/*
* 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 <math.h>
-#include "posic.h"
+#include "moldyn.h"
+#include "math/math.h"
+#include "init/init.h"
+#include "visual/visual.h"
-#define RAND(max) (max*(0.5-(1.0*rand()/RAND_MAX+1)));
+#include "posic.h"
int main(int argc,char **argv) {
+ t_moldyn md;
t_atom *si;
- //t_si *c;
- int i,j,runs,amount_si;
- double time;
- int fd1,fd2;
- unsigned char xyz[128];
- unsigned char scr[128];
- unsigned char ppm[128];
-
- 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;
+ t_visual vis;
+ t_random random;
+
+ int a,b,c;
+ double e,u;
+ double help;
+ t_3dvec p;
+ int count;
+
+ t_lj_params lj;
+ t_ho_params ho;
+
+ /* parse arguments */
+ a=moldyn_parse_argv(&md,argc,argv);
+ if(a<0) return -1;
/* 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;
-
-
- 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))
+ moldyn_log_init(&md,&vis);
+ rand_init(&random,NULL,1);
+ random.status|=RAND_STAT_VERBOSE;
+
+ /* testing random numbers */
+ //for(a=0;a<1000000;a++)
+ // printf("%f %f\n",rand_get_gauss(&random),
+ // rand_get_gauss(&random));
+
+ a=LEN_X;
+ b=LEN_Y;
+ c=LEN_Z;
+
+ /* set for 'bounding atoms' */
+ vis.dim.x=a*LC_SI;
+ vis.dim.y=b*LC_SI;
+ vis.dim.z=c*LC_SI;
+
+ /* init lattice
+ printf("placing silicon atoms ... ");
+ count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
+ printf("(%d) ok!\n",count); */
+ /* testing purpose */
+ count=2;
+ si=malloc(2*sizeof(t_atom));
+ si[0].r.x=0.35*sqrt(3.0)*LC_SI/2.0;
+ si[0].r.y=0;
+ si[0].r.z=0;
+ si[0].element=SI;
+ si[0].mass=M_SI;
+ si[1].r.x=-si[0].r.x;
+ si[1].r.y=0;
+ si[1].r.z=0;
+ si[1].element=SI;
+ si[1].mass=M_SI;
+ /* */
+
+ /* moldyn init (now si is a valid address) */
+ md.count=count;
+ md.atom=si;
+ md.potential=potential_lennard_jones;
+ md.force=force_lennard_jones;
+ //md.potential=potential_harmonic_oscillator;
+ //md.force=force_harmonic_oscillator;
+ md.cutoff=R_CUTOFF;
+ md.cutoff_square=(R_CUTOFF*R_CUTOFF);
+ md.pot_params=&lj;
+ //md.pot_params=&ho;
+ md.integrate=velocity_verlet;
+ //md.time_steps=RUNS;
+ //md.tau=TAU;
+ md.status=0;
+ md.visual=&vis;
+
+ printf("setting thermal fluctuations (T=%f K)\n",md.t);
+ //thermal_init(&md,&random,count);
+ for(a=0;a<count;a++) v3_zero(&(si[0].v));
+ //v3_zero(&(si[0].v));
+ //v3_zero(&(si[1].v));
+
+ /* check kinetic energy */
+
+ e=get_e_kin(si,count);
+ printf("kinetic energy: %.40f [J]\n",e);
+ printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*md.t);
+
+ /* check total momentum */
+ p=get_total_p(si,count);
+ printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
+
+ /* check potential energy */
+ lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
+ help=lj.sigma6*lj.sigma6;
+ lj.sigma6*=help;
+ lj.sigma12=lj.sigma6*lj.sigma6;
+ lj.epsilon=LJ_EPSILON_SI;
+
+ ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+ ho.spring_constant=LJ_EPSILON_SI;
+
+ u=get_e_pot(&md);
+
+ printf("potential energy: %.40f [J]\n",u);
+ printf("total energy (1): %.40f [J]\n",e+u);
+ printf("total energy (2): %.40f [J]\n",get_total_energy(&md));
+
+ md.dim.x=a*LC_SI;
+ md.dim.y=b*LC_SI;
+ md.dim.z=c*LC_SI;
+
+ printf("estimated accurate time step: %.30f [s]\n",
+ estimate_time_step(&md,3.0,md.t));
+
+
+ /*
+ * let's do the actual md algorithm now
*
+ * integration of newtons equations
*/
- 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);
- }
-
- if(!(runs%10)) {
-
- /* rasmol script & xyz file */
- sprintf(xyz,"./saves/si-%.15f.xyz",time);
- sprintf(scr,"./saves/si-%.15f.scr",time);
- sprintf(ppm,"./video/si-%.15f.ppm",time);
- fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
- fd2=open(scr,O_WRONLY|O_CREAT|O_TRUNC);
- if((fd1<0)||(fd2<0)) {
- perror("rasmol 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,"set write on\n");
- dprintf(fd2,"write ppm %s\n",ppm);
- dprintf(fd1,"%d\nsilicon\n",amount_si);
- 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);
- close(fd1);
- close(fd2);
-
- }
-
- /* increase time */
- time+=tau;
- printf(".");
- fflush(stdout);
-
- }
-
- printf(" done\n");
- free(si);
+ moldyn_integrate(&md);
+
+ printf("total energy (after integration): %.40f [J]\n",
+ get_total_energy(&md));
+
+ /* close */
+
+ rand_close(&random);
+
+ moldyn_shutdown(&md);
+
return 0;
}
projects / physik / posic.git / blobdiff