X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=d33de02efa776fa52dd3a10bbd5ca00d93ba7b4c;hb=15b4727e1137600f8f46af027aefd2b5c7a56420;hp=faa6b7c3ea6354a7f1ab08a51cca462d567fd405;hpb=2d562a1946322ae5b70bdce180321f32adbeab62;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index faa6b7c..d33de02 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -460,6 +460,28 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double temperature_calc(t_moldyn *moldyn) {
+
+	double double_ekin;
+	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+
+	for(i=0;i<moldyn->count;i++)
+		double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+	/* kinetic energy = 3/2 N k_B T */
+	moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+
+	return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+	return moldyn->t;
+}
+
 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
@@ -478,10 +500,11 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	count=0;
 	for(i=0;i<moldyn->count;i++) {
 		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
-			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 			count+=1;
 		}
 	}
+	e*=0.5;
 	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
@@ -515,6 +538,34 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double pressure_calc(t_moldyn *moldyn) {
+
+	int i;
+	t_atom *atom;
+	double p1,p2,p=0;
+	
+	for(i=0;i<moldyn->count;i++) {
+		
+
+	}
+
+	p1=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt1);
+	p1/=moldyn->volume;
+
+	p2=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt2);
+	p2/=moldyn->volume;
+
+	printf("compare pressures: %f %f\n",p1/ATM,p2/ATM);
+
+	return moldyn->p;
+}	
+
+double get_pressure(t_moldyn *moldyn) {
+
+	return moldyn->p;
+
+}
+
 int scale_volume(t_moldyn *moldyn) {
 
 	t_atom *atom;
@@ -592,11 +643,6 @@ double get_e_kin(t_moldyn *moldyn) {
 	return moldyn->ekin;
 }
 
-double get_e_pot(t_moldyn *moldyn) {
-
-	return moldyn->energy;
-}
-
 double update_e_kin(t_moldyn *moldyn) {
 
 	return(get_e_kin(moldyn));
@@ -659,6 +705,9 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
+	if(lc->cells<27)
+		printf("[moldyn] FATAL: less then 27 subcells!\n");
+
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
@@ -885,13 +934,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			scale_volume(moldyn);
 
 		/* check for log & visualization */
+//double ax;
+//double ao;
+//double av;
 		if(e) {
 			if(!(i%e))
+//ao=sqrt(0.1/M_SI);
+//ax=((0.28-0.25)*sqrt(3)*LC_SI/2)*cos(ao*i);
+//av=ao*(0.28-0.25)*sqrt(3)*LC_SI/2*sin(ao*i);
+				update_e_kin(moldyn);
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
-				        moldyn->time,update_e_kin(moldyn),
+				        moldyn->time,moldyn->ekin,
 				        moldyn->energy,
 				        get_total_energy(moldyn));
+//moldyn->atom[0].r.x,ax,av*av*M_SI,0.1*ax*ax,av*av*M_SI+0.1*ax*ax);
 		}
 		if(m) {
 			if(!(i%m)) {
@@ -946,7 +1003,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
 	int i,count;
-	double tau,tau_square;
+	double tau,tau_square,h;
 	t_3dvec delta;
 	t_atom *atom;
 
@@ -957,14 +1014,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 	for(i=0;i<count;i++) {
 		/* new positions */
+		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+		v3_scale(&delta,&(atom[i].f),h*tau_square);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		check_per_bound(moldyn,&(atom[i].r));
 
-		/* velocities */
-		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		/* velocities [actually v(t+tau/2)] */
+		v3_scale(&delta,&(atom[i].f),h*tau);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
@@ -975,7 +1033,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 	potential_force_calc(moldyn);
 
 	for(i=0;i<count;i++) {
-		/* again velocities */
+		/* 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);
 	}
@@ -986,7 +1044,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
@@ -1010,6 +1068,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset energy */
 	moldyn->energy=0.0;
+
+	moldyn->vt2=0.0;
 	
 	/* get energy and force of every atom */
 	for(i=0;i<count;i++) {
@@ -1025,6 +1085,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		virial->xy=0.0;
 		virial->xz=0.0;
 		virial->yz=0.0;
+		moldyn->vt1=0.0;
 
