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]));
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];
for(ci=-1;ci<=1;ci++) {
bx=0;
z=(z+nz)%nz;
bz=1;
}
- if(!(x|y|z)) continue;
+ if(!(ci|cj|ck)) continue;
if(bx|by|bz) {
cell[--count2]=lc->subcell[x+y*nx+z*a];
}
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;
}
int fd;
char fb[128];
+ /* initialize linked cell method */
+ link_cell_init(moldyn);
+
/* logging & visualization */
e=moldyn->ewrite;
m=moldyn->mwrite;
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);
/* integration step */
moldyn->integrate(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);
+ }
}
}
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+ /* neighbour list update */
+printf("list update ...\n");
+ link_cell_update(moldyn);
+printf("done\n");
+
/* forces depending on chosen potential */
+printf("calc potential/force ...\n");
moldyn->potential_force_function(moldyn);
+printf("done\n");
for(i=0;i<count;i++) {
/* again velocities */
equi_dist=params->equilibrium_distance;
count=moldyn->count;
+ /* reset energy counter */
u=0.0;
+
for(i=0;i<count;i++) {
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
/* 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;
c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
- /* processing cell of atom i */
+ /*
+ * processing cell of atom i
+ * => no need to check for empty list (1 element at minimum)
+ */
this=&(neighbour[0]);
- list_reset(this); /* list has 1 element at minimum */
+ list_reset(this);
do {
btom=this->current->data;
if(btom==&(atom[i]))
continue;
v3_sub(&distance,&(atom[i].r),&(btom->r));
d=v3_norm(&distance);
- u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
- v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
- v3_add(&(atom[i].f),&(atom[i].f),&force);
+ if(d<=moldyn->cutoff) {
+ u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ v3_scale(&force,&distance,
+ -sc*(1.0-(equi_dist/d)));
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ }
} while(list_next(this)!=L_NO_NEXT_ELEMENT);
- /* neighbours not doing boundary condition overflow */
+ /*
+ * direct neighbour cells
+ * => no boundary condition check necessary
+ */
for(j=1;j<c;j++) {
this=&(neighbour[j]);
list_reset(this); /* there might not be a single atom */
}
}
- /* neighbours due to boundary conditions */
+ /*
+ * indirect neighbour cells
+ * => check boundary conditions
+ */
for(j=c;j<27;j++) {
this=&(neighbour[j]);
list_reset(this); /* check boundary conditions */
}
}
- moldyn->energy=u;
+ moldyn->energy=0.5*u;
return 0;
}
sig6=params->sigma6;
sig12=params->sigma12;
+ /* reset energy counter */
u=0.0;
+
for(i=0;i<count;i++) {
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
/* 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;
c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
/* processing cell of atom i */
if(btom==&(atom[i]))
continue;
v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
- h1=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=eps*(sig12*h1-sig6*h2);
- h2*=d; /* 1/r^8 */
- h1*=d; /* 1/r^14 */
- h2*=6*sig6;
- h1*=12*sig12;
- d=-h1+h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(atom[i].f),&(atom[i].f),&force);
+ d=v3_absolute_square(&distance); /* 1/r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ u+=eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=+h1-h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ }
} while(list_next(this)!=L_NO_NEXT_ELEMENT);
/* neighbours not doing boundary condition overflow */
d=v3_absolute_square(&distance); /* r^2 */
if(d<=moldyn->cutoff_square) {
d=1.0/d; /* 1/r^2 */
- h1=d*d; /* 1/r^4 */
+ h2=d*d; /* 1/r^4 */
h2*=d; /* 1/r^6 */
h1=h2*h2; /* 1/r^12 */
u+=eps*(sig12*h1-sig6*h2);
h1*=d; /* 1/r^14 */
h2*=6*sig6;
h1*=12*sig12;
- d=-h1+h2;
+ d=+h1-h2;
d*=eps;
v3_scale(&force,&distance,d);
v3_add(&(atom[i].f),&(atom[i].f),
d=v3_absolute_square(&distance); /* r^2 */
if(d<=moldyn->cutoff_square) {
d=1.0/d; /* 1/r^2 */
- h1=d*d; /* 1/r^4 */
+ h2=d*d; /* 1/r^4 */
h2*=d; /* 1/r^6 */
h1=h2*h2; /* 1/r^12 */
u+=eps*(sig12*h1-sig6*h2);
h1*=d; /* 1/r^14 */
h2*=6*sig6;
h1*=12*sig12;
- d=-h1+h2;
+ d=+h1-h2;
d*=eps;
v3_scale(&force,&distance,d);
v3_add(&(atom[i].f),&(atom[i].f),
}
}
- moldyn->energy=u;
+ moldyn->energy=0.5*u;
+
+ return 0;
+}
+
+/* tersoff potential & force for 2 sorts of atoms */
+
+int tersoff(t_moldyn *moldyn) {
+
+ t_tersoff_params *params;
+ t_atom *atom,*btom,*ktom;
+ t_linkcell *lc;
+ t_list *this,*thisk,neighbour[27],neighbourk[27];
+ int i,j,k,c,ck;
+ int count;
+ double u;
+ int ni,nj,nk;
+ int ki,kj,kk;
+
+
+ params=moldyn->pot_params;
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+ count=moldyn->count;
+ /* reset enrgy counter */
+ u=0.0;
+
+ for(i=0;i<count;i++) {
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
+ /* determin cell neighbours */
+ 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;
+ c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+ /*
+ * processing cell of atom i
+ * => no need to check for empty list (1 element at minimum)
+ */
+ this=&(neighbour[0]);
+ list_reset(this);
+ do {
+ btom=this->current->data;
+ if(btom==&(atom[i]))
+ continue;
+
+ /* 2 body stuff */
+
+ /* determine cell neighbours of btom */
+ ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+ kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+ kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+ ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+ neighbourk);
+
+ /* cell of btom */
+ thisk=&(neighbourk[0]);
+ list_reset(thisk);
+ do {
+ ktom=thisk->current->data;
+ if(ktom==btom)
+ continue;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (1) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ /* direct neighbours of btom cell */
+ for(k=1;k<ck;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (2) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* indirect neighbours of btom cell */
+ for(k=ck;k<27;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /*
+ * direct neighbour cells of atom i
+ */
+ for(j=1;j<c;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+
+ /* 2 body stuff */
+
+
+ /* determine cell neighbours of btom */
+ ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+ kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+ kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+ ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+ neighbourk);
+
+ /* cell of btom */
+ thisk=&(neighbourk[0]);
+ list_reset(thisk);
+ do {
+ ktom=thisk->current->data;
+ if(ktom==btom)
+ continue;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (1) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ /* direct neighbours of btom cell */
+ for(k=1;k<ck;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (2) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* indirect neighbours of btom cell */
+ for(k=ck;k<27;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (3) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /*
+ * indirect neighbour cells of atom i
+ */
+ for(j=c;j<27;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+
+ /* 2 body stuff */
+
+
+ /* determine cell neighbours of btom */
+ ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+ kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+ kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+ ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+ neighbourk);
+
+ /* cell of btom */
+ thisk=&(neighbourk[0]);
+ list_reset(thisk);
+ do {
+ ktom=thisk->current->data;
+ if(ktom==btom)
+ continue;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (1) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ /* direct neighbours of btom cell */
+ for(k=1;k<ck;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (2) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* indirect neighbours of btom cell */
+ for(k=ck;k<27;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (3) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ }
+
+ moldyn->energy=0.5*u;
+
return 0;
}
projects / physik / posic.git / blobdiff