 memset(d3_l.status,0,i*sizeof(unsigned char));
1310 if((d3_l.extra=(int *)malloc(i*sizeof(int)))==NULL)
1312 puts("failed allocating concentration buffer");
1315 memset(d3_l.extra,0,i*sizeof(int));
1318 printf("loading file ...");
1319 load_from_file(l_file,&d3_l,&my_info);
1323 if(!strcmp(c_file,"")) sprintf(c_file,"%s_gnuplot",l_file);
1324 printf("converting file %s to %s\n",l_file,c_file);
1325 convert_file(c_file,&d3_l);
1330 printf("d3 lattice init ...");
1331 d3_lattice_init(&argc,argv,&d3_l);
1337 printf("event init ...");
1338 d3_event_init(&d3_l);
1343 strcpy(a_txt,"args:");
1344 sprintf(s_txt,"steps: %d",my_info.steps);
1345 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));
1346 sprintf(r_txt,"stress influence range: %d",my_info.range);
1347 sprintf(stress_txt,"stress term: %f",my_info.s);
1348 sprintf(ballistic_txt,"ballistic term: %f",my_info.b);
1349 sprintf(carbon_txt,"carbon term: %f",my_info.c);
1350 sprintf(dr_ac_txt,"a/c diffusion rate: %f",my_info.dr_ac);
1351 sprintf(zdiff_txt,"diffusion in z direction: yes");
1352 sprintf(diff_txt,"diffusion every %d steps",my_info.diff_rate);
1353 strcpy(mode_txt,"view: a/c mode");
1354 sprintf(hpi_txt,"hits per ion: %d",my_info.cpi);
1355 sprintf(srate_txt,"sputter rate (3nm/#c): %d",my_info.s_rate);
1356 get_amorphous_layer_info(&d3_l,&sai,&sacl,&eacl);
1357 sprintf(start_ai_txt,"start of a-inclusions: %d nm (%d)",3*sai,sai);
1358 sprintf(start_acl_txt,"start of a-layer: %d nm (%d)",3*sacl,sacl);
1359 sprintf(end_acl_txt,"end of a-layer: %d nm (%d)",3*eacl,eacl);
1362 arg_v[3]=status_txt;
1372 arg_v[13]=zdiff_txt;
1373 arg_v[14]=dr_ac_txt;
1374 arg_v[15]=ballistic_txt;
1375 arg_v[16]=carbon_txt;
1376 arg_v[17]=stress_txt;
1379 arg_v[20]=srate_txt;
1381 arg_v[22]=start_ai_txt;
1382 arg_v[23]=start_acl_txt;
1383 arg_v[24]=end_acl_txt;
1387 /* compute graphs for random number rejection method */
1388 printf("random rejection graphs ...");
1389 if((c_profile=(u32 *)malloc(d3_l.max_z*sizeof(unsigned int)))==NULL)
1391 puts("failed allocating memory for carbon profile graph");
1394 if((n_e_loss=(u32 *)malloc(d3_l.max_z*sizeof(unsigned int)))==NULL)
1396 puts("failed allocating memory for nuclear energy loss graph");
1399 ip_max=get_reject_graph(&my_info,&d3_l,p_file,c_profile);
1400 ne_max=get_reject_graph(&my_info,&d3_l,n_e_file,n_e_loss);
1403 if((!strcmp(l_file,""))||(c_step))
1406 /* this should be obsolete - z is high enough - we check now! */
1407 if(c_profile[d3_l.max_z-1]!=0)
1409 printf("max_z (%d) too small - sputtering not possible\n",d3_l.max_z);
1412 /* calculate ratio of c_simwindow / c_total */
1413 //if(get_c_ratio(&c_ratio,p_file,&my_info,&d3_l)!=1)
1415 // puts("failed calculating ratio");
1419 /* sputtering realy possible ?*/
1420 if(n_e_loss[d3_l.max_z-1]!=0)
1421 printf("warning: max_z (%d) too small - there may be amorphous volumes\n",d3_l.max_z);
1428 printf("%d\n",get_rand_reject(d3_l.max_z,ip_max,c_profile));
1431 printf("%d\n",get_rand_reject(d3_l.max_z,ne_max,n_e_loss));
1434 printf("%d\n",get_rand(d3_l.max_z));
