From: hackbard <hackbard>
Date: Wed, 7 Mar 2007 16:23:21 +0000 (+0000)
Subject: tersoff MAYBE fixed now!
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=e25ff194682ff5fac86c60701343103e74973bed;p=physik%2Fposic.git

tersoff MAYBE fixed now!
---

diff --git a/moldyn.c b/moldyn.c
index dae975c..ca6f84a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -162,28 +162,28 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 	return 0;
 }
 
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
 
 	moldyn->func1b=func;
 
 	return 0;
 }
 
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 
 	moldyn->func2b=func;
 
 	return 0;
 }
 
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
 
 	moldyn->func2b_post=func;
 
 	return 0;
 }
 
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
 
 	moldyn->func3b=func;
 
diff --git a/moldyn.h b/moldyn.h
index 1300998..b140372 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -230,9 +230,9 @@ typedef struct s_moldyn {
 #define LC_SI			(0.543105e-9*METER)		/* A */
 #define M_SI			28.08553			/* amu */
 
-//#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
+#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
 //#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
-#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)			/* A */
+//#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)			/* A */
 #define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
 
 #define TM_R_SI			(2.7e-10*METER)			/* A */
@@ -292,10 +292,11 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
 int set_nn_dist(t_moldyn *moldyn,double dist);
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params);
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func);
+int set_potential2b(t_moldyn *moldyn,pf_func2b func);
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func);
+int set_potential3b(t_moldyn *moldyn,pf_func3b func);
+int set_potential_params(t_moldyn *moldyn,void *params);
 
 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
diff --git a/potentials/lennard_jones.c b/potentials/lennard_jones.c
index 1738ea5..1277c46 100644
--- a/potentials/lennard_jones.c
+++ b/potentials/lennard_jones.c
@@ -35,10 +35,11 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&distance);
-	d=v3_absolute_square(&distance);	/* 1/r^2 */
+	d=v3_absolute_square(&distance);	/* r^2 */
 	if(d<=moldyn->cutoff_square) {
 		d=1.0/d; 			/* 1/r^2 */
 		h2=d*d;				/* 1/r^4 */
+		h2*=d;				/* 1/r^6 */
 		h1=h2*h2;			/* 1/r^12 */
 		moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
 		h2*=d;				/* 1/r^8 */
diff --git a/potentials/tersoff.c b/potentials/tersoff.c
index 972075d..01364ea 100644
--- a/potentials/tersoff.c
+++ b/potentials/tersoff.c
@@ -95,6 +95,9 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	double s_r;
 	double arg;
 
+	/* use newtons third law */
+	//if(ai<aj) return 0;
+
 	params=moldyn->pot_params;
 	brand=aj->brand;
 	exchange=&(params->exchange);
@@ -119,27 +122,11 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	 *
 	 */
 
-	/* constants */
-	if(brand==ai->brand) {
-		S=params->S[brand];
+	/* determine cutoff square */
+	if(brand==ai->brand)
 		S2=params->S2[brand];
-		R=params->R[brand];
-		A=params->A[brand];
-		B=params->B[brand];
-		lambda=params->lambda[brand];
-		mu=params->mu[brand];
-		exchange->chi=1.0;
-	}
-	else {
-		S=params->Smixed;
+	else
 		S2=params->S2mixed;
-		R=params->Rmixed;
-		A=params->Amixed;
-		B=params->Bmixed;
-		lambda=params->lambda_m;
-		mu=params->mu_m;
-		params->exchange.chi=params->chi;
-	}
 
 	/* dist_ij, d_ij */
 	v3_sub(&dist_ij,&(aj->r),&(ai->r));
@@ -166,12 +153,26 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	exchange->d_j=&(params->d[brand]);
 	exchange->h_j=&(params->h[brand]);
 	if(brand==ai->brand) {
+		S=params->S[brand];
+		R=params->R[brand];
+		A=params->A[brand];
+		B=params->B[brand];
+		lambda=params->lambda[brand];
+		mu=params->mu[brand];
+		exchange->chi=1.0;
 		exchange->betajnj=exchange->betaini;
 		exchange->cj2=exchange->ci2;
 		exchange->dj2=exchange->di2;
 		exchange->cj2dj2=exchange->ci2di2;
 	}
 	else {
+		S=params->Smixed;
+		R=params->Rmixed;
+		A=params->Amixed;
+		B=params->Bmixed;
+		lambda=params->lambda_m;
+		mu=params->mu_m;
+		params->exchange.chi=params->chi;
 		exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
 		exchange->cj2=params->c[brand]*params->c[brand];
 		exchange->dj2=params->d[brand]*params->d[brand];
diff --git a/sic.c b/sic.c
index e148709..167735f 100644
--- a/sic.c
+++ b/sic.c
@@ -51,6 +51,8 @@ int main(int argc,char **argv) {
 
