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;
}
projects / physik / posic.git / blobdiff