moldyn->vis.dim.z=z;
}
+ printf("[moldyn] dimensions in A:\n");
+ printf(" x: %f\n",moldyn->dim.x);
+ printf(" y: %f\n",moldyn->dim.y);
+ printf(" z: %f\n",moldyn->dim.z);
+ printf(" visualize simulation box: %s\n",visualize?"on":"off");
+
return 0;
}
return 0;
}
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+ moldyn->func2b_post=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
moldyn->func3b=func;
return 0;
}
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+ strncpy(moldyn->vlsdir,dir,127);
+
+ return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+ char filename[128];
+ int ret;
switch(type) {
case LOG_TOTAL_ENERGY:
moldyn->ewrite=timer;
- moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+ moldyn->efd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
if(moldyn->efd<0) {
- perror("[moldyn] efd open");
+ perror("[moldyn] energy log fd open");
return moldyn->efd;
}
dprintf(moldyn->efd,"# total energy log file\n");
break;
case LOG_TOTAL_MOMENTUM:
moldyn->mwrite=timer;
- moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+ moldyn->mfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
if(moldyn->mfd<0) {
- perror("[moldyn] mfd open");
+ perror("[moldyn] momentum log fd open");
return moldyn->mfd;
}
dprintf(moldyn->efd,"# total momentum log file\n");
break;
case SAVE_STEP:
moldyn->swrite=timer;
- strncpy(moldyn->sfb,fb,63);
break;
case VISUAL_STEP:
moldyn->vwrite=timer;
- strncpy(moldyn->vfb,fb,63);
- visual_init(&(moldyn->vis),fb);
+ ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ if(ret<0) {
+ printf("[moldyn] visual init failure\n");
+ return ret;
+ }
break;
default:
- printf("unknown log mechanism: %02x\n",type);
+ printf("[moldyn] unknown log mechanism: %02x\n",type);
return -1;
}
/* (temporary) hack for e,t = 0 */
if(e==0.0) {
moldyn->t=0.0;
- if(moldyn->t_ref!=0.0)
+ if(moldyn->t_ref!=0.0) {
thermal_init(moldyn,equi_init);
+ return 0;
+ }
else
return 0; /* no scaling needed */
}
scale*=2.0;
else
if(moldyn->pt_scale&T_SCALE_BERENDSEN)
- scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
scale=sqrt(scale);
/* velocity scaling */
- for(i=0;i<moldyn->count;i++)
+ for(i=0;i<moldyn->count;i++) {
if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
v3_scale(&(atom[i].v),&(atom[i].v),scale);
+ }
return 0;
}
/* 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;
}
lc->dnlc=count1;
- lc->countn=27;
- return count2;
+ return count1;
}
int link_cell_shutdown(t_moldyn *moldyn) {
t_moldyn_schedule *schedule;
t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
double ds;
schedule=&(moldyn->schedule);
/* 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 */
+ /* some stupid 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)
/* zero absolute time */
moldyn->time=0.0;
+
+ /* debugging, ignore */
+ moldyn->debug=0;
+
+ /* executing the schedule */
for(sched=0;sched<moldyn->schedule.content_count;sched++) {
/* setting amount of runs and finite time step size */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
- /* increase absolute time */
- moldyn->time+=moldyn->tau;
-
/* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
- "%.15f %.45f %.45f %.45f\n",
+ "%f %f %f %f\n",
moldyn->time,update_e_kin(moldyn),
moldyn->energy,
get_total_energy(moldyn));
if(!(i%m)) {
p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",moldyn->time,
- v3_norm(&p));
+ "%f %f\n",moldyn->time,v3_norm(&p));
}
}
if(s) {
if(!(i%s)) {
- snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
- moldyn->t,i*moldyn->tau);
- fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+ snprintf(dir,128,"%s/s-%07.f.save",
+ moldyn->vlsdir,moldyn->time);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
if(fd<0) perror("[moldyn] save fd open");
else {
write(fd,moldyn,sizeof(t_moldyn));
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d",sched,i);
+ printf("\rsched: %d, steps: %d, debug: %d",
+ sched,i,moldyn->debug);
fflush(stdout);
}
}
