#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
- //int ret;
-
- //ret=moldyn_parse_argv(moldyn,argc,argv);
- //if(ret<0) return ret;
-
memset(moldyn,0,sizeof(t_moldyn));
rand_init(&(moldyn->random),NULL,1);
moldyn->vis.dim.z=z;
}
- printf("[moldyn] dimensions in A and A^2 respectively:\n");
+ printf("[moldyn] dimensions in A and A^3 respectively:\n");
printf(" x: %f\n",moldyn->dim.x);
printf(" y: %f\n",moldyn->dim.y);
printf(" z: %f\n",moldyn->dim.z);
return 0;
}
+/*
+ * creating lattice functions
+ */
+
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
- u8 attr,u8 bnum,int a,int b,int c) {
+ u8 attr,u8 brand,int a,int b,int c) {
- int count;
+ int new,count;
int ret;
t_3dvec origin;
+ void *ptr;
+ t_atom *atom;
- count=a*b*c;
+ new=a*b*c;
+ count=moldyn->count;
/* how many atoms do we expect */
- if(type==FCC) count*=4;
- if(type==DIAMOND) count*=8;
+ if(type==FCC) new*=4;
+ if(type==DIAMOND) new*=8;
/* allocate space for atoms */
- moldyn->atom=malloc(count*sizeof(t_atom));
- if(moldyn->atom==NULL) {
- perror("malloc (atoms)");
+ ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (create lattice)");
return -1;
}
-
+ moldyn->atom=ptr;
+ atom=&(moldyn->atom[count]);
+
v3_zero(&origin);
switch(type) {
case FCC:
- ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+ ret=fcc_init(a,b,c,lc,atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+ ret=diamond_init(a,b,c,lc,atom,&origin);
break;
default:
printf("unknown lattice type (%02x)\n",type);
}
/* debug */
- if(ret!=count) {
+ if(ret!=new) {
printf("[moldyn] creating lattice failed\n");
printf(" amount of atoms\n");
- printf(" - expected: %d\n",count);
+ printf(" - expected: %d\n",new);
printf(" - created: %d\n",ret);
return -1;
}
- moldyn->count=count;
- printf("[moldyn] created lattice with %d atoms\n",count);
+ moldyn->count+=new;
+ printf("[moldyn] created lattice with %d atoms\n",new);
- while(count) {
- count-=1;
- moldyn->atom[count].element=element;
- moldyn->atom[count].mass=mass;
- moldyn->atom[count].attr=attr;
- moldyn->atom[count].bnum=bnum;
- check_per_bound(moldyn,&(moldyn->atom[count].r));
+ for(ret=0;ret<new;ret++) {
+ atom[ret].element=element;
+ atom[ret].mass=mass;
+ atom[ret].attr=attr;
+ atom[ret].brand=brand;
+ atom[ret].tag=count+ret;
+ check_per_bound(moldyn,&(atom[ret].r));
}
return ret;
}
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ int i,j;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+ double help[3];
+ double x,y,z;
+
+ x=a*lc;
+ y=b*lc;
+ z=c*lc;
+
+ if(origin) v3_copy(&o,origin);
+ else v3_zero(&o);
+
+ /* construct the basis */
+ for(i=0;i<3;i++) {
+ for(j=0;j<3;j++) {
+ if(i!=j) help[j]=0.5*lc;
+ else help[j]=.0;
+ }
+ v3_set(&basis[i],help);
+ }
+
+ v3_zero(&r);
+ count=0;
+
+ /* fill up the room */
+ r.x=o.x;
+ while(r.x<x) {
+ r.y=o.y;
+ while(r.y<y) {
+ r.z=o.z;
+ while(r.z<z) {
+ v3_copy(&(atom[count].r),&r);
+ atom[count].element=1;
+ count+=1;
+ for(i=0;i<3;i++) {
+ v3_add(&n,&r,&basis[i]);
+ if((n.x<x+o.x)&&
+ (n.y<y+o.y)&&
+ (n.z<z+o.z)) {
+ v3_copy(&(atom[count].r),&n);
+ count+=1;
+ }
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ help[0]=x/2.0;
+ help[1]=y/2.0;
+ help[2]=z/2.0;
+ v3_set(&n,help);
+ for(i=0;i<count;i++)
+ v3_sub(&(atom[i].r),&(atom[i].r),&n);
+
+ return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ t_3dvec o;
