int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
int i;
- t_ho_params hop;
- t_lj_params ljp;
- double s,e;
memset(moldyn,0,sizeof(t_moldyn));
moldyn->tau=MOLDYN_TAU;
moldyn->time_steps=MOLDYN_RUNS;
moldyn->integrate=velocity_verlet;
- moldyn->potential_force_function=lennard_jones;
/* parse argv */
for(i=1;i<argc;i++) {
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);
return 0;
}
-int create_lattice(unsigned char type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom) {
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+ u8 attr,u8 bnum,int a,int b,int c) {
int count;
int ret;
t_3dvec origin;
+ t_atom *atom;
count=a*b*c;
+ atom=moldyn->atom;
if(type==FCC) count*=4;
if(type==DIAMOND) count*=8;
- *atom=malloc(count*sizeof(t_atom));
- if(*atom==NULL) {
+ atom=malloc(count*sizeof(t_atom));
+ if(atom==NULL) {
perror("malloc (atoms)");
return -1;
}
switch(type) {
case FCC:
- ret=fcc_init(a,b,c,lc,*atom,&origin);
+ ret=fcc_init(a,b,c,lc,atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,*atom,&origin);
+ ret=diamond_init(a,b,c,lc,atom,&origin);
break;
default:
printf("unknown lattice type (%02x)\n",type);
}
while(count) {
- (*atom)[count-1].element=element;
- (*atom)[count-1].mass=mass;
+ atom[count-1].element=element;
+ atom[count-1].mass=mass;
+ atom[count-1].attr=attr;
+ atom[count-1].bnum=bnum;
count-=1;
}
return ret;
}
-int destroy_lattice(t_atom *atom) {
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+ t_3dvec r,t_3dvec v) {
- if(atom) free(atom);
+ t_atom *atom;
+ void *ptr;
+ int count;
+
+ atom=moldyn->atom;
+ count=++(moldyn->count);
+
+ ptr=realloc(atom,count*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (add atom)");
+ return -1;
+ }
+
+ atom=ptr;
+ atom->r=r;
+ atom->v=v;
+ atom->element=element;
+ atom->bnum=bnum;
+ atom->attr=attr;
+
+ return 0;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
+
+ if(moldyn->atom) free(moldyn->atom);
return 0;
}
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;
int ci,cj,ck;
int nx,ny,nz;
int x,y,z;
- unsigned char bx,by,bz;
+ u8 bx,by,bz;
lc=&(moldyn->lc);
nx=lc->nx;
}
}
+ lc->dnlc=count2;
+ lc->countn=27;
+
return count2;
}
return 0;
}
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau ) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=moldyn->schedule;
+ count=++(schedule->content_count);
+
+ ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ moldyn->schedule.runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ moldyn->schedule.tau[count-1]=tau;
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}
+
/*
*
* 'integration of newtons equation' - algorithms
int moldyn_integrate(t_moldyn *moldyn) {
- int i;
+ int i,sched;
unsigned int e,m,s,d,v;
t_3dvec p;
/* calculate initial forces */
moldyn->potential_force_function(moldyn);
+ for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+
+ /* setting amont of runs and finite time step size */
+ moldyn->tau=schedule->tau[sched];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->timesteps=schedule->runs[sched];
+
+ /* integration according to schedule */
+
for(i=0;i<moldyn->time_steps;i++) {
/* integration step */
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,
}
}
+ /* check for hooks */
+ if(schedule->hook)
+ schedule->hook(moldyn,schedule->hook_params);
+
return 0;
}
/* 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++) {
*
*/
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
-int harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
- t_ho_params *params;
- t_atom *atom,*btom;
+ int i,count;
+ t_atom *atom;
t_linkcell *lc;
- t_list *this,neighbour[27];
- int i,j,c;
- int count;
- t_3dvec force,distance;
- double d,u;
- double sc,equi_dist;
- int ni,nj,nk;
+ t_list neighbour[27];
+ t_list *this;
+ double u;
+ u8 bc,bc3;
+ int countn,dnlc;
- params=moldyn->pot_params;
+ count=moldyn->count;
atom=moldyn->atom;
lc=&(moldyn->lc);
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
- count=moldyn->count;
- /* reset energy counter */
- u=0.0;
+ /* reset energy */
+ moldyn->energy=0.0;
for(i=0;i<count;i++) {
+
/* reset force */
v3_zero(&(atom[i].f));
- /* determine 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;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_norm(&distance);
- 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);
-
- /*
- * 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 */
- if(this->start!=NULL) {
-
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_norm(&distance);
- 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);
