X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=posic.c;h=236e208bcce0bea5516bbe1a70d5efe1decda416;hb=c1a1e7ec0bdad968f7dbf80329740ec8843e3477;hp=8910dddecd353f04004e11d9eddc20135882703e;hpb=6eb09b305eb6f565d844979b68dd2542e9a0d5fa;p=physik%2Fposic.git

diff --git a/posic.c b/posic.c
index 8910ddd..236e208 100644
--- a/posic.c
+++ b/posic.c
@@ -1,202 +1,137 @@
 /*
  * 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;
-	amount_si=2;
-	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;
+	double help;
+	t_3dvec p;
+
+	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");
+	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 ... ");
+	md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
+	printf("(%d) ok!\n",md.count);
+	testing purpose */
+	md.count=2;
+	si=malloc(2*sizeof(t_atom));
+	si[0].r.x=0.13*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.atom=si;
+	md.potential_force_function=lennard_jones;
+	//md.potential_force_function=harmonic_oscillator;
+	md.cutoff=R_CUTOFF*LC_SI;
+	md.pot_params=&lj;
+	//md.pot_params=&ho;
+	md.status=0;
+	md.visual=&vis;
+	/* dimensions of the simulation cell */
+	md.dim.x=a*LC_SI;
+	md.dim.y=b*LC_SI;
+	md.dim.z=c*LC_SI;
+
+	printf("setting thermal fluctuations (T=%f K)\n",md.t);
+	// thermal_init(&md,&random);
+	for(a=0;a<md.count;a++) v3_zero(&(si[0].v));
+
+	/* check kinetic energy */
+
+	e=get_e_kin(si,md.count);
+	printf("kinetic energy: %.40f [J]\n",e);
+	printf("3/2 N k T = %.40f [J] (T=%f [K])\n",
+	       1.5*md.count*K_BOLTZMANN*md.t,md.t);
+
+	/* check total momentum */
+	p=get_total_p(si,md.count);
+	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
+
+	/* potential paramters */
+	lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
+	help=lj.sigma6*lj.sigma6;
+	lj.sigma6*=help;
+	lj.sigma12=lj.sigma6*lj.sigma6;
+	lj.epsilon4=4.0*LJ_EPSILON_SI;
+
+	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+	ho.spring_constant=1.0;
+
+	printf("estimated accurate time step: %.30f [s]\n",
+	       estimate_time_step(&md,3.0,md.t));
+
 	/*
-	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;
-	}
-	*/
-	si[0].x=-2.0;
-	si[1].x=+2.0;
-	si[0].y=0;
-	si[0].z=0;
-	si[1].y=0;
-	si[1].z=0;
-
-	/* time */
-	time=.0;
-	tau=TAU;
-	tau2=tau*tau;
-
-	/* rasmol script file */
-	sprintf(scr,"./saves/si.scr");
-	fd2=open(scr,O_WRONLY|O_CREAT|O_TRUNC);
-	if(fd2<0) {
-		perror("rasmol script 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))
+	 * 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);
-		/* 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%100)) {
-
-	/* 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,"spacefill\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,"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);
 
+	moldyn_integrate(&md);
+
+	printf("total energy (after integration): %.40f [J]\n",
+	       get_total_energy(&md));
+
+	/* close */
+
+	link_cell_shutdown(&md);
+
+	rand_close(&random);
+
+	moldyn_shutdown(&md);
+	
 	return 0;
 }