From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Fri, 1 Feb 2008 17:15:48 +0000 (+0100)
Subject: some changes (still invalid pointer freed!)
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=e84546faff88301a68958b58f66f546b03294503;p=physik%2Fposic.git

some changes (still invalid pointer freed!)
---

diff --git a/Makefile b/Makefile
index de46da4..28fd2b1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,12 +1,13 @@
 CC = gcc
 
 CFLAGS = -Wall
+#CFLAGS += -Wextra -pedantic
 CFLAGS += -O3
 CFLAGS += -g
 #CFLAGS += -ffloat-store
 
 CFLAGS += -DALBE
-CFLAGS += -DSTATIC_LISTS
+#CFLAGS += -DSTATIC_LISTS
 #CFLAGS += -DDEBUG
 CFLAGS += -DDSTART=400 -DDEND=600
 #CFLAGS += -DVDEBUG
diff --git a/moldyn.c b/moldyn.c
index 6d5f9e4..5681779 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1244,13 +1244,10 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 /* linked list / cell method */
 
-#ifdef STATIC_LISTS
-
 int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
 	int i;
-	int *foo;
 
 	lc=&(moldyn->lc);
 
@@ -1261,21 +1258,36 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 	lc->y=moldyn->dim.y/lc->ny;
 	lc->nz=moldyn->dim.z/moldyn->cutoff;
 	lc->z=moldyn->dim.z/lc->nz;
-
 	lc->cells=lc->nx*lc->ny*lc->nz;
+
+#ifdef STATIC_LISTS
 	lc->subcell=malloc(lc->cells*sizeof(int*));
+#else
+	lc->subcell=malloc(lc->cells*sizeof(t_list));
+#endif
+
+	if(lc->subcell==NULL) {
+		perror("[moldyn] cell init (malloc)");
+		return -1;
+	}
 
 	if(lc->cells<27)
 		printf("[moldyn] FATAL: less then 27 subcells!\n");
 
 	if(vol) {
+#ifdef STATIC_LISTS
 		printf("[moldyn] initializing 'static' linked cells (%d)\n",
 		       lc->cells);
+#else
+		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
+		       lc->cells);
+#endif
 		printf("  x: %d x %f A\n",lc->nx,lc->x);
 		printf("  y: %d x %f A\n",lc->ny,lc->y);
 		printf("  z: %d x %f A\n",lc->nz,lc->z);
 	}
 
+#ifdef STATIC_LISTS
 	/* list init */
 	for(i=0;i<lc->cells;i++) {
 		lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
@@ -1283,8 +1295,16 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 			perror("[moldyn] list init (malloc)");
 			return -1;
 		}
-//if(i==0) printf(" --- add one here! %d %p %p ----\n",i,lc->subcell,lc->subcell[0]);
+		/*
+		if(i==0)
+			printf(" ---> %d malloc %p (%p)\n",
+			       i,lc->subcell[0],lc->subcell);
+		*/
 	}
+#else
+	for(i=0;i<lc->cells;i++)
+		list_init_f(&(lc->subcell[i]));
+#endif
 
 	/* update the list */
 	link_cell_update(moldyn);
@@ -1298,7 +1318,9 @@ int link_cell_update(t_moldyn *moldyn) {
 	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+#ifdef STATIC_LISTS
 	int p;
+#endif
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
@@ -1307,13 +1329,18 @@ int link_cell_update(t_moldyn *moldyn) {
 	ny=lc->ny;
 
 	for(i=0;i<lc->cells;i++)
+#ifdef STATIC_LISTS
 		memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#else
+		list_destroy_f(&(lc->subcell[i]));
+#endif
 
 	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);
 
+#ifdef STATIC_LISTS
 		p=0;
 		while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
 			p++;
@@ -1324,12 +1351,27 @@ int link_cell_update(t_moldyn *moldyn) {
 		}
 
 		lc->subcell[i+j*nx+k*nx*ny][p]=count;
+#else
+		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
+		/*
+		if(j==0&&k==0)
+			printf(" ---> %d %d malloc %p (%p)\n",
+			       i,count,lc->subcell[i].current,lc->subcell);
+		*/
+#endif
 	}
 
 	return 0;
 }
 
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell) {
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
+#ifdef STATIC_LISTS
+                              int **cell
+#else
+                              t_list *cell
+#endif
+			     ) {
 
 	t_linkcell *lc;
 	int a;
@@ -1389,170 +1431,24 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 	int i;
 	t_linkcell *lc;
-	int *foo;
 
 	lc=&(moldyn->lc);
 