+
+ count=fcc_init(a,b,c,lc,atom,origin);
+
+ o.x=0.25*lc;
+ o.y=0.25*lc;
+ o.z=0.25*lc;
+
+ if(origin) v3_add(&o,&o,origin);
+
+ count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+ return count;
+}
+
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
t_3dvec *r,t_3dvec *v) {
t_atom *atom;
int count;
atom=moldyn->atom;
- count=++(moldyn->count);
+ count=(moldyn->count)++;
- ptr=realloc(atom,count*sizeof(t_atom));
+ ptr=realloc(atom,(count+1)*sizeof(t_atom));
if(!ptr) {
perror("[moldyn] realloc (add atom)");
return -1;
moldyn->atom=ptr;
atom=moldyn->atom;
- atom[count-1].r=*r;
- atom[count-1].v=*v;
- atom[count-1].element=element;
- atom[count-1].mass=mass;
- atom[count-1].bnum=bnum;
- atom[count-1].attr=attr;
+ atom[count].r=*r;
+ atom[count].v=*v;
+ atom[count].element=element;
+ atom[count].mass=mass;
+ atom[count].brand=brand;
+ atom[count].tag=count;
+ atom[count].attr=attr;
return 0;
}
t_linkcell *lc;
int i;
- int fd;
-
- fd=open("/dev/null",O_WRONLY);
lc=&(moldyn->lc);
printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
for(i=0;i<lc->cells;i++)
- //list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]),fd);
+ list_init_f(&(lc->subcell[i]));
link_cell_update(moldyn);
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny,nz;
+ int nx,ny;
t_atom *atom;
t_linkcell *lc;
+ double x,y,z;
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nz=lc->nz;
+
+ x=moldyn->dim.x/2;
+ y=moldyn->dim.y/2;
+ z=moldyn->dim.z/2;
for(i=0;i<lc->cells;i++)
- list_destroy(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(lc->subcell[i]));
for(count=0;count<moldyn->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]));
+ 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_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
}
return 0;
lc=&(moldyn->lc);
for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_shutdown(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(moldyn->lc.subcell[i]));
+
+ free(lc->subcell);
return 0;
}
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
-{
-printf("going to do p scale ...\n");
scale_volume(moldyn);
-printf("done\n");
-}
/* check for log & visualization */
if(e) {
v3_add(&(atom[i].r),&(atom[i].r),&delta);
v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
-//if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
check_per_bound(moldyn,&(atom[i].r));
-//if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
-//moldyn_bc_check(moldyn);
/* neighbour list update */
link_cell_update(moldyn);
/* reset viral of atom i */
v3_zero(&(itom[i].virial));
+ /* reset site energy */
+ itom[i].e=0.0;
+
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
moldyn->func1b(moldyn,&(itom[i]));
for(j=0;j<27;j++) {
this=&(neighbour_i[j]);
- list_reset(this);
+ list_reset_f(this);
if(this->start==NULL)
continue;
for(k=0;k<27;k++) {
that=&(neighbour_i2[k]);
- list_reset(that);
+ list_reset_f(that);
if(that->start==NULL)
continue;
ktom,
bc_ik|bc_ij);
- } while(list_next(that)!=\
+ } while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
jtom,bc_ij);
}
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
}
* periodic boundayr checking
*/
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
t_3dvec *dim;
/* tersoff 1 body part */
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
