#CFLAGS+=-DVDEBUG
LDFLAGS=-lm
-SOURCE=moldyn.c visual/visual.c random/random.c
+SOURCE=moldyn.c visual/visual.c random/random.c list/list.c
-POT_SRC=potentials/tersoff.c potentials/lennard_jones.c
-POT_SRC+= potentials/harmonic_oscillator.c
+POT_SRC=potentials/tersoff.c
+#POT_SRC=potentials/tersoff_orig.c
+POT_SRC+= potentials/lennard_jones.c potentials/harmonic_oscillator.c
all: sic
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_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
- moldyn->func2b_post=func;
+ moldyn->func3b_j1=func;
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
- moldyn->func3b=func;
+ 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;
}
perror("[moldyn] report fd open");
return moldyn->rfd;
}
+ printf("report -> ");
if(moldyn->efd) {
snprintf(filename,127,"%s/e_plot.scr",
moldyn->vlsdir);
}
dprintf(moldyn->epfd,e_plot_script);
close(moldyn->epfd);
+ printf("energy ");
}
if(moldyn->pfd) {
snprintf(filename,127,"%s/pressure_plot.scr",
}
dprintf(moldyn->ppfd,pressure_plot_script);
close(moldyn->ppfd);
+ printf("pressure ");
}
if(moldyn->tfd) {
snprintf(filename,127,"%s/temperature_plot.scr",
}
dprintf(moldyn->tpfd,temperature_plot_script);
close(moldyn->tpfd);
+ printf("temperature ");
}
dprintf(moldyn->rfd,report_start,
moldyn->rauthor,moldyn->rtitle);
+ printf("\n");
break;
default:
printf("unknown log type: %02x\n",type);
/* 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;
}
/* 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;
}
* dV: dx,y,z = 0.001 x,y,z
*/
- scale=1.00001;
+ scale=1.00000000000001;
printf("\n\nP-DEBUG:\n");
tp=&(moldyn->tp);
/* derivative with respect to x direction */
scale_dim(moldyn,scale,TRUE,0,0);
scale_atoms(moldyn,scale,TRUE,0,0);
- dv=0.00001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
+ 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)/dv;
p=tp->x*tp->x;
-printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn->energy-u)/moldyn->count/EV,dv);
/* restore atomic configuration + dim */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
/* derivative with respect to y direction */
scale_dim(moldyn,scale,0,TRUE,0);
scale_atoms(moldyn,scale,0,TRUE,0);
- dv=0.00001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+ 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);
/* derivative with respect to z direction */
scale_dim(moldyn,scale,0,0,TRUE);
scale_atoms(moldyn,scale,0,0,TRUE);
- dv=0.00001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+ 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);
}
-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]));
}
/* 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);
//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(p) {
if(!(i%p)) {
dprintf(moldyn->pfd,
- "%f %f\n",moldyn->time,moldyn->p/ATM);
+ "%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\n",moldyn->time,moldyn->t);
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->mean_t);
}
}
if(s) {
/* display progress */
if(!(i%10)) {
- printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+ printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
sched->count,i,
- moldyn->t,moldyn->p/ATM,moldyn->volume);
+ 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;
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ do {
+
+ ktom=that->current->data;
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==jtom)
+ continue;
+
+ 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;
}
/* potential force function and parameter pointers */
int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
- u8 bck);
+ int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func3b_k1)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func3b_k2)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
