+ for(y=0;y<d3_l->max_y;y++)
+ {
+ for(z=0;z<d3_l->max_z;z++)
+ {
+ count=0;
+ for(i=-range;i<=range;i++)
+ {
+ for(j=-range;j<=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) count+=((double)*(d3_l->extra+off))/(i*i+j*j);
+ }
+ }
+ }
+ if(count>max) max=count;
+ }
+ }
+ }
+
+ for(x=0;x<d3_l->max_x;x++)
+ {
+ for(y=0;y<d3_l->max_y;y++)
+ {
+ for(z=0;z<d3_l->max_z;z++)
+ {
+ count=0;
+ for(i=-range;i<=range;i++)
+ {
+ for(j=-range;j<=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) count+=((double)*(d3_l->extra+off))/(i*i+j*j);
+ }
+ }
+ }
+ *(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);
+ }
+ }
+ }
+
+ return 1;
+}
+
+int calc_max_extra(d3_lattice *d3_l)
+{
+ int x,y,z;
+ int off,max=0;
+
+ for(x=0;x<d3_l->max_x;x++)
+ {
+ for(y=0;y<d3_l->max_y;y++)
+ {
+ for(z=0;z<d3_l->max_z;z++)
+ {
+ off=x+y*d3_l->max_x+z*d3_l->max_x*d3_l->max_y;
+ if(*(d3_l->extra+off)>max) max=*(d3_l->extra+off);
+ }
+ }
+ }
+
+ return max;
+}
+
+int write_bmp(d3_lattice *d3_l,int window,u32 x,u32 y,u32 z)
+{
+ int fd,i,j,size=0,foo=0;
+ int width=0,height=0;
+ char bmpfile[MAX_CHARS];
+ char buf[128];
+
+ if(window==1)
+ {
+ 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;
+ }
+ 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;
+ }
+ if(window==3)
+ {
+ sprintf(bmpfile,"x-y_%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((fd=open(bmpfile,O_WRONLY|O_CREAT))<0)
+ {
+ puts("cannot open bmp file");
+ return -1;
+ }
+
+ /* bmpheader */
+ buf[0]='B'; /* std header start */
+ buf[1]='M';
+ buf[2]=(size+0x36)&0xff; /* file size */
+ buf[3]=(size+0x36)>>8;
+ memset(buf+4,0,6);
+ buf[10]=0x36; /* offset to data */
+ memset(buf+11,0,3);
+ buf[14]=0x28; /* length of bmp info header */
+ memset(buf+15,0,3);
+ buf[18]=width&0xff; /* width and height */
+ buf[19]=width>>8;
+ memset(buf+20,0,2);
+ buf[22]=height&0xff;
+ buf[23]=height>>8;
+ memset(buf+24,0,2);
+ buf[26]=1; /* # planes -> 1 */
+ buf[27]=0;
+ buf[28]=24; /* bits per pixel -> 2^24 (true color) */
+ buf[29]=0;
+ memset(buf+30,0,4); /* compression -> none */
+ buf[34]=size&0xff; /* data size */
+ buf[35]=size>>8;
+ memset(buf+36,0,2);
+ buf[38]=0x12; /* res: pixel/meter */
+ buf[39]=0x0b;
+ memset(buf+40,0,2);
+ buf[42]=0x12;
+ buf[43]=0x0b;
+ memset(buf+44,0,2);
+ memset(buf+46,0,8); /* no colors, no important colors */
+
+ if(write(fd,buf,54)<54)
+ {
+ puts("failed writing bmp header");
+ return -1;
+ }
+ if(window==1)
+ {
+ 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) memset(buf,0xff,3);
+ else memset(buf,0,3);
+ 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==2)
+ {
+ for(j=0;j<d3_l->max_z;j++)
+ {
+ for(i=0;i<d3_l->max_y;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) memset(buf,0xff,3);
