for(i=0;i<lc->cells;i++)
//list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]),lc->listfd);
+ 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;
+ for(count=0;count<moedyn->count;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;
list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
&(atom[count]));
}
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];
}
int fd;
char fb[128];
+ /* initialize linked cell method */
+ link_cell_init(moldyn);
+
/* logging & visualization */
e=moldyn->ewrite;
m=moldyn->mwrite;
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 energy 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 */
+
+ /* we need: f_c, df_c, f_r, df_r */
+
+ v3_sub(&dist_ij,btom,&(atom[i]));
+ d_ij=v3_norm(&dist_ij);
+ if(d_ij<=S) {
+
+ /* determine the tersoff parameters */
+ if(atom[i].element!=btom->element) {
+ S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
+ R=R_m;
+ A=;
+ lambda=;
+ B=;
+ mu=;
+ chi=;
+ beta=;
+ betaN=;
+
+ if(d_ij<=R) {
+ df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
+ v3_scale(&force,&dist_ij,df_r);
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ else {
+ s_r=S-R;
+ arg1=PI*(d_ij-R)/s_r;
+ f_c=0.5+0.5*cos(arg1);
+ df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
+ f_r=A*exp(-lambda*d_ij);
+ df_r=-lambda*f_r/d_ij;
+ scale=df_c*f_r+df_r*f_c;
+ v3_scale(&force,&dist_ij,scale);
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ }
+ else
+ continue;
+
+
+ /* end 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);
+
+ /* go for zeta - 3 body stuff! */
+ zeta=0.0;
+ d_ij2=d_ij*d_ij;
+
+ /* 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) */
+
+ v3_sub(&dist_ik,ktom,&(atom[i]));
+ d_ik=v3_norm(&dist_ik);
+ if(d_ik<=Sik) {
+
+ Rik=;
+ Sik=;
+ Aik=;
+ lambda_ik=;
+ Bik=;
+ mu_ik=;
+ omega_ik=;
+ c_i=;
+ d_i=;
+ h_i=;
+
+
+ if(d_ik<=Rik) {
+ f_cik=1.0;
+ df_cik=0.0;
+ }
+ else {
+ sik_rik=Sik-Rik;
+ arg1ik=PI*(d_ik-Rik)/sik_rik;
+ f_cik=0.5+0.5*cos(arg1ik);
+ df_cik=-0.5*sin(arg1ik)* \
+ (PI/(sik_rik*d_ik));
+ f_rik=Aik*exp(-lambda_ik*d_ik);
+ f_aik=-Bik*exp(-mu_ik*d_ik);
+ }
+
+ v3_sub(&distance_jk,ktom,btom);
+ cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
+ (2*d_ij*d_ik);
+ sin_theta=sqrt(1.0/\
+ (cos_theta*cos_theta));
+ theta=arccos(cos_theta);
+
+
+ }
+ else
+ continue;
+
+ /* end 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