void *pot_params;
- //int (*potential_force_function)(struct s_moldyn *moldyn);
+ unsigned char run3bp;
double cutoff; /* cutoff radius */
double cutoff_square; /* square of the cutoff radius */
double t_ref; /* reference temperature */
double t; /* actual temperature */
+ double t_sum; /* sum over all t */
+ double mean_t; /* mean value of t */
+
+ t_virial virial; /* global virial (absolute coordinates) */
+ double gp; /* pressure computed from global virial */
+ double gp_sum; /* sum over all gp */
+ double mean_gp; /* mean value of gp */
double p_ref; /* reference pressure */
double p; /* actual pressure (computed by virial) */
+ double p_sum; /* sum over all p */
+ double mean_p; /* mean value of p */
t_3dvec tp; /* thermodynamic pressure dU/dV */
double dv; /* dV for thermodynamic pressure calc */
double tau; /* delta t */
double time; /* absolute time */
double tau_square; /* delta t squared */
- double elapsed; /* total elapsed time */
+ int total_steps; /* total steps */
double energy; /* potential energy */
double ekin; /* kinetic energy */
#define P_SCALE_DIRECT 0x08 /* direct p control */
/*
- * default values
+ * default values & units
*
* - length unit: 1 A (1 A = 1e-10 m)
* - time unit: 1 fs (1 fs = 1e-15 s)
#define KILOGRAM (1.0/AMU) /* amu */
#define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
#define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
-#define ATM ((1.0133e5*PASCAL)) /* N / A^2 */
+#define BAR ((1.0e5*PASCAL)) /* N / A^2 */
+#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
+#define EV (1.6021765314e-19*METER*NEWTON) /* NA */
#define MOLDYN_TEMP 273.0
#define MOLDYN_TAU 1.0
#define QUIET 0
/*
- *
- * phsical values / constants
- *
+ * potential related phsical values / constants
*
*/
#define ONE_THIRD (1.0/3.0)
-#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
-#define EV (1.6021765314e-19*METER*NEWTON) /* NA */
-
#define C 0x06
#define M_C 12.011 /* amu */
*
*/
-typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
-typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
-typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
-typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func1b)(t_moldyn *,t_atom *);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
+typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
int set_potential1b(t_moldyn *moldyn,pf_func1b func);
int set_potential2b(t_moldyn *moldyn,pf_func2b func);
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func);
-int set_potential3b(t_moldyn *moldyn,pf_func3b func);
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
int set_potential_params(t_moldyn *moldyn,void *params);
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
-double get_e_kin(t_moldyn *moldyn);
-double update_e_kin(t_moldyn *moldyn);
+double e_kin_calc(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
t_3dvec get_total_p(t_moldyn *moldyn);
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 A,R,S,S2,lambda;
double f_r,df_r;
double f_c,df_c;
int brand;
double arg;
/* use newtons third law */
+ if(ai<aj) return 0;
params=moldyn->pot_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
- *
- */
/* determine cutoff square */
if(brand==ai->brand)
else
S2=params->S2mixed;
- /* dist_ij, d_ij */
+ /* dist_ij, d_ij2 */
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)
+ 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) {
S=params->S[brand];
R=params->R[brand];
A=params->A[brand];
- B=params->B[brand];
lambda=params->lambda[brand];
- mu=params->mu[brand];
- exchange->chi=1.0;
- exchange->betajnj=exchange->betaini;
- exchange->cj2=exchange->ci2;