-	for(i=0;i<lc->cells;i++)
-{
-//printf(" --- free %p , %d\n",lc->subcell[i],i);
+	for(i=0;i<lc->cells;i++) {
+#ifdef STATIC_LISTS
+		//printf(" ---> %d free %p\n",i,lc->subcell[i]);
 		free(lc->subcell[i]);
-}
-
-	free(lc->subcell);
-
-	return 0;
-}
-
 #else
-
-int link_cell_init(t_moldyn *moldyn,u8 vol) {
-
-	t_linkcell *lc;
-	int i;
-
-	lc=&(moldyn->lc);
-
-	/* partitioning the md cell */
-	lc->nx=moldyn->dim.x/moldyn->cutoff;
-	lc->x=moldyn->dim.x/lc->nx;
-	lc->ny=moldyn->dim.y/moldyn->cutoff;
-	lc->y=moldyn->dim.y/lc->ny;
-	lc->nz=moldyn->dim.z/moldyn->cutoff;
-	lc->z=moldyn->dim.z/lc->nz;
-
-	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");
-
-	if(vol) {
-		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
-		       lc->cells);
-		printf("  x: %d x %f A\n",lc->nx,lc->x);
-		printf("  y: %d x %f A\n",lc->ny,lc->y);
-		printf("  z: %d x %f A\n",lc->nz,lc->z);
-	}
-
-	for(i=0;i<lc->cells;i++)
-		list_init_f(&(lc->subcell[i]));
-
- 	link_cell_update(moldyn);
-	
-	return 0;
-}
-
-int link_cell_update(t_moldyn *moldyn) {
-
-	int count,i,j,k;
-	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;
-
-	x=moldyn->dim.x/2;
-	y=moldyn->dim.y/2;
-	z=moldyn->dim.z/2;
-
-	for(i=0;i<lc->cells;i++)
+		//printf(" ---> %d free %p\n",i,lc->subcell[i].start);
 		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_f(&(lc->subcell[i+j*nx+k*nx*ny]),
-		                     &(atom[count]));
-//if(i==0&&j==0&&k==0) printf(" --- add one here! %d %p ----\n",count,lc->subcell[0].current);
-	}
-
-	return 0;
-}
-
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
-
-	t_linkcell *lc;
-	int a;
-	int count1,count2;
-	int ci,cj,ck;
-	int nx,ny,nz;
-	int x,y,z;
-	u8 bx,by,bz;
-
-	lc=&(moldyn->lc);
-	nx=lc->nx;
-	ny=lc->ny;
-	nz=lc->nz;
-	count1=1;
-	count2=27;
-	a=nx*ny;
-
-	cell[0]=lc->subcell[i+j*nx+k*a];
-	for(ci=-1;ci<=1;ci++) {
-		bx=0;
-		x=i+ci;
-		if((x<0)||(x>=nx)) {
-			x=(x+nx)%nx;
-			bx=1;
-		}
-		for(cj=-1;cj<=1;cj++) {
-			by=0;
-			y=j+cj;
-			if((y<0)||(y>=ny)) {
-				y=(y+ny)%ny;
-				by=1;
-			}
-			for(ck=-1;ck<=1;ck++) {
-				bz=0;
-				z=k+ck;
-				if((z<0)||(z>=nz)) {
-					z=(z+nz)%nz;
-					bz=1;
-				}
-				if(!(ci|cj|ck)) continue;
-				if(bx|by|bz) {
-					cell[--count2]=lc->subcell[x+y*nx+z*a];
-				}
-				else {
-					cell[count1++]=lc->subcell[x+y*nx+z*a];
-				}
-			}
-		}
+#endif
 	}
 
-	lc->dnlc=count1;
-
-	return count1;
-}
-
-int link_cell_shutdown(t_moldyn *moldyn) {
-
-	int i;
-	t_linkcell *lc;
-
-	lc=&(moldyn->lc);
-
-printf("FOO:\n");
-	for(i=0;i<lc->nx*lc->ny*lc->nz;i++) {
-printf(" %d\n",i);
-		list_destroy_f(&(moldyn->lc.subcell[i]));
-printf(" %d!\n",i);
-}
-
 	free(lc->subcell);
 
 	return 0;
 }
 
-#endif
-
 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 
 	int count;
@@ -2306,7 +2202,7 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 		return cnt;
 	}
 
-	// hooks
+	// hooks etc ...
 
 	return 0;
 }
diff --git a/pair_correlation_calc.c b/pair_correlation_calc.c
index 2f93ab7..f193614 100644
--- a/pair_correlation_calc.c
+++ b/pair_correlation_calc.c
@@ -39,6 +39,8 @@ int main(int argc,char **argv) {
 		return -1;
 	}
 
+	memset(&moldyn,0,sizeof(t_moldyn));
+
 	ret=moldyn_read_save_file(&moldyn,argv[1]);
 	if(ret) {
 		printf("[pair corr calc] exit!\n");