From: hackbard Date: Thu, 31 Jan 2008 22:56:26 +0000 (+0100) Subject: added static lists (but: glibc double free prob (for both lists!)) X-Git-Url: https://www.hackdaworld.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=099c05fce45cacbbd7bbf6a7c5f1067e150d30ac;p=physik%2Fposic.git added static lists (but: glibc double free prob (for both lists!)) --- diff --git a/Makefile b/Makefile index 73645df..de46da4 100644 --- a/Makefile +++ b/Makefile @@ -6,6 +6,7 @@ CFLAGS += -g #CFLAGS += -ffloat-store CFLAGS += -DALBE +CFLAGS += -DSTATIC_LISTS #CFLAGS += -DDEBUG CFLAGS += -DDSTART=400 -DDEND=600 #CFLAGS += -DVDEBUG @@ -29,4 +30,4 @@ pair_correlation_calc: $(DEPS) .PHONY:clean clean: - rm -vf sic postproc fluctuation_calc *.o */*.o + rm -vf sic postproc fluctuation_calc pair_correlation_calc *.o */*.o diff --git a/moldyn.c b/moldyn.c index 2e0e468..6d5f9e4 100644 --- a/moldyn.c +++ b/moldyn.c @@ -1244,6 +1244,168 @@ 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); + + /* 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(int*)); + + if(lc->cells<27) + printf("[moldyn] FATAL: less then 27 subcells!\n"); + + if(vol) { + printf("[moldyn] initializing 'static' 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); + } + + /* list init */ + for(i=0;icells;i++) { + lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int)); + if(lc->subcell[i]==NULL) { + perror("[moldyn] list init (malloc)"); + return -1; + } +//if(i==0) printf(" --- add one here! %d %p %p ----\n",i,lc->subcell,lc->subcell[0]); + } + + /* update the list */ + 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; + int p; + + atom=moldyn->atom; + lc=&(moldyn->lc); + + nx=lc->nx; + ny=lc->ny; + + for(i=0;icells;i++) + memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int)); + + 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); + + p=0; + while(lc->subcell[i+j*nx+k*nx*ny][p]!=0) + p++; + + if(p>=MAX_ATOMS_PER_LIST) { + printf("[moldyn] FATAL: amount of atoms too high!\n"); + return -1; + } + + lc->subcell[i+j*nx+k*nx*ny][p]=count; + } + + return 0; +} + +int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **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]; + } + } + } + } + + lc->dnlc=count1; + + return count1; +} + +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); + free(lc->subcell[i]); +} + + free(lc->subcell); + + return 0; +} + +#else + int link_cell_init(t_moldyn *moldyn,u8 vol) { t_linkcell *lc; @@ -1266,7 +1428,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) { printf("[moldyn] FATAL: less then 27 subcells!\n"); if(vol) { - printf("[moldyn] initializing linked cells (%d)\n",lc->cells); + 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); @@ -1307,6 +1470,7 @@ int link_cell_update(t_moldyn *moldyn) { 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; @@ -1375,14 +1539,20 @@ int link_cell_shutdown(t_moldyn *moldyn) { lc=&(moldyn->lc); - for(i=0;inx*lc->ny*lc->nz;i++) +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; @@ -1676,15 +1846,24 @@ int potential_force_calc(t_moldyn *moldyn) { t_atom *itom,*jtom,*ktom; t_virial *virial; t_linkcell *lc; +#ifdef STATIC_LISTS + int *neighbour_i[27]; + int p,q; + t_atom *atom; +#else t_list neighbour_i[27]; t_list neighbour_i2[27]; t_list *this,*that; +#endif u8 bc_ij,bc_ik; int dnlc; count=moldyn->count; itom=moldyn->atom; lc=&(moldyn->lc); +#ifdef STATIC_LISTS + atom=moldyn->atom; +#endif /* reset energy */ moldyn->energy=0.0; @@ -1739,14 +1918,33 @@ int potential_force_calc(t_moldyn *moldyn) { if(moldyn->func2b) { for(j=0;j<27;j++) { + bc_ij=(jattr&ATOM_ATTR_2BP)& + (itom[i].attr&ATOM_ATTR_2BP)) { + moldyn->func2b(moldyn, + &(itom[i]), + jtom, + bc_ij); + } + } +#else this=&(neighbour_i[j]); list_reset_f(this); if(this->start==NULL) continue; - bc_ij=(jcurrent->data; @@ -1761,6 +1959,7 @@ int potential_force_calc(t_moldyn *moldyn) { bc_ij); } } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); +#endif } } @@ -1771,21 +1970,34 @@ int potential_force_calc(t_moldyn *moldyn) { continue; /* copy the neighbour lists */ +#ifdef STATIC_LISTS + /* no copy needed for static lists */ +#else memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list)); +#endif /* second loop over atoms j */ for(j=0;j<27;j++) { + bc_ij=(jstart==NULL) continue; - bc_ij=(jcurrent->data; +#endif if(jtom==&(itom[i])) continue; @@ -1811,17 +2023,24 @@ int potential_force_calc(t_moldyn *moldyn) { for(k=0;k<27;k++) { + bc_ik=(kstart==NULL) continue; - bc_ik=(kcurrent->data; +#endif if(!