-
- }
- }
+ /* single particle potential/force */
+ if(atom[i].attr&ATOM_ATTR_1BP)
+ moldyn->pf_func1b(moldyn,&(atom[i]));
- /*
- * indirect neighbour cells
- * => check boundary conditions
- */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
-
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_norm(&distance);
- 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);
+ /* 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;
- moldyn->energy=0.5*u;
+ for(j=0;j<countn;j++) {
- return 0;
-}
+ this=&(neighbour[j]);
+ list_reset(this);
-/* lennard jones potential & force for one sort of atoms */
-
-int lennard_jones(t_moldyn *moldyn) {
+ if(this->start==NULL)
+ continue;
- t_lj_params *params;
- t_atom *atom,*btom;
- t_linkcell *lc;
- t_list *this,neighbour[27];
- int i,j,c;
- int count;
- t_3dvec force,distance;
- double d,h1,h2,u;
- double eps,sig6,sig12;
- int ni,nj,nk;
+ bc=(j<dnlc)?0:1;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- count=moldyn->count;
- eps=params->epsilon4;
- sig6=params->sigma6;
- sig12=params->sigma12;
-
- /* reset energy counter */
- u=0.0;
+ do {
+ btom=this->current->data;
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
+ if(btom==&(atom[i]))
+ continue;
- /* determine 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 */
- this=&(neighbour[0]);
- list_reset(this); /* list has 1 element at minimum */
- do {
- btom=this->current->data;
- if(btom==&(atom[i]))
- continue;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- 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 */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* there might not be a single atom */
- if(this->start!=NULL) {
-
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_absolute_square(&distance); /* 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);
-
- }
- }
+ if((btom->attr&ATOM_ATTR_2BP)&
+ (atom[i].attr&ATOM_ATTR_2BP))
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),
+ btom,
+ bc);
- /* neighbours due to boundary conditions */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
-
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_absolute_square(&distance); /* 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);
+ /* 3 body potential/force */
- }
- }
- }
+ if(!(atom[i].attr&ATOM_ATTR_3BP)||
+ !(btom->attr&ATOM_ATTR_3BP))
+ continue;
- moldyn->energy=0.5*u;
-
- return 0;
-}
+ 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);
-/* tersoff potential & force for 2 sorts of atoms */
+ for(k=0;k<lc->countn;k++) {
-int tersoff(t_moldyn *moldyn) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+
+ if(thisk->start==NULL)
+ continue;
- 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;
-
+ bck=(k<lc->dnlc)?0:1;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- count=moldyn->count;
-
- /* reset energy counter */
- u=0.0;
+ do {
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
+ ktom=thisk->current->data;
- /* 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]))
+ if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- /* 2 body stuff */
+ if(ktom==btom)
+ continue;
- v3_sub(&dist_ij,btom,&(atom[i]));
- d_ij=v3_norm(&dist_ij);
- if(d_ij<=S) {
+ if(ktom==&(atom[i]))
+ continue;
- S=;
- R=;
- A=;
- lambda=;
- B=;
- mu=;
+ moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
- if(d_ij<=R) {
- f_c=1.0;
- df_c=0.0;
- }
- 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);
- f_a=-B*exp(-mu*d_ij);
- }
+ } while(list_next(thisk)!=\
+ L_NO_NEXT_ELEMENT);
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
}
- 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);
-
- /* 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) */
-
- theta_ijk=;
- sin_theta=;
- cos_theta=;
- hi_cos=;
- hi_cos_square=;
-
+ }
+ }
- /* end 3 body stuff (1) */
+ return 0;
+}
+/*
+ * periodic boundayr checking
+ */
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+
+ double x,y,z;
+
+ x=0.5*dim->x;
+ y=0.5*dim->y;
+ z=0.5*dim->z;
+
+ if(moldyn->MOLDYN_ATTR_PBX)
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
+ if(moldyn->MOLDYN_ATTR_PBY)
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
+ if(moldyn->MOLDYN_ATTR_PBZ)
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
- /* direct neighbours of btom cell */
- for(k=1;k<ck;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ return 0;
+}
+
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+/*
+ * example potentials
+ */
- /* 3 body stuff (2) */
+/* harmonic oscillator potential and force */
