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("-c <value> \t diffusion rate in cryst cells (default %f)\n",DR_CC);
69 printf("-e <value> \t do diffusion every <value> steps (default %d)\n",DIFF_RATE);
70 puts("-g <file> <step> continue simulation from file and step (step > 0)!");
71 printf("-W <value> \t write every <value> steps to save file (default %d)\n",RESAVE);
72 puts("-C <file> \t convert file to gnuplot format");
73 puts("-L <file> \t load from file");
74 puts("-S <file> \t save to file");
75 puts("-R <file> \t read from random file");
76 puts("-P <file> \t specify implantation profile file");
77 puts("-N <file> \t specify nuclear energy loss profile file");
78 printf("-H <value> \t collisions per ion in simulation window (default %d)\n",CPI);
79 puts("-m <value> \t specify c->a carbon saturation");
84 int process_cell(d3_lattice *d3_l,u32 x,u32 y,u32 z,info *my_info,u32 nel_z)
92 thiz=d3_l->status+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
93 conc=d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
95 for(i=-(my_info->range);i<=my_info->range;i++)
97 for(j=-(my_info->range);j<=my_info->range;j++)
101 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;
102 if(*(d3_l->status+off)&AMORPH) p+=my_info->s*(*(d3_l->extra+off))*URAND_MAX/(i*i+j*j);
106 p+=*conc*my_info->c*URAND_MAX;
109 if(get_rand(URAND_MAX)<=p) MAKE_AMORPH(thiz);
112 /* assume 1-p probability */
113 /* also look for neighbours ! */
114 q=(URAND_MAX-p)>0?URAND_MAX-p:0;
116 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;
117 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;
118 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;
119 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;
120 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;
121 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;
124 if(get_rand(URAND_MAX)>p) MAKE_CRYST(thiz);
130 int distrib_c(d3_lattice *d3_l,info *my_info,int step,double c_ratio,u32 rj_m,u32 *rj_g)
137 /* put one c ion somewhere in the lattice */
138 if(my_info->cc<c_ratio*step)
140 x=get_rand(d3_l->max_x);
141 y=get_rand(d3_l->max_y);
142 z=get_rand_reject(d3_l->max_z,rj_m,rj_g);
143 *(d3_l->extra+x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y)+=1;
147 if(step%my_info->diff_rate==0)
150 for(i=0;i<d3_l->max_x;i++)
152 for(j=0;j<d3_l->max_y;j++)
154 for(k=0;k<d3_l->max_z;k++)
156 offset=i+j*d3_l->max_x+k*d3_l->max_x*d3_l->max_y;
157 /* case amorph: amorph <- cryst diffusion */
158 if(*(d3_l->status+offset)&AMORPH && *(d3_l->extra+offset)<my_info->c_sat)
164 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;
166 if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
169 *(d3_l->extra+offset)+=carry;
170 *(d3_l->extra+off)-=carry;
178 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;
180 if(!(*(d3_l->status+off)&AMORPH)) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
