int moldyn_shutdown(t_moldyn *moldyn) {
+ printf("[moldyn] shutdown\n");
moldyn_log_shutdown(moldyn);
link_cell_shutdown(moldyn);
- moldyn_log_shutdown(moldyn);
rand_close(&(moldyn->random));
free(moldyn->atom);
return 0;
}
-int set_temperature(t_moldyn *moldyn,double t) {
-
- moldyn->t=t;
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+ moldyn->t_ref=t_ref;
+
+ return 0;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+ moldyn->pt_scale=(ptype|ttype);
+ moldyn->t_tc=ttc;
+ moldyn->p_tc=ptc;
return 0;
}
return 0;
}
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+ moldyn->nnd=dist;
+
+ return 0;
+}
+
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
if(x)
int moldyn_log_shutdown(t_moldyn *moldyn) {
+ printf("[moldyn] log shutdown\n");
if(moldyn->efd) close(moldyn->efd);
if(moldyn->mfd) close(moldyn->mfd);
- if(moldyn->visual) visual_tini(moldyn->visual);
+ if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
return 0;
}
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) {
+ moldyn->atom=malloc(count*sizeof(t_atom));
+ if(moldyn->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,moldyn->atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,atom,&origin);
+ ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
break;
default:
printf("unknown lattice type (%02x)\n",type);
}
moldyn->count=count;
+ printf("[moldyn] created lattice with %d atoms\n",count);
while(count) {
- atom[count-1].element=element;
- atom[count-1].mass=mass;
- atom[count-1].attr=attr;
- atom[count-1].bnum=bnum;
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));
}
+
return ret;
}
moldyn->atom=ptr;
atom=moldyn->atom;
- atom->r=*r;
- atom->v=*v;
- atom->element=element;
- atom->bnum=bnum;
- atom->attr=attr;
+ 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;
return 0;
}
return 0;
}
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
/*
* - gaussian distribution of velocities
/* gaussian distribution of velocities */
v3_zero(&p_total);
for(i=0;i<moldyn->count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* velocity scaling */
- scale_velocity(moldyn);
+ scale_velocity(moldyn,equi_init);
return 0;
}
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
int i;
- double e,c;
+ double e,scale;
t_atom *atom;
+ int count;
atom=moldyn->atom;
/*
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
+
+ /* get kinetic energy / temperature & count involved atoms */
e=0.0;
+ count=0;
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+ e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ count+=1;
+ }
+ }
+ if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+ else return 0; /* no atoms involved in scaling! */
+
+ /* (temporary) hack for e,t = 0 */
+ if(e==0.0) {
+ moldyn->t=0.0;
+ if(moldyn->t_ref!=0.0)
+ thermal_init(moldyn,equi_init);
+ else
+ return 0; /* no scaling needed */
+ }
+
+
+ /* get scaling factor */
+ scale=moldyn->t_ref/moldyn->t;
+ if(equi_init&TRUE)
+ scale*=2.0;
+ else
+ if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+ scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
+ scale=sqrt(scale);
+
+ /* velocity scaling */
for(i=0;i<moldyn->count;i++)
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
- for(i=0;i<moldyn->count;i++)
- v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+ v3_scale(&(atom[i].v),&(atom[i].v),scale);
return 0;
}
count2=27;
a=nx*ny;
-
cell[0]=lc->subcell[i+j*nx+k*a];
for(ci=-1;ci<=1;ci++) {
bx=0;
}
}
- lc->dnlc=count2;
+ lc->dnlc=count1;
lc->countn=27;
return count2;
unsigned int e,m,s,v;
t_3dvec p;
t_moldyn_schedule *schedule;
-
+ t_atom *atom;
int fd;
char fb[128];
+ double ds;
schedule=&(moldyn->schedule);
+ atom=moldyn->atom;
/* initialize linked cell method */
link_cell_init(moldyn);
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
-
/* calculate initial forces */
potential_force_calc(moldyn);
+ /* do some checks before we actually start calculating bullshit */
+ if(moldyn->cutoff>0.5*moldyn->dim.x)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.y)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
+
/* zero absolute time */
moldyn->time=0.0;
-
for(sched=0;sched<moldyn->schedule.content_count;sched++) {
/* setting amount of runs and finite time step size */
/* integration step */
moldyn->integrate(moldyn);
+ /* p/t scaling */
+ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+ scale_velocity(moldyn,FALSE);
+
/* increase absolute time */
moldyn->time+=moldyn->tau;
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);
- v3_per_bound(&(atom[i].r),&(moldyn->dim));
+ check_per_bound(moldyn,&(atom[i].r));
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
int potential_force_calc(t_moldyn *moldyn) {
int i,j,k,count;
- t_atom *atom,*btom,*ktom;
+ t_atom *itom,*jtom,*ktom;
t_linkcell *lc;
- t_list neighbour[27];
