printf("--- physics options ---\n");
printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
+ printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
printf("-R <runs> (%d)\n",MOLDYN_RUNS);
printf(" -- integration algo --\n");
printf(" -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
case 't':
moldyn->tau=atof(argv[++i]);
break;
+ case 'C':
+ moldyn->cutoff=atof(argv[++i]);
+ break;
case 'R':
moldyn->time_steps=atoi(argv[++i]);
break;
return 0;
}
-int moldyn_log_init(t_moldyn *moldyn,void *v) {
+int moldyn_log_init(t_moldyn *moldyn) {
moldyn->lvstat=0;
t_visual *vis;
- vis=v;
+ vis=&(moldyn->vis);
if(moldyn->ewrite) {
moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
return 0;
}
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
if(moldyn->efd) close(moldyn->efd);
if(moldyn->mfd) close(moldyn->efd);
return 0;
}
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+ int ret;
+
+ ret=moldyn_parse_argv(moldyn,argc,argv);
+ if(ret<0) return ret;
+
+ ret=moldyn_log_init(moldyn);
+ if(ret<0) return ret;
+
+ rand_init(&(moldyn->random),NULL,1);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
+
+ moldyn->status=0;
+
+ return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+ moldyn_log_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
+
+ return 0;
+}
+
int create_lattice(unsigned char type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom) {
return 0;
}
-int thermal_init(t_moldyn *moldyn,t_random *random) {
+int thermal_init(t_moldyn *moldyn) {
/*
* - gaussian distribution of velocities
double v,sigma;
t_3dvec p_total,delta;
t_atom *atom;
+ t_random *random;
atom=moldyn->atom;
+ random=&(moldyn->random);
/* gaussian distribution of velocities */
v3_zero(&p_total);
int link_cell_init(t_moldyn *moldyn) {
t_linkcell *lc;
+ int i;
lc=&(moldyn->lc);
+ /* list log fd */
+ lc->listfd=open("/dev/null",O_WRONLY);
+
/* partitioning the md cell */
lc->nx=moldyn->dim.x/moldyn->cutoff;
lc->x=moldyn->dim.x/lc->nx;
lc->nz=moldyn->dim.z/moldyn->cutoff;
lc->z=moldyn->dim.z/lc->nz;
- lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+ lc->cells=lc->nx*lc->ny*lc->nz;
+ lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+ printf("initializing linked cells (%d)\n",lc->cells);
+
+ for(i=0;i<lc->cells;i++)
+ list_init(&(lc->subcell[i]),1);
+ //list_init(&(lc->subcell[i]),lc->listfd);
link_cell_update(moldyn);
ny=lc->ny;
nz=lc->nz;
- for(i=0;i<nx*ny*nz;i++)
+ for(i=0;i<lc->cells;i++)
list_destroy(&(moldyn->lc.subcell[i]));
for(count=0;count<moldyn->count;count++) {
- i=atom[count].r.x/lc->x;
- j=atom[count].r.y/lc->y;
- k=atom[count].r.z/lc->z;
+ 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_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
&(atom[count]));
}
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nx=lc->nz;
+ nz=lc->nz;
count1=1;
count2=27;
a=nx*ny;
+
cell[0]=lc->subcell[i+j*nx+k*a];
+ printf("%d\n",i+j*nx+k*a);
for(ci=-1;ci<=1;ci++) {
bx=0;
x=i+ci;
z=(z+nz)%nz;
bz=1;
}
- if(!(x|y|z)) continue;
+ if(!(ci|cj|ck)) continue;
+ printf(" %d %d %d \n",x,y,z);
if(bx|by|bz) {
cell[--count2]=lc->subcell[x+y*nx+z*a];
+ printf("%d\n",x+y*nx+z*a);
+ printf("--- %d\n",count2);
}
else {
cell[count1++]=lc->subcell[x+y*nx+z*a];
+ printf("%d\n",x+y*nx+z*a);
+ printf("--- %d\n",count1);
}
}
}
for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
list_shutdown(&(moldyn->lc.subcell[i]));
+ if(lc->listfd) close(lc->listfd);
+
return 0;
}
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
- /* create the neighbour list */
- link_cell_update(moldyn);
-
/* calculate initial forces */
moldyn->potential_force_function(moldyn);
for(i=0;i<moldyn->time_steps;i++) {
- /* show runs */
- printf(".");
/* neighbour list update */
link_cell_update(moldyn);
}
if(v) {
- if(!(i%v))
+ if(!(i%v)) {
visual_atoms(moldyn->visual,i*moldyn->tau,
moldyn->atom,moldyn->count);
+ printf("\rsteps: %d",i);
+ fflush(stdout);
+ }
}
}
u=0.0;
for(i=0;i<count;i++) {
/* determine cell + neighbours */
- ni=atom[i].r.x/lc->x;
- nj=atom[i].r.y/lc->y;
- nk=atom[i].r.z/lc->z;
+ ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+ nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+ nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+ printf("%d %d %d\n",ni,nj,nk);
c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
/* processing cell of atom i */
u=0.0;
for(i=0;i<count;i++) {
/* determine cell + neighbours */
- ni=atom[i].r.x/lc->x;
- nj=atom[i].r.y/lc->y;
- nk=atom[i].r.z/lc->z;
+ ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+ nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+ nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+ printf("hier atom = %08x\n",&(atom[i]));
c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+ printf("da atom = %08x\n",&(atom[i]));
+ printf("da atom = %08x\n",&(moldyn->atom[i]));
+
+ printf("c = %d (%d %d %d)\n",c,ni,nj,nk);
/* processing cell of atom i */
this=&(neighbour[0]);
btom=this->current->data;
if(btom==&(atom[i]))
continue;
+ puts("foo");
v3_sub(&distance,&(atom[i].r),&(btom->r));
+ puts("foo");
d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
h1=d*d; /* 1/r^4 */
h2*=d; /* 1/r^6 */
d*=eps;
v3_scale(&force,&distance,d);
v3_add(&(atom[i].f),&(atom[i].f),&force);
+ printf("test!!\n");
} while(list_next(this)!=L_NO_NEXT_ELEMENT);
/* neighbours not doing boundary condition overflow */
if(this->start!=NULL) {
do {
+ printf("in bound: %d\n",j);
btom=this->current->data;
v3_sub(&distance,&(atom[i].r),&(btom->r));
d=v3_absolute_square(&distance); /* r^2 */
if(this->start!=NULL) {
do {
+ printf("out bound: %d\n",j);
btom=this->current->data;
v3_sub(&distance,&(atom[i].r),&(btom->r));
v3_per_bound(&distance,&(moldyn->dim));