+ else memset(buf,0,3);
+ 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==3)
+ {
+ 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) memset(buf,0xff,3);
+ else memset(buf,0,3);
+ 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;
+}
+
+int save_to_file(char *sf,d3_lattice *d3_l,info *my_inf)
+{
+ int sf_fd,c;
+
+ if((sf_fd=open(sf,O_WRONLY|O_CREAT))<0)
+ {
+ puts("cannot open save file");
+ return -1;
+ }
+ if(write(sf_fd,d3_l,sizeof(d3_lattice))<sizeof(d3_lattice))
+ {
+ puts("failed saving d3 lattice struct");
+ return -1;
+ }
+ if(write(sf_fd,my_inf,sizeof(info))<sizeof(info))
+ {
+ puts("failed saving info struct");
+ return-1;
+ }
+ c=d3_l->max_x*d3_l->max_y*d3_l->max_z;
+ if(write(sf_fd,d3_l->status,c*sizeof(unsigned char))<c*sizeof(unsigned char))
+ {
+ puts("failed saving status of d3 lattice sites");
+ return -1;
+ }
+ if(write(sf_fd,d3_l->extra,c*sizeof(int))<c*sizeof(int))
+ {
+ puts("failed saving sites concentration");
+ return -1;
+ }
+ close(sf_fd);
+
+ return 1;
+}
+
+int load_from_file(char *lf,d3_lattice *d3_l,info *my_inf)
+{
+ int lf_fd,c;
+
+ if((lf_fd=open(lf,O_RDONLY))<0)
+ {
+ puts("cannot open load file");
+ return -1;
+ }
+ if(read(lf_fd,d3_l,sizeof(d3_lattice))<sizeof(d3_lattice))
+ {
+ puts("failed reading d3 lattice struct");
+ return -1;
+ }
+ if(read(lf_fd,my_inf,sizeof(info))<sizeof(info))
+ {
+ puts("failed reading info struct");
+ return-1;
+ }
+ 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)
+ {
+ puts("cannot allocate status buffer");
+ return -1;
+ }
+ if((d3_l->extra=(int *)malloc(c*sizeof(int)))==NULL)
+ {
+ puts("cannot allocate concentration buffer");
+ return -1;
+ }
+ if(read(lf_fd,d3_l->status,c*sizeof(unsigned char))<c*sizeof(unsigned char))
+ {
+ puts("failed reading status of d3 lattice sites");
+ return -1;
+ }
+ if(read(lf_fd,d3_l->extra,c*sizeof(int))<c*sizeof(int))
+ {
+ puts("failed reading sites concentration");
+ return -1;
+ }
+ close(lf_fd);
+
+ return 1;
+}
+
+int convert_file(char *cf,d3_lattice *d3_l)
+{
+ int x,y,z;
+ int c_fd;
+
+ if((c_fd=open(cf,O_WRONLY|O_CREAT))<0)
+ {
+ puts("cannot open convert file");
+ return -1;
+ }
+ dprintf(c_fd,"# created by nlsop (gnuplot format)\n");
+ for(x=0;x<d3_l->max_x;x++)
+ {
+ for(y=0;y<d3_l->max_y;y++)
+ {
+ for(z=0;z<d3_l->max_z;z++)
+ {
+ 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);
+ }
+ }
+ }
+ close(c_fd);
+
+ return 1;
+}
+
+int get_c_ratio(double *c_ratio,char *pfile,info *my_info,d3_lattice *d3_l)
+{
+ double all,a,b,d;
+ int i,k;
+ int p_fd;
+ unsigned char buf[32];
+ char *p;
+ unsigned char c;
+
+ if((p_fd=open(pfile,O_RDONLY))<0)
+ {
+ puts("cannot open profile file");
+ return -1;
+ }
+ k=1;
+ d=0;
+ all=0;
+ while(k)
+ {
