pthread_mutex_t emutex;
#endif
+/* fully constrained relaxation technique - global pointers */
+u8 crtt;
+u8 *constraints;
+double *trafo_angle;
+
/*
* the moldyn functions
*/
pthread_mutex_init(&emutex,NULL);
#endif
-#ifdef CONSTRAINT_110_5832
- printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
- printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
-#endif
return 0;
}
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
- t_part_params *p_params,t_defect_params *d_params) {
+ t_part_params *p_params,t_defect_params *d_params,
+ t_offset_params *o_params) {
int new,count;
int ret;
switch(type) {
case CUBIC:
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
set_nn_dist(moldyn,lc);
ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
strcpy(name,"cubic");
case FCC:
if(!origin)
v3_scale(&orig,&orig,0.5);
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
strcpy(name,"fcc");
case DIAMOND:
if(!origin)
v3_scale(&orig,&orig,0.25);
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
strcpy(name,"diamond");
case DEFECT_STYPE_DB_Z:\
d_o.z=d_params->od;\
d_d.z=d_params->dd;\
-d_d.x=0.9;\
-d_d.y=0.9;\
break;\
case DEFECT_STYPE_DB_R:\
break;\
return 0;
}
+/* basis trafo */
+
+#define FORWARD 0
+#define BACKWARD 1
+
+int basis_trafo(t_3dvec *r,u8 dir,double z,double x) {
+
+ t_3dvec tmp;
+
+ if(dir==FORWARD) {
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(z)*tmp.x-sin(z)*tmp.y;
+ r->y=sin(z)*tmp.x+cos(z)*tmp.y;
+ }
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(x)*tmp.y-sin(x)*tmp.z;
+ r->z=sin(x)*tmp.y+cos(x)*tmp.z;
+ }
+ }
+ else {
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(-x)*tmp.y-sin(-x)*tmp.z;
+ r->z=sin(-x)*tmp.y+cos(-x)*tmp.z;
+ }
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(-z)*tmp.x-sin(-z)*tmp.y;
+ r->y=sin(-z)*tmp.x+cos(-z)*tmp.y;
+ }
+ }
+
+ return 0;
+}
+
/* velocity verlet */
int velocity_verlet(t_moldyn *moldyn) {
tau=moldyn->tau;
tau_square=moldyn->tau_square;
-#ifdef CONSTRAINT_110_5832
- if(count==5833) {
- atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
- atom[5832].f.y=-atom[5832].f.x;
- }
-#endif
for(i=0;i<count;i++) {
+
/* check whether fixed atom */
if(atom[i].attr&ATOM_ATTR_FP)
continue;
+
/* new positions */
h=0.5/atom[i].mass;
- v3_scale(&delta,&(atom[i].v),tau);
-#ifdef CONSTRAINT_110_5832
- if(i==5832) {
- delta.y=-delta.x;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
}
-#endif
+
#ifndef QUENCH
+ v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
#endif
v3_scale(&delta,&(atom[i].f),h*tau_square);
-#ifdef CONSTRAINT_110_5832
- if(i==5832) {
- delta.y=-delta.x;
- }
-#endif
v3_add(&(atom[i].r),&(atom[i].r),&delta);
//check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
check_per_bound(moldyn,&(atom[i].r));
albe_potential_force_calc(moldyn);
#endif
-#ifdef CONSTRAINT_110_5832
- if(count==5833) {
- atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
- atom[5832].f.y=-atom[5832].f.x;
- }
-#endif
for(i=0;i<count;i++) {
/* check whether fixed atom */
if(atom[i].attr&ATOM_ATTR_FP)
continue;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ }
+
/* again velocities [actually v(t+tau)] */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
return 0;
}
+int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ t_3dvec final_r;
+ double d2;
+ int a_cnt;
+ int b_cnt;
+
+ atom=moldyn->atom;
+ msd[0]=0;
+ msd[1]=0;
+ msd[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+ /* care for pb crossing */
+ if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+ printf("[moldyn] msd pb crossings for atom %d\n",i);
+ printf(" x: %d y: %d z: %d\n",
+ atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+ }
+ final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+ final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+ final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+ /* calculate distance */
+ v3_sub(&dist,&final_r,&(atom[i].r_0));
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ msd[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ msd[0]+=d2;
+ }
+
+ msd[2]+=d2;
+ }
+
+ msd[0]/=a_cnt;
+ msd[1]/=b_cnt;
+ msd[2]/=moldyn->count;
+
+ return 0;
+}
+
int bonding_analyze(t_moldyn *moldyn,double *cnt) {
return 0;