initial checkin

diff --git a/posic.c b/posic.c
new file mode 100644 (file)
index 0000000..006fd99
--- /dev/null
+++ b/posic.c
@@ -0,0 +1,154 @@
+/*
+ * posic.c - precipitation process of silicon carbide in silicon
+ *
+ * author: Frank Zirkelbach <hackbard@hackdaworld.org>
+ *
+ */
+ 
+#include "posic.h"
+
+#define RAND(max) (max*(0.5-(1.0*rand()/RAND_MAX+1)));
+
+int main(int argc,char **argv) {
+
+       t_atom *si;
+       //t_si *c;
+       int i,j,runs,amount_si;
+       double time;
+       int fd;
+
+       double tau,tau2,m,m2;
+       double deltax,deltay,deltaz,distance;
+       double deltax2,deltay2,deltaz2,tmp;
+       double lj1,lj2,lj;
+
+       /* silicon */
+       amount_si=AMOUNT_SI;
+       printf("simulating %d silicon atoms\n",amount_si);
+       si=malloc(amount_si*sizeof(t_atom));
+       if(!si) {
+               perror("silicon malloc");
+               return -1;
+       }
+       memset(si,0,amount_si*sizeof(t_atom));
+       m=SI_M; m2=2.0*m;
+
+       /* init */
+       printf("placing silicon atoms\n");
+       for(i=0;i<amount_si;i++) {
+               si[i].x=RAND(LEN_X);
+               si[i].y=RAND(LEN_Y);
+               si[i].z=RAND(LEN_Z);
+               si[i].vx=.0;
+               si[i].vy=.0;
+               si[i].vz=.0;
+               si[i].fx=.0;
+               si[i].fy=.0;
+               si[i].fz=.0;
+       }
+
+       /* time */
+       time=.0;
+       tau=TAU;
+       tau2=tau*tau;
+
+       /* rasmol */
+       printf("opening the rasmol file\n");
+       fd=open("rasmol.xyz",O_WRONLY);
+       if(fd<0) {
+               perror("rasmol file open");
+               return -1;
+       }
+
+       printf("starting velocity verlet: ");
+       fflush(stdout);
+
+       for(runs=0;runs<RUNS;runs++) {
+
+       /* 
+        * velocity verlet
+        *
+        * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
+        * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
+        *
+        */
+       for(i=0;i<amount_si;i++) {
+               /* calculation of new positions r(t+h) */
+               si[i].x+=si[i].vx*tau;
+               si[i].y+=si[i].vy*tau;
+               si[i].z+=si[i].vz*tau;
+               si[i].x+=(tau2*si[i].fx/m2);
+               if(si[i].x>LX) si[i].x-=LEN_X;
+               else if(si[i].x<-LX) si[i].x+=LEN_X;
+               si[i].y+=(tau2*si[i].fy/m2);
+               if(si[i].y>LY) si[i].y-=LEN_Y;
+               else if(si[i].y<-LY) si[i].y+=LEN_Y;
+               si[i].z+=(tau2*si[i].fz/m2);
+               if(si[i].z>LZ) si[i].z-=LEN_Z;
+               else if(si[i].z<-LZ) si[i].z+=LEN_Z;
+               /* calculation of velocities v(t+h/2) */
+               si[i].vx+=(tau*si[i].fx/m2);
+               si[i].vy+=(tau*si[i].fy/m2);
+               si[i].vz+=(tau*si[i].fz/m2);
+       }
+       for(i=0;i<amount_si;i++) {
+               /* calculation of forces at new positions r(t+h) */
+               for(j=0;j<i;j++) {
+                       deltax=si[i].x-si[j].x;
+                       if(deltax>LX) deltax-=LEN_X;
+                       else if(-deltax>LX) deltax+=LEN_X;
+                       deltax2=deltax*deltax;
+                       deltay=si[i].y-si[j].y;
+                       if(deltay>LY) deltay-=LEN_Y;
+                       else if(-deltay>LY) deltay+=LEN_Y;
+                       deltay2=deltay*deltay;
+                       deltaz=si[i].z-si[j].z;
+                       if(deltaz>LZ) deltaz-=LEN_Z;
+                       else if(-deltaz>LZ) deltaz+=LEN_Z;
+                       deltaz2=deltaz*deltaz;
+                       distance=deltax2+deltay2+deltaz2;
+                       if(distance<=R2_CUTOFF) {
+                               tmp=1.0/distance; // 1/r^2
+                               lj1=tmp; // 1/r^2
+                               tmp*=tmp; // 1/r^4
+                               lj1*=tmp; // 1/r^6
+                               tmp*=tmp; // 1/r^8
+                               lj2=tmp; // 1/r^8
+                               lj1*=tmp; // 1/r^14
+                               lj1*=LJ_SIGMA_12;
+                               lj2*=LJ_SIGMA_06;
+                               lj=-2*lj1+lj2;
+                               si[i].fx=lj*deltax;
+                               si[i].fy=lj*deltay;
+                               si[i].fz=lj*deltaz;
+                               si[i].fx=-lj*deltax;
+                               si[i].fy=-lj*deltay;
+                               si[i].fz=-lj*deltaz;
+                       }
+               }
+               /* calculation of new velocities v(t+h) */
+               si[i].vx+=(tau*si[i].fx/m2);
+               si[i].vy+=(tau*si[i].fy/m2);
+               si[i].vz+=(tau*si[i].fz/m2);
+       }
+
+       time+=tau;
+
+       /* print out positions in rasmol format */
+       dprintf(fd,"%d\nTime %f\n",amount_si,time);
+       for(i=0;i<amount_si;i++)
+               dprintf(fd,"Si %f %f %f %f\n",
+                       si[i].x,si[i].y,si[i].z,time);
+       printf(".");
+       fflush(stdout);
+       dprintf(fd,"\n");
+
+       }
+
+       printf("done\n");
+       close(fd);
+       free(si);
+
+       return 0;
+}
+

diff --git a/posic.h b/posic.h
new file mode 100644 (file)
index 0000000..93b7219
--- /dev/null
+++ b/posic.h
@@ -0,0 +1,54 @@
+/*
+ * posic.h - precipitation process of silicon carbide in silicon
+ *
+ * author: Frank Zirkelbach <hackbard@hackdaworl.org>
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+
+#ifndef POSIC_H
+#define POSIC_H
+
+#define LEN_X 5
+#define LX (1.0*LEN_X/2)
+#define LEN_Y 5
+#define LY (1.0*LEN_Y/2)
+#define LEN_Z 5
+#define LZ (1.0*LEN_Z/2)
+
+#define RUNS 1000
+#define TAU 0.001
+
+#define R_CUTOFF 2
+#define R2_CUTOFF (R_CUTOFF*R_CUTOFF)
+
+#define SI_M 1
+#define SI_LC 0.543105
+#define LJ_SIGMA SI_LC
+#define LJ_SIGMA_02 (LJ_SIGMA*LJ_SIGMA)
+#define LJ_SIGMA_06 (LJ_SIGMA_02*LJ_SIGMA_02*LJ_SIGMA_02)
+#define LJ_SIGMA_12 (LJ_SIGMA_06*LJ_SIGMA_06)
+
+#define AMOUNT_SI ((LEN_X/SI_LC)*(LEN_Y/SI_LC)*(LEN_Z/SI_LC)*2)
+
+typedef struct s_atom {
+       double x;
+       double y;
+       double z;
+       double vx;
+       double vy;
+       double vz;
+       double fx;
+       double fy;
+       double fz;
+} t_atom;
+
+#endif