moldyn->p_ref=p_ref;
- printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+ printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
return 0;
}
return 0;
}
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
moldyn->func1b=func;
- moldyn->pot1b_params=params;
return 0;
}
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
moldyn->func2b=func;
- moldyn->pot2b_params=params;
return 0;
}
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
- moldyn->func2b_post=func;
- moldyn->pot2b_params=params;
+ moldyn->func3b_j1=func;
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
- moldyn->func3b=func;
- moldyn->pot3b_params=params;
+ moldyn->func3b_j2=func;
+
+ return 0;
+}
+
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j3=func;
+
+ return 0;
+}
+
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k1=func;
+
+ return 0;
+}
+
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k2=func;
+
+ return 0;
+}
+
+int set_potential_params(t_moldyn *moldyn,void *params) {
+
+ moldyn->pot_params=params;
return 0;
}
dprintf(moldyn->efd,"# total momentum log file\n");
printf("total momentum (%d)\n",timer);
break;
+ case LOG_PRESSURE:
+ moldyn->pwrite=timer;
+ snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
+ moldyn->pfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->pfd<0) {
+ perror("[moldyn] pressure log file\n");
+ return moldyn->pfd;
+ }
+ dprintf(moldyn->pfd,"# pressure log file\n");
+ printf("pressure (%d)\n",timer);
+ break;
+ case LOG_TEMPERATURE:
+ moldyn->twrite=timer;
+ snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
+ moldyn->tfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tfd<0) {
+ perror("[moldyn] temperature log file\n");
+ return moldyn->tfd;
+ }
+ dprintf(moldyn->tfd,"# temperature log file\n");
+ printf("temperature (%d)\n",timer);
+ break;
case SAVE_STEP:
moldyn->swrite=timer;
printf("save file (%d)\n",timer);
perror("[moldyn] report fd open");
return moldyn->rfd;
}
- snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
- moldyn->pfd=open(filename,
- O_WRONLY|O_CREAT|O_EXCL,
- S_IRUSR|S_IWUSR);
- if(moldyn->pfd<0) {
- perror("[moldyn] plot fd open");
- return moldyn->pfd;
+ printf("report -> ");
+ if(moldyn->efd) {
+ snprintf(filename,127,"%s/e_plot.scr",
+ moldyn->vlsdir);
+ moldyn->epfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->epfd<0) {
+ perror("[moldyn] energy plot fd open");
+ return moldyn->epfd;
+ }
+ dprintf(moldyn->epfd,e_plot_script);
+ close(moldyn->epfd);
+ printf("energy ");
+ }
+ if(moldyn->pfd) {
+ snprintf(filename,127,"%s/pressure_plot.scr",
+ moldyn->vlsdir);
+ moldyn->ppfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->ppfd<0) {
+ perror("[moldyn] p plot fd open");
+ return moldyn->ppfd;
+ }
+ dprintf(moldyn->ppfd,pressure_plot_script);
+ close(moldyn->ppfd);
+ printf("pressure ");
+ }
+ if(moldyn->tfd) {
+ snprintf(filename,127,"%s/temperature_plot.scr",
+ moldyn->vlsdir);
+ moldyn->tpfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tpfd<0) {
+ perror("[moldyn] t plot fd open");
+ return moldyn->tpfd;
+ }
+ dprintf(moldyn->tpfd,temperature_plot_script);
+ close(moldyn->tpfd);
+ printf("temperature ");
}
dprintf(moldyn->rfd,report_start,
moldyn->rauthor,moldyn->rtitle);
- dprintf(moldyn->pfd,plot_script);
- close(moldyn->pfd);
+ printf("\n");
break;
default:
printf("unknown log type: %02x\n",type);
char sc[256];
printf("[moldyn] log shutdown\n");
- if(moldyn->efd) close(moldyn->efd);
+ if(moldyn->efd) {
+ close(moldyn->efd);
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_energy);
+ snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ }
if(moldyn->mfd) close(moldyn->mfd);
+ if(moldyn->pfd) {
+ close(moldyn->pfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_pressure);
+ snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->tfd) {
+ close(moldyn->tfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_temperature);
+ snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
if(moldyn->rfd) {
dprintf(moldyn->rfd,report_end);
close(moldyn->rfd);
- snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
- system(sc);
snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
system(sc);
snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
/* assume up to date kinetic energy, which is 3/2 N k_B T */
moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+ moldyn->t_sum+=moldyn->t;
+ moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
return moldyn->t;