- t_list *this,*thisk,*neighbourk;
- u8 bc,bck;
+ t_list neighbour_i[27];
+ t_list neighbour_i2[27];
+ //t_list neighbour_j[27];
+ t_list *this,*that;
+ u8 bc_ij,bc_ijk;
int countn,dnlc;
count=moldyn->count;
- atom=moldyn->atom;
+ itom=moldyn->atom;
lc=&(moldyn->lc);
/* reset energy */
moldyn->energy=0.0;
-printf("DEBUG: count = %d\n",count);
for(i=0;i<count;i++) {
-
+
/* reset force */
- v3_zero(&(atom[i].f));
+ v3_zero(&(itom[i].f));
/* single particle potential/force */
- if(atom[i].attr&ATOM_ATTR_1BP)
- moldyn->func1b(moldyn,&(atom[i]));
+ if(itom[i].attr&ATOM_ATTR_1BP)
+ moldyn->func1b(moldyn,&(itom[i]));
/* 2 body pair potential/force */
- if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+ if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-printf("DEBUG: processing atom %d\n",i);
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);
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour_i);
countn=lc->countn;
dnlc=lc->dnlc;
-printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
for(j=0;j<countn;j++) {
- this=&(neighbour[j]);
+ this=&(neighbour_i[j]);
list_reset(this);
if(this->start==NULL)
continue;
- bc=(j<dnlc)?0:1;
+ bc_ij=(j<dnlc)?0:1;
do {
- btom=this->current->data;
+ jtom=this->current->data;
- if(btom==&(atom[i]))
+ if(jtom==&(itom[i]))
continue;
- if((btom->attr&ATOM_ATTR_2BP)&
- (atom[i].attr&ATOM_ATTR_2BP))
-printf("DEBUG: calling func2b\n");
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP))
moldyn->func2b(moldyn,
- &(atom[i]),
- btom,
- bc);
+ &(itom[i]),
+ jtom,
+ bc_ij);
/* 3 body potential/force */
- if(!(atom[i].attr&ATOM_ATTR_3BP)||
- !(btom->attr&ATOM_ATTR_3BP))
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->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);
+ /*
+ * according to mr. nordlund, we dont need to take the
+ * sum over all atoms now, as 'this is centered' around
+ * atom i ...
+ * i am not quite sure though! there is a not vanishing
+ * part even if f_c_ik is zero ...
+ * this analytical potentials suck!
+ * switching from mc to md to dft soon!
+ */
+
+ // link_cell_neighbour_index(moldyn,
+ // (jtom->r.x+moldyn->dim.x/2)/lc->x,
+ // (jtom->r.y+moldyn->dim.y/2)/lc->y,
+ // (jtom->r.z+moldyn->dim.z/2)/lc->z,
+ // neighbour_j);
+
+// /* neighbours of j */
+// for(k=0;k<lc->countn;k++) {
+//
+// that=&(neighbour_j[k]);
+// list_reset(that);
+//
+// if(that->start==NULL)
+// continue;
+//
+// bc_ijk=(k<lc->dnlc)?0:1;
+//
+// do {
+//
+// ktom=that->current->data;
+//
+// if(!(ktom->attr&ATOM_ATTR_3BP))
+// continue;
+//
+// if(ktom==jtom)
+// continue;
+//
+// if(ktom==&(itom[i]))
+// continue;
+//
+// moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+//
+/* } while(list_next(that)!=\ */
+// L_NO_NEXT_ELEMENT);
+//
+// }
+
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
+
+ /* get neighbours of i */
+ for(k=0;k<countn;k++) {
+
+ that=&(neighbour_i2[k]);
+ list_reset(that);
- if(thisk->start==NULL)
+ if(that->start==NULL)
continue;
- bck=(k<lc->dnlc)?0:1;
+ bc_ijk=(k<dnlc)?0:1;
do {
- ktom=thisk->current->data;
+ ktom=that->current->data;
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==btom)
+ if(ktom==jtom)
continue;
- if(ktom==&(atom[i]))
+ if(ktom==&(itom[i]))
continue;
- moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
+printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+ moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
- } while(list_next(thisk)!=\
+ } while(list_next(that)!=\
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) {
d=+h1-h2;
d*=eps;
v3_scale(&force,&distance,d);
- v3_add(&(ai->f),&(aj->f),&force);
+ v3_add(&(ai->f),&(ai->f),&force);
}
return 0;
* tersoff potential & force for 2 sorts of atoms
*/
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+ printf("[moldyn] tersoff parameter completion\n");
+ p->Smixed=sqrt(p->S[0]*p->S[1]);
+ p->Rmixed=sqrt(p->R[0]*p->R[1]);
+ p->Amixed=sqrt(p->A[0]*p->A[1]);
+ p->Bmixed=sqrt(p->B[0]*p->B[1]);
+ p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+ p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+ return 0;
+}
+
/* tersoff 1 body part */
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
if(bc) check_per_bound(moldyn,&dist_ij);
- /* save for use in 3bp */ /* REALLY ?!?!?! */
- exchange->dist_ij=dist_ij;
+ d_ij=v3_norm(&dist_ij);
+
+ /* save for use in 3bp */
+ exchange->dist_ij=dist_ij; /* <- needed ? */
+ exchange->d_ij=d_ij;
/* constants */
if(num==aj->bnum) {
params->exchange.chi=params->chi;
}
- d_ij=v3_norm(&dist_ij);
-
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
-
if(d_ij>S)
return 0;
/* 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);
+ /* energy is 0.5 f_r f_c ... */
+ moldyn->energy+=(0.5*f_r*f_c);
/* save for use in 3bp */
exchange->f_c=f_c;
projects / physik / posic.git / blobdiff