183 *(d3_l->extra+offset)+=carry;
184 *(d3_l->extra+off)-=carry;
192 off=i+j*d3_l->max_x+(k-1)*d3_l->max_x*d3_l->max_y;
194 if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
197 *(d3_l->extra+off)-=carry;
198 *(d3_l->extra+offset)+=carry;
203 off=i+j*d3_l->max_x+(k+1)*d3_l->max_x*d3_l->max_y;
205 if(!*(d3_l->status+off)&AMORPH) carry=(int)(my_info->dr_ac*(*(d3_l->extra+off)));
208 *(d3_l->extra+off)-=carry;
209 *(d3_l->extra+offset)+=carry;
214 /* case not amorph: cryst <-> cryst diffusion */
215 if(my_info->c_diff) {
216 /* if there is c diff, no diff in z-direction */
222 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;
224 if(!(*(d3_l->status+off)&AMORPH))
226 carry=(int)(my_info->dr_cc*(*(d3_l->extra+off)-*(d3_l->extra+offset))/2);
229 *(d3_l->extra+offset)+=carry;
230 *(d3_l->extra+off)-=carry;
239 off=((i+c+d3_l->max_x)%d3_l->max_x)+j*d3_l->max_x+k*d3_l->max_x*d3_l->max_y;
241 if(!(*(d3_l->status+off)&AMORPH))
243 carry=(int)(my_info->dr_cc*(*(d3_l->extra+off)-*(d3_l->extra+offset))/2);
246 *(d3_l->extra+offset)+=carry;
247 *(d3_l->extra+off)-=carry;
260 } /* if step modulo diff_rate == 0 */
265 int calc_pressure(d3_lattice *d3_l,int range)
271 for(x=0;x<d3_l->max_x;x++)
273 for(y=0;y<d3_l->max_y;y++)
275 for(z=0;z<d3_l->max_z;z++)
278 for(i=-range;i<=range;i++)
280 for(j=-range;j<=range;j++)
284 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;
285 if(*(d3_l->status+off)&AMORPH) count+=((double)*(d3_l->extra+off))/(i*i+j*j);
289 if(count>max) max=count;
294 for(x=0;x<d3_l->max_x;x++)
296 for(y=0;y<d3_l->max_y;y++)
298 for(z=0;z<d3_l->max_z;z++)
301 for(i=-range;i<=range;i++)
303 for(j=-range;j<=range;j++)
307 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;
308 if(*(d3_l->status+off)&AMORPH) count+=((double)*(d3_l->extra+off))/(i*i+j*j);
312 *(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);
320 int calc_max_extra(d3_lattice *d3_l)
325 for(x=0;x<d3_l->max_x;x++)
327 for(y=0;y<d3_l->max_y;y++)
329 for(z=0;z<d3_l->max_z;z++)
331 off=x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
332 if(*(d3_l->extra+off)>max) max=*(d3_l->extra+off);
340 int write_ac_distr(d3_lattice *d3_l,int ac_distr)
347 si_count=d3_l->max_x*d3_l->max_y*SI_PER_VOLUME;
348 if(ac_distr==1) strcpy(file,"carbon_in_av.plot");
349 if(ac_distr==2) strcpy(file,"carbon_in_cv.plot");
350 if(ac_distr==3) strcpy(file,"carbon.plot");
351 if(ac_distr==4) strcpy(file,"amorphous_volumes.plot");
353 if((fd=open(file,O_WRONLY|O_CREAT))<0)
355 puts("cannot open plot file");
359 for(z=0;z<d3_l->max_z;z++)
362 for(x=0;x<d3_l->max_x;x++)
364 for(y=0;y<d3_l->max_y;y++)
366 offset=x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
368 if(*(d3_l->status+offset)&AMORPH) count+=*(d3_l->extra+offset);
370 if(!(*(d3_l->status+offset)&AMORPH)) count+=*(d3_l->extra+offset);
371 if(ac_distr==3) count+=*(d3_l->extra+offset);
