From b397d0e80a7191ae1f10a86e9a595dcb8668286e Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Tue, 7 Oct 2008 17:33:51 +0200
Subject: [PATCH] new imp of pthread approach

---
 potentials/albe_fast.c | 859 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 709 insertions(+), 150 deletions(-)

diff --git a/potentials/albe_fast.c b/potentials/albe_fast.c
index 05502c6..29c303b 100644
--- a/potentials/albe_fast.c
+++ b/potentials/albe_fast.c
@@ -29,13 +29,6 @@
 #include "../math/math.h"
 #include "albe.h"
 
-#ifdef PTHREADS
-typedef struct s_kdata {
-	t_moldyn *moldyn;
-	t_atom *itom,*jtom;
-} t_kdata;
-#endif
-
 /*
  * virial calculation
  */
@@ -47,115 +40,7 @@ typedef struct s_kdata {
 				a->virial.xz+=f->x*d->z; \
 				a->virial.yz+=f->y*d->z
 
-#if 0
-#ifdef PTHREADS
-void *k1_calc(void *ptr) {
-
-	/* albe 3 body potential function (first k loop) */
-	
-	t_albe_mult_params *params;
-	t_albe_exchange *exchange;
-	unsigned char brand_i;
-	double Rk,Sk,Sk2,gamma_i,c_i,d_i,h_i,ci2,di2,ci2di2;
-	t_atom *ai,*jtom,*ktom;
-	
-
-	if(kcount>ALBE_MAXN) {
-		printf("FATAL: neighbours = %d\n",kcount);
-		printf("  -> %d %d %d\n",ai->tag,jtom->tag,ktom->tag);
-	}
-
-	/* ik constants */
-	if(brand_i==ktom->brand) {
-		Rk=params->R[brand_i];
-		Sk=params->S[brand_i];
-		Sk2=params->S2[brand_i];
-		/* albe needs i,k depending c,d,h and gamma values */
-		gamma_i=params->gamma[brand_i];
-		c_i=params->c[brand_i];
-		d_i=params->d[brand_i];
-		h_i=params->h[brand_i];
-		ci2=params->c2[brand_i];
-		di2=params->d2[brand_i];
-		ci2di2=params->c2d2[brand_i];
-	}
-	else {
-		Rk=params->Rmixed;
-		Sk=params->Smixed;
-		Sk2=params->S2mixed;
-		/* albe needs i,k depending c,d,h and gamma values */
-		gamma_i=params->gamma_m;
-		c_i=params->c_mixed;
-		d_i=params->d_mixed;
-		h_i=params->h_mixed;
-		ci2=params->c2_mixed;
-		di2=params->d2_mixed;
-		ci2di2=params->c2d2_m;
-	}
-
-	/* dist_ik, d_ik2 */
-	v3_sub(&dist_ik,&(ktom->r),&(ai->r));
-	if(bc_ik) check_per_bound(moldyn,&dist_ik);
-	d_ik2=v3_absolute_square(&dist_ik);
-
-	/* store data for second k loop */
-	exchange->dist_ik[kcount]=dist_ik;
-	exchange->d_ik2[kcount]=d_ik2;
-
-	/* return if not within cutoff */
-	if(d_ik2>Sk2) {
-		kcount++;
-		continue;
-	}
-
-	/* d_ik */
-	d_ik=sqrt(d_ik2);
-
-	/* cos theta */
-	cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
-
-	/* g_ijk 
-	h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism
-	d2_h_cos2=exchange->di2+(h_cos*h_cos);
-	frac=exchange->ci2/d2_h_cos2;
-	g=*(exchange->gamma_i)*(1.0+exchange->ci2di2-frac);
-	dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f..
-	*/
-
-	h_cos=h_i+cos_theta; // + in albe formalism
-	d2_h_cos2=di2+(h_cos*h_cos);
-	frac=ci2/d2_h_cos2;
-	g=gamma_i*(1.0+ci2di2-frac);
-	dg=2.0*frac*gamma_i*h_cos/d2_h_cos2; // + in albe f..
-
-	/* zeta sum += f_c_ik * g_ijk */
-	if(d_ik<=Rk) {
-		zeta_ij+=g;
-		f_c_ik=1.0;
-		df_c_ik=0.0;
-	}
-	else {
-		s_r=Sk-Rk;
-		arg=M_PI*(d_ik-Rk)/s_r;
-		f_c_ik=0.5+0.5*cos(arg);
-		df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
-		zeta_ij+=f_c_ik*g;
-	}
-
-	/* store even more data for second k loop */
-	exchange->g[kcount]=g;
-	exchange->dg[kcount]=dg;
-	exchange->d_ik[kcount]=d_ik;
-	exchange->cos_theta[kcount]=cos_theta;
-	exchange->f_c_ik[kcount]=f_c_ik;
-	exchange->df_c_ik[kcount]=df_c_ik;
-
-	/* increase k counter */
-	kcount++;
-
-}
-#endif
-#endif
+#ifndef PTHREADS
 