1436 if(i==10000000) return 1;
1442 printf("starting simulation ... now! :)\n");
1445 i=(c_step?c_step:0);
1446 while((i<my_info.steps) && (quit==0) && (escape==0))
1449 if(i%refresh==0) printf("step: %d\n",i);
1451 for(j=0;j<my_info.cpi;j++)
1453 x_c=get_rand(d3_l.max_x);
1454 y_c=get_rand(d3_l.max_y);
1455 // z_c=get_rand_reject(d3_l.max_z,ne_max,n_e_loss);
1456 z_c=get_rand(d3_l.max_z);
1457 nel_z=URAND_MAX*(1.0*n_e_loss[z_c]/ne_max);
1458 process_cell(&d3_l,x_c,y_c,z_c,&my_info,nel_z);
1460 distrib_c(&d3_l,&my_info,i,ip_max,c_profile);
1464 sprintf(xyz_txt,"x: %d y: %d z: %d (%d nm)",x+1,y+1,z+1,z*3);
1465 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');
1466 sprintf(conc_txt,"carbon: %d",*(d3_l.extra+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y));
1467 sprintf(steps_txt,"step: %d",i);
1468 sprintf(cc_txt,"total c: %d",my_info.cc);
1469 get_amorphous_layer_info(&d3_l,&sai,&sacl,&eacl);
1470 sprintf(start_ai_txt,"start of a-inclusions: %d nm (%d)",3*sai,sai);
1471 sprintf(start_acl_txt,"start of a-layer: %d nm (%d)",3*sacl,sacl);
1472 sprintf(end_acl_txt,"end of a-layer: %d nm (%d)",3*eacl,eacl);
1473 d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,0,NULL,0,NULL,0);
1476 if(i%resave==0 && strcmp(s_file,"") && resave!=0 && i!=0)
1478 sprintf(s_file_tmp,"%s_%d_of_%d",s_file,i,my_info.steps);
1479 save_to_file(s_file_tmp,&d3_l,&my_info);
1481 printf("saved %s\n",s_file_tmp);
1485 if(i%my_info.s_rate==0) sputter(&d3_l);
1489 if(strcmp(s_file,""))
1491 printf("saved %s\n",s_file);
1492 save_to_file(s_file,&d3_l,&my_info);
1496 /* allocating buffer for pressure values */
1497 printf("allocating buffer for preassure values ...");
1498 if((d3_l.v_ptr=malloc(d3_l.max_x*d3_l.max_y*d3_l.max_z*sizeof(unsigned char)))==NULL)
1500 puts("cannot allocate buffer for pressure values");
1505 printf("calculating preassure values ...");
1506 calc_pressure(&d3_l,my_info.range);
1508 printf("finding maximum carbon concentration ...");
1509 max_extra=calc_max_extra(&d3_l);
1512 while((quit==0) && (escape==0) && (nowait==0))
1515 if(switchmode==0) mode=0;
1516 if(switchmode==1) mode=1;
1517 if(switchmode==2) mode=2;
1518 if(switchmode==3) mode=3;
1520 sprintf(xyz_txt,"x: %d y: %d z: %d (%d nm)",x+1,y+1,z+1,z*3);
1521 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');
1522 sprintf(conc_txt,"carbon: %d",*(d3_l.extra+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y));
1523 sprintf(steps_txt,"step: end");
1524 sprintf(cc_txt,"total c: %d",my_info.cc);
1525 if(switchmode==0) strcpy(mode_txt,"view: a/c mode");
1526 if(switchmode==1) strcpy(mode_txt,"view: c conc mode");
1527 if(switchmode==2) strcpy(mode_txt,"view: a pressure mode");
1528 if(switchmode==3) strcpy(mode_txt,"view: a/c + profiles mode");
1529 d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,max_extra,c_profile,ip_max,n_e_loss,ne_max);
1532 scan_event(&d3_l,&x,&y,&z,&quit,&escape,&switchmode,&bmp,&ac_distr);
1533 if(bmp) write_bmp(&d3_l,bmp,x,y,z,max_extra);
1534 if(ac_distr) write_ac_distr(&d3_l,ac_distr);
1537 d3_lattice_release(&d3_l);