X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=posic.c;h=236e208bcce0bea5516bbe1a70d5efe1decda416;hb=c1a1e7ec0bdad968f7dbf80329740ec8843e3477;hp=8bbfe0e39fa869bb5cdf7de287d851456374dcb9;hpb=bdb198c5a5fe38361d10f98e7db366b0915e56fb;p=physik%2Fposic.git

diff --git a/posic.c b/posic.c
index 8bbfe0e..236e208 100644
--- a/posic.c
+++ b/posic.c
@@ -22,10 +22,9 @@ int main(int argc,char **argv) {
 	t_random random;
 
 	int a,b,c;
-	double e,u;
+	double e;
 	double help;
 	t_3dvec p;
-	int count;
 
 	t_lj_params lj;
 	t_ho_params ho;
@@ -53,12 +52,12 @@ int main(int argc,char **argv) {
 	vis.dim.y=b*LC_SI;
 	vis.dim.z=c*LC_SI;
 
-	/* init lattice */
+	/* 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;
+	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;
@@ -70,40 +69,38 @@ int main(int argc,char **argv) {
 	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.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.integrate=velocity_verlet;
-	//md.time_steps=RUNS;
-	//md.tau=TAU;
 	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,count);
-	//for(a=0;a<count;a++) v3_zero(&(si[0].v));
+	// thermal_init(&md,&random);
+	for(a=0;a<md.count;a++) v3_zero(&(si[0].v));
 
 	/* check kinetic energy */
 
-	e=get_e_kin(si,count);
+	e=get_e_kin(si,md.count);
 	printf("kinetic energy: %.40f [J]\n",e);
-	printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*md.t);
+	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);
+	p=get_total_p(si,md.count);
 	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
-	/* check potential energy */
+	/* potential paramters */
 	lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
 	help=lj.sigma6*lj.sigma6;
 	lj.sigma6*=help;
@@ -113,20 +110,9 @@ int main(int argc,char **argv) {
 	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
 	ho.spring_constant=1.0;
 
-	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
 	 *
@@ -140,6 +126,8 @@ int main(int argc,char **argv) {
 
 	/* close */
 
+	link_cell_shutdown(&md);
+
 	rand_close(&random);
 
 	moldyn_shutdown(&md);