- exchange->dj2=exchange->di2;
- exchange->cj2dj2=exchange->ci2di2;
}
else {
S=params->Smixed;
R=params->Rmixed;
A=params->Amixed;
- B=params->Bmixed;
lambda=params->lambda_m;
- mu=params->mu_m;
- params->exchange.chi=params->chi;
- 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_ij, df_r_ij */
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) */
+ /* f_c, df_c */
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 {
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) */
+ /* add forces */
v3_add(&(ai->f),&(ai->f),&force);
+ v3_sub(&(aj->f),&(aj->f),&force);
+
+#ifdef DEBUG
+ if((ai==&(moldyn->atom[0]))|(aj==&(moldyn->atom[0]))) {
+ printf("force 2bp: [%d %d]\n",ai->tag,aj->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ if(ai==&(moldyn->atom[0]))
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+ if(aj==&(moldyn->atom[0]))
+ printf("total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+ }
+#endif
/* virial */
- virial_calc(ai,&force,&dist_ij);
+ //virial_calc(ai,&force,&dist_ij);
+ //virial_calc(aj,&force,&dist_ij);
//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.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));
+ /* energy 2bp contribution */
+ moldyn->energy+=f_r*f_c;
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
- *
- */
+/* tersoff 3 body potential function (first ij loop) */
+int tersoff_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
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;
+ unsigned char brand;
+ double S2;
+ t_3dvec dist_ij;
+ double d_ij2,d_ij;
params=moldyn->pot_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);
+ /* reset zeta sum */
+ exchange->zeta_ij=0.0;
- /* virial */
- virial_calc(ai,&force,dist_ij);
- //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;
+ /*
+ * set ij depending values
+ */
-#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
+ brand=ai->brand;
+
+ if(brand==aj->brand)
+ S2=params->S2[brand];
+ else
+ S2=params->S2mixed;
- /* add energy of 3bp sum */
- moldyn->energy+=(0.5*f_c*b*f_a);
+ /* dist_ij, d_ij2 */
+ v3_sub(&dist_ij,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ij);
+ d_ij2=v3_absolute_square(&dist_ij);
- /* 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);
+ /* if d_ij2 > S2 => no force & potential energy contribution */
+ if(d_ij2>S2) {
+ moldyn->run3bp=0;
+ return 0;
}
- 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
- virial_calc(ai,&force,dist_ij);
- //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;
+ /* d_ij */
+ d_ij=sqrt(d_ij2);
-#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
+ /* store values */
+ exchange->dist_ij=dist_ij;
+ exchange->d_ij2=d_ij2;
+ exchange->d_ij=d_ij;
+ /* reset k counter for first k loop */
+ exchange->kcount=0;
+
return 0;
}
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+/* tersoff 3 body potential function (first k loop) */
+int tersoff_mult_3bp_k1(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;
+ unsigned char brand;
+ double R,S,S2;
+ t_3dvec dist_ij,dist_ik;
+ double d_ik2,d_ik,d_ij;
+ double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg;
+ double f_c_ik,df_c_ik;
+ int kcount;
params=moldyn->pot_params;
exchange=&(params->exchange);
+ kcount=exchange->kcount;
- 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);
+ if(kcount>TERSOFF_MAXN) {
+ printf("FATAL: neighbours = %d\n",kcount);
+ printf(" -> %d %d %d\n",ai->tag,aj->tag,ak->tag);
+ }
/* ik constants */
brand=ai->brand;
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);
- }
+ /* dist_ik, d_ik2 */
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik2=v3_absolute_square(&dist_ik);
+
+ /* store data for second k loop */
+ exchange->dist_ik[kcount]=dist_ik;
