int i;
t_ho_params hop;
t_lj_params ljp;
+ t_tersoff_params tp;
double s,e;
memset(moldyn,0,sizeof(t_moldyn));
moldyn->mwrite=atoi(argv[++i]);
strncpy(moldyn->mfb,argv[++i],64);
break;
- case 'D':
- moldyn->dwrite=atoi(argv[++i]);
- strncpy(moldyn->dfb,argv[++i],64);
- break;
case 'S':
moldyn->swrite=atoi(argv[++i]);
strncpy(moldyn->sfb,argv[++i],64);
if(moldyn->swrite)
moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
- if(moldyn->dwrite) {
- moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->dfd<0) {
- perror("[moldyn] dfd open");
- return moldyn->dfd;
- }
- write(moldyn->dfd,moldyn,sizeof(t_moldyn));
- moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
- }
-
if((moldyn->vwrite)&&(vis)) {
moldyn->visual=vis;
visual_init(vis,moldyn->vfb);
for(i=0;i<lc->cells;i++)
list_destroy(&(moldyn->lc.subcell[i]));
- for(count=0;count<moldyn->count;count++) {
+ 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;
}
}
+ lc->dnlc=count2;
+ lc->countn=27;
+
return count2;
}
write(fd,moldyn->atom,
moldyn->count*sizeof(t_atom));
}
+ close(fd);
}
}
- if(d) {
- if(!(i%d))
- write(moldyn->dfd,moldyn->atom,
- moldyn->count*sizeof(t_atom));
-
- }
if(v) {
if(!(i%v)) {
visual_atoms(moldyn->visual,i*moldyn->tau,
/* forces depending on chosen potential */
printf("calc potential/force ...\n");
- moldyn->potential_force_function(moldyn);
+ potential_force_calc(moldyn);
+ //moldyn->potential_force_function(moldyn);
printf("done\n");
for(i=0;i<count;i++) {
*
*/
+/* generic potential and force calculation */
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+ int i,count;
+ t_atom *atom;
+ t_linkcell *lc;
+ 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 */
+ moldyn->energy=0.0;
+
+ for(i=0;i<count;i++) {
+
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
+ /* single particle potential/force */
+ if(atom[i].attr&ATOM_ATTR_1BP)
+ moldyn->pf_func1b(moldyn,&(atom[i]));
+
+ /* 2 body pair potential/force */
+ if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+
+ 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);
+
+ countn=lc->countn;
+ dnlc=lc->dnlc;
+
+ for(j=0;j<countn;j++) {
+
+ this=&(neighbour[j]);
+ list_reset(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc=(j<dnlc)?0:1;
+
+ do {
+ btom=this->current->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,
+ 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;k<lc->countn;k++) {
+
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+
+ if(thisk->start==NULL)
+ continue;
+
+ bck=(k<lc->dnlc)?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;
lc=&(moldyn->lc);
count=moldyn->count;
- /* reset enrgy counter */
+ /* reset energy counter */
u=0.0;
for(i=0;i<count;i++) {
/* 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;
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);
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);
projects / physik / posic.git / blobdiff