 int albe_potential_force_calc(t_moldyn *moldyn) {
 
@@ -366,17 +251,6 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 				/* first loop over atoms k */
 				for(k=0;k<27;k++) {
 
-#ifdef PTHREADS
-	// create threads
-	kdata.moldyn=moldyn;
-	kdata.jtom=jtom;
-	kdata.itom=&(itom[i]);
-	ret=pthread_create(&(kthread[k]),NULL,k1_thread,&(kdata[k]));
-	if(ret) {
-		perror("[albe fast] thread create");
-		return ret;
-	}
-#else
 					bc_ik=(k<dnlc)?0:1;
 #ifdef STATIC_LISTS
 					q=0;
@@ -412,15 +286,6 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 						if(ktom==&(itom[i]))
 							continue;
 
-#if 0
-//#ifdef PTHREADS
-	ret=pthread_create(&(k_thread[k]),NULL,k1_calc,k_data);
-	if(ret) {
-		perror("[albe fast] create thread\n");
-		return ret;
-	}
-#else
-
 /* k1 func here ... */
 /* albe 3 body potential function (first k loop) */
 
@@ -526,22 +391,8 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 					        L_NO_NEXT_ELEMENT);
 #endif
 
-#endif // PTHREADS
-
 				}
 
-#ifdef PTHREADS
-	// join threads
-	for(k=0;k<27;k++) {
-		ret=pthread_join(kthread[k],NULL);
-		if(ret) {
-			perror("[albe fast] join thread");
-			return ret;
-		}
-	}
-#endif
-
-
 /* j2 func here ... */
 
 
@@ -840,3 +691,711 @@ if(moldyn->time>DSTART&&moldyn->time<DEND) {
 	return 0;
 }
 