}
t_virial *virial;
/*
- * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
- *
- * virial = f_i r_i
+ * PV = NkT + <W>
+ * W = 1/3 sum_i f_i r_i
+ * virial = sum_i f_i r_i
+ *
+ * => P = (2 Ekin + virial) / (3V)
*/
v=0.0;
/* assume up to date kinetic energy */
moldyn->p=2.0*moldyn->ekin+v;
moldyn->p/=(3.0*moldyn->volume);
+ moldyn->p_sum+=moldyn->p;
+ moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
+
+ /* pressure from 'absolute coordinates' virial */
+ virial=&(moldyn->virial);
+ v=virial->xx+virial->yy+virial->zz;
+ moldyn->gp=2.0*moldyn->ekin+v;
+ moldyn->gp/=(3.0*moldyn->volume);
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
return moldyn->p;
}
t_3dvec dim,*tp;
double u,p;
- double scale;
+ double scale,dv;
t_atom *store;
+ /*
+ * dU = - p dV
+ *
+ * => p = - dU/dV
+ *
+ * dV: dx,y,z = 0.001 x,y,z
+ */
+
+ scale=1.00000000000001;
+printf("\n\nP-DEBUG:\n");
+
tp=&(moldyn->tp);
store=malloc(moldyn->count*sizeof(t_atom));
if(store==NULL) {
dim=moldyn->dim;
/* derivative with respect to x direction */
- scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
scale_dim(moldyn,scale,TRUE,0,0);
scale_atoms(moldyn,scale,TRUE,0,0);
+ dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- tp->x=(moldyn->energy-u)/moldyn->dv;
+ tp->x=(moldyn->energy-u)/dv;
p=tp->x*tp->x;
/* restore atomic configuration + dim */
moldyn->dim=dim;
/* derivative with respect to y direction */
- scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
scale_dim(moldyn,scale,0,TRUE,0);
scale_atoms(moldyn,scale,0,TRUE,0);
+ dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- tp->y=(moldyn->energy-u)/moldyn->dv;
+ tp->y=(moldyn->energy-u)/dv;
p+=tp->y*tp->y;
/* restore atomic configuration + dim */
moldyn->dim=dim;
/* derivative with respect to z direction */
- scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
scale_dim(moldyn,scale,0,0,TRUE);
scale_atoms(moldyn,scale,0,0,TRUE);
+ dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- tp->z=(moldyn->energy-u)/moldyn->dv;
+ tp->z=(moldyn->energy-u)/dv;
p+=tp->z*tp->z;
/* restore atomic configuration + dim */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
moldyn->dim=dim;
- printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
-
- scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
-
-printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
- scale_dim(moldyn,scale,1,1,1);
- scale_atoms(moldyn,scale,1,1,1);
- link_cell_shutdown(moldyn);
- link_cell_init(moldyn,QUIET);
- potential_force_calc(moldyn);
-printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
-
- printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
-
- /* restore atomic configuration + dim */
- memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
- moldyn->dim=dim;
-
/* restore energy */
moldyn->energy=u;
}
-double get_e_kin(t_moldyn *moldyn) {
+double e_kin_calc(t_moldyn *moldyn) {
int i;
t_atom *atom;
return moldyn->ekin;
}
-double update_e_kin(t_moldyn *moldyn) {
-
- return(get_e_kin(moldyn));
-}
-
double get_total_energy(t_moldyn *moldyn) {
return(moldyn->ekin+moldyn->energy);
if(lc->cells<27)
printf("[moldyn] FATAL: less then 27 subcells!\n");
- if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ if(vol) {
+ printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ printf(" x: %d x %f A\n",lc->nx,lc->x);
+ printf(" y: %d x %f A\n",lc->ny,lc->y);
+ printf(" z: %d x %f A\n",lc->nz,lc->z);
+ }
for(i=0;i<lc->cells;i++)
list_init_f(&(lc->subcell[i]));
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]),
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
&(atom[count]));
}
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- unsigned int e,m,s,v;
- t_3dvec p;
+ unsigned int e,m,s,v,p,t;
+ t_3dvec momentum;
t_moldyn_schedule *sched;
t_atom *atom;
int fd;
char dir[128];
double ds;
double energy_scale;
+ //double tp;
sched=&(moldyn->schedule);
atom=moldyn->atom;
m=moldyn->mwrite;
s=moldyn->swrite;
v=moldyn->vwrite;
+ p=moldyn->pwrite;
+ t=moldyn->twrite;
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
/* zero absolute time */
moldyn->time=0.0;
+ moldyn->total_steps=0;
/* debugging, ignore */
moldyn->debug=0;
moldyn->integrate(moldyn);
/* calculate kinetic energy, temperature and pressure */
- update_e_kin(moldyn);
+ e_kin_calc(moldyn);
temperature_calc(moldyn);
pressure_calc(moldyn);
- //thermodynamic_pressure_calc(moldyn);
+ //tp=thermodynamic_pressure_calc(moldyn);
+//printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
}
if(m) {
if(!(i%m)) {
- p=get_total_p(moldyn);
+ momentum=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%f %f\n",moldyn->time,v3_norm(&p));
+ "%f %f %f %f %f\n",moldyn->time,
+ momentum.x,momentum.y,momentum.z,
+ v3_norm(&momentum));
+ }
+ }
+ if(p) {
+ if(!(i%p)) {
+ dprintf(moldyn->pfd,
+ "%f %f %f %f %f\n",moldyn->time,
+ moldyn->p/BAR,moldyn->mean_p/BAR,
+ moldyn->gp/BAR,moldyn->mean_gp/BAR);
+ }
+ }
+ if(t) {
+ if(!(i%t)) {
+ dprintf(moldyn->tfd,
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->mean_t);
}
}
if(s) {
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
- sched->count,i,
- moldyn->t,moldyn->p/ATM,moldyn->volume);
- fflush(stdout);
}
}
+ /* display progress */
+ if(!(i%10)) {
+ printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
+ sched->count,i,
+ moldyn->mean_t,
+ moldyn->mean_p/BAR,
+ moldyn->mean_gp/BAR,
+ moldyn->volume);
+ fflush(stdout);
+ }
+
/* increase absolute time */
moldyn->time+=moldyn->tau;
+ moldyn->total_steps+=1;
}
/* reset energy */
moldyn->energy=0.0;
+ /* reset global virial */
+ memset(&(moldyn->virial),0,sizeof(t_virial));
+
/* reset force, site energy and virial of every atom */
for(i=0;i<count;i++) {
}
- /* get energy,force and virial of every atom */
+ /* get energy, force and virial of every atom */
+
+ /* first (and only) loop over atoms i */
for(i=0;i<count;i++) {
/* single particle potential/force */
dnlc=lc->dnlc;
+ /* first loop over atoms j */
+ if(moldyn->func2b) {
+ for(j=0;j<27;j++) {
+
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc_ij=(j<dnlc)?0:1;
+
+ do {
+ jtom=this->current->data;
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* 3 body potential/force */
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+
+ /* second loop over atoms j */
for(j=0;j<27;j++) {
this=&(neighbour_i[j]);
if(jtom==&(itom[i]))
continue;
- if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
- }
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- /* 3 body potential/force */
+ /* reset 3bp run */
+ moldyn->run3bp=1;
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
+ if(moldyn->func3b_j1)
+ moldyn->func3b_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+ /* in first j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
continue;
+
+ /* first loop over atoms k */
+ if(moldyn->func3b_k1) {
+
+ for(k=0;k<27;k++) {
+
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
+
+ bc_ik=(k<dnlc)?0:1;
+
+ do {
+
+ ktom=that->current->data;
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==jtom)
+ continue;
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func3b_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+
+ }
+
+ }
+
+ if(moldyn->func3b_j2)
+ moldyn->func3b_j2(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+ /* second loop over atoms k */
+ if(moldyn->func3b_k2) {
- /* get neighbours of i */
for(k=0;k<27;k++) {
that=&(neighbour_i2[k]);
if(ktom==&(itom[i]))
continue;
- moldyn->func3b(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func3b_k2(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
+
+ }
/* 2bp post function */
- if(moldyn->func2b_post) {
- moldyn->func2b_post(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ if(moldyn->func3b_j3) {
+ moldyn->func3b_j3(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
}
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
}
+
+#ifdef DEBUG
+ //printf("\n\n");
+#endif
+#ifdef VDEBUG
+ printf("\n\n");
+#endif
}
#ifdef DEBUG
-printf("\n\n");
-#endif
-#ifdef VDEBUG
-printf("\n\n");
+ printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
#endif
+ /* calculate global virial */
+ for(i=0;i<count;i++) {
+ moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+ moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+ moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+ moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+ moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+ moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+ }
+
return 0;
}
* virial calculation
*/
-inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
a->virial.xx+=f->x*d->x;
a->virial.yy+=f->y*d->y;
* periodic boundayr checking
*/
-inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
t_3dvec *dim;
return 0;
}
-
-/*
- * example potentials
- */
-
-/* harmonic oscillator potential and force */
-
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_ho_params *params;
- t_3dvec force,distance;
