From e3e1d8e2f7fc65748c8da0accb9b3e6b0b1eb049 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 1 Sep 2008 16:23:14 +0200
Subject: [PATCH] fixed static lists + first work on lowmem lists

---
 moldyn.c               | 36 +++++++++++++++++++++++++++++-------
 potentials/albe_fast.c |  6 +++---
 2 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index b73cd34..7a9709e 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1308,6 +1308,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 #ifdef STATIC_LISTS
 	lc->subcell=malloc(lc->cells*sizeof(int*));
+#elif LOWMEM_LIST
+	lc->subcell=malloc(t_lowmem_list);
 #else
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 #endif
@@ -1325,6 +1327,9 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 #ifdef STATIC_LISTS
 		printf("[moldyn] initializing 'static' linked cells (%d)\n",
 		       lc->cells);
+#elif LOWMEM_LIST
+		printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
+		       lc->cells);
 #else
 		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
 		       lc->cells);
@@ -1348,6 +1353,17 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 			       i,lc->subcell[0],lc->subcell);
 		*/
 	}
+#elif LOWMEM_LIST
+	lc->subcell->head=malloc(lc->cells*sizeof(int));
+	if(lc->subcell->head==NULL) {
+		perror("[moldyn] head init (malloc)");
+		return -1;
+	}
+	lc->subcell->list=malloc(moldyn->count*sizeof(int));
+	if(lc->subcell->list==NULL) {
+		perror("[moldyn] list init (malloc)");
+		return -1;
+	}
 #else
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
@@ -1377,7 +1393,9 @@ int link_cell_update(t_moldyn *moldyn) {
 
 	for(i=0;i<lc->cells;i++)
 #ifdef STATIC_LISTS
-		memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+		memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#elif LOWMEM_LIST
+		lc->subcell->head[i]=-1;
 #else
 		list_destroy_f(&(lc->subcell[i]));
 #endif
@@ -1389,7 +1407,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	
 #ifdef STATIC_LISTS
 		p=0;
-		while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+		while(lc->subcell[i+j*nx+k*nx*ny][p]!=-1)
 			p++;
 
 		if(p>=MAX_ATOMS_PER_LIST) {
@@ -1398,6 +1416,9 @@ int link_cell_update(t_moldyn *moldyn) {
 		}
 
 		lc->subcell[i+j*nx+k*nx*ny][p]=count;
+#elif LOWMEM_LIST
+		lc->subcell->list[count]=list->subcell->head[i+j*nx+k*nx*ny];
+		list->subcell->head=count;
 #else
 		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
 		                     &(atom[count]));
@@ -1851,6 +1872,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset force, site energy and virial of every atom */
 #ifdef PARALLEL
+	i=omp_get_thread_num();
 	#pragma omp parallel for private(virial)
 #endif
 	for(i=0;i<count;i++) {
@@ -1903,7 +1925,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 				p=0;
 
-				while(neighbour_i[j][p]!=0) {
+				while(neighbour_i[j][p]!=-1) {
 
 					jtom=&(atom[neighbour_i[j][p]]);
 					p++;
@@ -1956,7 +1978,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 			p=0;
 
-			while(neighbour_i[j][p]!=0) {
+			while(neighbour_i[j][p]!=-1) {
 
 				jtom=&(atom[neighbour_i[j][p]]);
 				p++;
@@ -2000,7 +2022,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 					q=0;
 
-					while(neighbour_i[j][q]!=0) {
+					while(neighbour_i[k][q]!=-1) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
@@ -2055,7 +2077,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 					q=0;
 
-					while(neighbour_i[j][q]!=0) {
+					while(neighbour_i[k][q]!=-1) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
@@ -2371,7 +2393,7 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 #ifdef STATIC_LISTS
 			p=0;
 
-			while(neighbour[j][p]!=0) {
+			while(neighbour[j][p]!=-1) {
 
 				jtom=&(moldyn->atom[neighbour[j][p]]);
 				p++;
diff --git a/potentials/albe_fast.c b/potentials/albe_fast.c
index 6331064..4523938 100644
--- a/potentials/albe_fast.c
+++ b/potentials/albe_fast.c
@@ -171,7 +171,7 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 			p=0;
 
-			while(neighbour_i[j][p]!=0) {
+			while(neighbour_i[j][p]!=-1) {
 
 				jtom=&(atom[neighbour_i[j][p]]);
 				p++;
@@ -236,7 +236,7 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 					q=0;
 
-					while(neighbour_i[j][q]!=0) {
+					while(neighbour_i[k][q]!=-1) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
@@ -466,7 +466,7 @@ if(moldyn->time>DSTART&&moldyn->time<DEND) {
 #ifdef STATIC_LISTS
 					q=0;
 
-					while(neighbour_i[j][q]!=0) {
+					while(neighbour_i[k][q]!=-1) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
-- 
2.20.1