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;
t_list neighbour[27];
t_list *this;
double u;
- unsigned char bc,bc3;
+ u8 bc,bc3;
int countn,dnlc;
count=moldyn->count;
return 0;
}
+/*
+ * 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;
+
+ return 0;
+}
+
+
/*
* example potentials
*/
/* harmonic oscillator potential and force */
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,unsigned char bc)) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
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 d;
double sc,equi_dist;
- int ni,nj,nk;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
+ params=moldyn->pot2b_params;
sc=params->spring_constant;
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+(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);
-
- }
- }
-
- /*
- * 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);
-
- }
- }
+ 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);
}
- moldyn->energy=0.5*u;
-
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) {
t_3dvec f; /* force */
int element; /* number of element in pse */
double mass; /* atom mass */
- unsigned char attr; /* attributes */
+ u8 bnum; /* brand number */
+ u8 attr; /* attributes */
} t_atom;
#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
t_3dvec dim; /* dimensions of the simulation volume */
- /* potential force function pointer and parameters */
+ /* potential force function and parameter pointers */
int (*pf_func1b)(struct s_moldyn *,t_atom *);
+ void *pot1b_params;
int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ void *pot2b_params;
int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ void *pot3b_params;
//int (*potential_force_function)(struct s_moldyn *moldyn);
- void *pot_params; /* parameters describing the potential */
double cutoff; /* cutoff radius */
double cutoff_square; /* square of the cutoff radius */
double energy; /* energy */
t_visual vis; /* visualization/log/save interface structure */
- unsigned char lvstat; /* log & vis properties */
+ u8 lvstat; /* log & vis properties */
unsigned int ewrite; /* how often to log energy */
char efb[64]; /* energy log filename */
int efd; /* fd for energy log */
void *visual; /* pointer (hack!) */
unsigned int swrite; /* how often to create a save file */
- unsigned char status; /* general moldyn properties */
+ u8 status; /* general moldyn properties */
t_random random; /* random interface */
} t_moldyn;
} t_lj_params;
typedef struct s_tersoff_params {
+ double S[2]; /* tersoff cutoff radii */
+ double R[2]; /* tersoff cutoff radii */
+ double Smixed /* mixed S radius */
+ double Rmixed /* mixed R radius */
+
double l_1,l_2;
double m_1,m_2;
double a_1,a_2;
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
-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 destroy_lattice(t_atom *atom);
int thermal_init(t_moldyn *moldyn);
projects / physik / posic.git / commitdiff