From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 1 Sep 2008 23:17:00 +0000 (+0200)
Subject: introduced lowmem lists
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=99a9305339d568641a7ec55783faa161b3c33311;p=physik%2Fposic.git

introduced lowmem lists
---

diff --git a/Makefile b/Makefile
index d1b78ec..4de3dcc 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-CC = gcc
+CC = gcc-4.3
 
 CFLAGS = -Wall -Winline
 #CFLAGS += -Wextra -pedantic
@@ -13,6 +13,7 @@ CFLAGS += -DALBE_FAST
 #CFLAGS += -DTERSOFF_ORIG
 
 #CFLAGS += -DSTATIC_LISTS
+CFLAGS += -DLOWMEM_LISTS
 
 #CFLAGS += -DDEBUG
 #CFLAGS += -DDSTART=-1 -DDEND=40 -DDATOM=0
diff --git a/moldyn.c b/moldyn.c
index 7a9709e..6da2b95 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -600,6 +600,15 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	}
 	moldyn->atom=ptr;
 
+#ifdef LOWMEM_LISTS
+	ptr=realloc(moldyn->lc.subcell->list,(count+1)*sizeof(int));
+	if(!ptr) {
+		perror("[moldyn] list realloc (add atom)");
+		return -1;
+	}
+	moldyn->lc.subcell->list=ptr;
+#endif
+
 	atom=moldyn->atom;
 
 	/* initialize new atom */
@@ -1293,7 +1302,9 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
+#ifndef LOWMEM_LISTS
 	int i;
+#endif
 
 	lc=&(moldyn->lc);
 
@@ -1308,8 +1319,8 @@ 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);
+#elif LOWMEM_LISTS
+	lc->subcell=malloc(sizeof(t_lowmem_list));
 #else
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 #endif
@@ -1327,7 +1338,7 @@ 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
+#elif LOWMEM_LISTS
 		printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
 		       lc->cells);
 #else
@@ -1353,7 +1364,7 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 			       i,lc->subcell[0],lc->subcell);
 		*/
 	}
-#elif LOWMEM_LIST
+#elif LOWMEM_LISTS
 	lc->subcell->head=malloc(lc->cells*sizeof(int));
 	if(lc->subcell->head==NULL) {
 		perror("[moldyn] head init (malloc)");
@@ -1378,23 +1389,25 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny;
+	int nx,nxy;
 	t_atom *atom;
 	t_linkcell *lc;
 #ifdef STATIC_LISTS
 	int p;
+#elif LOWMEM_LISTS
+	int p;
 #endif
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
-	ny=lc->ny;
+	nxy=nx*lc->ny;
 
 	for(i=0;i<lc->cells;i++)
 #ifdef STATIC_LISTS
 		memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
-#elif LOWMEM_LIST
+#elif LOWMEM_LISTS
 		lc->subcell->head[i]=-1;
 #else
 		list_destroy_f(&(lc->subcell[i]));
@@ -1407,7 +1420,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	
 #ifdef STATIC_LISTS
 		p=0;
-		while(lc->subcell[i+j*nx+k*nx*ny][p]!=-1)
+		while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
 			p++;
 
 		if(p>=MAX_ATOMS_PER_LIST) {
@@ -1415,12 +1428,13 @@ int link_cell_update(t_moldyn *moldyn) {
 			return -1;
 		}
 
-		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;
+		lc->subcell[i+j*nx+k*nxy][p]=count;
+#elif LOWMEM_LISTS
+		p=i+j*nx+k*nxy;
+		lc->subcell->list[count]=lc->subcell->head[p];
+		lc->subcell->head[p]=count;
 #else
-		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nxy]),
 		                     &(atom[count]));
 		/*
 		if(j==0&&k==0)
@@ -1436,6 +1450,8 @@ int link_cell_update(t_moldyn *moldyn) {
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 #ifdef STATIC_LISTS
                               int **cell
+#elif LOWMEM_LISTS
+                              int *cell
 #else
                               t_list *cell
 #endif
@@ -1461,7 +1477,11 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 		printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
 		       i,nx,j,ny,k,nz);
 