+ exchange->d_ik2[kcount]=d_ik2;
+
+ /* return if not within cutoff */
+ if(d_ik2>S2) {
+ exchange->kcount++;
+ return 0;
+ }
+
+ /* d_ik */
+ d_ik=sqrt(d_ik2);
+
+ /* dist_ij, d_ij */
+ dist_ij=exchange->dist_ij;
+ d_ij=exchange->d_ij;
+
+ /* cos theta */
+ cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
+
+ /* g_ijk */
+ h_cos=*(exchange->h_i)-cos_theta;
+ d2_h_cos2=exchange->di2+(h_cos*h_cos);
+ frac=exchange->ci2/d2_h_cos2;
+ g=1.0+exchange->ci2di2-frac;
+ dg=-2.0*frac*h_cos/d2_h_cos2;
+
+ /* zeta sum += f_c_ik * g_ijk */
+ if(d_ik<=R) {
+ exchange->zeta_ij+=g;
+ f_c_ik=1.0;
+ df_c_ik=0.0;
+ }
+ 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));
+ exchange->zeta_ij+=f_c_ik*g;
}
- /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+ /* store even more data for second k loop */
+ exchange->g[kcount]=g;
+ exchange->dg[kcount]=dg;
+ exchange->d_ik[kcount]=d_ik;
+ exchange->cos_theta[kcount]=cos_theta;
+ exchange->f_c_ik[kcount]=f_c_ik;
+ exchange->df_c_ik[kcount]=df_c_ik;
- /* 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);
+ /* increase k counter */
+ exchange->kcount++;
+
+ return 0;
+}
+
+int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec force;
+ double f_a,df_a,b,db,f_c,df_c;
+ double mu,B,chi;
+ double d_ij;
+ unsigned char brand;
+ double ni,tmp;
+ double S,R,s_r,arg;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
- /* jk constants */
brand=aj->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
+ if(brand==ai->brand) {
S=params->S[brand];
- S2=params->S2[brand];
+ R=params->R[brand];
B=params->B[brand];
mu=params->mu[brand];
chi=1.0;
}
else {
- R=params->Rmixed;
S=params->Smixed;
- S2=params->S2mixed;
+ R=params->Rmixed;
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;
+ d_ij=exchange->d_ij;
+
+ /* f_c, df_c */
+ if(d_ij<R) {
+ f_c=1.0;
+ df_c=0.0;
+ }
+ 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));
+ }
+
+ /* f_a, df_a */
+ f_a=-B*exp(-mu*d_ij);
+ df_a=mu*f_a/d_ij;
+
+ /* b, db */
+ if(exchange->zeta_ij==0.0) {
+ b=chi;
+ db=0.0;
+ }
+ else {
+ ni=*(exchange->n_i);
+ tmp=exchange->betaini*pow(exchange->zeta_ij,ni-1.0);
+ b=(1.0+exchange->zeta_ij*tmp);
+ db=chi*pow(b,-1.0/(2*ni)-1.0);
+ b=db*b;
+ db*=-0.5*tmp;
+ }
+
+ /* force contribution */
+ v3_scale(&force,&(exchange->dist_ij),df_a*f_c+f_a*df_c);
+ v3_scale(&force,&force,-0.5*b);
+ v3_add(&(ai->f),&(ai->f),&force);
+ v3_sub(&(aj->f),&(aj->f),&force);
#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);
-}
+ if((ai==&(moldyn->atom[0]))|(aj==&(moldyn->atom[0]))) {
+ printf("force 3bp (j2): [%d %d sum]\n",ai->tag,aj->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ if(ai==&(moldyn->atom[0]))
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+ if(aj==&(moldyn->atom[0]))
+ printf("total j: %f %f %f\n",aj->f.x,aj->f.y,aj->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);
+
+ /* virial */
+ //virial_calc(ai,&force,&(exchange->dist_ij));
+ //virial_calc(aj,&force,&(exchange->dist_ij));
+
+ /* dzeta prefactor = - 0.5 f_c f_a db */
+ exchange->pre_dzeta=-0.5*f_a*f_c*db;
+
+ /* energy contribution */
+ moldyn->energy+=0.5*f_c*b*f_a;
+
+ /* reset k counter for second k loop */
+ exchange->kcount=0;
+
+ return 0;
}
+
+/* tersoff 3 body potential function (second k loop) */
+int tersoff_mult_3bp_k2(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ int kcount;
+ t_3dvec dist_ik,dist_ij;
+ double d_ik2,d_ik,d_ij2,d_ij;
+ unsigned char brand;
+ double S2;
+ double g,dg,cos_theta;
+ double pre_dzeta;
+ double f_c_ik,df_c_ik;
+ double dijdik_inv,fcdg,dfcg;
+ t_3dvec dcosdri,dcosdrj,dcosdrk;
+ t_3dvec force,tmp;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+ kcount=exchange->kcount;
+
