X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=6da2b959c32fb3afbdd10b90a8903bc94925b5ab;hb=55fd772a75e72968f166743b495ee751a633b305;hp=b73cd3432b65971aabc055e7f126fc5efdb3deb4;hpb=cb2811d92cb79b1f24d11d4f4897426ce5f7dc3a;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index b73cd34..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);
 
@@ -1308,6 +1319,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 #ifdef STATIC_LISTS
 	lc->subcell=malloc(lc->cells*sizeof(int*));
+#elif LOWMEM_LISTS
+	lc->subcell=malloc(sizeof(t_lowmem_list));
 #else
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 #endif
@@ -1325,6 +1338,9 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 #ifdef STATIC_LISTS
 		printf("[moldyn] initializing 'static' linked cells (%d)\n",
 		       lc->cells);
+#elif LOWMEM_LISTS
+		printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
+		       lc->cells);
 #else
 		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
 		       lc->cells);
@@ -1348,6 +1364,17 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 			       i,lc->subcell[0],lc->subcell);
 		*/
 	}
+#elif LOWMEM_LISTS
+	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]));
@@ -1362,22 +1389,26 @@ 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],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+		memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#elif LOWMEM_LISTS
+		lc->subcell->head[i]=-1;
 #else
 		list_destroy_f(&(lc->subcell[i]));
 #endif
@@ -1389,7 +1420,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	
 #ifdef STATIC_LISTS
 		p=0;
-		while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+		while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
 			p++;
 
 		if(p>=MAX_ATOMS_PER_LIST) {
@@ -1397,9 +1428,13 @@ int link_cell_update(t_moldyn *moldyn) {
 			return -1;
 		}
 
-		lc->subcell[i+j*nx+k*nx*ny][p]=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)
@@ -1415,6 +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
@@ -1440,7 +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;
@@ -1464,10 +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
 				}
 			}
 		}
@@ -1480,11 +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]);
@@ -1493,6 +1551,7 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 		list_destroy_f(&(lc->subcell[i]));
 #endif
 	}
+#endif
 
 	free(lc->subcell);
 
@@ -1828,6 +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];
@@ -1851,6 +1913,7 @@ 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++) {
@@ -1903,10 +1966,17 @@ 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++;
+#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);
@@ -1930,6 +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
@@ -1945,6 +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
@@ -1956,10 +2030,17 @@ 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++;
+#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);
@@ -2000,10 +2081,17 @@ 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++;
+#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);
@@ -2031,6 +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);
@@ -2055,10 +2145,17 @@ 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++;
+#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);
@@ -2087,6 +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);
@@ -2104,6 +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
@@ -2345,6 +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;
@@ -2371,10 +2475,17 @@ 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++;
+#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);
@@ -2392,6 +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