From: hackbard Date: Wed, 22 Nov 2006 10:40:07 +0000 (+0000) Subject: security ci X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=0656efc2936da55ecf0b818fe33bb2acebc689c6;p=physik%2Fposic.git security ci --- diff --git a/moldyn.c b/moldyn.c index 57f76c4..d74b391 100644 --- a/moldyn.c +++ b/moldyn.c @@ -694,14 +694,6 @@ printf("done\n"); /* generic potential and force calculation */ -#define CREATE_CELL_LIST(nb_list) \ - link_cell_neighbour_index(moldyn,\ - (atom[i].r.x+moldyn->dim.x/2)/lc->x,\ - (atom[i].r.y+moldyn->dim.y/2)/lc->y,\ - (atom[i].r.z+moldyn->dim.z/2)/lc->z,\ - nb_list); - - int potential_force_calc(t_moldyn *moldyn) { int i,count; @@ -710,13 +702,15 @@ int potential_force_calc(t_moldyn *moldyn) { t_list neighbour[27]; t_list *this; double u; + unsigned char bc,bc3; + int countn,dnlc; count=moldyn->count; atom=moldyn->atom; lc=&(moldyn->lc); /* reset energy */ - u=0.0; + moldyn->energy=0.0; for(i=0;istatus&MOLDYN_STAT_1BP) + if(atom[i].attr&ATOM_ATTR_1BP) moldyn->pf_func1b(moldyn,&(atom[i])); /* 2 body pair potential/force */ - if(moldyn->status&MOLDYN_STAT_2BP) { + if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) { - CREATE_CELL_LIST(neighbour); + link_cell_neighbour_index(moldyn, + (atom[i].r.x+moldyn->dim.x/2)/lc->x, + (atom[i].r.y+moldyn->dim.y/2)/lc->y, + (atom[i].r.z+moldyn->dim.z/2)/lc->z, + neighbour); - /* - * processing cell of atom i - * => no need to check for empty list - * (1 element at minimum) - */ + countn=lc->countn; + dnlc=lc->dnlc; - this=&(neighbour[0]); - list_reset(this); - do { - btom=this->current->data; - if(btom!=&(atom[i])) - moldyn->pf_func2b(moldyn, - &(atom[i]),btom); - } while(list_next(this)!=L_NO_NEXT_ELEMENT); + for(j=0;j no boundary condition check necessary - */ - for(j=0;jdnlc;j++) { this=&(neighbour[j]); list_reset(this); - if(this->start!=NULL) { - do { - btom=this->current->data; - moldyn->pf_func2b(moldyn, - &(atom[i]), - btom); - } while(list_next(this)!=\ - L_NO_NEXT_ELEMENT); - } - /* - * neighbour cells due to periodic bc - * => check boundary conditions - */ - for(j=lc->dnlc;jcountn;j++) { - this=&(neighbour[j]); - list_reset(this); - if(this->start!=NULL) { - do { - btom=this->current->data; + if(this->start==NULL) + continue; + + bc=(jcurrent->data; + + if(btom==&(atom[i])) + continue; + + if((btom->attr&ATOM_ATTR_2BP)& + (atom[i].attr&ATOM_ATTR_2BP)) moldyn->pf_func2b(moldyn, &(atom[i]), - btom); + btom, + bc); - } + /* 3 body potential/force */ + if(!(atom[i].attr&ATOM_ATTR_3BP)|| + !(btom->attr&ATOM_ATTR_3BP)) + continue; + + link_cell_neighbour_index(moldyn, + (btom->r.x+moldyn->dim.x/2)/lc->x, + (btom->r.y+moldyn->dim.y/2)/lc->y, + (btom->r.z+moldyn->dim.z/2)/lc->z, + neighbourk); + + for(k=0;kcountn;k++) { + + thisk=&(neighbourk[k]); + list_reset(thisk); + + if(thisk->start==NULL) + continue; + + bck=(kdnlc)?0:1; + + do { + + ktom=thisk->current->data; + + if(!(ktom->attr&ATOM_ATTR_3BP)) + continue; + + if(ktom==btom) + continue; + + if(ktom==&(atom[i])) + continue; + + moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck); + + } while(list_next(thisk)!=\ + L_NO_NEXT_ELEMENT); + + } while(list_next(this)!=L_NO_NEXT_ELEMENT); + } } + } return 0; } +/* + * example potentials + */ /* harmonic oscillator potential and force */ -int harmonic_oscillator(t_moldyn *moldyn) { +int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,unsigned char bc)) { t_ho_params *params; t_atom *atom,*btom; diff --git a/moldyn.h b/moldyn.h index 717388a..66f774e 100644 --- a/moldyn.h +++ b/moldyn.h @@ -15,6 +15,7 @@ /* datatypes */ +typedef unsigned char u8; /* the atom of the md simulation */ @@ -30,6 +31,10 @@ typedef struct s_atom { #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */ #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */ +#define ATOM_ATTR_1BP 0x10 /* single paricle potential */ +#define ATOM_ATTR_2BP 0x20 /* pair potential */ +#define ATOM_ATTR_3BP 0x40 /* 3 body potential */ + /* cell lists */ typedef struct s_linkcell { @@ -99,9 +104,6 @@ typedef struct s_moldyn { #define MOLDYN_LVSTAT_VISUAL 0x08 #define MOLDYN_LVSTAT_INITIALIZED 0x10 -#define MOLDYN_STAT_1BP 0x01 -#define MOLDYN_STAT_2BP 0x02 /* define for pair potentials */ -#define MOLDYN_STAT_3BP 0x04 /* define for 3 body pot */ #define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */ #define MOLDYN_STAT_PBY 0x10 /* y */ #define MOLDYN_STAT_PBZ 0x20 /* and z direction */