 		/* reset site energy */
 		itom[i].e=0.0;
@@ -1130,6 +1191,33 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef DEBUG
 printf("\n\n");
 #endif
+#ifdef VDEBUG
+printf("\n\n");
+#endif
+
+	moldyn->vt2=0.0;
+	for(i=0;i<count;i++)
+		moldyn->vt2-=v3_scalar_product(&(itom[i].r),&(itom[i].f));
+
+printf("compare: vt1: %f vt2: %f\n",moldyn->vt1,moldyn->vt2);
+
+pressure_calc(moldyn);
+
+	return 0;
+}
+
+/*
+ * virial calculation
+ */
+
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+	a->virial.xx-=f->x*d->x;
+	a->virial.yy-=f->y*d->y;
+	a->virial.zz-=f->z*d->z;
+	a->virial.xy-=f->x*d->y;
+	a->virial.xz-=f->x*d->z;
+	a->virial.yz-=f->y*d->z;
 
 	return 0;
 }
@@ -1176,23 +1264,29 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_ho_params *params;
 	t_3dvec force,distance;
-	double d;
+	double d,f;
 	double sc,equi_dist;
 
 	params=moldyn->pot2b_params;
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
 
+	if(ai<aj) return 0;
+
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
-		/* energy is 1/2 (d-d0)^2, but we will add this twice ... */
-		moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+		moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
 		/* f = -grad E; grad r_ij = -1 1/r_ij distance */
-		v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+		f=sc*(1.0-equi_dist/d);
+		v3_scale(&force,&distance,f);
 		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
+		v3_scale(&force,&distance,-f);
+		v3_add(&(aj->f),&(aj->f),&force);
 	}
 
 	return 0;
@@ -1212,6 +1306,8 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
+	if(ai<aj) return 0;
+
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_absolute_square(&distance);	/* 1/r^2 */
@@ -1220,16 +1316,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		h2=d*d; 			/* 1/r^4 */
 		h2*=d;	 			/* 1/r^6 */
 		h1=h2*h2; 			/* 1/r^12 */
-		/* energy is eps*..., but we will add this twice ... */
-		moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+		moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
 		h2*=d;				/* 1/r^8 */
 		h1*=d;				/* 1/r^14 */
 		h2*=6*sig6;
 		h1*=12*sig12;
 		d=+h1-h2;
 		d*=eps;
+		v3_scale(&force,&distance,d);
+		v3_add(&(aj->f),&(aj->f),&force);
 		v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
 		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
+		moldyn->vt1-=v3_scalar_product(&force,&distance);
 	}
 
 	return 0;
@@ -1376,6 +1476,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	/* save for use in 3bp */
 	exchange->d_ij=d_ij;
+	exchange->d_ij2=d_ij2;
 	exchange->dist_ij=dist_ij;
 
 	/* more constants */
@@ -1443,6 +1544,14 @@ if(ai==&(moldyn->atom[0])) {
 	printf("%f | %f\n",force.y,ai->f.y);
 	printf("%f | %f\n",force.z,ai->f.z);
 }
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij, dVji (2bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
+}
 #endif
 
 	/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
@@ -1514,7 +1623,6 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	zeta=exchange->zeta_ij;
 	if(zeta==0.0) {
 		moldyn->debug++;		/* just for debugging ... */
-		db=0.0;
 		b=chi;
 		v3_scale(&force,dist_ij,df_a*b*f_c);
 	}
@@ -1551,6 +1659,14 @@ if(ai==&(moldyn->atom[0])) {
 	printf("%f | %f\n",force.y,ai->f.y);
 	printf("%f | %f\n",force.z,ai->f.z);
 }
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij (3bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
 #endif
 
 	/* add energy of 3bp sum */
@@ -1582,12 +1698,13 @@ if(ai==&(moldyn->atom[0])) {
 	v3_add(&(ai->f),&(ai->f),&force);
 
 	/* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-	ai->virial.xx+=force.x*dist_ij->x;
-	ai->virial.yy+=force.y*dist_ij->y;
-	ai->virial.zz+=force.z*dist_ij->z;
-	ai->virial.xy+=force.x*dist_ij->y;
-	ai->virial.xz+=force.x*dist_ij->z;
-	ai->virial.yz+=force.y*dist_ij->z;
+// TEST ... with a minus instead
+	ai->virial.xx-=force.x*dist_ij->x;
+	ai->virial.yy-=force.y*dist_ij->y;
+	ai->virial.zz-=force.z*dist_ij->z;
+	ai->virial.xy-=force.x*dist_ij->y;
+	ai->virial.xz-=force.x*dist_ij->z;
+	ai->virial.yz-=force.y*dist_ij->z;
 
