return 0;
}
-int create_lattice(unsigned char type,int element,double mass,double lc,
+int create_lattice(u8 type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom) {
int count;
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;
/* generic potential and force calculation */
-#define CREATE_CELL_LIST(nb_list) \
- 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,\
- nb_list);
-
-
int potential_force_calc(t_moldyn *moldyn) {
int i,count;
t_list neighbour[27];
t_list *this;
double u;
+ u8 bc,bc3;
+ int countn,dnlc;
count=moldyn->count;
atom=moldyn->atom;
lc=&(moldyn->lc);
/* reset energy */
- u=0.0;
+ moldyn->energy=0.0;
for(i=0;i<count;i++) {
v3_zero(&(atom[i].f));
/* single particle potential/force */
- if(moldyn->status&MOLDYN_STAT_1BP)
+ if(atom[i].attr&ATOM_ATTR_1BP)
moldyn->pf_func1b(moldyn,&(atom[i]));
/* 2 body pair potential/force */
- if(moldyn->status&MOLDYN_STAT_2BP) {
+ if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
- CREATE_CELL_LIST(neighbour);
+ 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);
- /*
- * processing cell of atom i
- * => no need to check for empty list
- * (1 element at minimum)
- */
+ countn=lc->countn;
+ dnlc=lc->dnlc;
- this=&(neighbour[0]);
- list_reset(this);
- do {
- btom=this->current->data;
- if(btom!=&(atom[i]))
- moldyn->pf_func2b(moldyn,
- &(atom[i]),btom);
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ for(j=0;j<countn;j++) {
- /*
- * direct neighbour cells
- * => no boundary condition check necessary
- */
- for(j=0;j<lc->dnlc;j++) {
this=&(neighbour[j]);
list_reset(this);
- if(this->start!=NULL) {
- do {
- btom=this->current->data;
- moldyn->pf_func2b(moldyn,
- &(atom[i]),
- btom);
- } while(list_next(this)!=\
- L_NO_NEXT_ELEMENT);
- }
- /*
- * neighbour cells due to periodic bc
- * => check boundary conditions
- */
- for(j=lc->dnlc;j<lc->countn;j++) {
- this=&(neighbour[j]);
- list_reset(this);
- if(this->start!=NULL) {
- do {
- btom=this->current->data;
- moldyn->pf_func2b(moldyn,
- &(atom[i]),
- btom);
+ if(this->start==NULL)
+ continue;
- }
+ bc=(j<dnlc)?0:1;
- }
+ do {
+ btom=this->current->data;
- return 0;
-}
+ 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 */
-/* harmonic oscillator potential and force */
+ if(!(atom[i].attr&ATOM_ATTR_3BP)||
+ !(btom->attr&ATOM_ATTR_3BP))
+ continue;
-int harmonic_oscillator(t_moldyn *moldyn) {
+ 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);
- t_ho_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,u;
- double sc,equi_dist;
- int ni,nj,nk;
+ for(k=0;k<lc->countn;k++) {
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
- count=moldyn->count;
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+
+ if(thisk->start==NULL)
+ continue;
- /* reset energy counter */
- u=0.0;
+ bck=(k<lc->dnlc)?0:1;
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
+ do {
- /* 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);
+ ktom=thisk->current->data;
- /*
- * 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;
- 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) {
+ if(ktom==btom)
+ continue;
- 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);
+ 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);
}
}
+ }
- /*
- * 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) {
+ return 0;
+}
- 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);
+/*
+ * periodic boundayr checking
+ */
- }
- }
- }
+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;
- moldyn->energy=0.5*u;
+ return 0;
+}
+
+
+/*
+ * example potentials
+ */
+
+/* harmonic oscillator potential and force */
+
+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;
+
+ params=moldyn->pot2b_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+
+ 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);
+ }
return 0;
}
/* lennard jones potential & force for one sort of atoms */
-int lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
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;
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;
+ 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);
+ }
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
+ return 0;
+}
- /* 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);
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
- /* 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) {
+/* tersoff 2 body part */
- 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);
-
- }
- }
+int tersoff_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 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) {
+ t_tersoff_params *params;
+ t_3dvec dist_ij;
+ double d_ij;
- 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);
+ params=moldyn->pot_params;
+
+ /*
+ * we need: f_c, df_c, f_r, df_r
+ *
+ * therefore we need: R, S
+ */
- }
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
+
+ if(bc) check_per_bound(moldyn,&dist_ij);
+
+ if(ai->bnum==aj->bnum) {
+ S=params->S[ai->bnum];
+ R=params->R[ai->bnum];
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ }
+
+ d_ij=v3_norm(&dist_ij);
+
+ if(d_ij<=S) {
+ f_r=A*exp(-lamda*d_ij);
+ df_r=-lambda*f_r/d_ij;
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 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);
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
+ moldyn->energy+=(f_r*f_c);
}
- moldyn->energy=0.5*u;
-
return 0;
}
-/* tersoff potential & force for 2 sorts of atoms */
+/* tersoff 3 body part */
-int tersoff(t_moldyn *moldyn) {
+int tersoff(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc,u8 bck) {
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;
-
+ t_3dvec dist_ij;
+ double d_ij;
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 */
+ /* 2 body part of the tersoff potential */
- v3_sub(&dist_ij,btom,&(atom[i]));
- d_ij=v3_norm(&dist_ij);
- if(d_ij<=S) {
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_ij);
+ d_ij=v3_norm(&dist_ij);
+ if(d_ij<=S) {
/* determine the tersoff parameters */
if(atom[i].element!=btom->element) {