X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=26f298fbb58f2488f048d04dd4fbaad550e9563e;hb=a33fe7f5d4d7e09b5b52f5f4dadd462cf868ec2f;hp=2f274c2da8fb7fcaeec9344f21bec718cb8585a8;hpb=8e98c9cbbddf1c9c852874f956b0dbe2f9a4a922;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 2f274c2..26f298f 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -41,9 +41,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 int moldyn_shutdown(t_moldyn *moldyn) {
 
+	printf("[moldyn] shutdown\n");
 	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
-	moldyn_log_shutdown(moldyn);
 	rand_close(&(moldyn->random));
 	free(moldyn->atom);
 
@@ -93,6 +93,13 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	return 0;
 }
 
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
+
+	return 0;
+}
+
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
 	if(x)
@@ -171,9 +178,10 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	printf("[moldyn] log shutdown\n");
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->mfd);
-	if(moldyn->visual) visual_tini(moldyn->visual);
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
@@ -184,17 +192,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	int count;
 	int ret;
 	t_3dvec origin;
-	t_atom *atom;
 
 	count=a*b*c;
-	atom=moldyn->atom;
 
 	if(type==FCC) count*=4;
 
 	if(type==DIAMOND) count*=8;
 
-	atom=malloc(count*sizeof(t_atom));
-	if(atom==NULL) {
+	moldyn->atom=malloc(count*sizeof(t_atom));
+	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
 		return -1;
 	}
@@ -203,10 +209,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	switch(type) {
 		case FCC:
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,atom,&origin);
+			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -222,15 +228,18 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	moldyn->count=count;
+	printf("[moldyn] created lattice with %d atoms\n",count);
 
 	while(count) {
-		atom[count-1].element=element;
-		atom[count-1].mass=mass;
-		atom[count-1].attr=attr;
-		atom[count-1].bnum=bnum;
 		count-=1;
+		moldyn->atom[count].element=element;
+		moldyn->atom[count].mass=mass;
+		moldyn->atom[count].attr=attr;
+		moldyn->atom[count].bnum=bnum;
+		check_per_bound(moldyn,&(moldyn->atom[count].r));
 	}
 
+
 	return ret;
 }
 
@@ -252,11 +261,12 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 	moldyn->atom=ptr;
 
 	atom=moldyn->atom;
-	atom->r=*r;
-	atom->v=*v;
-	atom->element=element;
-	atom->bnum=bnum;
-	atom->attr=attr;
+	atom[count-1].r=*r;
+	atom[count-1].v=*v;
+	atom[count-1].element=element;
+	atom[count-1].mass=mass;
+	atom[count-1].bnum=bnum;
+	atom[count-1].attr=attr;
 
 	return 0;
 }
@@ -311,15 +321,15 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn);
+	scale_velocity(moldyn,VSCALE_INIT_EQUI);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 type) {
 
 	int i;
-	double e,c;
+	double e,scale;
 	t_atom *atom;
 
 	atom=moldyn->atom;
@@ -327,12 +337,15 @@ int scale_velocity(t_moldyn *moldyn) {
 	/*
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
+
 	e=0.0;
 	for(i=0;i<moldyn->count;i++)
 		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+	if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
+	scale=sqrt(scale);
 	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+		v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
@@ -484,7 +497,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	count2=27;
 	a=nx*ny;
 
-
 	cell[0]=lc->subcell[i+j*nx+k*a];
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
@@ -518,7 +530,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
-	lc->dnlc=count2;
+	lc->dnlc=count1;
 	lc->countn=27;
 
 	return count2;
@@ -587,11 +599,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	unsigned int e,m,s,v;
 	t_3dvec p;
 	t_moldyn_schedule *schedule;
-
+	t_atom *atom;
 	int fd;
 	char fb[128];
+	double ds;
 
 	schedule=&(moldyn->schedule);
+	atom=moldyn->atom;
 
 	/* initialize linked cell method */
 	link_cell_init(moldyn);
@@ -605,13 +619,22 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
-
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
+	/* do some checks before we actually start calculating bullshit */
+	if(moldyn->cutoff>0.5*moldyn->dim.x)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.y)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.z)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+	if(ds>0.05*moldyn->nnd)
+		printf("[moldyn] warning: forces too high / tau too small!\n");
+
 	/* zero absolute time */
 	moldyn->time=0.0;
-
 	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 
 		/* setting amount of runs and finite time step size */
@@ -700,7 +723,7 @@ 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);
-		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+		check_per_bound(moldyn,&(atom[i].r));
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -735,106 +758,134 @@ int velocity_verlet(t_moldyn *moldyn) {
 int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,j,k,count;
-	t_atom *atom,*btom,*ktom;
+	t_atom *itom,*jtom,*ktom;
 	t_linkcell *lc;
-	t_list neighbour[27];
-	t_list *this,*thisk,*neighbourk;
-	u8 bc,bck;
+	t_list neighbour_i[27],neighbour_j[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ijk;
 	int countn,dnlc;
 
 	count=moldyn->count;
-	atom=moldyn->atom;
+	itom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	/* reset energy */
 	moldyn->energy=0.0;
 