+ if(kcount>TERSOFF_MAXN)
+ printf("FATAL: neighbours!\n");
+
+ /* d_ik2 */
+ d_ik2=exchange->d_ik2[kcount];
+
+ brand=ak->brand;
+ if(brand==ai->brand)
+ S2=params->S2[brand];
+ else
+ S2=params->S2mixed;
+
+ /* return if d_ik > S */
+ if(d_ik2>S2) {
+ exchange->kcount++;
+ return 0;
+ }
+
+ /* prefactor dzeta */
+ pre_dzeta=exchange->pre_dzeta;
+
+ /* dist_ik, d_ik */
+ dist_ik=exchange->dist_ik[kcount];
+ d_ik=exchange->d_ik[kcount];
+
+ /* f_c_ik, df_c_ik */
+ f_c_ik=exchange->f_c_ik[kcount];
+ df_c_ik=exchange->df_c_ik[kcount];
+
+ /* dist_ij, d_ij2, d_ij */
+ dist_ij=exchange->dist_ij;
+ d_ij2=exchange->d_ij2;
+ d_ij=exchange->d_ij;
+
+ /* g, dg, cos_theta */
+ g=exchange->g[kcount];
+ dg=exchange->dg[kcount];
+ cos_theta=exchange->cos_theta[kcount];
+
+ /* cos_theta derivatives wrt i,j,k */
+ dijdik_inv=1.0/(d_ij*d_ik);
+ v3_scale(&dcosdrj,&dist_ik,dijdik_inv);
+ v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
+ v3_add(&dcosdrj,&dcosdrj,&tmp);
+ v3_scale(&dcosdrk,&dist_ij,dijdik_inv);
+ v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
+ v3_add(&dcosdrk,&dcosdrk,&tmp);
+ v3_add(&dcosdri,&dcosdrj,&dcosdrk);
+ v3_scale(&dcosdri,&dcosdri,-1.0);
+
+ /* f_c_ik * dg, df_c_ik * g */
+ fcdg=f_c_ik*dg;
+ dfcg=df_c_ik*g;
+
+ /* derivative wrt i */
+ v3_scale(&force,&dist_ik,dfcg);
+ v3_scale(&tmp,&dcosdri,fcdg);
+ v3_add(&force,&force,&tmp);
+ v3_scale(&force,&force,pre_dzeta);
+
+ /* force contribution */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+#ifdef DEBUG
+ if(ai==&(moldyn->atom[0])) {
+ printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+ }
+#endif
+
+ /* virial */
+ //virial_calc(ai,&force,&dist_ij);
+
+ /* derivatice wrt j */
+ v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
+
+ /* force contribution */
+ v3_add(&(aj->f),&(aj->f),&force);
+
+#ifdef DEBUG
+ if(aj==&(moldyn->atom[0])) {
+ printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ printf("total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+ }
#endif
+ /* virial */
+ //virial_calc(aj,&force,&dist_ij);
+
+ /* derivative wrt k */
+ v3_scale(&force,&dist_ik,dfcg);
+ v3_scale(&tmp,&dcosdrk,fcdg);
+ v3_add(&force,&force,&tmp);
+ v3_scale(&force,&force,pre_dzeta);
+
+ /* force contribution */
+ v3_add(&(ak->f),&(ak->f),&force);
+
+#ifdef DEBUG
+ if(ak==&(moldyn->atom[0])) {
+ printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ printf("total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z);
}
+#endif
+
+ /* virial */
+ virial_calc(ak,&force,&dist_ik);
+
+ /* increase k counter */
+ exchange->kcount++;
return 0;
-}
+}
#ifndef TERSOFF_H
#define TERSOFF_H
+#define TERSOFF_MAXN 16*27
+
/* tersoff exchange type */
typedef struct s_tersoff_echange {
- double f_c,df_c;
- double f_a,df_a;
t_3dvec dist_ij;
double d_ij2;
double d_ij;
- double chi;
+ t_3dvec dist_ik[TERSOFF_MAXN];
+ double d_ik2[TERSOFF_MAXN];
+ double d_ik[TERSOFF_MAXN];
+
+ double f_c_ik[TERSOFF_MAXN];
+ double df_c_ik[TERSOFF_MAXN];
+
+ double g[TERSOFF_MAXN];
+ double dg[TERSOFF_MAXN];
+ double cos_theta[TERSOFF_MAXN];
double *beta_i;
- double *beta_j;
double *n_i;
- double *n_j;
double *c_i;
- double *c_j;
double *d_i;
- double *d_j;
double *h_i;
- double *h_j;
double ci2;
- double cj2;
double di2;
- double dj2;
double ci2di2;
- double cj2dj2;
double betaini;
- double betajnj;
-
- u8 run3bp;
- u8 run2bp_post;
- u8 d_ij_between_rs;
double zeta_ij;
- double zeta_ji;
- t_3dvec dzeta_ij;
- t_3dvec dzeta_ji;
+ double pre_dzeta;
+
+ int kcount;
} t_tersoff_exchange;
/* tersoff mult (2!) potential parameters */
int tersoff_mult_complete_params(t_tersoff_mult_params *p);
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
