From e84546faff88301a68958b58f66f546b03294503 Mon Sep 17 00:00:00 2001 From: hackbard Date: Fri, 1 Feb 2008 18:15:48 +0100 Subject: [PATCH] some changes (still invalid pointer freed!) --- Makefile | 3 +- moldyn.c | 212 ++++++++++------------------------------ pair_correlation_calc.c | 2 + 3 files changed, 58 insertions(+), 159 deletions(-) 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;icells;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;icells;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;icells;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;countcount;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;icells;i++) -{ -//printf(" --- free %p , %d\n",lc->subcell[i],i); + for(i=0;icells;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;icells;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;icells;i++) + //printf(" ---> %d free %p\n",i,lc->subcell[i].start); list_destroy_f(&(lc->subcell[i])); - - for(count=0;countcount;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;inx*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"); -- 2.20.1