+
+#else // PTHREADS
+
+
+typedef struct s_pft_data {
+	t_moldyn *moldyn;
+	int i;
+} t_pft_data;
+
+void *potential_force_thread(void *ptr) {
+
+	t_pft_data *pft_data;
+	t_moldyn *moldyn;
+	t_albe_exchange ec;
+
+	int i,j,k,count;
+	t_atom *itom,*jtom,*ktom;
+	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour_i[27];
+	int p,q;
+#elif LOWMEM_LISTS
+	int neighbour_i[27];
+	int p,q;
+#else
+	t_list neighbour_i[27];
+	t_list neighbour_i2[27];
+	t_list *this,*that;
+#endif
+	u8 bc_ij,bc_ik;
+	int dnlc;
+
+	// needed to work
+	t_atom *ai;
+
+	// optimized
+	t_albe_mult_params *params;
+	t_albe_exchange *exchange;
+	t_3dvec dist_ij;
+	double d_ij2;
+	double d_ij;
+	u8 brand_i;
+	double S2;
+	int kcount;
+	double zeta_ij;
+	double pre_dzeta;
+
+	// more ...
+	double Rk,Sk,Sk2;
+	t_3dvec dist_ik;
+	double d_ik2,d_ik;
+	double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg;
+	double f_c_ik,df_c_ik;
+
+	t_3dvec force;
+	double f_a,df_a,b,db,f_c,df_c;
+	double f_r,df_r;
+	double scale;
+	double mu,B;
+	double lambda,A;
+	double r0;
+	double S,R;
+	double energy;
+
+	double dijdik_inv,fcdg,dfcg;
+	t_3dvec dcosdrj,dcosdrk;
+	t_3dvec tmp;
+
+	// even more ...
+	double gamma_i;
+	double c_i;
+	double d_i;
+	double h_i;
+	double ci2;
+	double di2;
+	double ci2di2;
+
+	pft_data=ptr;
+	moldyn=pft_data->moldyn;
+	exchange=&ec;
+
+	count=moldyn->count;
+	itom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	// optimized
+	params=moldyn->pot_params;
+
+
+	/* get energy, force and virial of every atom */
+
+	/* first (and only) loop over atoms i */
+	for(i=0;i<count;i++) {
+
+		if(!(itom[i].attr&ATOM_ATTR_3BP))
+			continue;
+
+		link_cell_neighbour_index(moldyn,
+		                          (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+		                          (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+		                          (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+		                          neighbour_i);
+
+		dnlc=lc->dnlc;
+
+		/* copy the neighbour lists */
+#ifdef STATIC_LISTS
+#elif LOWMEM_LISTS
+#else
+		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
+
+		ai=&(itom[i]);
+		brand_i=ai->brand;
+
+		/* loop over atoms j */
+		for(j=0;j<27;j++) {
+
+			bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+			p=0;
+
+			while(neighbour_i[j][p]!=-1) {
+
+				jtom=&(itom[neighbour_i[j][p]]);
+				p++;
+#elif LOWMEM_LISTS
+			p=neighbour_i[j];
+
+			while(p!=-1) {
+
+				jtom=&(itom[p]);
+				p=lc->subcell->list[p];
+#else
+			this=&(neighbour_i[j]);
+			list_reset_f(this);
+
+			if(this->start==NULL)
+				continue;
+
+			do {
+
+				jtom=this->current->data;
+#endif
+
+				if(jtom==&(itom[i]))
+					continue;
+
+				if(!(jtom->attr&ATOM_ATTR_3BP))
+					continue;
+
+				/* reset 3bp run */
+				moldyn->run3bp=1;
+
+
+/* j1 func here ... */
+/* albe 3 body potential function (first ij loop) */
+
+	/* reset zeta sum */
+	zeta_ij=0.0;
+
+	/*
+	 * set ij depending values
+	 */
+
+	if(brand_i==jtom->brand) {
+		S2=params->S2[brand_i];
+	}
+	else {
+		S2=params->S2mixed;
+	}
+
+	/* dist_ij, d_ij2 */
+	v3_sub(&dist_ij,&(jtom->r),&(ai->r));
+	if(bc_ij) check_per_bound(moldyn,&dist_ij);
+	d_ij2=v3_absolute_square(&dist_ij);
+
+	/* if d_ij2 > S2 => no force & potential energy contribution */
+	if(d_ij2>S2)
+		continue;
+
+	/* d_ij */
+	d_ij=sqrt(d_ij2);
+
+	/* reset k counter for first k loop */
+	kcount=0;
+
+				/* first loop over atoms k */
+				for(k=0;k<27;k++) {
+
+					bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+					q=0;
+
+					while(neighbour_i[k][q]!=-1) {
+
+						ktom=&(itom[neighbour_i[k][q]]);
+						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
+#else
