X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=d715c52a11f91aa9f43244b014c281f3c2a00cc4;hb=fe84cdc3fc897581636aff89b6f4fd12db1d2718;hp=15dcedef5fd105b05ce69e2c9d49ad5a8c4c353e;hpb=f0e4c6422ec1aff0cf86597fef919335bba75c1b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 15dcede..d715c52 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -55,6 +55,11 @@ pthread_mutex_t *amutex;
 pthread_mutex_t emutex;
 #endif
 
+/* fully constrained relaxation technique - global pointers */
+u8 crtt;
+u8 *constraints;
+double *trafo_angle;
+
 /*
  * the moldyn functions
  */
@@ -78,10 +83,6 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 	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;
 }
 
@@ -2256,6 +2257,43 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
 	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) {
@@ -2270,33 +2308,34 @@ 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) {
+			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]);
 		}
-#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));
@@ -2323,16 +2362,25 @@ int velocity_verlet(t_moldyn *moldyn) {
 	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) {
+			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]);
+		}
+
 		/* 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);
@@ -3197,6 +3245,57 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
 	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;