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
}
/* check for hooks */
if(schedule->hook)
schedule->hook(moldyn,schedule->hook_params);
+ /* get a new info line */
+ printf("\n");
+
}
return 0;
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+moldyn_bc_check(moldyn);
/* neighbour list update */
link_cell_update(moldyn);
/* forces depending on chosen potential */
potential_force_calc(moldyn);
- //moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
/* again velocities */
t_list neighbour_i2[27];
//t_list neighbour_j[27];
t_list *this,*that;
- u8 bc_ij,bc_ijk;
- int countn,dnlc;
+ u8 bc_ij,bc_ik;
+ int dnlc;
count=moldyn->count;
itom=moldyn->atom;
/* reset energy */
moldyn->energy=0.0;
+ /* get energy and force of every atom */
for(i=0;i<count;i++) {
/* reset force */
if(itom[i].attr&ATOM_ATTR_1BP)
moldyn->func1b(moldyn,&(itom[i]));
+ if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+ continue;
+
/* 2 body pair potential/force */
- if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
- link_cell_neighbour_index(moldyn,
- (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);
+ link_cell_neighbour_index(moldyn,
+ (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);
+
+ dnlc=lc->dnlc;
+
+ for(j=0;j<27;j++) {
- countn=lc->countn;
- dnlc=lc->dnlc;
+ this=&(neighbour_i[j]);
+ list_reset(this);
+
+ if(this->start==NULL)
+ continue;
- for(j=0;j<countn;j++) {
+ bc_ij=(j<dnlc)?0:1;
- this=&(neighbour_i[j]);
- list_reset(this);
+ do {
+ jtom=this->current->data;
- if(this->start==NULL)
+ if(jtom==&(itom[i]))
continue;
- bc_ij=(j<dnlc)?0:1;
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
- do {
- jtom=this->current->data;
+ /* 3 body potential/force */
- if(jtom==&(itom[i]))
- continue;
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP))
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
- /* 3 body potential/force */
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
+ that=&(neighbour_i2[k]);
+ list_reset(that);
+
+ if(that->start==NULL)
continue;
- /*
- * 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(that->start==NULL)
- continue;
+ bc_ik=(k<dnlc)?0:1;
- bc_ijk=(k<dnlc)?0:1;
+ do {
- do {
+ ktom=that->current->data;
- ktom=that->current->data;
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- if(!(ktom->attr&ATOM_ATTR_3BP))
- continue;
+ if(ktom==jtom)
+ continue;
- if(ktom==jtom)
- continue;
+ if(ktom==&(itom[i]))
+ continue;
- if(ktom==&(itom[i]))
- continue;
+ moldyn->func3b(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
-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(that)!=\
+ L_NO_NEXT_ELEMENT);
- } while(list_next(that)!=\
- L_NO_NEXT_ELEMENT);
+ }
- }
+ /* 2bp post function */
+ if(moldyn->func2b_post) {
+ moldyn->func2b_post(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+ }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- }
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
}
+
}
return 0;
sc=params->spring_constant;
equi_dist=params->equilibrium_distance;
- v3_sub(&distance,&(ai->r),&(aj->r));
+ v3_sub(&distance,&(aj->r),&(ai->r));
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)));
+ /* f = -grad E; grad r_ij = -1 1/r_ij distance */
+ v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
v3_add(&(ai->f),&(ai->f),&force);
}
sig6=params->sigma6;
sig12=params->sigma12;
- v3_sub(&distance,&(ai->r),&(aj->r));
+ v3_sub(&distance,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&distance);
d=v3_absolute_square(&distance); /* 1/r^2 */
if(d<=moldyn->cutoff_square) {
h1*=12*sig12;
d=+h1-h2;
d*=eps;
- v3_scale(&force,&distance,d);
+ v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
v3_add(&(ai->f),&(ai->f),&force);
}
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 (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (A) | %f | %f | %f\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;
}
* their right values
*/
- exchange->beta=&(params->beta[num]);
- exchange->n=&(params->n[num]);