+#ifndef LOWMEM_LISTS
 	cell[0]=lc->subcell[i+j*nx+k*a];
+#else
+	cell[0]=lc->subcell->head[i+j*nx+k*a];
+#endif
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
 		x=i+ci;
@@ -1485,10 +1505,19 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 				}
 				if(!(ci|cj|ck)) continue;
 				if(bx|by|bz) {
+#ifndef LOWMEM_LISTS
 					cell[--count2]=lc->subcell[x+y*nx+z*a];
+#else
+				cell[--count2]=lc->subcell->head[x+y*nx+z*a];
+#endif
+					
 				}
 				else {
+#ifndef LOWMEM_LISTS
 					cell[count1++]=lc->subcell[x+y*nx+z*a];
+#else
+				cell[count1++]=lc->subcell->head[x+y*nx+z*a];
+#endif
 				}
 			}
 		}
@@ -1501,11 +1530,19 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 
 int link_cell_shutdown(t_moldyn *moldyn) {
 
+#ifndef LOWMEM_LISTS
 	int i;
+#endif
 	t_linkcell *lc;
 
 	lc=&(moldyn->lc);
 
+#if LOWMEM_LISTS
+	free(lc->subcell->head);
+	free(lc->subcell->list);
+
+#else
+
 	for(i=0;i<lc->cells;i++) {
 #ifdef STATIC_LISTS
 		free(lc->subcell[i]);
@@ -1514,6 +1551,7 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 		list_destroy_f(&(lc->subcell[i]));
 #endif
 	}
+#endif
 
 	free(lc->subcell);
 
@@ -1849,6 +1887,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 	int *neighbour_i[27];
 	int p,q;
 	t_atom *atom;
+#elif LOWMEM_LISTS
+	int neighbour_i[27];
+	int p,q;
 #else
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
@@ -1929,6 +1970,13 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 					jtom=&(atom[neighbour_i[j][p]]);
 					p++;
+#elif LOWMEM_LISTS
+				p=neighbour_i[j];
+
+				while(p!=-1) {
+
+					jtom=&(itom[p]);
+					p=lc->subcell->list[p];
 #else
 				this=&(neighbour_i[j]);
 				list_reset_f(this);
@@ -1952,6 +2000,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 					}
 #ifdef STATIC_LISTS
 				}
+#elif LOWMEM_LISTS
+				}
 #else
 				} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif
@@ -1967,6 +2017,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 		/* copy the neighbour lists */
 #ifdef STATIC_LISTS
 		/* no copy needed for static lists */
+#elif LOWMEM_LISTS
+		/* no copy needed for lowmem lists */
 #else
 		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
 #endif
@@ -1982,6 +2034,13 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 				jtom=&(atom[neighbour_i[j][p]]);
 				p++;
+#elif LOWMEM_LISTS
+				p=neighbour_i[j];
+
+				while(p!=-1) {
+
+					jtom=&(itom[p]);
+					p=lc->subcell->list[p];
 #else
 			this=&(neighbour_i[j]);
 			list_reset_f(this);
@@ -2026,6 +2085,13 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
 #else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
@@ -2053,6 +2119,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 						                  bc_ik|bc_ij);
 #ifdef STATIC_LISTS
 					}
+#elif LOWMEM_LISTS
+					}
 #else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
@@ -2081,6 +2149,13 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
 #else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
@@ -2109,6 +2184,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 #ifdef STATIC_LISTS
 					}
+#elif LOWMEM_LISTS
+					}
 #else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
@@ -2126,6 +2203,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 				}
 #ifdef STATIC_LISTS
 			}
+#elif LOWMEM_LISTS
+			}
 #else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif
@@ -2367,6 +2446,9 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 #ifdef STATIC_LISTS
 	int *neighbour[27];
 	int p;
+#elif LOWMEM_LISTS
+	int neighbour[27];
+	int p;
 #else
 	t_list neighbour[27];
 	t_list *this;
@@ -2397,6 +2479,13 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 				jtom=&(moldyn->atom[neighbour[j][p]]);
 				p++;
+#elif LOWMEM_LISTS
+			p=neighbour[j];
+
+			while(p!=-1) {
+
+				jtom=&(itom[p]);
+				p=lc->subcell->list[p];
 #else
 			this=&(neighbour[j]);
 			list_reset_f(this);
@@ -2414,6 +2503,8 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 #ifdef STATIC_LISTS
 			}
+#elif LOWMEM_LISTS
+			}
 #else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif
diff --git a/moldyn.h b/moldyn.h
index c3b8c6b..da951b5 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -58,6 +58,12 @@ typedef struct s_atom {
 