373 if(*(d3_l->status+offset)&AMORPH) count+=1;
376 if(ac_distr==4) dprintf(fd,"%d %d\n",z*CELL_LENGTH,count);
377 else dprintf(fd,"%d %f\n",z*CELL_LENGTH,100.0*count/si_count);
384 int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z,int max)
386 int fd,i,j,size=0,foo=0,k,sum;
387 int width=0,height=0;
388 char bmpfile[MAX_CHARS];
393 sprintf(bmpfile,"x-z_%d.bmp",y);
395 size=(foo+(4-foo%4))*d3_l->max_z;
401 sprintf(bmpfile,"y-z_%d.bmp",x);
403 size=(foo+(4-foo%4))*d3_l->max_z;
409 sprintf(bmpfile,"x-y_%d.bmp",z);
411 size=(foo+(4-foo%4))*d3_l->max_y;
417 sprintf(bmpfile,"x-z_cdistr_%d.bmp",y);
419 size=(foo+(4-foo%4))*d3_l->max_z;
425 sprintf(bmpfile,"y-z_cdistr_%d.bmp",x);
427 size=(foo+(4-foo%4))*d3_l->max_z;
433 sprintf(bmpfile,"x-y_cdistr_%d.bmp",z);
435 size=(foo+(4-foo%4))*d3_l->max_y;
441 sprintf(bmpfile,"x-z_a_cdistr_%d.bmp",y);
443 size=(foo+(4-foo%4))*d3_l->max_z;
449 sprintf(bmpfile,"y-z_a_cdistr_%d.bmp",x);
451 size=(foo+(4-foo%4))*d3_l->max_z;
457 sprintf(bmpfile,"x-y_a_cdistr_%d.bmp",z);
459 size=(foo+(4-foo%4))*d3_l->max_y;
465 sprintf(bmpfile,"x-z_c_cdistr_%d.bmp",y);
467 size=(foo+(4-foo%4))*d3_l->max_z;
473 sprintf(bmpfile,"y-z_c_cdistr_%d.bmp",x);
475 size=(foo+(4-foo%4))*d3_l->max_z;
481 sprintf(bmpfile,"x-y_c_cdistr_%d.bmp",z);
483 size=(foo+(4-foo%4))*d3_l->max_y;
487 if((fd=open(bmpfile,O_WRONLY|O_CREAT))<0)
489 puts("cannot open bmp file");
494 buf[0]='B'; /* std header start */
496 buf[2]=(size+0x36)&0xff; /* file size */
497 buf[3]=(size+0x36)>>8;
499 buf[10]=0x36; /* offset to data */
501 buf[14]=0x28; /* length of bmp info header */
503 buf[18]=width&0xff; /* width and height */
509 buf[26]=1; /* # planes -> 1 */
511 buf[28]=24; /* bits per pixel -> 2^24 (true color) */
513 memset(buf+30,0,4); /* compression -> none */
514 buf[34]=size&0xff; /* data size */
517 buf[38]=0x12; /* res: pixel/meter */
523 memset(buf+46,0,8); /* no colors, no important colors */
525 if(write(fd,buf,54)<54)
527 puts("failed writing bmp header");
532 for(j=0;j<d3_l->max_z;j++)
534 for(i=0;i<d3_l->max_x;i++)
538 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;
540 memset(buf,(unsigned char)sum,3);
541 if(write(fd,buf,3)<3)
543 puts("failed writing rgb values to bmp file");
549 memset(buf,0,4-foo%4);
550 if(write(fd,buf,4-foo%4)<4-foo%4)
552 puts("failed writing 4 byte ending");
560 for(j=0;j<d3_l->max_z;j++)
562 for(i=0;i<d3_l->max_y;i++)
566 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;
568 memset(buf,(unsigned char)sum,3);
569 if(write(fd,buf,3)<3)
571 puts("failed writing rgb values to bmp file");
577 memset(buf,0,4-foo%4);
578 if(write(fd,buf,4-foo%4)<4-foo%4)
580 puts("failed writing 4 byte ending");
588 for(j=0;j<d3_l->max_y;j++)
590 for(i=0;i<d3_l->max_x;i++)
592 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);
593 else memset(buf,0,3);
594 if(write(fd,buf,3)<3)