(ktom->attr&ATOM_ATTR_3BP)) continue; @@ -1837,9 +2056,12 @@ int potential_force_calc(t_moldyn *moldyn) { jtom, ktom, bc_ik|bc_ij); - +#ifdef STATIC_LISTS + } +#else } while(list_next_f(that)!=\ L_NO_NEXT_ELEMENT); +#endif } @@ -1856,17 +2078,24 @@ int potential_force_calc(t_moldyn *moldyn) { for(k=0;k<27;k++) { + bc_ik=(kstart==NULL) continue; - bc_ik=(kcurrent->data; +#endif if(!(ktom->attr&ATOM_ATTR_3BP)) continue; @@ -1883,8 +2112,12 @@ int potential_force_calc(t_moldyn *moldyn) { ktom, bc_ik|bc_ij); +#ifdef STATIC_LISTS + } +#else } while(list_next_f(that)!=\ L_NO_NEXT_ELEMENT); +#endif } @@ -1896,8 +2129,11 @@ int potential_force_calc(t_moldyn *moldyn) { &(itom[i]), jtom,bc_ij); } - +#ifdef STATIC_LISTS + } +#else } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); +#endif } @@ -2116,7 +2352,12 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) { double *stat; int i,j; t_linkcell *lc; +#ifdef STATIC_LISTS + int *neighbour[27]; + int p; +#else t_list neighbour[27]; +#endif t_atom *itom,*jtom; t_list *this; unsigned char bc; @@ -2130,6 +2371,12 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) { slots=(int)(moldyn->cutoff/dr); o=2*slots; + printf("[moldyn] pair correlation calc info:\n"); + printf(" time: %f\n",moldyn->time); + printf(" count: %d\n",moldyn->count); + printf(" cutoff: %f\n",moldyn->cutoff); + printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg); + if(ptr!=NULL) { stat=(double *)ptr; } @@ -2159,20 +2406,27 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) { ibrand=itom[i].brand; for(j=0;j<27;j++) { - /* prepare the neighbour cell list */ + + bc=(jdnlc)?0:1; + +#ifdef STATIC_LISTS + p=0; + + while(neighbour[j][p]!=0) { + + jtom=&(moldyn->atom[neighbour[j][p]]); + p++; +#else this=&(neighbour[j]); list_reset_f(this); - /* check for atoms */ if(this->start==NULL) continue; - /* boundary check */ - bc=(jdnlc)?0:1; - do { - jtom=this->current->data; + jtom=this->current->data; +#endif if(jtom==&(itom[i])) continue; @@ -2211,21 +2465,24 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) { stat[s+o]+=1; } +#ifdef STATIC_LISTS + } +#else } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); +#endif } } - /* normalization */ + /* normalization for(i=1;i 2 pi r r dr - */ + // normalization: 4 pi r r dr + // here: not double counting pairs -> 2 pi r r dr norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr; stat[i]/=norm; stat[slots+i]/=norm; stat[o+i]/=norm; } + */ if(ptr==NULL) { /* todo: store/print pair correlation function */ @@ -2268,7 +2525,12 @@ int visual_atoms(t_moldyn *moldyn) { t_atom *atom; t_atom *btom; t_linkcell *lc; +#ifdef STATIC_LISTS + int *neighbour[27]; + int p; +#else t_list neighbour[27]; +#endif u8 bc; t_3dvec dist; double d2; @@ -2322,12 +2584,19 @@ int visual_atoms(t_moldyn *moldyn) { (atom[i].r.z+moldyn->dim.z/2)/lc->z, neighbour); for(j=0;j<27;j++) { + bc=jdnlc?0:1; +#ifdef STATIC_LISTS + p=0; + while(neighbour[j][p]!=0) { + btom=&(atom[neighbour[j][p]]); + p++; +#else list_reset_f(&neighbour[j]); if(neighbour[j].start==NULL) continue; - bc=jdnlc?0:1; do { btom=neighbour[j].current->data; +#endif if(btom==&atom[i]) // skip identical atoms continue; //if(btom<&atom[i]) // skip half of them @@ -2347,7 +2616,11 @@ int visual_atoms(t_moldyn *moldyn) { dprintf(fd,"# [B] %f %f %f %f %f %f\n", atom[i].r.x,atom[i].r.y,atom[i].r.z, btom->r.x,btom->r.y,btom->r.z); +#ifdef STATIC_LISTS + } +#else } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT); +#endif } } diff --git a/moldyn.h b/moldyn.h index a7a81e9..ee45228 100644 --- a/moldyn.h +++ b/moldyn.h @@ -62,10 +62,16 @@ typedef struct s_linkcell { int cells; /* total amount of cells */ double len; /* prefered cell edge length */ double x,y,z; /* the actual cell lengthes */ +#ifdef STATIC_LISTS + int **subcell; /* pointer to the cell lists */ +#else t_list *subcell; /* pointer to the cell lists */ +#endif int dnlc; /* direct neighbour lists counter */ } t_linkcell; +#define MAX_ATOMS_PER_LIST 10 + /* moldyn schedule structure */ typedef struct s_moldyn_schedule { int count; @@ -454,7 +460,11 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist); 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); +#else int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell); +#endif int link_cell_shutdown(t_moldyn *moldyn); typedef int (*set_hook)(void *,void *);