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
+					
+					if(that->start==NULL)
+						continue;
+
+					do {
+						ktom=that->current->data;
+#endif
+
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
+
+						if(ktom==jtom)
+							continue;
+
+						if(ktom==&(itom[i]))
+							continue;
+
+/* k1 func here ... */
+/* albe 3 body potential function (first k loop) */
+
+	if(kcount>ALBE_MAXN) {
+		printf("FATAL: neighbours = %d\n",kcount);
+		printf("  -> %d %d %d\n",ai->tag,jtom->tag,ktom->tag);
+	}
+
+	/* ik constants */
+	if(brand_i==ktom->brand) {
+		Rk=params->R[brand_i];
+		Sk=params->S[brand_i];
+		Sk2=params->S2[brand_i];
+		/* albe needs i,k depending c,d,h and gamma values */
+		gamma_i=params->gamma[brand_i];
+		c_i=params->c[brand_i];
+		d_i=params->d[brand_i];
+		h_i=params->h[brand_i];
+		ci2=params->c2[brand_i];
+		di2=params->d2[brand_i];
+		ci2di2=params->c2d2[brand_i];
+	}
+	else {
+		Rk=params->Rmixed;
+		Sk=params->Smixed;
+		Sk2=params->S2mixed;
+		/* albe needs i,k depending c,d,h and gamma values */
+		gamma_i=params->gamma_m;
+		c_i=params->c_mixed;
+		d_i=params->d_mixed;
+		h_i=params->h_mixed;
+		ci2=params->c2_mixed;
+		di2=params->d2_mixed;
+		ci2di2=params->c2d2_m;
+	}
+
+	/* dist_ik, d_ik2 */
+	v3_sub(&dist_ik,&(ktom->r),&(ai->r));
+	if(bc_ik) check_per_bound(moldyn,&dist_ik);
+	d_ik2=v3_absolute_square(&dist_ik);
+
+	/* store data for second k loop */
+	exchange->dist_ik[kcount]=dist_ik;
+	exchange->d_ik2[kcount]=d_ik2;
+
+	/* return if not within cutoff */
+	if(d_ik2>Sk2) {
+		kcount++;
+		continue;
+	}
+
+	/* d_ik */
+	d_ik=sqrt(d_ik2);
+
+	/* cos theta */
+	cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
+
+	/* g_ijk 
+	h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism
+	d2_h_cos2=exchange->di2+(h_cos*h_cos);
+	frac=exchange->ci2/d2_h_cos2;
+	g=*(exchange->gamma_i)*(1.0+exchange->ci2di2-frac);
+	dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f..
+	*/
+
+	h_cos=h_i+cos_theta; // + in albe formalism
+	d2_h_cos2=di2+(h_cos*h_cos);
+	frac=ci2/d2_h_cos2;
+	g=gamma_i*(1.0+ci2di2-frac);
+	dg=2.0*frac*gamma_i*h_cos/d2_h_cos2; // + in albe f..
+
+	/* zeta sum += f_c_ik * g_ijk */
+	if(d_ik<=Rk) {
+		zeta_ij+=g;
+		f_c_ik=1.0;
+		df_c_ik=0.0;
+	}
+	else {
+		s_r=Sk-Rk;
+		arg=M_PI*(d_ik-Rk)/s_r;
+		f_c_ik=0.5+0.5*cos(arg);
+		df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
+		zeta_ij+=f_c_ik*g;
+	}
+
+	/* store even more data for second k loop */
+	exchange->g[kcount]=g;
+	exchange->dg[kcount]=dg;
+	exchange->d_ik[kcount]=d_ik;
+	exchange->cos_theta[kcount]=cos_theta;
+	exchange->f_c_ik[kcount]=f_c_ik;
+	exchange->df_c_ik[kcount]=df_c_ik;
+
+	/* increase k counter */
+	kcount++;
+
+#ifdef STATIC_LISTS
+					}
+#elif LOWMEM_LISTS
+					}
+#else
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+#endif
+
+				}
+
+/* j2 func here ... */
+
+
+	if(brand_i==jtom->brand) {
+		S=params->S[brand_i];
+		R=params->R[brand_i];
+		B=params->B[brand_i];
+		A=params->A[brand_i];
+		r0=params->r0[brand_i];
+		mu=params->mu[brand_i];
+		lambda=params->lambda[brand_i];
+	}
+	else {
+		S=params->Smixed;
+		R=params->Rmixed;
+		B=params->Bmixed;
+		A=params->Amixed;
+		r0=params->r0_mixed;
+		mu=params->mu_m;
+		lambda=params->lambda_m;
+	}
+
+	/* f_c, df_c */
+	if(d_ij<R) {
+		f_c=1.0;
+		df_c=0.0;
+	}
+	else {
+		s_r=S-R;
+		arg=M_PI*(d_ij-R)/s_r;
+		f_c=0.5+0.5*cos(arg);
+		df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
+	}
+
+	/* f_a, df_a */
+	f_a=-B*exp(-mu*(d_ij-r0));
+	df_a=mu*f_a/d_ij;
+
+	/* f_r, df_r */
+	f_r=A*exp(-lambda*(d_ij-r0));
+	df_r=lambda*f_r/d_ij;
+
+	/* b, db */
+	if(zeta_ij==0.0) {
+		b=1.0;
+		db=0.0;
+	}
+	else {
+		b=1.0/sqrt(1.0+zeta_ij);
+		db=-0.5*b/(1.0+zeta_ij);
+	}
+