- exchange->c=&(params->c[num]);
- exchange->d=&(params->d[num]);
- exchange->h=&(params->h[num]);
+ 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->betan=pow(*(exchange->beta),*(exchange->n));
- exchange->c2=params->c[num]*params->c[num];
- exchange->d2=params->d[num]*params->d[num];
- exchange->c2d2=exchange->c2/exchange->d2;
+ 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->ci2di2=exchange->ci2/exchange->di2;
return 0;
}
int num;
double s_r;
double arg;
- double scale;
params=moldyn->pot2b_params;
- num=ai->bnum;
+ num=aj->bnum;
exchange=&(params->exchange);
+ /* clear 3bp and 2bp post run */
exchange->run3bp=0;
+ exchange->run2bp_post=0;
+
+ /* reset S > r > R mark */
+ exchange->d_ij_between_rs=0;
/*
- * we need: f_c, df_c, f_r, df_r
+ * calc of 2bp contribution of V_ij and dV_ij/ji
+ *
+ * for Vij and dV_ij we need:
+ * - f_c_ij, df_c_ij
+ * - f_r_ij, df_r_ij
+ *
+ * for dV_ji we need:
+ * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+ * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
*
- * therefore we need: R, S, A, lambda
*/
- v3_sub(&dist_ij,&(ai->r),&(aj->r));
-
+ /* dist_ij, d_ij */
+ v3_sub(&dist_ij,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&dist_ij);
-
d_ij=v3_norm(&dist_ij);
/* save for use in 3bp */
- exchange->dist_ij=dist_ij; /* <- needed ? */
exchange->d_ij=d_ij;
+ exchange->dist_ij=dist_ij;
/* constants */
- if(num==aj->bnum) {
+ if(num==ai->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;
+ exchange->chi=1.0;
}
else {
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;
}
+ /* if d_ij > S => no force & potential energy contribution */
if(d_ij>S)
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->betajnj=exchange->betaini;
+ exchange->cj2=exchange->ci2;
+ exchange->dj2=exchange->di2;
+ exchange->cj2dj2=exchange->ci2di2;
+ }
+ 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->cj2dj2=exchange->cj2/exchange->dj2;
+ }
+
+ /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
f_r=A*exp(-lambda*d_ij);
- df_r=-lambda*f_r/d_ij;
+ df_r=lambda*f_r/d_ij;
- /* f_a, df_a calc + save for 3bp use */
+ /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=-mu*exchange->f_a/d_ij;
+ exchange->df_a=mu*exchange->f_a/d_ij;
+ /* f_c, df_c calc (again, same for ij and ji) */
if(d_ij<R) {
/* f_c = 1, df_c = 0 */
f_c=1.0;
df_c=0.0;
- v3_scale(&force,&dist_ij,df_r);
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_r);
}
else {
s_r=S-R;
arg=M_PI*(d_ij-R)/s_r;
f_c=0.5+0.5*cos(arg);
df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
- scale=df_c*f_r+df_r*f_c;
- v3_scale(&force,&dist_ij,scale);
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
+ /* tell 3bp that S > r > R */
+ exchange->d_ij_between_rs=1;
}
- /* add forces */
+ /* add forces of 2bp (ij, ji) contribution
+ * dVij = dVji and we sum up both: no 1/2) */
v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c ... */
+
+ /* energy 2bp contribution (ij, ji) 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;
exchange->df_c=df_c;
- /* enable the run of 3bp function */
+ /* enable the run of 3bp function and 2bp post processing */
exchange->run3bp=1;
+ exchange->run2bp_post=1;
+
+ /* reset 3bp sums */
+ exchange->zeta_ij=0.0;
+ exchange->zeta_ji=0.0;
+ v3_zero(&(exchange->dzeta_ij));
+ v3_zero(&(exchange->dzeta_ji));
+
+ return 0;
+}
+
+/* tersoff 2 body post part */
+
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ /*
+ * here we have to allow for the 3bp sums
+ *
+ * that is:
+ * - zeta_ij, dzeta_ij
+ * - zeta_ji, dzeta_ji
+ *
+ * to compute the 3bp contribution to:
+ * - Vij, dVij
+ * - dVji
+ *
+ */
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ t_3dvec force,temp;
+ t_3dvec *dist_ij;
+ double b,db,tmp;
+ double f_c,df_c,f_a,df_a;
+ double chi,ni,betaini,nj,betajnj;
+ double zeta;
+
+ params=moldyn->pot2b_params;
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was detected to be 0! */
+ if(!(exchange->run2bp_post))
+ return 0;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+ f_a=exchange->f_a;
+ df_a=exchange->df_a;
+ betaini=exchange->betaini;
+ betajnj=exchange->betajnj;
+ ni=*(exchange->n_i);
+ nj=*(exchange->n_j);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
+
+ /* Vij and dVij */
+ zeta=exchange->zeta_ij;
+ if(zeta==0.0) {
+ moldyn->debug++; /* just for debugging ... */
+ db=0.0;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* add energy of 3bp sum */
+ moldyn->energy+=(0.5*f_c*b*f_a);
+
+ /* dVji */
+ zeta=exchange->zeta_ji;
+ if(zeta==0.0) {
+ moldyn->debug++;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
return 0;
}
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec temp,force;
+ t_3dvec temp1,temp2;
+ t_3dvec *dzeta;
double R,S,s_r;
- double d_ij,d_ij2,d_ik,d_jk;
- double f_c,df_c,b_ij,f_a,df_a;
+ double B,mu;
+ double d_ij,d_ik,d_jk;
+ double rr,dd;
+ double f_c,df_c;
double f_c_ik,df_c_ik,arg;
- double scale;
- double chi;
- double n,c,d,h,beta,betan;
+ double f_c_jk;
+ double n,c,d,h;
double c2,d2,c2d2;
- double numer,denom;
- double theta,cos_theta,sin_theta;
- double d_theta,d_theta1,d_theta2;
- double h_cos,h_cos2,d2_h_cos2;
- double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
- double bracket3,bracket3_pow_1,bracket3_pow;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac,g,zeta,chi;
+ double tmp;
int num;
params=moldyn->pot3b_params;
- num=ai->bnum;
exchange=&(params->exchange);
if(!(exchange->run3bp))
return 0;
/*
- * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+ * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+ * 2bp contribution of dV_jk
*
- * we got f_c, df_c, f_a, df_a from 2bp calculation
+ * for Vij and dV_ij we still need:
+ * - b_ij, db_ij (zeta_ij)
+ * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
+ *
+ * for dV_ji we still need:
+ * - b_ji, db_ji (zeta_ji)
+ * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+ *
+ * for dV_jk we need:
+ * - f_c_jk
+ * - f_a_jk
+ * - db_jk (zeta_jk)
+ * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
+ *
+ */
+
+ /*
+ * get exchange data
*/
+ /* dist_ij, d_ij - this is < S_ij ! */
+ dist_ij=exchange->dist_ij;
d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
- f_a=params->exchange.f_a;
- df_a=params->exchange.df_a;
-
- /* d_ij is <= S, as we didn't return so far! */
+ /* f_c_ij, df_c_ij (same for ji) */
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
/*
- * calc of b_ij (scalar) and db_ij (vector)
- *
- * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
- *
- * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
- * w_ik,
- *
+ * calculate unknown values now ...
*/
-
- v3_sub(&dist_ik,&(ai->r),&(ak->r));
+ /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+
+ /* dist_ik, d_ik */
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
if(bc) check_per_bound(moldyn,&dist_ik);
d_ik=v3_norm(&dist_ik);
- /* constants for f_c_ik calc */
+ /* ik constants */
+ num=ai->bnum;
if(num==ak->bnum) {
R=params->R[num];
S=params->S[num];
S=params->Smixed;
}
- /* calc of f_c_ik */
- if(d_ik>S)
- return 0;
+ /* zeta_ij/dzeta_ij contribution only for d_ik < S */
+ if(d_ik<S) {
+
+ /* get constants_i from exchange data */
+ n=*(exchange->n_i);
+ c=*(exchange->c_i);
+ d=*(exchange->d_i);
+ h=*(exchange->h_i);
+ c2=exchange->ci2;
+ d2=exchange->di2;
+ c2d2=exchange->ci2di2;
+
+ /* cosine of theta_ijk by scalaproduct */
+ rr=v3_scalar_product(&dist_ij,&dist_ik);
+ dd=d_ij*d_ik;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ tmp=1.0/dd;
+ d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
+ d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_ij,d_costheta1);
+ v3_scale(&temp2,&dist_ik,d_costheta2);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* f_c_ik & df_c_ik + {d,}zeta contribution */
+ dzeta=&(exchange->dzeta_ij);
+ if(d_ik<R) {
+ /* {d,}f_c_ik */
+ // => f_c_ik=1.0;
+ // => df_c_ik=0.0; of course we do not set this!
