From: hackbard <hackbard>
Date: Thu, 3 May 2007 16:40:02 +0000 (+0000)
Subject: put repulsive part to 3bp/j2 function
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=57847266c05bc38218bf162efdb08e8dd40894d7;p=physik%2Fposic.git

put repulsive part to 3bp/j2 function
---

diff --git a/moldyn.c b/moldyn.c
index 4d73617..705a28c 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1711,7 +1711,7 @@ int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
 }
 
 /*
- * periodic boundayr checking
+ * periodic boundary checking
  */
 
 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
diff --git a/potentials/tersoff.c b/potentials/tersoff.c
index b6533e1..a4a87e3 100644
--- a/potentials/tersoff.c
+++ b/potentials/tersoff.c
@@ -94,6 +94,9 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	double s_r;
 	double arg;
 
+	printf("WARNING! - tersoff_mult_2bp is obsolete.\n");
+	printf("WARNING! - repulsive part handled in 3bp/j2 routine.\n");
+
 	/* use newtons third law */
 	if(ai<aj) return 0;
 
@@ -167,14 +170,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 #endif
 
 	/* virial */
-	//virial_calc(ai,&force,&dist_ij);
-	//virial_calc(aj,&force,&dist_ij);
-	//ai->virial.xx-=force.x*dist_ij.x;
-	//ai->virial.yy-=force.y*dist_ij.y;
-	//ai->virial.zz-=force.z*dist_ij.z;
-	//ai->virial.xy-=force.x*dist_ij.y;
-	//ai->virial.xz-=force.x*dist_ij.z;
-	//ai->virial.yz-=force.y*dist_ij.z;
+	virial_calc(ai,&force,&dist_ij);
 
 	/* energy 2bp contribution */
 	moldyn->energy+=f_r*f_c;
@@ -336,7 +332,10 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	t_tersoff_exchange *exchange;
 	t_3dvec force;
 	double f_a,df_a,b,db,f_c,df_c;
+	double f_r,df_r;
+	double scale;
 	double mu,B,chi;
+	double lambda,A;
 	double d_ij;
 	unsigned char brand;
 	double ni,tmp;
@@ -350,14 +349,18 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		S=params->S[brand];
 		R=params->R[brand];
 		B=params->B[brand];
+		A=params->A[brand];
 		mu=params->mu[brand];
+		lambda=params->lambda[brand];
 		chi=1.0;
 	}
 	else {
 		S=params->Smixed;
 		R=params->Rmixed;
 		B=params->Bmixed;
+		A=params->Amixed;
 		mu=params->mu_m;
+		lambda=params->lambda_m;
 		chi=params->chi;
 	}
 
@@ -379,6 +382,10 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	f_a=-B*exp(-mu*d_ij);
 	df_a=mu*f_a/d_ij;
 
+	/* f_r, df_r */
+	f_r=A*exp(-lambda*d_ij);
+	df_r=lambda*f_r/d_ij;
+
 	/* b, db */
 	if(exchange->zeta_ij==0.0) {
 		b=chi;
@@ -394,8 +401,8 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	}
 
 	/* force contribution */
-	v3_scale(&force,&(exchange->dist_ij),df_a*f_c+f_a*df_c);
-	v3_scale(&force,&force,-0.5*b);
+	scale=-0.5*(f_c*(df_r+b*df_a)+df_c*(f_r+b*df_a));
+	v3_scale(&force,&(exchange->dist_ij),scale);
 	v3_add(&(ai->f),&(ai->f),&force);
 	v3_sub(&(aj->f),&(aj->f),&force); // dri rij = - drj rij
 
@@ -411,14 +418,13 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 #endif
 
 	/* virial */
-	//virial_calc(ai,&force,&(exchange->dist_ij));
-	//virial_calc(aj,&force,&(exchange->dist_ij));
+	virial_calc(ai,&force,&(exchange->dist_ij));
 
 	/* dzeta prefactor = - 0.5 f_c f_a db */
 	exchange->pre_dzeta=-0.5*f_a*f_c*db;
 
 	/* energy contribution */
-	moldyn->energy+=0.5*f_c*b*f_a;
+	moldyn->energy+=0.5*f_c*(b*f_a+f_r);
 
 	/* reset k counter for second k loop */
 	exchange->kcount=0;
@@ -537,10 +543,11 @@ int tersoff_mult_3bp_k2(t_moldyn *moldyn,
 #endif
 
 	/* virial */
-	//virial_calc(aj,&force,&dist_ij);
+	//v3_scale(&force,&force,-1.0);
+	virial_calc(ai,&force,&dist_ij);
 
 	/* derivative wrt k */
-	v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rij = - drj rij
+	v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik
 	v3_scale(&tmp,&dcosdrk,fcdg);
 	v3_add(&force,&force,&tmp);
 	v3_scale(&force,&force,pre_dzeta);
@@ -557,7 +564,8 @@ int tersoff_mult_3bp_k2(t_moldyn *moldyn,
 #endif
 
 	/* virial */
-	virial_calc(ak,&force,&dist_ik);
+	//v3_scale(&force,&force,-1.0);
+	virial_calc(ai,&force,&dist_ik);
 	
 	/* increase k counter */
 	exchange->kcount++;	
diff --git a/sic.c b/sic.c
index 714710b..2221025 100644
--- a/sic.c
+++ b/sic.c
@@ -97,7 +97,7 @@ int main(int argc,char **argv) {
 
 	/* choose potential */
 	set_potential1b(&md,tersoff_mult_1bp);
-	set_potential2b(&md,tersoff_mult_2bp);
+	//set_potential2b(&md,tersoff_mult_2bp);
 	//set_potential3b_j1(&md,tersoff_mult_2bp);
 	//set_potential3b_k1(&md,tersoff_mult_3bp);
 	//set_potential3b_j3(&md,tersoff_mult_post_2bp);