 #define DEFAULT_ATOM_ATTR	0x74	// 1,2,3 body interaction + visualize
 
+/* special list structure for low mem approach */
+typedef struct s_lowmem_list {
+	int *head;
+	int *list;
+} t_lowmem_list;
+
 /* cell lists */
 typedef struct s_linkcell {
 	int nx,ny,nz;		/* amount of cells in x, y and z direction */
@@ -66,6 +72,8 @@ typedef struct s_linkcell {
 	double x,y,z;		/* the actual cell lengthes */
 #ifdef STATIC_LISTS
 	int **subcell;		/* pointer to the cell lists */
+#elif LOWMEM_LISTS
+	t_lowmem_list *subcell; /* low mem approach list */
 #else
 	t_list *subcell;	/* pointer to the cell lists */
 #endif
@@ -424,6 +432,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol);
 int link_cell_update(t_moldyn *moldyn);
 #ifdef STATIC_LISTS
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+#elif LOWMEM_LISTS
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int *cell);
 #else
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 #endif
diff --git a/potentials/albe_fast.c b/potentials/albe_fast.c
index 4523938..45ebff9 100644
--- a/potentials/albe_fast.c
+++ b/potentials/albe_fast.c
@@ -45,7 +45,9 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 	int *neighbour_i[27];
 	int p,q;
-	t_atom *atom;
+#elif LOWMEM_LISTS
+	int neighbour_i[27];
+	int p,q;
 #else
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
@@ -102,9 +104,6 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 	count=moldyn->count;
 	itom=moldyn->atom;
 	lc=&(moldyn->lc);
-#ifdef STATIC_LISTS
-	atom=moldyn->atom;
-#endif
 
 	// optimized
 	params=moldyn->pot_params;
@@ -157,7 +156,9 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 		dnlc=lc->dnlc;
 
 		/* copy the neighbour lists */
-#ifndef STATIC_LISTS
+#ifdef STATIC_LISTS
+#elif LOWMEM_LISTS
+#else
 		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
 #endif
 
@@ -173,8 +174,15 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 
 			while(neighbour_i[j][p]!=-1) {
 
-				jtom=&(atom[neighbour_i[j][p]]);
+				jtom=&(itom[neighbour_i[j][p]]);
 				p++;
+#elif LOWMEM_LISTS
+			p=neighbour_i[j];
+
+			while(p!=-1) {
+
+				jtom=&(itom[p]);
+				p=lc->subcell->list[p];
 #else
 			this=&(neighbour_i[j]);
 			list_reset_f(this);
@@ -238,8 +246,15 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 
 					while(neighbour_i[k][q]!=-1) {
 
-						ktom=&(atom[neighbour_i[k][q]]);
+						ktom=&(itom[neighbour_i[k][q]]);
 						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
 #else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
@@ -359,6 +374,8 @@ int albe_potential_force_calc(t_moldyn *moldyn) {
 
 #ifdef STATIC_LISTS
 					}
+#elif LOWMEM_LISTS
+					}
 #else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
@@ -468,8 +485,15 @@ if(moldyn->time>DSTART&&moldyn->time<DEND) {
 
 					while(neighbour_i[k][q]!=-1) {
 
-						ktom=&(atom[neighbour_i[k][q]]);
+						ktom=&(itom[neighbour_i[k][q]]);
 						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
 #else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
@@ -597,6 +621,8 @@ if(moldyn->time>DSTART&&moldyn->time<DEND) {
 
 #ifdef STATIC_LISTS
 					}
+#elif LOWMEM_LISTS
+					}
 #else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
@@ -606,6 +632,8 @@ if(moldyn->time>DSTART&&moldyn->time<DEND) {
 				
 #ifdef STATIC_LISTS
 			}
+#elif LOWMEM_LISTS
+			}
 #else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif