X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=db9185911137ca3862f77fb5135fa83c9ec029d4;hb=150c5f804a5088a01ef2bb1e934b5e65d10ac23e;hp=5aa6d87bb4490ad4585d9a196ec6b4d3867fc511;hpb=c0a8b254109929fba10795e644187c51742108a8;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 5aa6d87..db91859 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -519,7 +519,8 @@ int scale_volume(t_moldyn *moldyn) {
 
 	t_atom *atom;
 	t_3dvec *dim,*vdim;
-	double virial,scale;
+	double scale,v;
+	t_virial virial;
 	t_linkcell *lc;
 	int i;
 
@@ -528,12 +529,23 @@ int scale_volume(t_moldyn *moldyn) {
 	vdim=&(moldyn->vis.dim);
 	lc=&(moldyn->lc);
 
-	for(i=0;i<moldyn->count;i++)
-		virial+=v3_norm(&(atom[i].virial));
+	memset(&virial,0,sizeof(t_virial));
+
+	for(i=0;i<moldyn->count;i++) {
+		virial.xx+=atom[i].virial.xx;
+		virial.yy+=atom[i].virial.yy;
+		virial.zz+=atom[i].virial.zz;
+		virial.xy+=atom[i].virial.xy;
+		virial.xz+=atom[i].virial.xz;
+		virial.yz+=atom[i].virial.yz;
+	}
+
+	/* just a guess so far ... */
+	v=sqrt(virial.xx*virial.xx+virial.yy*virial.yy+virial.zz+virial.zz);
 
-printf("%f\n",virial);
+printf("%f\n",v);
 	/* get pressure from virial */
-	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*v;
 	moldyn->p/=moldyn->volume;
 printf("%f\n",moldyn->p/(ATM));
 
@@ -984,6 +996,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,j,k,count;
 	t_atom *itom,*jtom,*ktom;
+	t_virial *virial;
 	t_linkcell *lc;
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
@@ -1005,7 +1018,13 @@ int potential_force_calc(t_moldyn *moldyn) {
 		v3_zero(&(itom[i].f));
 
 		/* reset viral of atom i */
-		v3_zero(&(itom[i].virial));
+		virial=&(itom[i].virial);
+		virial->xx=0.0;
+		virial->yy=0.0;
+		virial->zz=0.0;
+		virial->xy=0.0;
+		virial->xz=0.0;
+		virial->yz=0.0;
 
 		/* reset site energy */
 		itom[i].e=0.0;
@@ -1224,7 +1243,10 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
 
 	printf("[moldyn] tersoff parameter completion\n");
+	p->S2[0]=p->S[0]*p->S[0];
+	p->S2[1]=p->S[1]*p->S[1];
 	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	p->S2mixed=p->Smixed*p->Smixed;
 	p->Rmixed=sqrt(p->R[0]*p->R[1]);
 	p->Amixed=sqrt(p->A[0]*p->A[1]);
 	p->Bmixed=sqrt(p->B[0]*p->B[1]);
@@ -1285,8 +1307,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	t_tersoff_mult_params *params;
 	t_tersoff_exchange *exchange;
 	t_3dvec dist_ij,force;
-	double d_ij;
-	double A,B,R,S,lambda,mu;
+	double d_ij,d_ij2;
+	double A,B,R,S,S2,lambda,mu;
 	double f_r,df_r;
 	double f_c,df_c;
 	int brand;
@@ -1317,18 +1339,10 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	 *
 	 */
 
-	/* dist_ij, d_ij */
-	v3_sub(&dist_ij,&(aj->r),&(ai->r));
-	if(bc) check_per_bound(moldyn,&dist_ij);
-	d_ij=v3_norm(&dist_ij);
-
-	/* save for use in 3bp */
-	exchange->d_ij=d_ij;
-	exchange->dist_ij=dist_ij;
-
 	/* constants */
 	if(brand==ai->brand) {
 		S=params->S[brand];
+		S2=params->S2[brand];
 		R=params->R[brand];
 		A=params->A[brand];
 		B=params->B[brand];
@@ -1338,6 +1352,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	}
 	else {
 		S=params->Smixed;
+		S2=params->S2mixed;
 		R=params->Rmixed;
 		A=params->Amixed;
 		B=params->Bmixed;
@@ -1346,10 +1361,23 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		params->exchange.chi=params->chi;
 	}
 
-	/* if d_ij > S => no force & potential energy contribution */
-	if(d_ij>S)
+	/* dist_ij, d_ij */
+	v3_sub(&dist_ij,&(aj->r),&(ai->r));
+	if(bc) check_per_bound(moldyn,&dist_ij);
+	d_ij2=v3_absolute_square(&dist_ij);
+
+	/* if d_ij2 > S2 => no force & potential energy contribution */
+	if(d_ij2>S2)
 		return 0;
 
+	/* now we will need the distance */
+	//d_ij=v3_norm(&dist_ij);
+	d_ij=sqrt(d_ij2);
+
+	/* save for use in 3bp */
+	exchange->d_ij=d_ij;
+	exchange->dist_ij=dist_ij;
+
 	/* more constants */
 	exchange->beta_j=&(params->beta[brand]);
 	exchange->n_j=&(params->n[brand]);
@@ -1389,7 +1417,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		s_r=S-R;
 		arg=M_PI*(d_ij-R)/s_r;
 		f_c=0.5+0.5*cos(arg);
-		//df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));	/* MARK! */
 		df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
 		/* two body contribution (ij, ji) */
 		v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
@@ -1685,7 +1712,6 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			s_r=S-R;
 			arg=M_PI*(d_ik-R)/s_r;
 			f_c_ik=0.5+0.5*cos(arg);
-			//df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
 			df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 
 			/* zeta_ij */