2 * posic.c - precipitation process of silicon carbide in silicon
4 * author: Frank Zirkelbach <hackbard@hackdaworld.org>
10 #define RAND(max) (max*(0.5-(1.0*rand()/RAND_MAX+1)));
12 int main(int argc,char **argv) {
16 int i,j,runs,amount_si;
19 unsigned char xyz[128];
20 unsigned char scr[128];
21 unsigned char ppm[128];
24 double deltax,deltay,deltaz,distance;
25 double deltax2,deltay2,deltaz2,tmp;
30 printf("simulating %d silicon atoms\n",amount_si);
31 si=malloc(amount_si*sizeof(t_atom));
33 perror("silicon malloc");
36 memset(si,0,amount_si*sizeof(t_atom));
40 printf("placing silicon atoms\n");
41 for(i=0;i<amount_si;i++) {
58 /* rasmol script file */
59 sprintf(scr,"./saves/si.scr");
60 fd2=open(scr,O_WRONLY|O_CREAT|O_TRUNC);
62 perror("rasmol script file open");
66 printf("starting velocity verlet: ");
69 for(runs=0;runs<RUNS;runs++) {
74 * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
75 * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
78 for(i=0;i<amount_si;i++) {
79 /* calculation of new positions r(t+h) */
80 si[i].x+=si[i].vx*tau;
81 si[i].y+=si[i].vy*tau;
82 si[i].z+=si[i].vz*tau;
83 si[i].x+=(tau2*si[i].fx/m2);
84 if(si[i].x>LX) si[i].x-=LEN_X;
85 else if(si[i].x<-LX) si[i].x+=LEN_X;
86 si[i].y+=(tau2*si[i].fy/m2);
87 if(si[i].y>LY) si[i].y-=LEN_Y;
88 else if(si[i].y<-LY) si[i].y+=LEN_Y;
89 si[i].z+=(tau2*si[i].fz/m2);
90 if(si[i].z>LZ) si[i].z-=LEN_Z;
91 else if(si[i].z<-LZ) si[i].z+=LEN_Z;
92 /* calculation of velocities v(t+h/2) */
93 si[i].vx+=(tau*si[i].fx/m2);
94 si[i].vy+=(tau*si[i].fy/m2);
95 si[i].vz+=(tau*si[i].fz/m2);
97 for(i=0;i<amount_si;i++) {
98 /* calculation of forces at new positions r(t+h) */
100 deltax=si[i].x-si[j].x;
101 if(deltax>LX) deltax-=LEN_X;
102 else if(-deltax>LX) deltax+=LEN_X;
103 deltax2=deltax*deltax;
104 deltay=si[i].y-si[j].y;
105 if(deltay>LY) deltay-=LEN_Y;
106 else if(-deltay>LY) deltay+=LEN_Y;
107 deltay2=deltay*deltay;
108 deltaz=si[i].z-si[j].z;
109 if(deltaz>LZ) deltaz-=LEN_Z;
110 else if(-deltaz>LZ) deltaz+=LEN_Z;
111 deltaz2=deltaz*deltaz;
112 distance=deltax2+deltay2+deltaz2;
113 if(distance<=R2_CUTOFF) {
114 tmp=1.0/distance; // 1/r^2
132 /* calculation of new velocities v(t+h) */
133 si[i].vx+=(tau*si[i].fx/m2);
134 si[i].vy+=(tau*si[i].fy/m2);
135 si[i].vz+=(tau*si[i].fz/m2);
140 /* rasmol script & xyz file */
141 sprintf(xyz,"./saves/si-%.15f.xyz",time);
142 sprintf(ppm,"./video/si-%.15f.ppm",time);
143 fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
145 perror("rasmol xyz file open");
148 dprintf(fd2,"load xyz %s\n",xyz);
149 dprintf(fd2,"spacefill 200\n");
150 dprintf(fd2,"rotate x 11\n");
151 dprintf(fd2,"rotate y 13\n");
152 dprintf(fd2,"set ambient 20\n");
153 dprintf(fd2,"set specular on\n");
154 dprintf(fd2,"write ppm %s\n",ppm);
155 dprintf(fd2,"zap\n");
156 dprintf(fd1,"%d\nsilicon\n",amount_si);
157 for(i=0;i<amount_si;i++)
158 dprintf(fd1,"Si %f %f %f %f\n",
159 si[i].x,si[i].y,si[i].z,time);