596 puts("failed writing rgb values to bmp file");
602 memset(buf,0,4-foo%4);
603 if(write(fd,buf,4-foo%4)<4-foo%4)
605 puts("failed writing 4 byte ending");
613 for(j=0;j<d3_l->max_z;j++)
615 for(i=0;i<d3_l->max_x;i++)
617 sum=*(d3_l->extra+i+y*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
619 memset(buf,(unsigned char)sum,3);
620 if(write(fd,buf,3)<3)
622 puts("failed writing rgb values to bmp file");
628 memset(buf,0,4-foo%4);
629 if(write(fd,buf,4-foo%4)<4-foo%4)
631 puts("failed writing 4 byte ending");
639 for(j=0;j<d3_l->max_z;j++)
641 for(i=0;i<d3_l->max_x;i++)
643 sum=*(d3_l->extra+x+i*d3_l->max_x+(d3_l->max_z-j-1)*d3_l->max_x*d3_l->max_y);
645 memset(buf,(unsigned char)sum,3);
646 if(write(fd,buf,3)<3)
648 puts("failed writing rgb values to bmp file");
654 memset(buf,0,4-foo%4);
655 if(write(fd,buf,4-foo%4)<4-foo%4)
657 puts("failed writing 4 byte ending");
665 for(j=0;j<d3_l->max_y;j++)
667 for(i=0;i<d3_l->max_x;i++)
669 sum=*(d3_l->extra+i+(d3_l->max_y-j-1)*d3_l->max_x+z*d3_l->max_x*d3_l->max_y);
671 memset(buf,(unsigned char)sum,3);
672 if(write(fd,buf,3)<3)
674 puts("failed writing rgb values to bmp file");
680 memset(buf,0,4-foo%4);
681 if(write(fd,buf,4-foo%4)<4-foo%4)
683 puts("failed writing 4 byte ending");
691 for(j=0;j<d3_l->max_z;j++)
693 for(i=0;i<d3_l->max_x;i++)
695 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);
698 memset(buf,(unsigned char)sum,3);
699 if(write(fd,buf,3)<3)
701 puts("failed writing rgb values to bmp file");
707 memset(buf,0,4-foo%4);
708 if(write(fd,buf,4-foo%4)<4-foo%4)
710 puts("failed writing 4 byte ending");
718 for(j=0;j<d3_l->max_z;j++)
720 for(i=0;i<d3_l->max_x;i++)
722 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);
725 memset(buf,(unsigned char)sum,3);
726 if(write(fd,buf,3)<3)
728 puts("failed writing rgb values to bmp file");
734 memset(buf,0,4-foo%4);
735 if(write(fd,buf,4-foo%4)<4-foo%4)
737 puts("failed writing 4 byte ending");
745 for(j=0;j<d3_l->max_y;j++)
747 for(i=0;i<d3_l->max_x;i++)
749 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);
752 memset(buf,(unsigned char)sum,3);
753 if(write(fd,buf,3)<3)
755 puts("failed writing rgb values to bmp file");
761 memset(buf,0,4-foo%4);
762 if(write(fd,buf,4-foo%4)<4-foo%4)
764 puts("failed writing 4 byte ending");
772 for(j=0;j<d3_l->max_z;j++)
774 for(i=0;i<d3_l->max_x;i++)
776 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);
779 memset(buf,(unsigned char)sum,3);
780 if(write(fd,buf,3)<3)
782 puts("failed writing rgb values to bmp file");
788 memset(buf,0,4-foo%4);
789 if(write(fd,buf,4-foo%4)<4-foo%4)
791 puts("failed writing 4 byte ending");
799 for(j=0;j<d3_l->max_z;j++)
801 for(i=0;i<d3_l->max_x;i++)
803 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);
806 memset(buf,(unsigned char)sum,3);
807 if(write(fd,buf,3)<3)
809 puts("failed writing rgb values to bmp file");
