X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=posic.c;h=5ff3bc1b7f03a6378bb549009e7c8db9e9806256;hb=45b27e01673a6cc5bebecb49c51d7f587917483e;hp=6d1256fbf6513d40b0ce32146c60b3a7bc5d9ed9;hpb=706aed2512544b99ff34308fdb673b19ee884ce0;p=physik%2Fposic.git

diff --git a/posic.c b/posic.c
index 6d1256f..5ff3bc1 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"
@@ -14,29 +16,138 @@
 
 int main(int argc,char **argv) {
 
-	t_atom *si;
-	int a,b,c;
+	t_moldyn md;
 
-	char fb[32]="saves/fcc_test";
+	t_atom *si;
 
 	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 */
+
+	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;
-	
-	visual_init(&vis,fb);
 
-	/* init */
-	printf("placing silicon atoms\n");
-	count=create_lattice(FCC,Si,M_SI,LC_SI,a,b,c,&si);
+	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;
 
-	visual_atoms(&vis,0.0,si,count);
+	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);