+ for(i=0;i<32;i++)
+ {
+ k=read(p_fd,&c,1);
+ buf[i]=c;
+ if(c=='\n') break;
+ }
+ if(k)
+ {
+ p=strtok(buf," ");
+ 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;
+ all+=b;
+ }
+ }
+ *c_ratio=d/all;
+ close(p_fd);
+
+ return 1;
+}
+
+int main(int argc,char **argv)
+{
+ u32 x,y,z,x_c,y_c,z_c;
+ int i,quit,escape,switchmode,nowait,bmp;
+ 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 convert;
+ char r_file[MAX_CHARS];
+#ifdef USE_DFB_API
+ char xyz_txt[MAX_TXT];
+ char status_txt[MAX_TXT];
+ char conc_txt[MAX_TXT];
+ char steps_txt[MAX_TXT];
+ 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 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 *arg_v[MAX_ARGV];
+#endif
+ d3_lattice d3_l;
+ info my_info;
+ unsigned char mode;
+ double c_ratio;
+#ifdef USE_DFB_API
+ int max_extra;
+#endif
+
+ d3_l.max_x=X;
+ d3_l.max_y=Y;
+ d3_l.max_z=Z;
+ my_info.steps=STEPS;
+ my_info.range=RANGE;
+ refresh=REFRESH;
+ resave=RESAVE;
+ my_info.z_diff=0;
+ c_diff=1;
+ 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.a_ap=A_AP;
+ my_info.b_ap=B_AP;
+ my_info.a_cp=A_CP;
+ my_info.cc=CC;
+ my_info.dr_ac=DR_AC;
+ my_info.dr_cc=DR_CC;
+ my_info.diff_rate=DIFF_RATE;
+ 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);
+ convert=0;
+ strcpy(r_file,"");
+ mode=0;
+
+ amorph_count=0;
+ cryst_count=0;
+
+ for(i=1;i<argc;i++)
+ {
+ if(argv[i][0]=='-')
+ {
+ switch(argv[i][1])
+ {
+ case 'h':
+ usage();
+ return -1;
+ 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;
+ case 'y':
+ d3_l.max_y=atoi(argv[++i]);
+ break;
+ case 'z':
+ d3_l.max_z=atoi(argv[++i]);
+ break;
+ case 'Z':
+ my_info.z_diff=1;
+ break;
+ case 'i':
+ c_diff=0;
+ break;
+ case 's':
+ my_info.steps=atoi(argv[++i]);
+ break;
+ case 'd':
+ refresh=atoi(argv[++i]);
+ break;
+ case 'r':
+ my_info.range=atoi(argv[++i]);
+ break;
+ case 'f':
+ my_info.a_ap=atof(argv[++i]);
+ break;
+ case 'p':
+ my_info.b_ap=atof(argv[++i]);
+ break;
+ 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;
+ case 'C':
+ strcpy(l_file,argv[++i]);
+ if(i<argc-1) if(argv[i+1][0]!='-') strcpy(c_file,argv[++i]);
+ convert=1;
+ break;
+ case 'D':
+ my_info.dr_ac=atof(argv[++i]);
+ break;
+ case 'c':
+ my_info.dr_cc=atof(argv[++i]);
+ break;
+ case 'e':
+ my_info.diff_rate=atoi(argv[++i]);
+ break;
+ case 'L':
+ strcpy(l_file,argv[++i]);
+ break;
+ case 'S':
+ strcpy(s_file,argv[++i]);
+ break;
+ case 'R':
+ strcpy(r_file,argv[++i]);
+ break;
+ case 'P':
+ strcpy(p_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;
+ default:
+ usage();
+ return -1;
+ }
+ } else usage();
+ }
+
+ x=d3_l.max_x/2-1;
+ y=d3_l.max_y/2-1;
+ z=d3_l.max_z/2-1;
+
+#ifdef NODFB
+ if(!strcmp(s_file,""))
+ {
+ puts("NODFB defined, run with -S option");
+ return -1;