815 memset(buf,0,4-foo%4);
816 if(write(fd,buf,4-foo%4)<4-foo%4)
818 puts("failed writing 4 byte ending");
826 for(j=0;j<d3_l->max_y;j++)
828 for(i=0;i<d3_l->max_x;i++)
830 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);
833 memset(buf,(unsigned char)sum,3);
834 if(write(fd,buf,3)<3)
836 puts("failed writing rgb values to bmp file");
842 memset(buf,0,4-foo%4);
843 if(write(fd,buf,4-foo%4)<4-foo%4)
845 puts("failed writing 4 byte ending");
856 int save_to_file(char *sf,d3_lattice *d3_l,info *my_inf)
860 if((sf_fd=open(sf,O_WRONLY|O_CREAT))<0)
862 puts("cannot open save file");
865 if(write(sf_fd,d3_l,sizeof(d3_lattice))<sizeof(d3_lattice))
867 puts("failed saving d3 lattice struct");
870 if(write(sf_fd,my_inf,sizeof(info))<sizeof(info))
872 puts("failed saving info struct");
875 c=d3_l->max_x*d3_l->max_y*d3_l->max_z;
876 if(write(sf_fd,d3_l->status,c*sizeof(unsigned char))<c*sizeof(unsigned char))
878 puts("failed saving status of d3 lattice sites");
881 if(write(sf_fd,d3_l->extra,c*sizeof(int))<c*sizeof(int))
883 puts("failed saving sites concentration");
891 int load_from_file(char *lf,d3_lattice *d3_l,info *my_inf)
894 int lf_fd,c,pos,end,data,data_len,strip;
896 if((lf_fd=open(lf,O_RDONLY))<0)
898 puts("cannot open load file");
901 if(read(lf_fd,d3_l,sizeof(d3_lattice))<sizeof(d3_lattice))
903 puts("failed reading d3 lattice struct");
906 pos=lseek(lf_fd,0,SEEK_CUR);
907 printf("psition: %d (%d)\n",pos,sizeof(d3_lattice));
908 data=d3_l->max_x*d3_l->max_y*d3_l->max_z;
909 data_len=data*(sizeof(int)+sizeof(unsigned char));
910 printf("there are %d volumes so we need %d of bytes\n",data,data_len);
911 end=lseek(lf_fd,0,SEEK_END);
913 printf("end: %d => length: %d => guessed info size: %d bytes\n",end,end-pos,c);
914 strip=sizeof(info)-c;
915 printf("as real programs info size is %d, we strip %d bytes\n",sizeof(info),strip);
916 lseek(lf_fd,pos,SEEK_SET);
918 if(strip>0) c-=strip;
921 puts("info smaller then strip size");
924 if(read(lf_fd,my_inf,c)<c)
926 puts("failed reading info struct");
929 if(strip>0) memset(my_inf+c,0,strip);
930 if(strip<0) lseek(lf_fd,(-1*strip),SEEK_CUR);
931 c=d3_l->max_x*d3_l->max_y*d3_l->max_z;
932 if((d3_l->status=(unsigned char*)malloc(c*sizeof(unsigned char)))==NULL)
934 puts("cannot allocate status buffer");
937 if((d3_l->extra=(int *)malloc(c*sizeof(int)))==NULL)
939 puts("cannot allocate concentration buffer");
942 if(read(lf_fd,d3_l->status,c*sizeof(unsigned char))<c*sizeof(unsigned char))
944 puts("failed reading status of d3 lattice sites");
947 if(read(lf_fd,d3_l->extra,c*sizeof(int))<c*sizeof(int))
949 puts("failed reading sites concentration");
957 int convert_file(char *cf,d3_lattice *d3_l)
962 if((c_fd=open(cf,O_WRONLY|O_CREAT))<0)
964 puts("cannot open convert file");
967 dprintf(c_fd,"# created by nlsop (gnuplot format)\n");
968 for(x=0;x<d3_l->max_x;x++)
