X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=7d2796507452a5f49dc3082f152677d5ca533d05;hb=20409ee0c545235c9246edde2d3cda5de0ddabde;hp=992d112622ce35341fa2e3bab745c8b8b683f0e3;hpb=998262afd7a8593832a8cbb80f02c0eb42a493ff;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index 992d112..7d27965 100644 --- a/moldyn.c +++ b/moldyn.c @@ -510,6 +510,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, atom[ret].brand=brand; atom[ret].tag=count+ret; check_per_bound(moldyn,&(atom[ret].r)); + atom[ret].r_0=atom[ret].r; } /* update total system mass */ @@ -518,6 +519,40 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, return ret; } +int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr, + t_3dvec *r,t_3dvec *v) { + + t_atom *atom; + void *ptr; + int count; + + atom=moldyn->atom; + count=(moldyn->count)++; + + ptr=realloc(atom,(count+1)*sizeof(t_atom)); + if(!ptr) { + perror("[moldyn] realloc (add atom)"); + return -1; + } + moldyn->atom=ptr; + + atom=moldyn->atom; + atom[count].r=*r; + atom[count].v=*v; + atom[count].element=element; + atom[count].mass=mass; + atom[count].brand=brand; + atom[count].tag=count; + atom[count].attr=attr; + check_per_bound(moldyn,&(atom[count].r)); + atom[count].r_0=atom[count].r; + + /* update total system mass */ + total_mass_calc(moldyn); + + return 0; +} + /* cubic init */ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { @@ -630,38 +665,6 @@ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { return count; } -int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr, - t_3dvec *r,t_3dvec *v) { - - t_atom *atom; - void *ptr; - int count; - - atom=moldyn->atom; - count=(moldyn->count)++; - - ptr=realloc(atom,(count+1)*sizeof(t_atom)); - if(!ptr) { - perror("[moldyn] realloc (add atom)"); - return -1; - } - moldyn->atom=ptr; - - atom=moldyn->atom; - atom[count].r=*r; - atom[count].v=*v; - atom[count].element=element; - atom[count].mass=mass; - atom[count].brand=brand; - atom[count].tag=count; - atom[count].attr=attr; - - /* update total system mass */ - total_mass_calc(moldyn); - - return 0; -} - int destroy_atoms(t_moldyn *moldyn) { if(moldyn->atom) free(moldyn->atom); @@ -1097,8 +1100,10 @@ double e_kin_calc(t_moldyn *moldyn) { atom=moldyn->atom; moldyn->ekin=0.0; - for(i=0;icount;i++) - moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v)); + for(i=0;icount;i++) { + atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v)); + moldyn->ekin+=atom[i].ekin; + } return moldyn->ekin; } @@ -1391,7 +1396,8 @@ return 0; printf("[moldyn] integration start, go get a coffee ...\n"); /* executing the schedule */ - for(sched->count=0;sched->counttotal_sched;sched->count++) { + sched->count=0; + while(sched->counttotal_sched) { /* setting amount of runs and finite time step size */ moldyn->tau=sched->tau[sched->count]; @@ -1489,13 +1495,15 @@ return 0; } /* check for hooks */ - if(sched->count+1total_sched) - if(sched->hook) { - printf("\n ## schedule hook %d/%d start ##\n", - sched->count+1,sched->total_sched); - sched->hook(moldyn,sched->hook_params); - printf(" ## schedule hook end ##\n"); - } + if(sched->hook) { + printf("\n ## schedule hook %d/%d start ##\n", + sched->count+1,sched->total_sched-1); + sched->hook(moldyn,sched->hook_params); + printf(" ## schedule hook end ##\n"); + } + + /* increase the schedule counter */ + sched->count+=1; }