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
- }
- }
+ t_ho_params *params;
+ t_3dvec force,distance;
+ double d;
+ double sc,equi_dist;
- /* indirect neighbours of btom cell */
- for(k=ck;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ params=moldyn->pot2b_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ v3_sub(&distance,&(ai->r),&(aj->r);
+
+ v3_per_bound(&distance,&(moldyn->dim));
+ if(bc) check_per_bound(moldyn,&distance);
+ d=v3_norm(&distance);
+ if(d<=moldyn->cutoff) {
+ /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
+ moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+ v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
- /* 3 body stuff */
+ return 0;
+}
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/* lennard jones potential & force for one sort of atoms */
+
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
- }
- }
+ t_lj_params *params;
+ t_3dvec force,distance;
+ double d,h1,h2,u;
+ double eps,sig6,sig12;
+ params=moldyn->pot_params;
+ eps=params->epsilon4;
+ sig6=params->sigma6;
+ sig12=params->sigma12;
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ v3_sub(&distance,&(ai->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&distance);
+ 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 */
+ /* energy is eps*..., but we will add this twice ... */
+ moldyn->energy+=0.5*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(&(ai->f),&(aj->f),&force);
+ }
- /*
- * direct neighbour cells of atom i
- */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this);
- if(this->start!=NULL) {
+ return 0;
+}
- do {
- btom=this->current->data;
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
- /* 2 body stuff */
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+ int num;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ num=ai->bnum;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
- /* 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);
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * their right values
+ */
- /* 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) */
+ exchange->beta=&(params->beta[num]);
+ exchange->n=&(params->n[num]);
+ exchange->c=&(params->c[num]);
+ exchange->d=&(params->d[num]);
+ exchange->h=&(params->h[num]);
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ exchange->betan=pow(*(exchange->beta),*(exchange->n));
+ exchange->c2=params->c[num]*params->c[num];
+ exchange->d2=params->d[num]*params->d[num];
+ exchange->c2d2=exchange->c2/exchange->d2;
- /* direct neighbours of btom cell */
- for(k=1;k<ck;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ return 0;
+}
+
+/* tersoff 2 body part */
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij;
+ double d_ij;
+ double A,B,R,S,lambda;
+ int num;
- /* 3 body stuff (2) */
+ params=moldyn->pot_params;
+ num=ai->bnum;
+ exchange=&(params->exchange);
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ exchange->run3bp=0;
+
+ /*
+ * we need: f_c, df_c, f_r, df_r
+ *
+ * therefore we need: R, S, A, lambda
+ */
- }
- }
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
- /* indirect neighbours of btom cell */
- for(k=ck;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ if(bc) check_per_bound(moldyn,&dist_ij);
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ /* save for use in 3bp */ /* REALLY ?!?!?! */
+ exchange->dist_ij=dist_ij;
- /* 3 body stuff (3) */
+ /* constants */
+ if(num==aj->bnum) {
+ S=params->S[num];
+ R=params->R[num];
+ A=params->A[num];
+ lambda=params->lambda[num];
+ /* more constants depending of atoms i and j, needed in 3bp */
+ params->exchange.B=&(params->B[num]);
+ params->exchange.mu=params->mu[num];
+ params->exchange.chi=1.0;
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ lambda=params->lambda_m;
+ /* more constants depending of atoms i and j, needed in 3bp */
+ params->exchange.B=&(params->Bmixed);
+ params->exchange.mu=&(params->mu_m);
+ params->exchange.chi=params->chi;
+ }
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ d_ij=v3_norm(&dist_ij);
- }
- }
+ /* save for use in 3bp */
+ exchange->d_ij=d_ij;
+ if(d_ij>S)
+ return 0;
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ f_r=A*exp(-lamda*d_ij);
+ df_r=-lambda*f_r/d_ij;
- }
- }
+ /* f_a, df_a calc + save for 3bp use */
+ exchange->f_a=-B*exp(-mu*d_ij);
+ exchange->df_a=-mu*exchange->f_a/d_ij;
- /*
- * 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) */
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ f_c=1.0;
+ df_c=0.0;