970 for(y=0;y<d3_l->max_y;y++)
972 for(z=0;z<d3_l->max_z;z++)
974 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);
983 int get_c_ratio(double *c_ratio,char *pfile,info *my_info,d3_lattice *d3_l)
988 unsigned char buf[32];
992 if((p_fd=open(pfile,O_RDONLY))<0)
994 puts("cannot open profile file");
1011 a=atof(p)/10; /* nm */
1014 if(a<=d3_l->max_z*CELL_LENGTH) d+=b;
1024 u32 get_reject_graph(info *my_info,d3_lattice *d3_l,char *file,u32 *graph) {
1029 unsigned char *flag;
1033 if((fd=open(file,O_RDONLY))<0)
1035 puts("cannot open file to calculate rejection graph");
1038 if((flag=(unsigned char *)malloc(d3_l->max_z))==NULL)
1040 puts("cannot malloc flag memory for rejection graph");
1043 memset(flag,0,d3_l->max_z);
1044 memset(graph,0,d3_l->max_z*sizeof(u32));
1051 k=read(fd,&buf[i],1);
1052 if((buf[i]=='\n')||(k==0)) break;
1057 a=atof(p)/10; /* nm */
1060 if(a>d3_l->max_z*CELL_LENGTH) k=0;
1063 graph[(int)(a/CELL_LENGTH)]=(int)(URAND_MAX/100*b);
1064 flag[(int)(a/CELL_LENGTH)]=1;
1068 /* do (linear) interpolation here! */
1071 while(i<d3_l->max_z)
1073 /* graph[0] is 0! */
1076 while(flag[i]==0&&i<d3_l->max_z) i++;
1077 for(k=j+1;k<i;k++) graph[k]=(int)((k-j)*((int)graph[i]-(int)graph[j])/(i-j))+graph[j];
1078 if(graph[i]>max) max=graph[i];
1083 #ifdef DEBUG_INTERPOL_PROFILE
1084 printf("debug: %s (interpolated profile)\n",file);
1085 for(i=0;i<d3_l->max_z;i++) printf("%d %d\n",i,graph[i]);
1091 int main(int argc,char **argv)
1093 u32 x,y,z,x_c,y_c,z_c;
1094 int i,j,quit,escape,switchmode,nowait,bmp,ac_distr;
1097 char s_file[MAX_CHARS];
1098 char s_file_tmp[MAX_CHARS];
1099 char l_file[MAX_CHARS];
1100 char c_file[MAX_CHARS];
1101 char p_file[MAX_CHARS];
1102 char n_e_file[MAX_CHARS];
1104 char r_file[MAX_CHARS];
1106 char xyz_txt[MAX_TXT];
1107 char status_txt[MAX_TXT];
1108 char conc_txt[MAX_TXT];
1109 char steps_txt[MAX_TXT];
1110 char cc_txt[MAX_TXT];
1111 char a_txt[MAX_TXT];
1112 char s_txt[MAX_TXT];
1113 char ballistic_txt[MAX_TXT];
1114 char carbon_txt[MAX_TXT];
1115 char stress_txt[MAX_TXT];
1116 char r_txt[MAX_TXT];
1117 char zdiff_txt[MAX_TXT];
1118 char diff_txt[MAX_TXT];
1119 char dr_ac_txt[MAX_TXT];
1120 char dr_cc_txt[MAX_TXT];
1121 char dose_txt[MAX_TXT];
1122 char mode_txt[MAX_TXT];
1123 char hpi_txt[MAX_TXT];
1124 char csat_txt[MAX_TXT];
1125 char *arg_v[MAX_ARGV];
1142 my_info.steps=STEPS;
1143 my_info.range=RANGE;
1152 my_info.dr_ac=DR_AC;
1153 my_info.dr_cc=DR_CC;
1154 my_info.diff_rate=DIFF_RATE;
1156 my_info.c_sat=C_SAT;
1165 strcpy(p_file,IMP_PROFILE);
1166 strcpy(n_e_file,NEL_PROFILE);
1186 d3_l.max_x=atoi(argv[++i]);
1189 d3_l.max_y=atoi(argv[++i]);
1192 d3_l.max_z=atoi(argv[++i]);
1202 my_info.steps=atoi(argv[++i]);
1205 refresh=atoi(argv[++i]);
1208 my_info.range=atoi(argv[++i]);
1211 my_info.s=atof(argv[++i]);
1214 my_info.b=atof(argv[++i]);
1217 my_info.c=atof(argv[++i]);
1220 resave=atoi(argv[++i]);
