X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=posic.c;h=cd1a2e2bc1b616b75964546643a8bad9b604a873;hb=refs%2Fheads%2Forigin;hp=6d901b4097298df45e88b695189e138da92c9ff6;hpb=85abe46fecc79a3d7885ff6124186b2be2ca96ac;p=physik%2Fposic.git

diff --git a/posic.c b/posic.c
index 6d901b4..cd1a2e2 100644
--- a/posic.c
+++ b/posic.c
@@ -1,9 +1,11 @@
 /*
  * 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 "moldyn.h"
 #include "math/math.h"
@@ -16,84 +18,134 @@ int main(int argc,char **argv) {
 
 	t_moldyn md;
 
-	t_atom *si;
-
-	t_visual vis;
-
-	t_random random;
+	t_lj_params lj;
+	t_ho_params ho;
+	t_tersoff_mult_params tp;
 
 	int a,b,c;
-	double t,e,u;
+	double e;
 	double help;
 	t_3dvec p;
-	int count;
 
-	t_lj_params lj;
+	/*
+	 *  moldyn init
+	 *
+	 * - parsing argv
+	 * - log init
+	 * - random init
+	 *
+	 */
+	a=moldyn_init(&md,argc,argv);
+	if(a<0) return a;
 
-	char fb[32]="saves/fcc_test";
+	/*
+	 * the following overrides possibly set interaction methods by argv !!
+	 */
 
-	/* init */
+	/* params */
+	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;
+	/* assignement */
+	md.potential_force_function=lennard_jones;
+	//md.potential_force_function=harmonic_oscillator;
+	md.pot_params=&lj;
+	//md.pot_params=&ho;
+	/* cutoff radius */
+	md.cutoff=R_CUTOFF*LC_SI;
 
-	rand_init(&random,NULL,1);
-	random.status|=RAND_STAT_VERBOSE;
+	/*
+	 * testing random numbers
+	 */
 
-	/* testing random numbers */
-	//for(a=0;a<1000000;a++)
-	//	printf("%f %f\n",rand_get_gauss(&random),
-	//	                 rand_get_gauss(&random));
+#ifdef DEBUG_RANDOM_NUMBER
+	for(a=0;a<1000000;a++)
+		printf("%f %f\n",rand_get_gauss(&(md.random)),
+		                 rand_get_gauss(&(md.random)));
+	return 0;
+#endif
 
-	visual_init(&vis,fb);
+	/*
+	 * geometry & particles
+	 */
 
+	/* simulation cell volume in lattice constants */
 	a=LEN_X;
 	b=LEN_Y;
 	c=LEN_Z;
+	md.dim.x=a*LC_SI;
+	md.dim.y=b*LC_SI;
+	md.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);
-
-	printf("setting thermal fluctuations\n");
-	thermal_init(si,&random,count,t);
+	/* (un)set to (not) get visualized 'bounding atoms' */
+	md.vis.dim.x=a*LC_SI;
+	md.vis.dim.y=b*LC_SI;
+	md.vis.dim.z=c*LC_SI;
 
-	/* visualize */
+	/*
+	 * particles
+	 */
 
-	visual_atoms(&vis,0.0,si,count);
+	/* lattice init */
+
+#ifndef SIMPLE_TESTING
+	md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&(md.atom));
+	printf("created silicon lattice (#atoms = %d)\n",md.count);
+#else
+	md.count=2;
+	md.atom=malloc(md.count*sizeof(t_atom));
+	md.atom[0].r.x=0.23*sqrt(3.0)*LC_SI/2.0;
+	md.atom[0].r.y=0;
+	md.atom[0].r.z=0;
+	md.atom[0].element=SI;
+	md.atom[0].mass=M_SI;
+	md.atom[1].r.x=-md.atom[0].r.x;
+	md.atom[1].r.y=0;
+	md.atom[1].r.z=0;
+	md.atom[1].element=SI;
+	md.atom[1].mass=M_SI;
+
+	//md.atom[2].r.x=0.5*(a-1)*LC_SI;
+	//md.atom[2].r.y=0.5*(b-1)*LC_SI;
+	//md.atom[2].r.z=0;
+	//md.atom[2].element=C;
+	//md.atom[2].mass=M_C;
+
+	//md.atom[3].r.x=0.5*(a-1)*LC_SI;
+	//md.atom[3].r.y=0;
+	//md.atom[3].r.z=0;
+	//md.atom[3].element=SI;
+	//md.atom[3].mass=M_SI;
+#endif
+
+	/* initial thermal fluctuations of particles */
+
+#ifndef SIMPLE_TESTING
+	printf("setting thermal fluctuations (T=%f K)\n",md.t);
+	thermal_init(&md);
+#else
+	for(a=0;a<md.count;a++) v3_zero(&(md.atom[0].v));
+	md.atom[2].v.x=-320;
+	md.atom[2].v.y=-320;
+#endif
 
 	/* 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);
+	e=get_e_kin(md.atom,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,count);
-	printf("total momentum: %f\n",v3_norm(&p));
-
-	/* check potential energy */
-	md.count=count;
-	md.atom=si;
-	md.potential=potential_lennard_jones;
-	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));
+	p=get_total_p(md.atom,md.count);
+	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
-	md.dim.x=a*LC_SI;
-	md.dim.y=b*LC_SI;
-	md.dim.z=c*LC_SI;
+	/* check time step */
+	printf("estimated accurate time step: %.30f [s]\n",
+	       estimate_time_step(&md,3.0,md.t));
 
 	/*
 	 * let's do the actual md algorithm now
@@ -101,139 +153,17 @@ int main(int argc,char **argv) {
 	 * integration of newtons equations
 	 */
 
-	/* close */
-
-	visual_tini(&vis);
-
-	rand_close(&random);
-	
+	moldyn_integrate(&md);
 
-	//printf("starting velocity verlet: ");
-	//fflush(stdout);
+	printf("total energy (after integration): %.40f [J]\n",
+	       get_total_energy(&md));
 
-	//for(runs=0;runs<RUNS;runs++) {
+	/* close */
 
-	/* 
-	 * 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);
-//
+	link_cell_shutdown(&md);
 
+	moldyn_shutdown(&md);
+	
 	return 0;
 }