- double d,f;
- double sc,equi_dist;
-
- params=moldyn->pot2b_params;
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
-
- if(ai<aj) return 0;
-
- v3_sub(&distance,&(aj->r),&(ai->r));
-
- if(bc) check_per_bound(moldyn,&distance);
- d=v3_norm(&distance);
- if(d<=moldyn->cutoff) {
- moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
- /* f = -grad E; grad r_ij = -1 1/r_ij distance */
- f=sc*(1.0-equi_dist/d);
- v3_scale(&force,&distance,f);
- v3_add(&(ai->f),&(ai->f),&force);
- virial_calc(ai,&force,&distance);
- virial_calc(aj,&force,&distance); /* f and d signe switched */
- v3_scale(&force,&distance,-f);
- v3_add(&(aj->f),&(aj->f),&force);
- }
-
- return 0;
-}
-
-/* lennard jones potential & force for one sort of atoms */
-
-int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_lj_params *params;
- t_3dvec force,distance;
- double d,h1,h2;
- double eps,sig6,sig12;
-
- params=moldyn->pot2b_params;
- eps=params->epsilon4;
- sig6=params->sigma6;
- sig12=params->sigma12;
-
- if(ai<aj) return 0;
-
- 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) {
- d=1.0/d; /* 1/r^2 */
- h2=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
- 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(&(aj->f),&(aj->f),&force);
- v3_scale(&force,&force,-1.0); /* f = - grad E */
- v3_add(&(ai->f),&(ai->f),&force);
- virial_calc(ai,&force,&distance);
-if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
- virial_calc(aj,&force,&distance); /* f and d signe switched */
- }
-
- 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->S2[0]=p->S[0]*p->S[0];
- p->S2[1]=p->S[1]*p->S[1];
- p->Smixed=sqrt(p->S[0]*p->S[1]);
- p->S2mixed=p->Smixed*p->Smixed;
- 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 (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;
-}
-
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
-
- int brand;
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
-
- brand=ai->brand;
- params=moldyn->pot1b_params;
- exchange=&(params->exchange);
-
- /*
- * simple: point constant parameters only depending on atom i to
- * their right values
- */
-
- 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[brand]*params->c[brand];
- exchange->di2=params->d[brand]*params->d[brand];
- exchange->ci2di2=exchange->ci2/exchange->di2;
-
- return 0;
-}
-
-/* tersoff 2 body part */
-int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,force;
- double d_ij,d_ij2;
- double A,B,R,S,S2,lambda,mu;
- double f_r,df_r;
- double f_c,df_c;
- int brand;
- double s_r;
- double arg;
-
- params=moldyn->pot2b_params;
- brand=aj->brand;
- 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;
-
- /*
- * 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
- *
- */
-
- /* constants */
- if(brand==ai->brand) {
- S=params->S[brand];
- S2=params->S2[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 {
- S=params->Smixed;
- S2=params->S2mixed;
- R=params->Rmixed;
- A=params->Amixed;
- B=params->Bmixed;
- lambda=params->lambda_m;
- mu=params->mu_m;
- params->exchange.chi=params->chi;
- }
-
- /* dist_ij, d_ij */
- v3_sub(&dist_ij,&(aj->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ij);
- d_ij2=v3_absolute_square(&dist_ij);
-
- /* if d_ij2 > S2 => no force & potential energy contribution */
- if(d_ij2>S2)
- return 0;
-
- /* now we will need the distance */
- //d_ij=v3_norm(&dist_ij);
- d_ij=sqrt(d_ij2);
-
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
- exchange->d_ij2=d_ij2;
- exchange->dist_ij=dist_ij;
-
- /* more constants */
- 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;
- exchange->cj2dj2=exchange->ci2di2;
- }
- else {
- exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
- exchange->cj2=params->c[brand]*params->c[brand];
- exchange->dj2=params->d[brand]*params->d[brand];
- 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;
-
- /* 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;
-
- /* 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;
- /* 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));
- /* 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 of 2bp (ij, ji) contribution
- * dVij = dVji and we sum up both: no 1/2) */
- v3_add(&(ai->f),&(ai->f),&force);
-
- /* virial */
- ai->virial.xx-=force.x*dist_ij.x;
- ai->virial.yy-=force.y*dist_ij.y;
- ai->virial.zz-=force.z*dist_ij.z;
- ai->virial.xy-=force.x*dist_ij.y;
- ai->virial.xz-=force.x*dist_ij.z;
- ai->virial.yz-=force.y*dist_ij.z;
-
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