1223 strcpy(l_file,argv[++i]);
1224 if(i<argc-1) if(argv[i+1][0]!='-') strcpy(c_file,argv[++i]);
1228 my_info.dr_ac=atof(argv[++i]);
1231 my_info.dr_cc=atof(argv[++i]);
1234 my_info.diff_rate=atoi(argv[++i]);
1237 strcpy(l_file,argv[++i]);
1240 strcpy(s_file,argv[++i]);
1243 strcpy(r_file,argv[++i]);
1246 strcpy(p_file,argv[++i]);
1249 strcpy(n_e_file,argv[++i]);
1252 strcpy(l_file,argv[++i]);
1253 if(i<argc-1) if(argv[i+1][0]!='-') c_step=atoi(argv[++i]);
1256 my_info.cpi=atoi(argv[++i]);
1259 my_info.c_sat=atoi(argv[++i]);
1273 if(!strcmp(s_file,""))
1275 puts("NODFB defined, run with -S option");
1280 if(!strcmp(r_file,"")) rand_init(NULL);
1281 else rand_init(r_file);
1283 if(!strcmp(l_file,""))
1285 i=d3_l.max_x*d3_l.max_y*d3_l.max_z;
1287 d3_lattice_init(&argc,argv,&d3_l);
1289 if((d3_l.status=(unsigned char *)malloc(i*sizeof(unsigned char)))==NULL)
1291 puts("failed allocating status buffer");
1294 memset(d3_l.status,0,i*sizeof(unsigned char));
1295 if((d3_l.extra=(int *)malloc(i*sizeof(int)))==NULL)
1297 puts("failed allocating concentration buffer");
1300 memset(d3_l.extra,0,i*sizeof(int));
1303 load_from_file(l_file,&d3_l,&my_info);
1306 if(!strcmp(c_file,"")) sprintf(c_file,"%s_gnuplot",l_file);
1307 printf("converting file %s to %s\n",l_file,c_file);
1308 convert_file(c_file,&d3_l);
1313 else d3_lattice_init(&argc,argv,&d3_l);
1318 d3_event_init(&d3_l);
1322 strcpy(a_txt,"args:");
1323 sprintf(s_txt,"steps: %d",my_info.steps);
1324 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));
1325 sprintf(r_txt,"pressure range: %d",my_info.range);
1326 sprintf(stress_txt,"stress term: %f",my_info.s);
1327 sprintf(ballistic_txt,"ballistic term: %f",my_info.b);
1328 sprintf(carbon_txt,"carbon term: %f",my_info.c);
1329 sprintf(dr_ac_txt,"a/c diffusion rate: %f",my_info.dr_ac);
1330 if(my_info.c_diff!=0) sprintf(dr_cc_txt,"c/c diffusion rate: %f",my_info.dr_cc);
1331 else sprintf(dr_cc_txt,"c/c diffusion rate: none");
1332 sprintf(zdiff_txt,"diffusion in z direction: %c",my_info.z_diff?'y':'n');
1333 sprintf(diff_txt,"diffusion every %d steps",my_info.diff_rate);
1334 strcpy(mode_txt,"view: a/c mode");
1335 sprintf(hpi_txt,"hits per ion: %d",my_info.cpi);
1336 sprintf(csat_txt,"carbon saturation: %d",my_info.c_sat);
1339 arg_v[3]=status_txt;
1349 arg_v[13]=zdiff_txt;
1351 arg_v[15]=ballistic_txt;
1352 arg_v[16]=carbon_txt;
1353 arg_v[17]=stress_txt;
1354 arg_v[18]=dr_ac_txt;
1355 arg_v[19]=dr_cc_txt;
1364 /* compute graphs for random number rejection method */
1365 if((c_profile=(u32 *)malloc(d3_l.max_z*sizeof(unsigned int)))==NULL)
1367 puts("failed allocating memory for carbon profile graph");
1370 if((n_e_loss=(u32 *)malloc(d3_l.max_z*sizeof(unsigned int)))==NULL)
1372 puts("failed allocating memory for nuclear energy loss graph");
1375 ip_max=get_reject_graph(&my_info,&d3_l,p_file,c_profile);