+	/* force contribution for atom i */
+	scale=-0.5*(f_c*(df_r-b*df_a)+df_c*(f_r-b*f_a)); // - in albe formalism
+	v3_scale(&force,&(dist_ij),scale);
+	v3_add(&(ai->f),&(ai->f),&force);
+
+	/* force contribution for atom j */
+	v3_scale(&force,&force,-1.0); // dri rij = - drj rij
+	v3_add(&(jtom->f),&(jtom->f),&force);
+
+	/* virial */
+	virial_calc(ai,&force,&(dist_ij));
+
+#ifdef DEBUG
+if(moldyn->time>DSTART&&moldyn->time<DEND) {
+	if((ai==&(moldyn->atom[DATOM]))|(jtom==&(moldyn->atom[DATOM]))) {
+		printf("force 3bp (j2): [%d %d sum]\n",ai->tag,jtom->tag);
+		printf("  adding %f %f %f\n",force.x,force.y,force.z);
+		if(ai==&(moldyn->atom[0]))
+			printf("  total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+		if(jtom==&(moldyn->atom[0]))
+			printf("  total j: %f %f %f\n",jtom->f.x,jtom->f.y,jtom->f.z);
+		printf("  energy: %f = %f %f %f %f\n",0.5*f_c*(b*f_a+f_r),
+		                                    f_c,b,f_a,f_r);
+		printf("          %f %f %f\n",zeta_ij,.0,.0);
+	}
+}
+#endif
+
+	/* dzeta prefactor = - f_c f_a db, (* -0.5 due to force calc) */
+	pre_dzeta=0.5*f_a*f_c*db;
+
+	/* energy contribution */
+	energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
+	moldyn->energy+=energy;
+	ai->e+=energy;
+
+	/* reset k counter for second k loop */
+	kcount=0;
+		
+
+				/* second loop over atoms k */
+				for(k=0;k<27;k++) {
+
+					bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+					q=0;
+
+					while(neighbour_i[k][q]!=-1) {
+
+						ktom=&(itom[neighbour_i[k][q]]);
+						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
+#else
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
+					
+					if(that->start==NULL)
+						continue;
+
+					do {
+						ktom=that->current->data;
+#endif
+
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
+
+						if(ktom==jtom)
+							continue;
+
+						if(ktom==&(itom[i]))
+							continue;
+
+
+/* k2 func here ... */
+/* albe 3 body potential function (second k loop) */
+
+	if(kcount>ALBE_MAXN)
+		printf("FATAL: neighbours!\n");
+
+	/* d_ik2 */
+	d_ik2=exchange->d_ik2[kcount];
+
+	if(brand_i==ktom->brand)
+		Sk2=params->S2[brand_i];
+	else
+		Sk2=params->S2mixed;
+
+	/* return if d_ik > S */
+	if(d_ik2>Sk2) {
+		kcount++;
+		continue;
+	}
+
+	/* dist_ik, d_ik */
+	dist_ik=exchange->dist_ik[kcount];
+	d_ik=exchange->d_ik[kcount];
+
+	/* f_c_ik, df_c_ik */
+	f_c_ik=exchange->f_c_ik[kcount];
+	df_c_ik=exchange->df_c_ik[kcount];
+
+	/* g, dg, cos_theta */
+	g=exchange->g[kcount];
+	dg=exchange->dg[kcount];
+	cos_theta=exchange->cos_theta[kcount];
+
+	/* cos_theta derivatives wrt j,k */
+	dijdik_inv=1.0/(d_ij*d_ik);
+	v3_scale(&dcosdrj,&dist_ik,dijdik_inv);		// j
+	v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
+	v3_add(&dcosdrj,&dcosdrj,&tmp);
+	v3_scale(&dcosdrk,&dist_ij,dijdik_inv);		// k
+	v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
+	v3_add(&dcosdrk,&dcosdrk,&tmp);
+
+	/* f_c_ik * dg, df_c_ik * g */
+	fcdg=f_c_ik*dg;
+	dfcg=df_c_ik*g;
+
+	/* derivative wrt j */
+	v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
+
+	/* force contribution */
+	v3_add(&(jtom->f),&(jtom->f),&force);
+
+#ifdef DEBUG
+if(moldyn->time>DSTART&&moldyn->time<DEND) {
+	if(jtom==&(moldyn->atom[DATOM])) {
+		printf("force 3bp (k2): [%d %d %d]\n",ai->tag,jtom->tag,ktom->tag);
+		printf("  adding %f %f %f\n",force.x,force.y,force.z);
+		printf("  total j: %f %f %f\n",jtom->f.x,jtom->f.y,jtom->f.z);
+		printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+		printf("    d ij ik = %f %f\n",d_ij,d_ik);
+	}
+}
+#endif
+
+	/* virial */
+	virial_calc(ai,&force,&dist_ij);
+
+	/* force contribution to atom i */
+	v3_scale(&force,&force,-1.0);
+	v3_add(&(ai->f),&(ai->f),&force);
+
+	/* derivative wrt k */