 	/* testing location & velocity vector */
 	t_3dvec r,v;
+	memset(&r,0,sizeof(t_3dvec));
+	memset(&v,0,sizeof(t_3dvec));
 
 	/* initialize moldyn */
 	moldyn_init(&md,argc,argv);
@@ -59,17 +61,20 @@ int main(int argc,char **argv) {
 	set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 
 	/* choose potential */
-	//set_potential1b(&md,tersoff_mult_1bp,&tp);
-	//set_potential2b(&md,tersoff_mult_2bp,&tp);
-	//set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
-	//set_potential3b(&md,tersoff_mult_3bp,&tp);
-	set_potential2b(&md,lennard_jones,&lj);
-	//set_potential2b(&md,harmonic_oscillator,&ho);
+	set_potential1b(&md,tersoff_mult_1bp);
+	set_potential2b(&md,tersoff_mult_2bp);
+	set_potential2b_post(&md,tersoff_mult_post_2bp);
+	set_potential3b(&md,tersoff_mult_3bp);
+	//set_potential2b(&md,lennard_jones);
+	//set_potential2b(&md,harmonic_oscillator);
+	set_potential_params(&md,&tp);
+	//set_potential_params(&md,&lj);
+	//set_potential_params(&md,&ho);
 
 	/* cutoff radius */
-	//set_cutoff(&md,TM_S_SI);
-	//set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
-	set_cutoff(&md,2.0*LC_SI);
+	set_cutoff(&md,TM_S_SI);
+	//set_cutoff(&md,LC_SI*sqrt(3.0));
+	//set_cutoff(&md,2.0*LC_SI);
 
 	/*
 	 * potential parameters
@@ -83,8 +88,8 @@ int main(int argc,char **argv) {
 	lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 
 	/* harmonic oscillator */
-	//ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-	ho.equilibrium_distance=LC_SI;
+	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+	//ho.equilibrium_distance=LC_SI;
 	ho.spring_constant=LJ_EPSILON_SI;
 
 	/*
@@ -126,16 +131,16 @@ int main(int argc,char **argv) {
 
 	/* create the lattice / place atoms */
 	//create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
-	create_lattice(&md,FCC,LC_SI,SI,M_SI,
-	//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-	//               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
-	               ATOM_ATTR_2BP|ATOM_ATTR_HB,
+	//create_lattice(&md,FCC,LC_SI,SI,M_SI,
+	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	//               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 	               0,6,6,6);
 	moldyn_bc_check(&md);
 
 	/* testing configuration */
-	//r.x=0.28*sqrt(3)*LC_SI/2;	v.x=0;
-	//r.x=1.75*LC_SI;	v.x=-0.01;
+	//r.x=0.27*sqrt(3.0)*LC_SI/2.0;	v.x=0;
+	//r.x=(TM_S_SI+TM_R_SI)/4.0;	v.x=0;
 	//r.y=0;		v.y=0;
 	//r.z=0;		v.z=0;
 	//add_atom(&md,SI,M_SI,0,
@@ -149,6 +154,13 @@ int main(int argc,char **argv) {
 	//           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 	//           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 	//           &r,&v);
+	//r.x=0;		v.x=0;
+	//r.y=0;	v.y=0;
+	//r.z=sin(M_PI*60.0/180.0)*(TM_S_SI+TM_R_SI)/4.0;	v.z=0;
+	//add_atom(&md,SI,M_SI,0,
+	//           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	//           ATOM_ATTR_2BP|ATOM_ATTR_HB,
+	//           &r,&v);
 
 	/* set temperature & pressure */
 	set_temperature(&md,atof(argv[2])+273.0);
@@ -164,7 +176,7 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	moldyn_add_schedule(&md,101,1.0);
+	moldyn_add_schedule(&md,10001,1.0);
 	//moldyn_add_schedule(&md,501,1.0);
 	//moldyn_add_schedule(&md,501,1.0);
 
@@ -175,7 +187,7 @@ int main(int argc,char **argv) {
 	moldyn_set_log_dir(&md,argv[1]);
 	moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 	moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
-	moldyn_set_log(&md,VISUAL_STEP,1);
+	moldyn_set_log(&md,VISUAL_STEP,100);
 	moldyn_set_log(&md,CREATE_REPORT,0);
 
 	/*