1376 ne_max=get_reject_graph(&my_info,&d3_l,n_e_file,n_e_loss);
1378 if((!strcmp(l_file,""))||(c_step))
1380 /* calculate ratio of c_simwindow / c_total */
1381 if(get_c_ratio(&c_ratio,p_file,&my_info,&d3_l)!=1)
1383 puts("failed calculating ratio");
1392 printf("%d\n",get_rand_reject(d3_l.max_z,ip_max,c_profile));
1395 printf("%d\n",get_rand_reject(d3_l.max_z,ne_max,n_e_loss));
1398 printf("%d\n",get_rand(d3_l.max_z));
1400 if(i==10000000) return 1;
1405 i=(c_step?c_step:0);
1406 while((i<my_info.steps) && (quit==0) && (escape==0))
1408 for(j=0;j<my_info.cpi;j++)
1410 x_c=get_rand(d3_l.max_x);
1411 y_c=get_rand(d3_l.max_y);
1412 // z_c=get_rand_reject(d3_l.max_z,ne_max,n_e_loss);
1413 z_c=get_rand(d3_l.max_z);
1414 nel_z=URAND_MAX*(1.0*n_e_loss[z_c]/ne_max);
1415 process_cell(&d3_l,x_c,y_c,z_c,&my_info,nel_z);
1417 distrib_c(&d3_l,&my_info,i,c_ratio,ip_max,c_profile);
1421 sprintf(xyz_txt,"x: %d y: %d z: %d",x+1,y+1,z+1);
1422 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');
1423 sprintf(conc_txt,"conc: %d",*(d3_l.extra+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y));
1424 sprintf(steps_txt,"step: %d",i);
1425 sprintf(cc_txt,"total c: %d",my_info.cc);
1426 d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,0,NULL,0,NULL,0);
1429 if(i%resave==0 && strcmp(s_file,"") && resave!=0 && i!=0)
1431 sprintf(s_file_tmp,"%s_%d_of_%d",s_file,i,my_info.steps);
1432 save_to_file(s_file_tmp,&d3_l,&my_info);
1434 printf("saved %s\n",s_file_tmp);
1441 if(strcmp(s_file,""))
1443 printf("saved %s\n",s_file);
1444 save_to_file(s_file,&d3_l,&my_info);
1448 /* allocating buffer for pressure values */
1449 if((d3_l.v_ptr=malloc(d3_l.max_x*d3_l.max_y*d3_l.max_z*sizeof(unsigned char)))==NULL)
1451 puts("cannot allocate buffer for pressure values");
1455 calc_pressure(&d3_l,my_info.range);
1456 max_extra=calc_max_extra(&d3_l);
1458 while((quit==0) && (escape==0) && (nowait==0))
1461 if(switchmode==0) mode=0;
1462 if(switchmode==1) mode=1;
1463 if(switchmode==2) mode=2;
1464 if(switchmode==3) mode=3;
1466 sprintf(xyz_txt,"x: %d y: %d z: %d",x+1,y+1,z+1);
1467 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');
1468 sprintf(conc_txt,"conc: %d",*(d3_l.extra+x+y*d3_l.max_x+z*d3_l.max_x*d3_l.max_y));
1469 sprintf(steps_txt,"step: end");
1470 sprintf(cc_txt,"total c: %d",my_info.cc);
1471 if(switchmode==0) strcpy(mode_txt,"view: a/c mode");
1472 if(switchmode==1) strcpy(mode_txt,"view: c conc mode");
1473 if(switchmode==2) strcpy(mode_txt,"view: a pressure mode");
1474 if(switchmode==3) strcpy(mode_txt,"view: a/c + profiles mode");
1475 d3_lattice_draw(&d3_l,x,y,z,25,arg_v,mode,max_extra,c_profile,ip_max,n_e_loss,ne_max);
1478 scan_event(&d3_l,&x,&y,&z,&quit,&escape,&switchmode,&bmp,&ac_distr);
1479 if(bmp) write_bmp(&d3_l,bmp,x,y,z,max_extra);
1480 if(ac_distr) write_ac_distr(&d3_l,ac_distr);
1483 d3_lattice_release(&d3_l);