+	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);
+
+	/* force contribution */
+	v3_add(&(ktom->f),&(ktom->f),&force);
+
+#ifdef DEBUG
+if(moldyn->time>DSTART&&moldyn->time<DEND) {
+	if(ktom==&(moldyn->atom[DATOM])) {
+		printf("force 3bp (k2): [%d %d %d]\n",ai->tag,jtom->tag,ktom->tag);
+		printf("  adding %f %f %f\n",force.x,force.y,force.z);
+		printf("  total k: %f %f %f\n",ktom->f.x,ktom->f.y,ktom->f.z);
+		printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+		printf("    d ij ik = %f %f\n",d_ij,d_ik);
+	}
+}
+#endif
+
+	/* virial */
+	virial_calc(ai,&force,&dist_ik);
+	
+	/* force contribution to atom i */
+	v3_scale(&force,&force,-1.0);
+	v3_add(&(ai->f),&(ai->f),&force);
+
+	/* increase k counter */
+	kcount++;	
+
+
+
+#ifdef STATIC_LISTS
+					}
+#elif LOWMEM_LISTS
+					}
+#else
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+#endif
+
+				}
+				
+#ifdef STATIC_LISTS
+			}
+#elif LOWMEM_LISTS
+			}
+#else
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+		
+		}
+		
+#ifdef DEBUG
+	//printf("\n\n");
+#endif
+#ifdef VDEBUG
+	printf("\n\n");
+#endif
+
+	}
+
+#ifdef DEBUG
+	//printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
+	if(moldyn->time>DSTART&&moldyn->time<DEND) {
+		printf("force:\n");
+		printf("  x: %0.40f\n",moldyn->atom[DATOM].f.x);
+		printf("  y: %0.40f\n",moldyn->atom[DATOM].f.y);
+		printf("  z: %0.40f\n",moldyn->atom[DATOM].f.z);
+	}
+#endif
+
+	/* some postprocessing */
+#ifdef PARALLEL
+	#pragma omp parallel for
+#endif
+	for(i=0;i<count;i++) {
+		/* calculate global virial */
+		moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
+		moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
+		moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
+		moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
+		moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
+		moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
+
+		/* check forces regarding the given timestep */
+		if(v3_norm(&(itom[i].f))>\
+                   0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+			printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
+			       i);
+	}
+
+	return 0;
+}
+
+int albe_potential_force_calc(t_moldyn *moldyn) {
+
+	int i,ret;
+	t_pft_data *pft_data;
+	int count;
+	pthread_t *pft_thread;
+	t_atom *itom;
+	t_virial *virial;
+
+	count=moldyn->count;
+	itom=moldyn->atom;
+
+	/* reset energy */
+	moldyn->energy=0.0;
+
+	/* reset global virial */
+	memset(&(moldyn->gvir),0,sizeof(t_virial));
+
+	/* reset force, site energy and virial of every atom */
+	for(i=0;i<count;i++) {
+
+		/* reset force */
+		v3_zero(&(itom[i].f));
+
+		/* reset virial */
+		virial=&(itom[i].virial);
+		virial->xx=0.0;
+		virial->yy=0.0;
+		virial->zz=0.0;
+		virial->xy=0.0;
+		virial->xz=0.0;
+		virial->yz=0.0;
+	
+		/* reset site energy */
+		itom[i].e=0.0;
+
+	}
+
+	/* alloc thread memory */
+	pft_thread=malloc(count*sizeof(pthread_t));
+	if(pft_thread==NULL) {
+		perror("[albe fast] alloc thread mem");
+		return -1;
+	}
+	pft_data=malloc(count*sizeof(t_pft_data));
+	if(pft_data==NULL) {
+		perror("[albe fast] alloc thread mem");
+		return -1;
+	}
+
+	/* start threads */
+	for(i=0;i<count;i++) {
+
+		/* prepare thread data */
+		pft_data[i].moldyn=moldyn;
+		pft_data[i].i=i;
+
+		ret=pthread_create(&(pft_thread[i]),NULL,
+                                   potential_force_thread,&(pft_data[i]));
+		if(ret)  {
+			perror("[albe fast] pf thread create");
+			return ret;
+		}
+	}
+
+	/* join threads */
+	for(i=0;i<count;i++) {
+		ret=pthread_join(pft_thread[i],NULL);
+		if(ret) {
+			perror("[albe fast] pf thread join");
+			return ret;
+		}
+	}
+
+	return 0;
+}
+
+#endif // PTHREADS
-- 
2.20.1