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {
@@ -1596,6 +1713,14 @@ if(ai==&(moldyn->atom[0])) {
 	printf("%f | %f\n",force.y,ai->f.y);
 	printf("%f | %f\n",force.z,ai->f.z);
 }
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVji (3bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
 #endif
 
 	return 0;
@@ -1610,9 +1735,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	t_3dvec dist_ij,dist_ik,dist_jk;
 	t_3dvec temp1,temp2;
 	t_3dvec *dzeta;
-	double R,S,s_r;
+	double R,S,S2,s_r;
 	double B,mu;
-	double d_ij,d_ik,d_jk;
+	double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
 	double rr,dd;
 	double f_c,df_c;
 	double f_c_ik,df_c_ik,arg;
@@ -1658,6 +1783,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	/* dist_ij, d_ij - this is < S_ij ! */
 	dist_ij=exchange->dist_ij;
 	d_ij=exchange->d_ij;
+	d_ij2=exchange->d_ij2;
 
 	/* f_c_ij, df_c_ij (same for ji) */
 	f_c=exchange->f_c;
@@ -1672,21 +1798,26 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	/* dist_ik, d_ik */
 	v3_sub(&dist_ik,&(ak->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&dist_ik);
-	d_ik=v3_norm(&dist_ik);
+	d_ik2=v3_absolute_square(&dist_ik);
 
 	/* ik constants */
 	brand=ai->brand;
 	if(brand==ak->brand) {
 		R=params->R[brand];
 		S=params->S[brand];
+		S2=params->S2[brand];
 	}
 	else {
 		R=params->Rmixed;
 		S=params->Smixed;
+		S2=params->S2mixed;
 	}
 
 	/* zeta_ij/dzeta_ij contribution only for d_ik < S */
-	if(d_ik<S) {
+	if(d_ik2<S2) {
+
+		/* now we need d_ik */
+		d_ik=sqrt(d_ik2);
 
 		/* get constants_i from exchange data */
 		n=*(exchange->n_i);
@@ -1704,8 +1835,8 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
 		/* d_costheta */
 		tmp=1.0/dd;
-		d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
-		d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+		d_costheta1=cos_theta/d_ij2-tmp;
+		d_costheta2=cos_theta/d_ik2-tmp;
 
 		/* some usefull values */
 		h_cos=(h-cos_theta);
@@ -1757,13 +1888,14 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	/* dist_jk, d_jk */
 	v3_sub(&dist_jk,&(ak->r),&(aj->r));
 	if(bc) check_per_bound(moldyn,&dist_jk);
-	d_jk=v3_norm(&dist_jk);
+	d_jk2=v3_absolute_square(&dist_jk);
 
 	/* jk constants */
 	brand=aj->brand;
 	if(brand==ak->brand) {
 		R=params->R[brand];
 		S=params->S[brand];
+		S2=params->S2[brand];
 		B=params->B[brand];
 		mu=params->mu[brand];
 		chi=1.0;
@@ -1771,13 +1903,17 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	else {
 		R=params->Rmixed;
 		S=params->Smixed;
+		S2=params->S2mixed;
 		B=params->Bmixed;
 		mu=params->mu_m;
 		chi=params->chi;
 	}
 
 	/* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
-	if(d_jk<S) {
+	if(d_jk2<S2) {
+
+		/* now we need d_ik */
+		d_jk=sqrt(d_jk2);
 
 		/* constants_j from exchange data */
 		n=*(exchange->n_j);
@@ -1795,7 +1931,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
 		/* d_costheta */
 		d_costheta1=1.0/dd;
-		d_costheta2=cos_theta/(d_ij*d_ij);
+		d_costheta2=cos_theta/d_ij2;
 
 		/* some usefull values */
 		h_cos=(h-cos_theta);
@@ -1805,10 +1941,11 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		/* g(cos_theta) */
 		g=1.0+c2d2-frac;
 
-		/* d_costheta_ij and dg(cos_theta) - needed in any case! */
+		/* d_costheta_jik and dg(cos_theta) - needed in any case! */
 		v3_scale(&temp1,&dist_jk,d_costheta1);
 		v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
-		v3_add(&temp1,&temp1,&temp2);
+		//v3_add(&temp1,&temp1,&temp2);
+		v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
 		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
 
 		/* store dg in temp2 and use it for dVjk later */
@@ -1873,6 +2010,14 @@ if(ai==&(moldyn->atom[0])) {
 	printf("%f | %f\n",temp2.y,ai->f.y);
 	printf("%f | %f\n",temp2.z,ai->f.z);
 }
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVjk (3bp) contrib:\n");
+	printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
+	printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
+	printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
+}
 #endif
 
 	}