- int num;
+ int brand;
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
- num=ai->bnum;
+ brand=ai->brand;
params=moldyn->pot1b_params;
exchange=&(params->exchange);
* their right values
*/
- exchange->beta_i=&(params->beta[num]);
- exchange->n_i=&(params->n[num]);
- exchange->c_i=&(params->c[num]);
- exchange->d_i=&(params->d[num]);
- exchange->h_i=&(params->h[num]);
+ exchange->beta_i=&(params->beta[brand]);
+ exchange->n_i=&(params->n[brand]);
+ exchange->c_i=&(params->c[brand]);
+ exchange->d_i=&(params->d[brand]);
+ exchange->h_i=&(params->h[brand]);
exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
- exchange->ci2=params->c[num]*params->c[num];
- exchange->di2=params->d[num]*params->d[num];
+ exchange->ci2=params->c[brand]*params->c[brand];
+ exchange->di2=params->d[brand]*params->d[brand];
exchange->ci2di2=exchange->ci2/exchange->di2;
return 0;
double A,B,R,S,lambda,mu;
double f_r,df_r;
double f_c,df_c;
- int num;
+ int brand;
double s_r;
double arg;
params=moldyn->pot2b_params;
- num=aj->bnum;
+ brand=aj->brand;
exchange=&(params->exchange);
/* clear 3bp and 2bp post run */
exchange->dist_ij=dist_ij;
/* constants */
- if(num==ai->bnum) {
- S=params->S[num];
- R=params->R[num];
- A=params->A[num];
- B=params->B[num];
- lambda=params->lambda[num];
- mu=params->mu[num];
+ if(brand==ai->brand) {
+ S=params->S[brand];
+ R=params->R[brand];
+ A=params->A[brand];
+ B=params->B[brand];
+ lambda=params->lambda[brand];
+ mu=params->mu[brand];
exchange->chi=1.0;
}
else {
return 0;
/* more constants */
- exchange->beta_j=&(params->beta[num]);
- exchange->n_j=&(params->n[num]);
- exchange->c_j=&(params->c[num]);
- exchange->d_j=&(params->d[num]);
- exchange->h_j=&(params->h[num]);
- if(num==ai->bnum) {
+ exchange->beta_j=&(params->beta[brand]);
+ exchange->n_j=&(params->n[brand]);
+ exchange->c_j=&(params->c[brand]);
+ exchange->d_j=&(params->d[brand]);
+ exchange->h_j=&(params->h[brand]);
+ if(brand==ai->brand) {
exchange->betajnj=exchange->betaini;
exchange->cj2=exchange->ci2;
exchange->dj2=exchange->di2;
}
else {
exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
- exchange->cj2=params->c[num]*params->c[num];
- exchange->dj2=params->d[num]*params->d[num];
+ exchange->cj2=params->c[brand]*params->c[brand];
+ exchange->dj2=params->d[brand]*params->d[brand];
exchange->cj2dj2=exchange->cj2/exchange->dj2;
}
double h_cos,d2_h_cos2;
double frac,g,zeta,chi;
double tmp;
- int num;
+ int brand;
params=moldyn->pot3b_params;
exchange=&(params->exchange);
d_ik=v3_norm(&dist_ik);
/* ik constants */
- num=ai->bnum;
- if(num==ak->bnum) {
- R=params->R[num];
- S=params->S[num];
+ brand=ai->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
}
else {
R=params->Rmixed;
d_jk=v3_norm(&dist_jk);
/* jk constants */
- num=aj->bnum;
- if(num==ak->bnum) {
- R=params->R[num];
- S=params->S[num];
- B=params->B[num];
- mu=params->mu[num];
+ brand=aj->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ B=params->B[brand];
+ mu=params->mu[brand];
chi=1.0;
}
else {
t_atom *atom;
t_3dvec *dim;
int i;
-double x;
-u8 byte;
-int j,k;
+ double x;
+ u8 byte;
+ int j,k;
atom=moldyn->atom;
dim=&(moldyn->dim);
-x=dim->x/2;
+ x=dim->x/2;
for(i=0;i<moldyn->count;i++) {
if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
return 0;
}
-
projects / physik / posic.git / blobdiff