From ff1bf111f517d9fa69903cd56181c1e9e38665ff Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Tue, 12 Dec 2006 14:28:10 +0000
Subject: [PATCH] fixed 2bp, todo: adjust create lattice, then go for 3bp

---
 moldyn.c | 14 +++++++++++---
 sic.c    | 28 ++++++++++++++++------------
 2 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index 7ea5d50..aaab0de 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -99,6 +99,12 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
+	printf("[moldyn] dimensions in A:\n");
+	printf("  x: %f\n",moldyn->dim.x);
+	printf("  y: %f\n",moldyn->dim.y);
+	printf("  z: %f\n",moldyn->dim.z);
+	printf("  visualize simulation box: %s\n",visualize?"on":"off");
+
 	return 0;
 }
 
@@ -802,6 +808,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
+moldyn_bc_check(moldyn);
 	/* neighbour list update */
 	link_cell_update(moldyn);
 
@@ -885,11 +892,12 @@ int potential_force_calc(t_moldyn *moldyn) {
 					continue;
 
 				if((jtom->attr&ATOM_ATTR_2BP)&
-				   (itom[i].attr&ATOM_ATTR_2BP))
+				   (itom[i].attr&ATOM_ATTR_2BP)) {
 					moldyn->func2b(moldyn,
 					               &(itom[i]),
 					               jtom,
 					               bc_ij);
+				}
 
 				/* 3 body potential/force */
 
@@ -1212,7 +1220,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	/* f_a, df_a calc (again, same for ij and ji) | save for later use! */
 	exchange->f_a=-B*exp(-mu*d_ij);
-	exchange->df_a=-mu*exchange->f_a/d_ij;
+	exchange->df_a=mu*exchange->f_a/d_ij;
 
 	/* f_c, df_c calc (again, same for ij and ji) */
 	if(d_ij<R) {
@@ -1354,7 +1362,7 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	v3_scale(&force,&force,-0.5);
 
 	/* add force */
-	v3_sub(&(ai->f),&(ai->f),&force);
+	v3_add(&(ai->f),&(ai->f),&force);
 
 	return 0;
 }
diff --git a/sic.c b/sic.c
index 1e29a85..5edb699 100644
--- a/sic.c
+++ b/sic.c
@@ -107,20 +107,24 @@ int main(int argc,char **argv) {
 	set_pbc(&md,TRUE,TRUE,TRUE);
 
 	/* create the lattice / place atoms */
-	//printf("[sic] creating atoms\n");
-	//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-	//               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
-	//               0,5,5,5);
+	printf("[sic] creating atoms\n");
+	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	               0,5,5,5);
 
 	/* testing configuration */
-	r.x=2.7/2;	v.x=0;
-	r.y=0;		v.y=0;
-	r.z=0;		v.z=0;
-	add_atom(&md,SI,M_SI,0,ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,&r,&v);
-	r.x=-2.7/2;	v.x=0;
-	r.y=0;		v.y=0;
-	r.z=0;		v.z=0;
-	add_atom(&md,SI,M_SI,0,ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,&r,&v);
+	//r.x=2.45/2;	v.x=0;
+	//r.y=0;		v.y=0;
+	//r.z=0;		v.z=0;
+	//add_atom(&md,SI,M_SI,0,
+	//           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	//           &r,&v);
+	//r.x=-2.45/2;	v.x=0;
+	//r.y=0;		v.y=0;
+	//r.z=0;		v.z=0;
+	//add_atom(&md,SI,M_SI,0,
+	//           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	//           &r,&v);
 
 	/* setting a nearest neighbour distance for the moldyn checks */
 	set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
-- 
2.20.1