+ v3_scale(&force,&dist_ij,df_r);
+ }
+ else {
+ s_r=S-R;
+ arg=PI*(d_ij-R)/s_r;
+ f_c=0.5+0.5*cos(arg);
+ df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+ scale=df_c*f_r+df_r*f_c;
+ v3_scale(&force,&dist_ij,scale);
+ }
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /* add forces */
+ v3_add(&(ai->f),&(ai->f),&force);
+ /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
+ moldyn->energy+=(0.25*f_r*f_c);
- /* direct neighbours of btom cell */
- for(k=1;k<ck;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ /* save for use in 3bp */
+ exchange->f_c=f_c;
+ exchange->df_c=df_c;
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ /* enable the run of 3bp function */
+ exchange->run3bp=1;
- /* 3 body stuff (2) */
+ return 0;
+}
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/* tersoff 3 body part */
- }
- }
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
- /* indirect neighbours of btom cell */
- for(k=ck;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,dist_ik,dist_jk;
+ t_3dvec temp,force;
+ double R,S,s_r;
+ double d_ij,d_ik,d_jk;
+ double f_c,df_c,b_ij,f_a,df_a;
+ double n,c,d,h,neta,betan,betan_1;
+ double theta,cos_theta,sin_theta;
+ int num;
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ params=moldyn->pot_params;
+ num=ai->bnum;
+ exchange=params->exchange;
- /* 3 body stuff (3) */
+ if(!(exchange->run3bp))
+ return 0;
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /*
+ * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+ *
+ * we got f_c, df_c, f_a, df_a from 2bp calculation
+ */
- }
- }
+ d_ij=exchange->d_ij;
+ d_ij2=exchange->d_ij2;
+ f_a=params->exchange.f_a;
+ df_a=params->exchange.df_a;
+
+ /* d_ij is <= S, as we didn't return so far! */
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ /*
+ * calc of b_ij (scalar) and db_ij (vector)
+ *
+ * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
+ *
+ * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
+ * w_ik,
+ *
+ */
- }
- }
-
+
+ v3_sub(&dist_ik,&(aj->i),&(ak->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik=v3_norm(&dist_ik);
+
+ /* constants for f_c_ik calc */
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
}
- moldyn->energy=0.5*u;
+ /* calc of f_c_ik */
+ if(d_ik>S)
+ return 0;
+ if(d_ik<R) {
+ /* f_c_ik = 1, df_c_ik = 0 */
+ f_c_ik=1.0;
+ df_c_ik=0.0;
+ }
+ else {
+ s_r=S-R;
+ arg=PI*(d_ik-R)/s_r;
+ f_c_ik=0.5+0.5*cos(arg);
+ df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
+ }
+
+ v3_sub(&dist_jk,&(aj->r),&(ak->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk=v3_norm(&dist_jk);
+
+ beta=*(exchange->beta);
+ betan=exchange->betan;
+ n=*(exchange->n);
+ c=*(exchange->c);
+ d=*(exchange->d);
+ h=*(exchange->h);
+ c2=exchange->c2;
+ d2=exchange->d2;
+ c2d2=exchange->c2d2;
+
+ numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
+ denom=2*d_ij*d_ik;
+ cos_theta=numer/denom;
+ sin_theta=sqrt(1.0-(cos_theta*cos_theta));
+ theta=arccos(cos_theta);
+ d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
+ d_theta1=2*denom-numer*2*d_ik/d_ij;
+ d_theta2=2*denom-numer*2*d_ij/d_ik;
+ d_theta1*=d_theta;
+ d_theta2*=d_theta;
+
+ h_cos=(h-cos_theta);
+ h_cos2=h_cos*h_cos;
+ d2_h_cos2=d2-h_cos2;
+
+ /* some usefull expressions */
+ frac1=c2/(d2-h_cos2);
+ bracket1=1+c2d2-frac1;
+ bracket2=f_c_ik*bracket1;
+ bracket2_n_1=pow(bracket2,n-1.0);
+ bracket2_n=bracket2_n_1*bracket2;
+ bracket3=1+betan*bracket2_n;
+ bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
+ bracket3_pow=bracket3_pow_1*bracket3;
+
+ /* now go on with calc of b_ij and derivation of b_ij */
+ b_ij=chi*bracket3_pow;
+
+ /* derivation of theta */
+ v3_scale(&force,&dist_ij,d1_theta);
+ v3_scale(&temp,&dist_ik,d_theta2);
+ v3_add(&force,&force,&temp);
+
+ /* part 1 of derivation of b_ij */
+ v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
+
+ /* part 2 of derivation of b_ij */
+ v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
+
+ /* sum up and scale ... */
+ v3_add(&temp,&temp,&force);
+ scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
+ v3_scale(&temp,&temp,scale);
+
+ /* now construct an energy and a force out of that */
+ v3_scale(&temp,&temp,f_a);
+ v3_scale(&force,&dist_ij,df_a*b_ij);
+ v3_add(&temp,&temp,&force);
+ v3_scale(&temp,&temp,f_c);
+ v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
+ v3_add(&force,&force,&temp);
+
+ /* add forces */
+ v3_add(&(ai->f),&(ai->f),&force);
+ /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
+ moldyn->energy+=(0.25*f_a*b_ij*f_c);
+
return 0;
}