X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=posic.c;h=5ff3bc1b7f03a6378bb549009e7c8db9e9806256;hb=45b27e01673a6cc5bebecb49c51d7f587917483e;hp=006fd99a298211458df528cb3986d3765a138f7a;hpb=9ae5e8af9192b47fba3743ab7f4ef6d0c34d507d;p=physik%2Fposic.git

diff --git a/posic.c b/posic.c
index 006fd99..5ff3bc1 100644
--- a/posic.c
+++ b/posic.c
@@ -1,69 +1,157 @@
 /*
  * 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 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;
+
+	t_visual vis;
+
+	t_random random;
+
+	int a,b,c;
+	double t,e,u;
+	double help;
+	t_3dvec p;
+	int count;
+
+	t_lj_params lj;
+	t_ho_params ho;
+
+	char fb[32]="saves/lj_test";
 
 	/* 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++) {
+
+	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));
+
+	visual_init(&vis,fb);
+
+	a=LEN_X;
+	b=LEN_Y;
+	c=LEN_Z;
+
+	vis.dim.x=a*LC_SI;
+	vis.dim.y=b*LC_SI;
+	vis.dim.z=c*LC_SI;
+
+	t=TEMPERATURE;
+
+	printf("placing silicon atoms ... ");
+	//count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
+	//printf("(%d) ok!\n",count);
+	count=2;
+	si=malloc(2*sizeof(t_atom));
+	si[0].r.x=0.16e-9;
+	si[0].r.y=0;
+	si[0].r.z=0;
+	si[0].element=SI;
+	si[0].mass=M_SI;
+	si[1].r.x=-0.16e-9;
+	si[1].r.y=0;
+	si[1].r.z=0;
+	si[1].element=SI;
+	si[1].mass=M_SI;
+
+	printf("setting thermal fluctuations\n");
+	//thermal_init(si,&random,count,t);
+	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*t);
+
+	/* check total momentum */
+	p=get_total_p(si,count);
+	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
+
+	/* check potential energy */
+	md.count=count;
+	md.atom=si;
+	md.potential=potential_lennard_jones;
+	//md.potential=potential_harmonic_oscillator;
+	md.force=force_lennard_jones;
+	//md.force=force_harmonic_oscillator;
+	//md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
+	md.cutoff=(0.4e-9);
+	md.cutoff_square=(0.6e-9*0.6e-9);
+	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;
+	md.write=WRITE_FILE;
+
+	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=0.3e-9;
+	ho.spring_constant=1.0e-9;
+
+	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,t));
+
+
+	/*
+	 * let's do the actual md algorithm now
+	 *
+	 * integration of newtons equations
+	 */
+
+	moldyn_integrate(&md);
+
+	printf("total energy (after integration): %.40f [J]\n",
+	       get_total_energy(&md));
+
+	/* close */
+
+	visual_tini(&vis);
+
+	rand_close(&random);
+	
+
+	//printf("starting velocity verlet: ");
+	//fflush(stdout);
+
+	//for(runs=0;runs<RUNS;runs++) {
 
 	/* 
 	 * velocity verlet
@@ -72,82 +160,119 @@ int main(int argc,char **argv) {
 	 * 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);
+	//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;
 }