put repulsive part to 3bp/j2 function

diff --git a/moldyn.c b/moldyn.c
index 4d73617..705a28c 100644 (file)
--- 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 (file)
--- 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 - tersoff_mult_2bp is obsolete.\n");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 (file)
--- 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);