+int tersoff_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int tersoff_mult_3bp_k1(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
+int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int tersoff_mult_3bp_k2(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
#endif
--- /dev/null
+/*
+ * tersoff_orig.c - tersoff potential
+ *
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <math.h>
+
+#include "../moldyn.h"
+#include "../math/math.h"
+#include "tersoff_orig.h"
+
+/* 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->pot_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;
+
+ /* use newtons third law */
+ //if(ai<aj) return 0;
+
+ params=moldyn->pot_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
+ *
+ */
+
+ /* determine cutoff square */
+ if(brand==ai->brand)
+ S2=params->S2[brand];
+ else
+ S2=params->S2mixed;
+
+ /* 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) {
+ S=params->S[brand];
+ R=params->R[brand];
+ A=params->A[brand];
+ B=params->B[brand];
+ lambda=params->lambda[brand];
+ mu=params->mu[brand];
+ exchange->chi=1.0;
+ exchange->betajnj=exchange->betaini;
+ exchange->cj2=exchange->ci2;
+ exchange->dj2=exchange->di2;
+ exchange->cj2dj2=exchange->ci2di2;
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ B=params->Bmixed;
+ lambda=params->lambda_m;
+ mu=params->mu_m;
+ exchange->chi=params->chi;
+ 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 */
+ virial_calc(ai,&force,&dist_ij);
+ //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: [%d %d]\n",ai->tag,aj->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,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->pot_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 */
+ virial_calc(ai,&force,dist_ij);
+ //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: [%d %d sum]\n",ai->tag,aj->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,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
+ virial_calc(ai,&force,dist_ij);
+ //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: [%d %d sum]\n",ai->tag,aj->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,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->pot_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: [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
+ printf("adding %f %f %f\n",temp2.x,temp2.y,temp2.z);
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,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;
+}
+
--- /dev/null
+/*
+ * tersoff_orig.h - tersoff potential header file
+ *
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
+ *
+ */
+
+#ifndef TERSOFF_H
+#define TERSOFF_H
+
+/* tersoff exchange type */
+typedef struct s_tersoff_echange {
+ double f_c,df_c;
+ double f_a,df_a;
+
+ t_3dvec dist_ij;
+ double d_ij2;
+ double d_ij;
+
+ double chi;
+
+ double *beta_i;
+ double *beta_j;
+ double *n_i;
+ double *n_j;
+ double *c_i;
+ double *c_j;
+ double *d_i;
+ double *d_j;
+ double *h_i;
+ double *h_j;
+
+ double ci2;
+ double cj2;
+ double di2;
+ double dj2;
+ double ci2di2;
+ double cj2dj2;
+ double betaini;
+ double betajnj;
+
+ u8 run3bp;
+ u8 run2bp_post;
+ u8 d_ij_between_rs;
+
+ double zeta_ij;
+ double zeta_ji;
+ t_3dvec dzeta_ij;
+ t_3dvec dzeta_ji;
+} t_tersoff_exchange;
+
+/* tersoff mult (2!) potential parameters */
+typedef struct s_tersoff_mult_params {
+ double S[2]; /* tersoff cutoff radii */
+ double S2[2]; /* tersoff cutoff radii squared */
+ double R[2]; /* tersoff cutoff radii */
+ double Smixed; /* mixed S radius */
+ double S2mixed; /* mixed S radius squared */
+ double Rmixed; /* mixed R radius */
+ double A[2]; /* factor of tersoff attractive part */
+ double B[2]; /* factor of tersoff repulsive part */
+ double Amixed; /* mixed A factor */
