introduced lowmem lists

diff --git a/Makefile b/Makefile
index d1b78ec..4de3dcc 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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