bc check probs

diff --git a/moldyn.c b/moldyn.c
index 1f6391fdaa23a1a03c424f7b9f4da2c113b8620c..4ddc42e98eb8bf1e6d2fa735ad4fd614de5f5f9b 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -781,12 +781,15 @@ int velocity_verlet(t_moldyn *moldyn) {
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
                v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
+//if(i==0) printf("und dann %.20f\n",atom[i].r.x*1e10);
                check_per_bound(moldyn,&(atom[i].r));
+//if(i==0) printf("und danach %.20f\n",atom[i].r.x);
 
                /* velocities */
                v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
                v3_add(&(atom[i].v),&(atom[i].v),&delta);
        }
+moldyn_bc_check(moldyn);
 
        /* neighbour list update */
        link_cell_update(moldyn);
@@ -1189,7 +1192,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
        f_r=A*exp(-lambda*d_ij);
-       df_r=-lambda*f_r/d_ij;
+       df_r=lambda*f_r/d_ij;
 
        /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
        exchange->f_a=-B*exp(-mu*d_ij);
@@ -1289,6 +1292,7 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                moldyn->debug++;                /* just for debugging ... */
                db=0.0;
                b=chi;
+               v3_scale(&force,dist_ij,df_a*b*f_c);
        }
        else {
                tmp=betaini*pow(zeta,ni-1.0);           /* beta^n * zeta^n-1 */
@@ -1300,13 +1304,13 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                v3_scale(&temp,dist_ij,df_a*b);
                v3_add(&force,&force,&temp);
                v3_scale(&force,&force,f_c);
-               v3_scale(&temp,dist_ij,df_c*b*f_a);
-               v3_add(&force,&force,&temp);
-               v3_scale(&force,&force,-0.5);
-
-               /* add force */
-               v3_add(&(ai->f),&(ai->f),&force);
        }
+       v3_scale(&temp,dist_ij,df_c*b*f_a);
+       v3_add(&force,&force,&temp);
+       v3_scale(&force,&force,-0.5);
+
+       /* add force */
+       v3_add(&(ai->f),&(ai->f),&force);
 
        /* add energy of 3bp sum */
        moldyn->energy+=(0.5*f_c*b*f_a);
@@ -1314,8 +1318,9 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        /* dVji */
        zeta=exchange->zeta_ji;
        if(zeta==0.0) {
-               // do nothing ... (db=0, b=chi)
                moldyn->debug++;
+               b=chi;
+               v3_scale(&force,dist_ij,df_a*b*f_c);
        }
        else {
                tmp=betajnj*pow(zeta,nj-1.0);           /* beta^n * zeta^n-1 */
@@ -1327,13 +1332,13 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                v3_scale(&temp,dist_ij,df_a*b);
                v3_add(&force,&force,&temp);
                v3_scale(&force,&force,f_c);
-               v3_scale(&temp,dist_ij,0.5*df_c*b*f_a);
-               v3_add(&force,&force,&temp);
-               v3_scale(&force,&force,-0.5);
-
-               /* add force */
-               v3_sub(&(ai->f),&(ai->f),&force);
        }
+       v3_scale(&temp,dist_ij,df_c*b*f_a);
+       v3_add(&force,&force,&temp);
+       v3_scale(&force,&force,-0.5);
+
+       /* add force */
+       v3_sub(&(ai->f),&(ai->f),&force);
 
        return 0;
 }
@@ -1596,3 +1601,32 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
        return 0;
 }
 
+
+/*
+ * debugging / critical check functions
+ */
+
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+       t_atom *atom;
+       t_3dvec *dim;
+       int i;
+
+       atom=moldyn->atom;
+       dim=&(moldyn->dim);
+
+       for(i=0;i<moldyn->count;i++) {
+               if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2)
+                       printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+                              i,atom[i].r.x*1e10,dim->x/2*1e10);
+               if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+                       printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+                              i,atom[i].r.y*1e10,dim->y/2*1e10);
+               if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+                       printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+                              i,atom[i].r.z*1e10,dim->z/2*1e10);
+       }
+
+       return 0;
+}
+

diff --git a/moldyn.h b/moldyn.h
index d62ec47c6fa26841e9e6b1be9cb620badef7679e..534287bd0e615d9e54bfd325f6fd6292ae13d40d 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -388,4 +388,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
 
+int moldyn_bc_check(t_moldyn *moldyn);
+
 #endif

diff --git a/sic.c b/sic.c
index cbb81a3b5fe5d9311c699c304c34eecc69c1936c..0d3b79802010a03284162f6a0ffb4c1c678c8076 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -108,20 +108,19 @@ int main(int argc,char **argv) {
 
        /* 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,
-         //             //ATOM_ATTR_2BP|ATOM_ATTR_HB,
-          //            0,5,5,5);
+       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=-0.55*0.25*sqrt(3.0)*LC_SI; 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=+0.55*0.25*sqrt(3.0)*LC_SI; 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=-0.55*0.25*sqrt(3.0)*LC_SI;       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=+0.55*0.25*sqrt(3.0)*LC_SI;       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 ! */
@@ -141,12 +140,12 @@ int main(int argc,char **argv) {
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,1000,1.0e-15);
+       moldyn_add_schedule(&md,100,1.0e-15);
 
        /* activate logging */
        printf("[sic] activate logging\n");
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",10);
-       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",10);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
+       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
 
        /*
         * let's do the actual md algorithm now