int moldyn_shutdown(t_moldyn *moldyn) {
- link_cell_shutdown(moldyn);
+ printf("[moldyn] shutdown\n");
moldyn_log_shutdown(moldyn);
+ link_cell_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)
strncpy(moldyn->sfb,fb,63);
break;
case VISUAL_STEP:
- moldyn->mwrite=timer;
+ moldyn->vwrite=timer;
strncpy(moldyn->vfb,fb,63);
visual_init(&(moldyn->vis),fb);
break;
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;
}
int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
- t_3dvec r,t_3dvec v) {
+ t_3dvec *r,t_3dvec *v) {
t_atom *atom;
void *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;
+ 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;
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;
}
return p_total;
}
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
double tau;
- tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
- tau*=1.0E-9;
- if(tau<moldyn->tau)
- printf("[moldyn] warning: time step (%f > %.15f)\n",
- moldyn->tau,tau);
+ /* nn_dist is the nearest neighbour distance */
+
+ if(moldyn->t==5.0) {
+ printf("[moldyn] i do not estimate timesteps below %f K!\n",
+ MOLDYN_CRITICAL_EST_TEMP);
+ return 23.42;
+ }
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
}
t_linkcell *lc;
int i;
+ int fd;
+
+ fd=open("/dev/null",O_WRONLY);
lc=&(moldyn->lc);
lc->cells=lc->nx*lc->ny*lc->nz;
lc->subcell=malloc(lc->cells*sizeof(t_list));
- printf("initializing linked cells (%d)\n",lc->cells);
+ 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]),1);
+ list_init(&(lc->subcell[i]),fd);
link_cell_update(moldyn);
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;
perror("[moldyn] realloc (runs)");
return -1;
}
+ moldyn->schedule.runs=ptr;
moldyn->schedule.runs[count-1]=runs;
ptr=realloc(schedule->tau,count*sizeof(double));
perror("[moldyn] realloc (tau)");
return -1;
}
+ moldyn->schedule.tau=ptr;
moldyn->schedule.tau[count-1]=tau;
return 0;
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);
s=moldyn->swrite;
v=moldyn->vwrite;
- if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
- printf("[moldyn] warning, lv system not initialized\n");
- return -1;
- }
-
/* 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;
}
if(v) {
if(!(i%v)) {
- visual_atoms(moldyn->visual,i*moldyn->tau,
+ visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsteps: %d",i);
+ printf("\rsched: %d, steps: %d",sched,i);
fflush(stdout);
}
}
+
}
/* check for hooks */
if(schedule->hook)
schedule->hook(moldyn,schedule->hook_params);
+ }
+
return 0;
}
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);
}
/* neighbour list update */
-printf("list update ...\n");
link_cell_update(moldyn);
-printf("done\n");
/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
potential_force_calc(moldyn);
//moldyn->potential_force_function(moldyn);
-printf("done\n");
for(i=0;i<count;i++) {
/* again velocities */
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;
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)) {
+
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;
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))
+ 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);
}
} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /* 2bp post function */
+ if(moldyn->func2b_post)
+ mlodyn->func2b_post(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+
}
}
}
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]);
+
+ printf("[moldyn] tersoff mult parameter info:\n");
+ printf(" S (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (m) | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
+ printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
+ printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
+ printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
+ p->lambda_m);
+ printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
+ printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+ printf(" n | %f | %f\n",p->n[0],p->n[1]);
+ printf(" c | %f | %f\n",p->c[0],p->c[1]);
+ printf(" d | %f | %f\n",p->d[0],p->d[1]);
+ printf(" h | %f | %f\n",p->h[0],p->h[1]);
+ printf(" chi | %f \n",p->chi);
+
+ 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 ?!?!?! */
+ d_ij=v3_norm(&dist_ij);
+
+ /* save for use in 3bp */
+ exchange->d_ij=d_ij;
exchange->dist_ij=dist_ij;
+ exchange->d_ij2=d_ij*d_ij;
/* constants */
if(num==aj->bnum) {
S=params->S[num];
R=params->R[num];
A=params->A[num];
+ B=params->B[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]);
mu=params->mu[num];
params->exchange.chi=1.0;
}
S=params->Smixed;
R=params->Rmixed;
A=params->Amixed;
+ B=params->Bmixed;
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);
mu=params->mu_m;
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;
/* enable the run of 3bp function */
exchange->run3bp=1;
+ /* reset 3bp sums */
+ exchange->3bp_sum1=0.0;
+ exchange->3bp_sum2=0.0;
+
+ return 0;
+}
+
+/* tersoff 2 body post part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ /* here we have to allow for the 3bp sums */
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ t_3dvec force,temp,*db_ij;
+ double db_ij_scale1,db_ij_scale2;
+ double b_ij;
+ double f_c,df_c,f_a,df_a;
+
+ params=moldyn->pot2b_params;
+ exchange=&(moldyn->exchange);
+
+ db_ij=&(exchange->db_ij);
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+ f_a=exchange->f_a;
+ df_a=exchange->df_a;
+
+ db_ij_scale1=(1+betan*3bp_sum1);
+ db_ij_scale2=(n*betan*3bp_sum2);
+ help=pow(db_ij_scale1,-1.0/(2*n)-1);
+ b_ij=chi*db_ij_scale1*help;
+ db_ij_scale1=-chi/(2*n)*help;
+
+ v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
+ v3_scale(db_ij,db_ij,f_a);
+
+ v3_scale(&temp,dist_ij,b_ij*df_a);
+
+ v3_add(&force,&temp,db_ij);
+ v3_scale(&force,&force,f_c);
+
+ v3_scale(&temp,&dist_ij,f_a*b_ij*df_c);
+
+ /* add energy of 3bp sum */
+ moldyn->energy+=(0.5*f_c*b_ij*f_a);
+ /* add force of 3bp calculation */
+ v3_add(&(ai->f),&temp,&force);
+
return 0;
}
d_ij=exchange->d_ij;
d_ij2=exchange->d_ij2;
+ dist_ij=exchange->dist_ij;
f_a=params->exchange.f_a;
df_a=params->exchange.df_a;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
/* d_ij is <= S, as we didn't return so far! */
*
*/
-
v3_sub(&dist_ik,&(ai->r),&(ak->r));
if(bc) check_per_bound(moldyn,&dist_ik);
d_ik=v3_norm(&dist_ik);
}
/* calc of f_c_ik */
- if(d_ik>S)
- return 0;
-
- if(d_ik<R) {
- /* f_c_ik = 1, df_c_ik = 0 */
+ if(d_ik>S) {
+ f_c_ik=0.0;
+ df_c_ik=0.0;
+ }
+ else if(d_ik<R) {
f_c_ik=1.0;
df_c_ik=0.0;
}
c=*(exchange->c);
d=*(exchange->d);
h=*(exchange->h);
+ chi=exchange->chi;
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;
+ //cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
sin_theta=sqrt(1.0-(cos_theta*cos_theta));
theta=acos(cos_theta);
d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
h_cos=(h-cos_theta);
h_cos2=h_cos*h_cos;
- d2_h_cos2=d2-h_cos2;
+ d2_h_cos2=d2+h_cos2;
/* some usefull expressions */
- frac1=c2/(d2-h_cos2);
+ 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;
+ if(f_c_ik==0.0) {
+ bracket2=0.0;
+ bracket2_n_1=0.0;
+ bracket2_n=0.0;
+ bracket3=1.0;
+ printf("Foo -> 0: ");
+ }
+ else {
+ bracket2=f_c_ik*bracket1;
+ bracket2_n_1=pow(bracket2,n-1.0);
+ bracket2_n=bracket2_n_1*bracket2;
+ bracket3=1.0+betan*bracket2_n;
+ printf("Foo -> 1: ");
+ }
bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
bracket3_pow=bracket3_pow_1*bracket3;
+printf("%.15f %.15f %.15f\n",bracket2_n_1,bracket2_n);
/* now go on with calc of b_ij and derivation of b_ij */
b_ij=chi*bracket3_pow;
/* 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);
+ /* energy is 0.5 f_r f_c */
+ moldyn->energy+=(0.5*f_a*b_ij*f_c);
return 0;
}
projects / physik / posic.git / blobdiff