X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=551e07a89ea47bde8a3ad8439308f9a94a6f93e8;hb=72ce33393b80034e6407f506de88652895ffab23;hp=b6fa8d3df41dbf12e89c0596463a6cba4207255b;hpb=88ea16029cc07a837977f737f4536fa3e881dcee;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index b6fa8d3..551e07a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -17,20 +17,8 @@
 
 #include "moldyn.h"
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
-	//int ret;
-
-	//ret=moldyn_parse_argv(moldyn,argc,argv);
-	//if(ret<0) return ret;
-
 	memset(moldyn,0,sizeof(t_moldyn));
 
 	rand_init(&(moldyn->random),NULL,1);
@@ -108,7 +96,7 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
-	printf("[moldyn] dimensions in A and A^2 respectively:\n");
+	printf("[moldyn] dimensions in A and A^3 respectively:\n");
 	printf("  x: %f\n",moldyn->dim.x);
 	printf("  y: %f\n",moldyn->dim.y);
 	printf("  z: %f\n",moldyn->dim.z);
@@ -237,6 +225,10 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * creating lattice functions
+ */
+
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                    u8 attr,u8 bnum,int a,int b,int c) {
 
@@ -295,6 +287,90 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	return ret;
 }
 
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j;
+	t_3dvec o,r,n;
+	t_3dvec basis[3];
+	double help[3];
+	double x,y,z;
+
+	x=a*lc;
+	y=b*lc;
+	z=c*lc;
+
+	if(origin) v3_copy(&o,origin);
+	else v3_zero(&o);
+
+	/* construct the basis */
+	for(i=0;i<3;i++) {
+		for(j=0;j<3;j++) {
+			if(i!=j) help[j]=0.5*lc;
+			else help[j]=.0;
+		}
+		v3_set(&basis[i],help);
+	}
+
+	v3_zero(&r);
+	count=0;
+	
+	/* fill up the room */
+	r.x=o.x;
+	while(r.x<x) {
+		r.y=o.y;
+		while(r.y<y) {
+			r.z=o.z;
+			while(r.z<z) {
+				v3_copy(&(atom[count].r),&r);
+				atom[count].element=1;
+				count+=1;
+				for(i=0;i<3;i++) {
+					v3_add(&n,&r,&basis[i]);
+					if((n.x<x+o.x)&&
+					   (n.y<y+o.y)&&
+					   (n.z<z+o.z)) {
+						v3_copy(&(atom[count].r),&n);
+						count+=1;
+					}
+				}
+				r.z+=lc;	
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	/* coordinate transformation */
+	help[0]=x/2.0;
+	help[1]=y/2.0;
+	help[2]=z/2.0;
+	v3_set(&n,help);
+	for(i=0;i<count;i++)
+		v3_sub(&(atom[i].r),&(atom[i].r),&n);
+		
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}
+
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
              t_3dvec *r,t_3dvec *v) {
 
@@ -551,9 +627,6 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
-	int fd;
-
-	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -571,8 +644,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),fd);
+		list_init_f(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -582,26 +654,30 @@ int link_cell_init(t_moldyn *moldyn) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny,nz;
+	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+	double x,y,z;
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
 	ny=lc->ny;
-	nz=lc->nz;
+
+	x=moldyn->dim.x/2;
+	y=moldyn->dim.y/2;
+	z=moldyn->dim.z/2;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(lc->subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
-		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
-		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
-		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
-		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[count]));
+		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
 	}
 
 	return 0;
@@ -671,7 +747,9 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	lc=&(moldyn->lc);
 
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_shutdown(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
 
 	return 0;
 }
@@ -786,11 +864,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
-{
-printf("going to do p scale ...\n");
 			scale_volume(moldyn);
-printf("done\n");
-}
 
 		/* check for log & visualization */
 		if(e) {
@@ -869,16 +943,13 @@ 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);
-//if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 		check_per_bound(moldyn,&(atom[i].r));
-//if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
-//moldyn_bc_check(moldyn);
 	/* neighbour list update */
 	link_cell_update(moldyn);
 
@@ -930,6 +1001,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 		/* reset viral of atom i */
 		v3_zero(&(itom[i].virial));
 
+		/* reset site energy */
+		itom[i].e=0.0;
+
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
 			moldyn->func1b(moldyn,&(itom[i]));
@@ -950,7 +1024,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		for(j=0;j<27;j++) {
 
 			this=&(neighbour_i[j]);
-			list_reset(this);
+			list_reset_f(this);
 
 			if(this->start==NULL)
 				continue;
@@ -985,7 +1059,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 				for(k=0;k<27;k++) {
 
 					that=&(neighbour_i2[k]);
-					list_reset(that);
+					list_reset_f(that);
 					
 					if(that->start==NULL)
 						continue;
@@ -1011,7 +1085,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 						               ktom,
 						               bc_ik|bc_ij);
 
-					} while(list_next(that)!=\
+					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
 
 				}
@@ -1023,7 +1097,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 					                    jtom,bc_ij);
 				}
 					
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 		
 		}
 
@@ -1036,7 +1110,7 @@ int potential_force_calc(t_moldyn *moldyn) {
  * periodic boundayr checking
  */
 
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
 	double x,y,z;
 	t_3dvec *dim;
@@ -1755,4 +1829,3 @@ x=dim->x/2;
 
 	return 0;
 }
-