-}
-#endif
-
- /* 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 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 ... */
- 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);
-
- /* virial */
- ai->virial.xx-=force.x*dist_ij->x;
- ai->virial.yy-=force.y*dist_ij->y;
- ai->virial.zz-=force.z*dist_ij->z;
- ai->virial.xy-=force.x*dist_ij->y;
- ai->virial.xz-=force.x*dist_ij->z;
- ai->virial.yz-=force.y*dist_ij->z;
-
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
-}
-#endif
-
- /* 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);
-
- /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-// TEST ... with a minus instead
- ai->virial.xx-=force.x*dist_ij->x;
- ai->virial.yy-=force.y*dist_ij->y;
- ai->virial.zz-=force.z*dist_ij->z;
- ai->virial.xy-=force.x*dist_ij->y;
- ai->virial.xz-=force.x*dist_ij->z;
- ai->virial.yz-=force.y*dist_ij->z;
-
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
-}
-#endif
-
- return 0;
-}
-
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec temp1,temp2;
- t_3dvec *dzeta;
- double R,S,S2,s_r;
- double B,mu;
- double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
- double rr,dd;
- double f_c,df_c;
- double f_c_ik,df_c_ik,arg;
- double f_c_jk;
- double n,c,d,h;
- double c2,d2,c2d2;
- double cos_theta,d_costheta1,d_costheta2;
- double h_cos,d2_h_cos2;
- double frac,g,zeta,chi;
- double tmp;
- int brand;
-
- params=moldyn->pot3b_params;
- exchange=&(params->exchange);
-
- if(!(exchange->run3bp))
- return 0;
-
- /*
- * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
- * 2bp contribution of dV_jk
- *
- * 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_c_ij, df_c_ij (same for ji) */
- f_c=exchange->f_c;
- df_c=exchange->df_c;
-
- /*
- * calculate unknown values now ...
- */
-
- /* 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_ik2=v3_absolute_square(&dist_ik);
-
- /* ik constants */
- brand=ai->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- }
-
- /* zeta_ij/dzeta_ij contribution only for d_ik < S */
- if(d_ik2<S2) {
-
- /* now we need d_ik */
- d_ik=sqrt(d_ik2);
-
- /* 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_ij2-tmp;
- d_costheta2=cos_theta/d_ik2-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_jk2=v3_absolute_square(&dist_jk);
-
- /* jk constants */
- brand=aj->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- B=params->B[brand];
- mu=params->mu[brand];
- chi=1.0;
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- B=params->Bmixed;
- mu=params->mu_m;
- chi=params->chi;
- }
-
- /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
- if(d_jk2<S2) {
-
- /* now we need d_ik */
- d_jk=sqrt(d_jk2);
-
- /* 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); /* -1, as ij -> ji */
- dd=d_ij*d_jk;
- cos_theta=rr/dd;
-
- /* d_costheta */
- d_costheta1=1.0/dd;
- d_costheta2=cos_theta/d_ij2;
-
- /* 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_jik 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_sub(&temp1,&temp1,&temp2); /* there is a minus! */
- v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
-
- /* store dg in temp2 and use it for dVjk later */
- v3_copy(&temp2,&temp1);
-
- /* 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_ji */
- v3_scale(&temp1,&temp1,f_c_jk);
- v3_add(dzeta,dzeta,&temp1);
- }
-
- /* dV_jk stuff | add force contribution on atom i immediately */
- if(exchange->d_ij_between_rs) {
- zeta=f_c*g;
- v3_scale(&temp1,&temp2,f_c);
- v3_scale(&temp2,&dist_ij,df_c*g);
- v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
- }
- else {
- zeta=g;
- // dzeta_jk is simply dg, which is stored in temp2
- }
- /* 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(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
- v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
- /* scaled with 0.5 ^ */
-
- /* virial */
- ai->virial.xx-=temp2.x*dist_jk.x;
- ai->virial.yy-=temp2.y*dist_jk.y;
- ai->virial.zz-=temp2.z*dist_jk.z;
- ai->virial.xy-=temp2.x*dist_jk.y;
- ai->virial.xz-=temp2.x*dist_jk.z;
- ai->virial.yz-=temp2.y*dist_jk.z;
-
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x,ai->f.x);
- printf("%f | %f\n",temp2.y,ai->f.y);
- printf("%f | %f\n",temp2.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
- printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
- printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
-}
-#endif
-
- }
-
- return 0;
-}
-
-
/*
* debugging / critical check functions
*/