/*
* posic.c - precipitation process of silicon carbide in silicon
*
- * author: Frank Zirkelbach <hackbard@hackdaworld.org>
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
*
*/
-
-#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
+
+/* main include file */
#include "posic.h"
-int main(int argc,char **argv) {
+/* functions */
- t_moldyn md;
- t_atom *si;
- t_visual vis;
+/* main code */
- t_random random;
+int parse_config_file() {
- int a,b,c;
- double t,e,u;
- double help;
- t_3dvec p;
- int count;
+ return 0;
+}
- t_lj_params lj;
+int main(int argc,char **argv) {
- char fb[32]="saves/fcc_test";
+ t_moldyn md;
- /* init */
+ t_lj_params *lj;
+ t_ho_params *ho;
+ t_tersoff_mult_params *tp;
+ t_albe_mult_params *ap;
- rand_init(&random,NULL,1);
- random.status|=RAND_STAT_VERBOSE;
+ lj=NULL;
+ ho=NULL;
+ tp=NULL;
+ ap=NULL;
- /* testing random numbers */
- //for(a=0;a<1000000;a++)
- // printf("%f %f\n",rand_get_gauss(&random),
- // rand_get_gauss(&random));
+ memset(&md,0,sizeof(t_moldyn));
- visual_init(&vis,fb);
-
- a=LEN_X;
- b=LEN_Y;
- c=LEN_Z;
-
- t=TEMPERATURE;
-
- printf("placing silicon atoms ... ");
- count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
- printf("(%d) ok!\n",count);
-
- printf("setting thermal fluctuations\n");
- thermal_init(si,&random,count,t);
-
- /* visualize */
-
- visual_atoms(&vis,0.0,si,count);
-
- /* check kinetic energy */
-
- e=get_e_kin(si,count);
- printf("kinetic energy: %f\n",e);
- printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
-
- /* check total momentum */
- p=get_total_p(si,count);
- printf("total momentum: %f\n",v3_norm(&p));
-
- /* check potential energy */
- md.count=count;
- md.atom=si;
- md.potential=potential_lennard_jones;
- md.force=force_lennard_jones;
- md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
- md.pot_params=&lj;
- md.force=NULL;
- md.status=0;
-
- lj.sigma6=3.0/16.0*LC_SI*LC_SI;
- help=lj.sigma6*lj.sigma6;
- lj.sigma6*=help;
- lj.sigma12=lj.sigma6*lj.sigma6;
- lj.epsilon=1;
-
- u=get_e_pot(&md);
-
- printf("potential energy: %f\n",u);
- printf("total energy (1): %f\n",e+u);
- printf("total energy (2): %f\n",get_total_energy(&md));
-
- md.dim.x=a*LC_SI;
- md.dim.y=b*LC_SI;
- md.dim.z=c*LC_SI;
-
- /*
- * let's do the actual md algorithm now
- *
- * integration of newtons equations
- */
-
- /* close */
-
- visual_tini(&vis);
-
- rand_close(&random);
-
-
- //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);
-// /* reset of forces */
-// si[i].fx=.0;
-// si[i].fy=.0;
-// si[i].fz=.0;
-// }
-// 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[j].fx+=lj*deltax;
-// si[j].fy+=lj*deltay;
-// si[j].fz+=lj*deltaz;
-// }
-// }
-// }
-// for(i=0;i<amount_si;i++) {
-// /* 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);
-// }
-//
-// if(!(runs%150)) {
-//
-// /* rasmol script & xyz file */
-// sprintf(xyz,"./saves/si-%.15f.xyz",time);
-// sprintf(ppm,"./video/si-%.15f.ppm",time);
-// fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
-// if(fd1<0) {
-// perror("rasmol xyz file open");
-// return -1;
-// }
-// dprintf(fd2,"load xyz %s\n",xyz);
-// dprintf(fd2,"spacefill 200\n");
-// dprintf(fd2,"rotate x 11\n");
-// dprintf(fd2,"rotate y 13\n");
-// dprintf(fd2,"set ambient 20\n");
-// dprintf(fd2,"set specular on\n");
-// dprintf(fd2,"zoom 400\n");
-// dprintf(fd2,"write ppm %s\n",ppm);
-// dprintf(fd2,"zap\n");
-// dprintf(fd1,"%d\nsilicon\n",amount_si+9);
-// for(i=0;i<amount_si;i++)
-// dprintf(fd1,"Si %f %f %f %f\n",
-// si[i].x,si[i].y,si[i].z,time);
-// dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
-// close(fd1);
-//
-// }
-//
-// /* increase time */
-// time+=tau;
-// printf(".");
-// fflush(stdout);
-//
-// }
-//
-// printf(" done\n");
-// close(fd2);
-// free(si);
-//
return 0;
}
projects / physik / posic.git / blobdiff