+ double Bmixed; /* mixed B factor */
+ double lambda[2]; /* tersoff lambda */
+ double lambda_m; /* mixed lambda */
+ double mu[2]; /* tersoff mu */
+ double mu_m; /* mixed mu */
+
+ double chi;
+
+ double beta[2];
+ double n[2];
+ double c[2];
+ double d[2];
+ double h[2];
+
+ t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
+} t_tersoff_mult_params;
+
+/* function prototypes */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p);
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
+
+#endif
set ytic auto \n\
set title 'Pressure vs. time' \n\
set xlabel 'Time [fs]' \n\
-set ylabel 'Pressure [atm]' \n\
+set ylabel 'Pressure [bar]' \n\
set terminal postscript eps enhanced color solid lw 1 'Helvetica' 14 \n\
set output 'pressure.eps' \n\
-plot \"pressure\" using 1:2 title 'Pressure' with lines \
+plot \"pressure\" using 1:2 title 'P' with lines , \"pressure\" using 1:3 title '<P>' with lines , \"pressure\" using 1:4 title 'P (global virial)' with lines , \"pressure\" using 1:5 title '<P (global virial)>' with lines \
";
static char temperature_plot_script[]="\
set ylabel 'Temperature [K]' \n\
set terminal postscript eps enhanced color solid lw 1 'Helvetica' 14 \n\
set output 'temperature.eps' \n\
-plot \"temperature\" using 1:2 title 'Temperature' with lines \
+plot \"temperature\" using 1:2 title 'T' with lines , \"temperature\" using 1:3 title '<T>' with lines \
";
#endif
#include "potentials/harmonic_oscillator.h"
#include "potentials/lennard_jones.h"
#include "potentials/tersoff.h"
+//#include "potentials/tersoff_orig.h"
-#define INJECT 20
-#define NR_ATOMS 20
+#define INJECT 1
+#define NR_ATOMS 4
int hook(void *moldyn,void *hook_params) {
/* choose potential */
set_potential1b(&md,tersoff_mult_1bp);
set_potential2b(&md,tersoff_mult_2bp);
- set_potential2b_post(&md,tersoff_mult_post_2bp);
- set_potential3b(&md,tersoff_mult_3bp);
+ //set_potential3b_j1(&md,tersoff_mult_2bp);
+ //set_potential3b_k1(&md,tersoff_mult_3bp);
+ //set_potential3b_j3(&md,tersoff_mult_post_2bp);
+ set_potential3b_j1(&md,tersoff_mult_3bp_j1);
+ set_potential3b_k1(&md,tersoff_mult_3bp_k1);
+ set_potential3b_j2(&md,tersoff_mult_3bp_j2);
+ set_potential3b_k2(&md,tersoff_mult_3bp_k2);
//set_potential2b(&md,lennard_jones);
//set_potential2b(&md,harmonic_oscillator);
set_potential_params(&md,&tp);
/* set temperature & pressure */
set_temperature(&md,atof(argv[2])+273.0);
- set_pressure(&md,ATM);
+ set_pressure(&md,BAR);
/* set p/t scaling */
//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
/* create the simulation schedule */
/* initial configuration */
- moldyn_add_schedule(&md,500,1.0);
+ moldyn_add_schedule(&md,10000,1.0);
/* adding atoms */
- for(inject=0;inject<INJECT;inject++) {
- /* injecting atom and run with enabled t scaling */
- moldyn_add_schedule(&md,400,1.0);
- /* continue running with disabled t scaling */
- moldyn_add_schedule(&md,100,1.0);
- }
+ //for(inject=0;inject<INJECT;inject++) {
+ // /* injecting atom and run with enabled t scaling */
+ // moldyn_add_schedule(&md,900,1.0);
+ // /* continue running with disabled t scaling */
+ // moldyn_add_schedule(&md,1100,1.0);
+ //}
/* schedule hook function */
moldyn_set_schedule_hook(&md,&hook,NULL);
/* activate logging */
moldyn_set_log_dir(&md,argv[1]);
moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,10);
- moldyn_set_log(&md,LOG_TEMPERATURE,10);
- moldyn_set_log(&md,LOG_PRESSURE,10);
+ moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
+ moldyn_set_log(&md,LOG_TEMPERATURE,1);
+ moldyn_set_log(&md,LOG_PRESSURE,1);
moldyn_set_log(&md,VISUAL_STEP,100);
moldyn_set_log(&md,SAVE_STEP,100);
moldyn_set_log(&md,CREATE_REPORT,0);
projects / physik / posic.git / commitdiff