+
+ /* zeta_ij */
+ exchange->zeta_ij+=g;
+
+ /* dzeta_ij */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* {d,}f_c_ik */
+ s_r=S-R;
+ arg=M_PI*(d_ik-R)/s_r;
+ f_c_ik=0.5+0.5*cos(arg);
+ df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+
+ /* zeta_ij */
+ exchange->zeta_ij+=f_c_ik*g;
+
+ /* dzeta_ij */
+ v3_scale(&temp1,&temp1,f_c_ik);
+ v3_scale(&temp2,&dist_ik,g*df_c_ik);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ }
+
+ /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+
+ /* dist_jk, d_jk */
+ v3_sub(&dist_jk,&(ak->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk=v3_norm(&dist_jk);
- if(d_ik<R) {
- /* f_c_ik = 1, df_c_ik = 0 */
- f_c_ik=1.0;
- df_c_ik=0.0;
+ /* 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];
+ chi=1.0;
}
else {
- s_r=S-R;
- arg=M_PI*(d_ik-R)/s_r;
- f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+ R=params->Rmixed;
+ S=params->Smixed;
+ B=params->Bmixed;
+ mu=params->mu_m;
+ chi=params->chi;
}
-
- v3_sub(&dist_jk,&(aj->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk=v3_norm(&dist_jk);
- beta=*(exchange->beta);
- betan=exchange->betan;
- n=*(exchange->n);
- c=*(exchange->c);
- d=*(exchange->d);
- h=*(exchange->h);
- 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;
- 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);
- d_theta1=2*denom-numer*2*d_ik/d_ij;
- d_theta2=2*denom-numer*2*d_ij/d_ik;
- d_theta1*=d_theta;
- d_theta2*=d_theta;
-
- h_cos=(h-cos_theta);
- h_cos2=h_cos*h_cos;
- d2_h_cos2=d2-h_cos2;
-
- /* some usefull expressions */
- 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;
- bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
- bracket3_pow=bracket3_pow_1*bracket3;
-
- /* now go on with calc of b_ij and derivation of b_ij */
- b_ij=chi*bracket3_pow;
-
- /* derivation of theta */
- v3_scale(&force,&dist_ij,d_theta1);
- v3_scale(&temp,&dist_ik,d_theta2);
- v3_add(&force,&force,&temp);
+ /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+ if(d_jk<S) {
+
+ /* constants_j from exchange data */
+ n=*(exchange->n_j);
+ c=*(exchange->c_j);
+ d=*(exchange->d_j);
+ h=*(exchange->h_j);
+ c2=exchange->cj2;
+ d2=exchange->dj2;
+ c2d2=exchange->cj2dj2;
+
+ /* cosine of theta_jik by scalaproduct */
+ rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+ dd=d_ij*d_jk;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ d_costheta1=1.0/(d_jk*d_ij);
+ d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_jk,d_costheta1);
+ v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+ dzeta=&(exchange->dzeta_ji);
+ if(d_jk<R) {
+ /* f_c_jk */
+ f_c_jk=1.0;
+
+ /* zeta_ji */
+ exchange->zeta_ji+=g;
+
+ /* dzeta_ji */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* f_c_jk */
+ s_r=S-R;
+ arg=M_PI*(d_jk-R)/s_r;
+ f_c_jk=0.5+0.5*cos(arg);
+
+ /* zeta_ji */
+ exchange->zeta_ji+=f_c_jk*g;
+
+ /* dzeta_ij */
+ v3_scale(&temp1,&temp1,f_c_jk);
+ v3_add(dzeta,dzeta,&temp1);
+ }
- /* part 1 of derivation of b_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
+ /* dV_jk stuff | add force contribution on atom i immediately */
+ if(exchange->d_ij_between_rs) {
+ zeta=f_c*g;
+ v3_scale(&temp1,&temp1,f_c);
+ v3_scale(&temp2,&dist_ij,df_c);
+ v3_add(&temp1,&temp1,&temp2);
+ }
+ else {
+ zeta=g;
+ // dzeta_jk is simply dg, which is temp1
+ }
+ /* betajnj * zeta_jk ^ nj-1 */
+ tmp=exchange->betajnj*pow(zeta,(n-1.0));
+ tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
+ v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+ v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+ /* scaled with 0.5 ^ */
+ }
+
+ return 0;
+}
- /* part 2 of derivation of b_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
- /* sum up and scale ... */
- v3_add(&temp,&temp,&force);
- scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
- v3_scale(&temp,&temp,scale);
+/*
+ * debugging / critical check functions
+ */
- /* now construct an energy and a force out of that */
- v3_scale(&temp,&temp,f_a);
- v3_scale(&force,&dist_ij,df_a*b_ij);
- v3_add(&temp,&temp,&force);
- v3_scale(&temp,&temp,f_c);
- v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
- v3_add(&force,&force,&temp);
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+ t_atom *atom;
+ t_3dvec *dim;
+ int i;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2)
+ printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+ i,atom[i].r.x*1e10,dim->x/2*1e10);
+ if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+ printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+ i,atom[i].r.y*1e10,dim->y/2*1e10);
+ if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+ printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+ i,atom[i].r.z*1e10,dim->z/2*1e10);
+ }
- /* 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);
-
return 0;
}
projects / physik / posic.git / blobdiff