-printf("DEBUG: count = %d\n",count);
 	for(i=0;i<count;i++) {
-	
+
 		/* reset force */
-		v3_zero(&(atom[i].f));
+		v3_zero(&(itom[i].f));
 
 		/* single particle potential/force */
-		if(atom[i].attr&ATOM_ATTR_1BP)
-			moldyn->func1b(moldyn,&(atom[i]));
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
 
 		/* 2 body pair potential/force */
-		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 	
-printf("DEBUG: processing atom %d\n",i);
 			link_cell_neighbour_index(moldyn,
-				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
-				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
-				(atom[i].r.z+moldyn->dim.z/2)/lc->z,
-				neighbour);
+				(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);
 
 			countn=lc->countn;
 			dnlc=lc->dnlc;
 
-printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 			for(j=0;j<countn;j++) {
 
-				this=&(neighbour[j]);
+				this=&(neighbour_i[j]);
 				list_reset(this);
 
 				if(this->start==NULL)
 					continue;
 
-				bc=(j<dnlc)?0:1;
+				bc_ij=(j<dnlc)?0:1;
 
 				do {
-					btom=this->current->data;
+					jtom=this->current->data;
 
-					if(btom==&(atom[i]))
+					if(jtom==&(itom[i]))
 						continue;
 
-					if((btom->attr&ATOM_ATTR_2BP)&
-					   (atom[i].attr&ATOM_ATTR_2BP))
-printf("DEBUG: calling func2b\n");
+					if((jtom->attr&ATOM_ATTR_2BP)&
+					   (itom[i].attr&ATOM_ATTR_2BP))
 						moldyn->func2b(moldyn,
-						               &(atom[i]),
-						               btom,
-						               bc);
+						               &(itom[i]),
+						               jtom,
+						               bc_ij);
 
 					/* 3 body potential/force */
 
-					if(!(atom[i].attr&ATOM_ATTR_3BP)||
-					   !(btom->attr&ATOM_ATTR_3BP))
+					if(!(itom[i].attr&ATOM_ATTR_3BP)||
+					   !(jtom->attr&ATOM_ATTR_3BP))
 						continue;
 
 					link_cell_neighbour_index(moldyn,
-					   (btom->r.x+moldyn->dim.x/2)/lc->x,
-					   (btom->r.y+moldyn->dim.y/2)/lc->y,
-					   (btom->r.z+moldyn->dim.z/2)/lc->z,
-					   neighbourk);
+					   (jtom->r.x+moldyn->dim.x/2)/lc->x,
+					   (jtom->r.y+moldyn->dim.y/2)/lc->y,
+					   (jtom->r.z+moldyn->dim.z/2)/lc->z,
+					   neighbour_j);
 
+					/* neighbours of j */
 					for(k=0;k<lc->countn;k++) {
 
-						thisk=&(neighbourk[k]);
-						list_reset(thisk);
+						that=&(neighbour_j[k]);
+						list_reset(that);
+					
+						if(that->start==NULL)
+							continue;
+
+						bc_ijk=(k<lc->dnlc)?0:1;
+
+						do {
+
+			ktom=that->current->data;
+
+			if(!(ktom->attr&ATOM_ATTR_3BP))
+				continue;
+
+			if(ktom==jtom)
+				continue;
+
+			if(ktom==&(itom[i]))
+				continue;
+
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+
+						} while(list_next(that)!=\
+						        L_NO_NEXT_ELEMENT);
+
+					}
 					
-						if(thisk->start==NULL)
+					/* neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i[k]);
+						list_reset(that);
+					
+						if(that->start==NULL)
 							continue;
 
-						bck=(k<lc->dnlc)?0:1;
+						bc_ijk=(k<dnlc)?0:1;
 
 						do {
 
-			ktom=thisk->current->data;
+			ktom=that->current->data;
 
 			if(!(ktom->attr&ATOM_ATTR_3BP))
 				continue;
 
-			if(ktom==btom)
+			if(ktom==jtom)
 				continue;
 
-			if(ktom==&(atom[i]))
+			if(ktom==&(itom[i]))
 				continue;
 
-			moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 
-						} while(list_next(thisk)!=\
+						} while(list_next(that)!=\
 						        L_NO_NEXT_ELEMENT);
 
 					}
@@ -898,7 +949,6 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	v3_sub(&distance,&(ai->r),&(aj->r));
 	
-	v3_per_bound(&distance,&(moldyn->dim));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
@@ -942,7 +992,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		d=+h1-h2;
 		d*=eps;
 		v3_scale(&force,&distance,d);
-		v3_add(&(ai->f),&(aj->f),&force);
+		v3_add(&(ai->f),&(ai->f),&force);
 	}
 
 	return 0;
@@ -952,6 +1002,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
  * tersoff potential & force for 2 sorts of atoms
  */
 
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+	printf("[moldyn] tersoff parameter completion\n");
+	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	p->Rmixed=sqrt(p->R[0]*p->R[1]);
+	p->Amixed=sqrt(p->A[0]*p->A[1]);
+	p->Bmixed=sqrt(p->B[0]*p->B[1]);
+	p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+	p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+	return 0;
+}
+
 /* tersoff 1 body part */
 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {